Cattle Genome Analysis Data Repository
Data Repository
Name Size Time Last Modified
ARS-UCD1.2_HISAT2Index 9 files2018-04-26 09:34:04
BTA4_masked.tgz 1.13 GB2010-05-24 08:29:48
Bov58kSNP_pos_Btau4_7.7.2008.README 1.53 KB2009-07-20 20:25:25
Bov58kSNP_pos_Btau4_7.7.2008.tab 4.6 MB2009-07-20 20:25:26
BovineHD_Ensembl_vep_76.txt.gz 15.46 MB2015-02-05 18:55:26
BovineHD_rs-ss-name-map2.xls.gz 30.69 MB2016-09-21 21:42:38
BovineHD_rs_111105.csv.gz 9.55 MB2011-11-06 08:11:18
BovineLD_Ensembl_vep_76.txt.gz 248.93 KB2015-02-05 18:57:09
BovineSNP50_Ensembl_vep_76.txt.gz 1.56 MB2015-02-05 19:01:55
Genome_annotations 192 files2016-09-10 21:52:23
ILumina_770K_nonagreement_markers.xlsx 92.76 KB2011-12-02 16:19:17
ISU_annotations.54kSNP.txt.gz 2.05 MB2012-03-22 09:29:30
ISU_annotations.770kSNP.txt.gz 12.86 MB2012-04-09 16:37:53
ISU_annotations.README 6.3 KB2012-04-10 07:35:07
Illinoi_Beever_Project.2012 9 files2014-05-23 17:43:09
LinkageMap.2009.txt.gz 117.19 KB2013-09-12 12:07:45
Related_genes_by_TOM_connectivity.txt.gz 1.54 GB2016-02-09 20:32:43
Repeats_in_assembly_3.1.tgz 1.31 MB2010-05-24 08:25:04
UMC_bovine_coordinates 2 files2018-10-30 21:00:04
UMD3.1_masked.tgz 899.08 MB2010-05-24 08:24:09
UMD3_56ksnps.gff 4.84 MB2011-01-23 21:12:19
UMD3_RepeatMasked.tar.gz 970.2 MB2009-10-29 13:17:14
UMD3_chr.gff.tar.gz 770.35 MB2010-12-16 17:10:19
nagrp_share 3 files2018-08-28 17:57:08
The NAGRP Data Repository: 231 data files at the current location
Data sources/credits:

Bov58kSNP_pos_Btau4_7.7.2008.tab
 - Positions of 58k SNP panel on the bovine genome assembly Btau_4.0

BovineHD_rs-ss-name-map2.xls.gz
 - 770K HD SNP chip: dbSNP "rs"/"ss"/custom SNP names/map locations match
 - Data source: NCBI dbSNP; Process/scripts by Zhiliang Hu[zhuiastate.edu]
 - Fields: 1. rs numbers
           2. ss numbers
           3. custom names
           4. BTAU map locations
           5. UMD map locations

BovineHD_rs_111105.csv.gz
 - 770K HD SNP chip: rs/ss numbers (Cattle High Density SNP Chip
   Consortium; file sent by Robert Schnabel [schnabelrmissouri.edu])
 - Fields: 1. snp_number
           2. snp50_snp_number
           3. marker_name
           4. rs_id
           5. ss_id

BovineHD_Ensembl_vep_76.txt.gz
 - Ensembl VEP annotated bovine high density SNP data (770K SNP panel)
  (Ensembl Release 76)

BovineLD_Ensembl_vep_76.txt.gz
 - Ensembl VEP annotated bovine low density SNP data (6K SNP panel)
  (Ensembl Release 76)

BovineSNP50_Ensembl_vep_76.txt.gz
 - Ensembl VEP annotated bovine 50K SNP chip data

BTA4_masked.tgz
 - Contributed by Dave Adelson [david.adelsonadelaide.edu.au]
 - ( http://genomes.sapac.edu.au/bovine_pub/ )

ILumina_770K_nonagreement_markers.xlsx
 - 770K ILumina HD SNPs - structural genomics analysis
   Contributed by James Reecy [ jreecyiastate.edu ]

ISU_annotations.54kSNP.txt.gz
ISU_annotations.770kSNP.txt.gz
 - By James Koltes [jekoltesmail.iastate.edu] (Iowa State University)

LinkageMap.2009.txt.gz
 - Additional data for the publication by JA Arias, M Keehan, P Fisher,
   W Coppieters and R Spelman (2009). "A high density linkage map of
   the bovine genome". (BMC Genetics 2009, 10:18).
   ( http://link.springer.com/article/10.1186%2F1471-2156-10-18 )

Repeats_in_assembly_3.1.tgz
 - Contributed by Dave Adelson [david.adelsonadelaide.edu.au]
 - ( http://genomes.sapac.edu.au/bovine_pub/ )

Genome_Annotattions
 o Versions: Both UMD and BTAU versions are available
 o Data types: 1. fasta
               2. genbank
               3. masked fasta

Related_genes_by_TOM_connectivity.txt.gz
 Weighted correlation network analysis on the GEO archive data was
 performed to estimate the gene expression connectivity using
 "Topological Overlap Measure (TOM)" ( Langfelder P, Horvath S:
 BMC bioinformatics 2008, 9:559) to find 137,887,921 connectivities
 among 11,125 genes represented by 16,608 probe sets.  There is also
 a web query tool built for this data set to allow extraction of TOM
 connectivity information on targeted genes. For more information,
 contact:
  Hamid Beiki (beikiiastate.edu) or
  James Reecy (jreecyiastate.edu)

UMC_bovine_coordinates
 Genome coordinates from genotyping assays
 - Data from Robert Schnabel (schnabelrmissouri.edu)
   University of Missouri

UMD3.1_masked.tgz
 - Contributed by Dave Adelson [david.adelsonadelaide.edu.au]
 - ( http://genomes.sapac.edu.au/bovine_pub/ )

UMD3_56ksnps.gff
 - Converted from "BovPortfoliCoord_20100801" data file forwarded
   by Jim Reecy.  __Zhiliang

UMD3_RepeatMasked.tar.gz
 - Contributed by Lakshmi Matukumalli [lmatukumanri.barc.usda.gov]
 - ( http://bfgl.anri.barc.usda.gov/tmp/UMD3_RepeatMasked.tar.gz )

UMD3_chr.gff.tar.gz
 - Converted from NCBI UMD3 data (http://eutils.ncbi.nlm.nih.gov)
   with Bioperl scripts.    __Zhiliang

nagrp_share
 - NAGRP (NRSP-8) community members shared files. Password required.
 
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