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 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](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=600).
- 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)
  
  **2019-12-01: LSRU CC Male Midbrain RNA-Seq (Dec19) TPM Log2.** profiling by array entered into GeneNetwork.
   
@@ -151,6 +104,55 @@
 
  This dataset is publicly available in most cases. For more information
  on how to access the data please refer to the link above.
+ 
+**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](http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=600).
+ 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**