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author | acenteno | 2021-06-15 15:08:15 -0500 |
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committer | acenteno | 2021-06-15 15:08:15 -0500 |
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Update news.md
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diff --git a/general/news/news.md b/general/news/news.md index f90f789..e52d2ad 100644 --- a/general/news/news.md +++ b/general/news/news.md @@ -35,54 +35,7 @@ 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** |