GeneNetwork News

2019-Sep-24: BXD Genotypes file: Sequence-based improvements coming soon

The BXD sequencing consortium has generated full genome sequence for 152 extant BXD strains. Dr. David Ashbrook has extracted the most informative 40,000 SNPs from sequence data, and compared sequence-based genotypes with those based on array platforms (see entries below).  In general there is excellent concordance for all but a handful of the BXD strains that are in widespread use (BXD1 to BXD102). However, there are some problems and mixups that we list below. We are currently working on harmonizing data when possible, and understanding and fixing errors, when not.

This evaluation of genotypes is based on data extracted from whole-genome sequencing of BXD male spleen samples obtained in January 2017 from the Jackson Laboratory whenever possible, and from the UTHSC colony in all other cases. All animals were born between January and December 2016.

1.  BXD65b (sourced from JAX). The sequence-based genotypes correlate better to array-based 2017 genotypes of BXD65 and BXD65a than with the BXD65b array-based genotypes. It is possible that there are two somewhat distinct sub-strains now called BXD65b—one at JAX and one at UTHSC. Recommended Action: Sourcing BXD65b animals from JAX.

2. BXD53 array-based genotypes do not correlate well with sequence-based genotypes for BXD53/2. BXD53 was rederived a second time by JAX and is now referred to formally at BXD53/2RwwJ (Stock 017749). The likely reason for the discrepancy is that we sequenced BXD53/2RwwJ (Stock 017749) rather than the older BXD53 (sourced from UTHSC) for array-based genotyping. BXD53 sequence-based genotypes correlate well with eQTL data for BXD53. Recommended Action: If using BXD53/2RwwJ, please obtain current sequence-based genotypes from David Ashbrook.

3. BXD68 animals at UTHSC used from about 2012 to 2017 were BXD34 animals. Genotypes in the 2017 array-based file HAVE or HAVE  NOT been corrected. We have corrected this error in some phenotype data sets. BXD68 from The Jackson Laboratory are genuine BXD68. We sequenced BXD68 DNA from JAX. Recommended Action: None unless you have used BXD68 animals obtained from UTHSC between 2012 and 2017. If so, these animals should be relabeled BXD34.

4. BXD81 sequence-based genotypes correlate well with the new array-based genotypes (r = 0.81) but less well with old array-based genotypes (r = 0.66). This is presumably due to more complete inbreeding. The new sequence-based genotypes are for BXD81 sources from JAX. Recommended Action: None

5. BXD88 sequence-based genotypes do not correlate well with either of the two array-based genotype files (r = 0.50 and 0.54). Like BXD53, BXD88 was rederived a second time by JAX and is now referred to formally at BXD88/2RwwJ (Stock 007110). BXD88 was admixed at some point in the last decade that has since been rederived. BXD88/2RwwJ is only available at JAX. Recommended Action: Sourcing BXD88/2RwwJ from JAX; do not treat as equivalent to old BXD88.

6. BXD100 (JAX stock 007143) sequence-based genotypes correlates well with the older array-based genotypes (r = 0.96) but not so well with newer 2017 array data (r = 0.55). This suggests some admixture in the last decade at UTHSC that has since been fixed. Recommended Action: If you used BXD100s between 2006 and 2014, we recommend using genotypes from the older array-based file for this strain. If you are using new BXD100 animals sourced from JAX, then use the newer 2017 array-based genotypes or the sequence-based genotypes.

7. BXD151 (UTHSC stock) sequence-based genotypes do not correlate with the array-based genotypes at all (r = -0.79 and -0.06). BXD151 sequence-based genotypes correlate very well with older array-based sequence for the now (formally) extinct BXD128a (r = 0.97 and 0.99 with the two array-based files). We need to check sequence of BXD151/RwwJ (JAX 029868). Recommended Action: None. It appears likely that BXD151 may be equivalent to what we used to call BXD128a. BXD128a is no longer officially available and we will retain the name BXD151. 

8. BXD155 (UTHSC stock) sequence-based genotypes do not correlate with arrays (r = 0.21 and 0.18). BXD155 has an excellent correlation with previous array-based genotypes for strain BXD152 (r = 0.95 and 0.95 with arrays, 0.99 with sequence). Likely reading error or strain swap at UTHSC. BXD152 (Stock 029869, non-agouti black coat color) can be obtained from JAX, but BXD155 (gray coat color) is not yet available from JAX. Recommended Action: Check with David Ashbrook or Rob Williams on whether this issue has been resolved. It seems likely that the BXD155 sample that we sequenced was actually at BXD152.

9. BXD162 (UTHSC stock) sequence-based genotypes correlate poorly well with new array genotypes (r = 0.65 and 0.69). This strain also has a reasonable correlation with BXD170 in older array genotypes (r = 0.7). Possible admixture. BXD162 is not yet available from JAX. Recommended Action: Check with David Ashbrook or Rob Williams in you use this strain regarding correct nomenclature.

10. BXD194 (UTHSC stock) sequence-based genotypes correlated with BXD87 (JAX stock) sequence-based genotypes. Probably a sample error at UTHSC when preparing samples for sequencing. We need to check the JAX BXD194/RwwJ (Stock 030878). Recommended Action: Check with David Ashbrook or Rob Williams in you use this strain regarding correct nomenclature. 

2018-12-19: BXD Genotypes file status (December 2018)

In September and October 2016, Robert Williams, Jesse Ingels, Lu Lu, and Danny Arends released new genotype files for many of the original BXD strains (BXD1 through BXD102), and for all of the new strains (BXD104 to BXD220). Genotypes were generated at about 74,000 SNPs using the GigaMUGA array developed by Drs. Fernando Pardo-Manuel de Villena (University of North Carolina) and Gary Churchill (The Jackson Laboratory). Genotypes were generated at GeneSeek (Neogen Inc) with financial support from the University of Tennessee Center for Integrative and Translational Genomics.

Update The new genotypes are now available in GeneNetwork as the 2019 Genotype file. All SNPs were mapped to the older July 2007 mm9 NCBI Build 37 assembly and to the newer Dec 2011, mm10, GRCm38 assembly. Of the 74,000 GigaMUGA and many other markers we have typed, only about 6800 are useful (informative) in defining recombination events in the current set of BXDs. These informative markers either define unique recombination patterns across the 198 BXD strains (including extinct strains) or they define the proximal and distal ends of regions that do not contain any known recombinations in the BXD family.

This file provides consensus genotypes for 198 BXD strains and for the two progenitor strains and the reciprocal F1s. Of the 198 BXD strains, 191 are independent, whereas 7 are substrains (e.g., BXD48 and BXD48a). This file provides approximate locations of 10300 recombinations, an average of 52 per strain. Genotypes were generated using Affymetrix, MUGA, MegaMUGA, and GigaMUGA Illumina platforms. Microsatellites and eQTL genotypes were generated by the Williams/Lu laboratory. Unknown genotypes were imputed as B or D, or were called as H (heterozygous) if the genotype was uncertain. Genotypes were manually curated by RW Williams. Genotypes were smoothed to remove unlikely recombination events. Almost all recombinations are supported by multiple markers, although only one or two representative markers may be provided in this file. The original parent file (BXD_El_Grande_Master_Used_to_Proof_Final_Genotypes_2016.xlxs) contains data for approximately 37000 markers. A subset of the most informative 7300 markers are included here. Genotypes for Chr Y and Chr M are provisional.

The file does not include any markers for Chr Y or the mitochondrion.

As of December 2018 GeneNetwork uses mm10 coordinates for mapping functions.

(Updated Dec 19, 2018 by RW Williams)

2018-09-12: GeneNetwork 1 will be supported in 2018 but GeneNetwork 2 will become the main production server

GeneNetwork 2 is ready for testing and research projects. GeneNetwork 1 (GN1) and GeneNetwork 2 (GN2) share the a single database, but they use different code and algorithms for mapping and data analysis. There are some benefits of using GN2, including more powerful linear mixed model mapping methods that account for kinship structure.

The interface of GN2 is still a work in progress. Please send any suggestion, requests, or bug reports to rwilliams@uthsc.edu.

2018-09-12: Notes on new BXD names.
  1. BXD73, BXD73a (original known as BXD80), and BXD73b (originally known as BXD103) are genetically very similar. BXD73 and BXD80 are genetically identical at 82264 of 100290 markers (82% identical by descent). BXD73 keeps its original name and JAX identifier number (JR#7117), whereas BXD80 is now referred to as BXD73a (JR#7124). BXD73 and BXD103 are genetically identical at 90917 of 100290 markers (90.6% identical by descent). BXD103 is now referred to as BXD73b (JR#7146).
  2. BXD48 and BXD48a (originally known as BXD96) are sister substrains, and are genetically identical at 93485 of 100290 markers (93.2% identical by descent). BXD48 retains its original name and JAX identifier number (JAX JR#7097) whereas BXD96 is now referred to as BXD48a (JR#7139).
  3. BXD65, BXD65a (originally known as BXD97), and BXD65b (originally known as BXD92) are sister substrains. BXD65 and BXD97 are genetically identical at 92225 of 100290 markers (92% identical by descent). BXD97 is now referred to as BXD65a (JR#7140). BXD65 and BXD92 are genetically identical at 6155 of 6459 markers (95.3% identical by descent). BXD65 retains its original name and JAX identifier (JR#7110) whereas BXD92 is now referred to as BXD65b (JR#9677).
2018-09-08: UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Log2 and raw data. profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-08-23: HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) rlog profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-08-14: EPFL/LISP BXD HFD+CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-08-10: NIA Aging BXD CD Liver RNA-Seq (Aug18) Log2 profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-08-07: NIA Aging BXD CD Liver Affy Clariom S Gene Level (Aug18) RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-08-06: UTHSC BXD Liver Affy Clariom S GeneLevel Main (Aug18) RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-04-27: JAX Retina (Apr18) RNA-Seq log2-Z profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-04-11: UCSD AIL Prefrontal Cortex (Apr18) RNA-Seq profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-04-11: UCSD AIL Striatum (Apr18) RNA-Seq profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-04-11: UCSD AIL Hippocampus (Apr18) RNA-Seq profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2018-01-04: UTHSC BXD Harvested Liver RNA-Seq (Aug18) Log2 ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-09-29: UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-09-12: EPFL/LISP BXD HFD Gastrointestinal Affy Clariom S GeneLevel Main (Sep17) RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-09-12: EPFL/LISP BXD CD Gastrointestinal Affy Clariom S GeneLevel Main (Sep17) RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-09-12: EPFL/LISP BXD CD+HFD Gastrointestinal Affy Clariom S GeneLevel Main (Sep17) RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, HFD Cohorts (Mar 2017) log2 profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction B, Chow Diet Cohorts (Mar 2017) log2 profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, HFD Cohorts (Mar 2017) log2 profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-08-24: UTHSC/ETHZ/EPFL BXD Liver Polar Metabolites Extraction A, Chow Diet Cohorts (Mar 2017) log2 profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-04-27: INIA-UTHSC Midbrain CIE Affy MTA 1.0 Exon Level (Apr17) RMA profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-05-05: INIA-UTHSC Striatum CIE Affy MTA 1.0 GeneLevel (Apr17) RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-05-05: INIA-UTHSC Prefrontal Cortex CIE Affy MTA 1.0 GeneLevel (Apr17) RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-05-05: INIA-UTHSC Hippocampus CIE Affy MTA 1.0 GeneLevel (Mar18) RMA profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-04-28: INIA-UTHSC Midbrain CIE Affy MTA 1.0 GeneLevel (Apr17) RMA profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-25: UTHSC Hippocampus Ethanol-Stress Affy MTA 1.0 Gene Level (Mar17) RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-26: UTHSC Hippocampus Stress Affy MTA 1.0 Gene Level (Mar17) RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-27: UTHSC Hippocampus Ethanol Affy MTA 1.0 Gene Level (Mar17) RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-28: UTHSC Hippocampus Saline Affy MTA 1.0 Gene Level (Mar17) RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-29: UTHSC Hippocampus All Treatments Affy MTA 1.0 Gene Level (Mar17) RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-24: UTHSC Human Islets Affy Human Gene 2.0 ST (Mar17) RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-02: UCLA CXB Liver Affy M430 2.0 (Jan16) RMA profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-02: UCLA AXB/BXA Liver Affy M430 2.0 (Jan16) RMA profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-02: UCLA CXB Aorta Affy M430 2.0 (Jan16) RMA profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-02: UCLA AXB/BXA Aorta Affy M430 2.0 (Jan16) RMA profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-02: UCLA BXD Aorta Affy M430 2.0 (Jan16) RMA profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-03-02: UCLA BXD Liver Affy M430 2.0 (Jan16) RMA profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-02-04: UCSD CFW Prefrontal Cortex (Jan17) RNA-Seq Log2 Z-score profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-02-04: UCSD CFW Striatum (Jan17) RNA-Seq Log2 Z-score profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-02-04: UCSD CFW Hippocampus (Jan17) RNA-Seq Log2 Z-score profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-01-17: UCSD CFW Prefrontal Cortex (Jan17) RNA-Seq profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-01-17: UCSD CFW Striatum (Jan17) RNA-Seq profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2017-01-17: UCSD CFW Hippocampus (Jan17) RNA-Seq profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2016-11-28: EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2016-11-28: EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2016-11-04: UTHSC B6D2 Retina Affy miRNA-4.0 (Nov16) RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2016-10-02: BXD Genotypes file status (October 2016)

In September and October 2016, Robert Williams, Jesse Ingels, Lu Lu, and Danny Arends released new genotype files for many of the original BXD strains (BXD1 through BXD102), and for all of the new strains (BXD104 to BXD220). Genotypes were generated at about 74,000 SNPs using the GigaMUGA array developed by Drs. Fernando Pardo-Manuel de Villena (University of North Carolina) and Gary Churchill (The Jackson Laboratory). Genotypes were generated at GeneSeek (Neogen Inc) with financial support from the University of Tennessee Center for Integrative and Translational Genomics.

The new genotypes are now available in GeneNetwork as the 2017 Genotype file. All SNPs were mapped to the older July 2007 mm9 NCBI Build 37 assembly and to the newer Dec 2011, mm10, GRCm38 assembly. Of the 74,000 GigaMUGA and many other markers we have typed, only about 6800 are useful (informative) in defining recombination events in the current set of BXDs. These informative markers either define unique recombination patterns across the 198 BXD strains (including extinct strains) or they define the proximal and distal ends of regions that do not contain any known recombinations in the BXD family.

The file does not include any markers for Chr Y or the mitochondrion.

As of October 2016 GeneNetwork still uses mm9 coordinates for mapping functions.

(Updated Oct 2, 2016 by RW Williams)

2016-09-29: TIGEM Human Retina RNA-Seq (Sep16) RPKM log2 profiling by array entered into GeneNetwork. This dataset is public available, please contact Michele Pinelli at Telethon Institute of Genetics and Medicine (TIGEM) for further information. (Implemented by Michele Pinelli, Arthur Centeno and Rob Williams).
2016-09-09: UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Exon Level RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2016-09-09: UTHSC B6D2 Retina Affy MoGene 1.0ST (Sep16) Gene Level RMA ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2016-07-26: Raw and processed data from our Hippocampus studies based on publication "Genetics of the hippocampal transcriptome in mouse: a systematic survey and online neurogenomics resource" can be accessed now through GEO series GSE84767.
2016-07-16: Gene expression data for 39 inbred mice strains for CD4+ T cells profiling by array entered into GeneNetwork. GEO Series: GSE60337. To determine the breadth and underpinning of changes in immunocyte gene expression due to genetic variation in mice, we performed, as part of the Immunological Genome Project, gene expression profiling for CD4(+) T cells and neutrophils purified from 39 inbred strains of the Mouse Phenome Database.
2016-05-16: FGUCAS BXH/HXB Brown Adipose Affy Rat Gene 2.0 ST (May16) log2 profiling by array entered into GeneNetwork. Currently this dataset is confidential, please contact Michal Pravenec Czech Academy of Sciences for further information. (Implemented by Michal Pravenec, Arthur Centeno and Rob Williams).
2016-04-16: EPFL/ETHZ BXD Brown Adipose Proteome (Apr16) profiling by array entered into GeneNetwork. Currently this dataset is confidential, please contact Johan Auwerx Ecole Polytechnique Federale de Lausanne for further information. (Implemented by Johan Auwerx, Arthur Centeno and Rob Williams).
2016-04-16: DoD TATRC Retina Affy MoGene 2.0 ST profiling by array entered into GeneNetwork. Currently this dataset is confidential, please contact Eldon Geisert Emory Eye Center for further information. (Implemented by Eldon Geisert, Arthur Centeno and Rob Williams).
2016-04-16: VCU BXD NAc EtOH vs CIE Air M430 2.0 profiling by array entered into GeneNetwork. Currently this dataset is confidential, please contact Michael Miles Virginia Commonwealth University for further information. (Implemented by Michael Miles, Arthur Centeno and Rob Williams).
2016-02-16: UCAMC LXS Whole Brain Saline and Ethanol RNA Sequence FPKM profiling by array entered into GeneNetwork. Currently this dataset is confidential, please contact Richard Radcliffe University of Colorado at Denver for further information. (Implemented by Richard Radcliffe, Arthur Centeno and Rob Williams).
2016-02-16: UTHSC Hippocampus Illumina v6.1 NOS, NOE, RSS, and RSE data sets profiling by array entered into GeneNetwork.

This is untreated control "Base" group gene expression data for the hippocampus of BXD strains of mice (n = 27 strains and n = 35 animals). These data NON data are useful as baseline for comparison with NOS, NOE, RSS, and RSE data sets. NON = NON = No stress and no saline control injection; NOS = No restraint stress and given only saline injections prior to sacrifice; NOE = No restraint stress and given an ethanol injection prior to sacrifice; RSS = short restraint stress (1 episode) followed by a saline injection; and finally, RSE = Restraint stress followed by an ethanol injection.

For more details on the precise experimental paradigm, please see Ziebarth et al 2010 or the original paper that used this paradigm by Kerns RT, Ravindranathan A, Hassan S, Cage MP, York T, Williams RW, Miles MF (2005) Ethanol-responsive brain region expression networks: implications for behavioral responses to acute ethanol in DBA/2J versus C57BL/6J mice. Journal of Neuroscience 25: 2255-2266.

Please contact Rob Williams University of Tennessee Health Science Center for further information. (Implemented by Lu Lu, Arthur Centeno and Rob Williams).
2016-02-16: EPFL/LISP BXD CD+HFD Subcutaneous WAT Affy MTA 1.0 GeneLevel Main (Feb16) RMA profiling by array entered into GeneNetwork.

The BXD genetic reference population is a recombinant inbred panel descended from crosses between the C57BL/6 (B6) and DBA/2 (D2) strains of mice, which segregate for about 5 million sequence variants. Recently, some these variants have been established with effects on general metabolic phenotypes such as glucose response and bone strength. In this study, we examined both genetic variants across 40 strains of BXD and the two founder lines, in addition to a major environmental influence—long term feeding with chow diet (CD) or high fat diet (HFD)—to see how metabolic gene expression varies by genotype and environment, and gene-by-environment interactions. The basic heart phenotypes quantified in these cohorts were not affected by HFD feeding (e.g. blood pressure and heart rate).

Currently this dataset is confidential, please contact Johan Auwerx Ecole Polytechnique Federale de Lausanne for further information. (Implemented by Johan Auwerx, Arthur Centeno and Rob Williams).
2015-12-09: INIA LCM (11 Regions) RNA-seq Transcript Level (Dec15) profiling by array entered into GeneNetwork. This dataset is now public, please contact Megan Mulligan University of Tennessee Health Science Center for further information. (Implemented by Megan Mulligan, Arthur Centeno and Rob Williams).
2015-12-07: UTHSC Affy MoGene 1.0 ST Spleen profiling by array entered into GeneNetwork. This is a preliminary release with known errors of a spleen gene expression data set generated by a DOD-funded consortium (Byrne, Kotb, Williams, and Lu). Please contact Lu Lu or Robert Williams regarding status of this data set. Animals were generated at UTHSC by Lu Lu and colleagues. The spleen of untreated young adult mice was profiled using the Affymetrix GeneChip Mouse Gene 1.0 ST array that contains approximately 34,728 probe sets that target approximately 29,000 well defined transcripts (RefSeq mRNA isoforms) and essentially all known protein coding genes in mouse. This array is an "exon style" array with multiple probes in all known exons of each gene (an average of about 27 per gene) and is an abridged version of the Affymetrix Exon 1.0 ST array. However, it also does contain some probes that target non-coding RNAs and even miRNA precursors (search "ncrna").This dataset is now public, please contact Robert Williams University of Tennessee Health Science Center for further information. (Implemented by Lu Lu, Arthur Centeno and Rob Williams).
2015-11-10: Hippocampus Mouse Transcriptome Assay 1.0 GeneLevel Main (Nov15) RMA profiling by array entered into GeneNetwork. Please contact Megan Mulligan University of Tennessee Health Science Center for further information. (Implemented by Megan Mulligan, Arthur Centeno and Rob Williams).
2015-10-13: UTHSC BXD Hippocampus ILM v6.1 RSE Balanced (Feb17) RankInv profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2015-10-14: UTHSC BXD Hippocampus ILM v6.1 RSS Balanced (Feb17) RankInv profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2015-10-15: UTHSC BXD Hippocampus ILM v6.1 NOE Balanced (Feb17) RankInv profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2015-10-16: UTHSC BXD Hippocampus ILM v6.1 NOS Balanced (Feb17) RankInv profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2015-09-14: The Genotype-Tissue Expression (GTEx) is providing a comprehensive atlas of gene expression and regulation across 53 human tissues. The latest GTEx data release (dbGaP release phs000424.v5.p1) is now available on GeneNetwork.

Note: Please disregard confusing legend provided in Study tab of the study page which claims that study contains 552 subjects with genotypes - those totals are counts of subjects with all molecular data types, not just molecular genotypes.

More detailed representation of subject counts in molecular datasets (including genotypes) may be found in 'Molecular Data' tab at Common Fund (CF) Genotype-Tissue Expression Project (GTEx) dbGaP Study Accession: phs000424.v5.p1.

2015-05-30: UTHSC BXD Aged Hippocampus Affy Mouse Gene 1.0 ST (Jun15) Exon Level RMA profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.


See More News

2014-10-21: HZI Lung Flu Infected BXD (Nov16) RNA-Seq ** profiling by array entered into GeneNetwork. This dataset is publicly available in most cases. For more information on how to access the data please refer to the link above.
2014-10-10: BXD Elicited Peritoneal Neutrophils Gene Expression profiling by array entered into GeneNetwork. Currently this dataset is confidential, please contact Marko Radic University of Tennessee Health Science Center for further information. (Implemented by Marko Radic, Indira Neeli, Teruki Hagiwara, Arthur Centeno and Rob Williams).
2014-08-29: Mouse Diversity Panel Hippocampus Antidepressant profiling by array entered into GeneNetwork. Currently this dataset is confidential, please contact Brooke Miller University of Florida for further information. (Implemented by Brooke Miller, Arthur Centeno and Rob Williams).
2014-08-10: RTI RCMRC BXD Fecal Metabolites CD+HFD (Aug14) Log2 profiling by array entered into GeneNetwork.

The goal of this project is to study expression of a large set of defined and undefined metabolites in fecal samples from a genetically diverse set of BXD mouse strains (females) raised either on a high fat diet or low fat diet. Samples were taken from animals at sacrifices directly from the large intestine.

Aim: Effect of genetics and diet on fecal metabolomics
Use UPLC-MS Broad Spectrum Metabolomics to study:Mice fecal samples To capture the most signal, all samples were analyzed under positive and negative ion mode using a reversed-phase separation. Please contact Robert Clark RTI International for further information. (Implemented by Robert Clark, Arthur Centeno and Rob Williams).

2014-05-02: BXD Liver, Soluble Proteins CD and Hi-Fat Gene Expression profiling by array entered into GeneNetwork. Currently this dataset is confidential, please contact Johan Auwerx Ecole Polytechnique Federale de Lausanne for further information. (Implemented by Johan Auwerx, Evan Williams, Arthur Centeno and Rob Williams).
2014-04-03: UTHSC Mouse BXD Gastrointestinal Affy MoGene 1.0 ST Gene Level (Apr14) RMA profiling by array entered into GeneNetwork.

Currently this dataset is confidential, please contact Dennis D Black UT Le Bonheur Pediatric Specialists for further information. (Implemented by Dennis D Black, Arthur Centeno and Rob Williams).

2014-03-07: The Genotype-Tissue Expression (GTEx) is providing a comprehensive atlas of gene expression and regulation across multiple human tissues. The latest GTEx data release (dbGaP release phs000424.v4.p1) is now available on