Dataset Open Access

Human-specific tandem repeat expansion and differential gene expression during primate evolution

Sulovari, Arvis; Li, Ruiyang; Audano, Peter; Porubsky, David; Vollger, Mitchell; Logsdon, Glennis; Warren, Wesley; Pollen, Alex; Chaisson, Mark; Eichler, Evan

THIS DATASET IS PART OF THE FOLLOWING STUDY:
https://www.pnas.org/content/early/2019/10/22/1912175116

 

THE RAW SEQUENCING 10x GENOMICS READS CAN BE DOWNLOADED FROM SRA:
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA593056


ORIGINAL UPLOAD: 09/06/2019

UPDATES: 10/28/2019; 01/27/2020

DESCRIPTION: Contigs were assembled using Phased-SV (Chaisson et al, Nature Communications 2019) on six human haplotypes (i.e., H0 and H1 in NA19240, HG00514, and HG00733), and six nonhuman haplotypes (this study, H0 and H1 in Clint the chimpanzee, Kamilah the gorilla, and Susie the orangutan). The long read data (PacBio CLR) from NHPs were phased into haplotypes H0 and H1 using linked reads from 10X Genomics prior to assembly, whenever possible. If not possible (e.g., in the case of long runs of homozygosity regions), long reads from both haplotypes were used to generate a "squished assembly". Using human haplotype data, we identified  21,442 polymorphic STRs/VNTRs, followed by a targetted phasing of these regions in the three NHPs. All of the human and nonhuman primate contigs were padded by 2 kbp both upstream and downstream, followed by mapping against the human reference (GRCh38). We did the same for "squished assemblies" from a Yoruban individual, CHM13, and three NHPs as described in Kronenberg et al, Science 2018. The BAM and BAI files in this dataset contain the alignment of all these contigs against GRCh38.

These BAM files contain all ~20,000 STR/VNTR contigs used in the study "Human-specific tandem repeat expansion and differential gene expression during primate evolution". Each locus is flanked by ~2 kbp of unique sequence to facilitate their anchoring in GRCh38.p12.
Files (506.0 MB)
Name Size
chm13_hsa.bam
md5:7c633d3dc110acc08709314a8a8ea22d
28.0 MB Download
chm13_hsa.bam.bai
md5:cb26845295e3152ccc544b56ce8f84c0
1.8 MB Download
clint_ptr.bam
md5:fe32a5f202101fdea18c8ddb57f37b00
33.9 MB Download
clint_ptr.bam.bai
md5:a26ae103fd2f184f79cc4571427d014c
1.8 MB Download
clint_ptr_h0.bam
md5:84654f8e61a1f0e17f4b2da62aed86fb
25.9 MB Download
clint_ptr_h0.bam.bai
md5:5ae4077767a052944fca1d59f1ca9341
1.8 MB Download
clint_ptr_h1.bam
md5:4211e06211e824bbc24ef8660b28632c
25.8 MB Download
clint_ptr_h1.bam.bai
md5:aac62802e7ab26c3da6ffa27d5f12e0d
1.8 MB Download
HG00514_h0.bam
md5:66cd808cce55c83133ce491cf6b99292
26.2 MB Download
HG00514_h0.bam.bai
md5:8f2105339402fd78ed138b3724769c16
1.8 MB Download
HG00514_h1.bam
md5:5f224bf273fc9e65c040522a238d1d9c
26.1 MB Download
HG00514_h1.bam.bai
md5:035a24c8b66b2a2b7282f91fdb913897
1.8 MB Download
HG00733_h0.bam
md5:40a1718f2e038847b5dbf3a402a37c63
27.3 MB Download
HG00733_h0.bam.bai
md5:a64945baa4756acf868ff4d04104b4eb
1.8 MB Download
HG00733_h1.bam
md5:6c47126992c55eab197fbcf1d1e2ac19
27.3 MB Download
HG00733_h1.bam.bai
md5:b0b82f1256f055f21af874610704c65a
1.8 MB Download
kamilah_ggo_h0.bam
md5:e6736f1d0fdf8abd12473cf8f5491590
24.0 MB Download
kamilah_ggo_h0.bam.bai
md5:ef5aa4e55eed4a1a7f27f9febe347dea
1.8 MB Download
kamilah_ggo_h1.bam
md5:0485a9216a1bb315ab6bcc5837fca180
24.4 MB Download
kamilah_ggo_h1.bam.bai
md5:224790fcdbaa8ea617174eefaae961c4
1.8 MB Download
NA19240_h0.bam
md5:926972f11a0015e156d9d4e6a319c747
27.2 MB Download
NA19240_h0.bam.bai
md5:1af8576744aa089fdd4e1e80c6dd366a
1.8 MB Download
NA19240_h1.bam
md5:676fa3864c03efdaa059f1770ff3a8df
27.2 MB Download
NA19240_h1.bam.bai
md5:8b4094a3294703caf0bf167d989d735e
1.8 MB Download
susie_ggo.bam
md5:4eafa26d1319e49332a164d00ff0ec0c
33.0 MB Download
susie_ggo.bam.bai
md5:a9b1cc031a6823182a3b51d990b57d94
1.8 MB Download
susie_pab.bam
md5:ededf4d60e93bbe07ab03dbc1fab575f
38.2 MB Download
susie_pab.bam.bai
md5:a8296af6f055aa118cc47659b4d146b1
1.8 MB Download
susie_pab_h0.bam
md5:6077220d0df721192376b97a6fea53cc
26.4 MB Download
susie_pab_h0.bam.bai
md5:0d649825b4eb1f60e88d0bd2cff1400c
1.8 MB Download
susie_pab_h1.bam
md5:fb7ac44a5388adcd27c3ee263cd3deb1
26.4 MB Download
susie_pab_h1.bam.bai
md5:1c481502b32bfdcdfc459606366a8ef4
1.8 MB Download
yoruban_hsa.bam
md5:cdda58a9855353f9a4d7177edb9c1960
28.0 MB Download
yoruban_hsa.bam.bai
md5:7d82926279f22360eefdf3ea9ae2c859
1.8 MB Download
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