Degner12, Variation in DNaseI sensitivity among individuals

Description

DNaseI sequencing was used to measure chromatin accessibility in 70 Yoruba lymphoblastoid cell lines, for which genome-wide genotypes and estimates of gene expression levels are also available.

Source

Files downloaded from FTP site: ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP007/SRP007821
Input file format: SRA

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly

Filename Description Feature GEO-ID
1 GSM778663.sga GM18486 - DNaseI DNaseI GSM778663
2 GSM778664.sga GM18498 - DNaseI DNaseI GSM778664
3 GSM778665.sga GM18499 - DNaseI DNaseI GSM778665
4 GSM778666.sga GM18501 - DNaseI DNaseI GSM778666
5 GSM778667.sga GM18502 - DNaseI DNaseI GSM778667
6 GSM778668.sga GM18504 - DNaseI DNaseI GSM778668
7 GSM778669.sga GM18505 - DNaseI DNaseI GSM778669
8 GSM778670.sga GM18507 - DNaseI DNaseI GSM778670
9 GSM778671.sga GM18508 - DNaseI DNaseI GSM778671
10 GSM778672.sga GM18510 - DNaseI DNaseI GSM778672
11 GSM778673.sga GM18511 - DNaseI DNaseI GSM778673
12 GSM778674.sga GM18516 - DNaseI DNaseI GSM778674
13 GSM778675.sga GM18517 - DNaseI DNaseI GSM778675
14 GSM778676.sga GM18519 - DNaseI DNaseI GSM778676
15 GSM778677.sga GM18520 - DNaseI DNaseI GSM778677
16 GSM778678.sga GM18522 - DNaseI DNaseI GSM778678
17 GSM778679.sga GM18852 - DNaseI DNaseI GSM778679
18 GSM778680.sga GM18853 - DNaseI DNaseI GSM778680
19 GSM778681.sga GM18855 - DNaseI DNaseI GSM778681
20 GSM778682.sga GM18856 - DNaseI DNaseI GSM778682
21 GSM778683.sga GM18858 - DNaseI DNaseI GSM778683
22 GSM778684.sga GM18859 - DNaseI DNaseI GSM778684
23 GSM778685.sga GM18861 - DNaseI DNaseI GSM778685
24 GSM778686.sga GM18862 - DNaseI DNaseI GSM778686
25 GSM778687.sga GM18870 - DNaseI DNaseI GSM778687
26 GSM778688.sga GM18907 - DNaseI DNaseI GSM778688
27 GSM778689.sga GM18909 - DNaseI DNaseI GSM778689
28 GSM778690.sga GM18912 - DNaseI DNaseI GSM778690
29 GSM778691.sga GM18913 - DNaseI DNaseI GSM778691
30 GSM778692.sga GM18916 - DNaseI DNaseI GSM778692
31 GSM778693.sga GM19092 - DNaseI DNaseI GSM778693
32 GSM778694.sga GM19093 - DNaseI DNaseI GSM778694
33 GSM778695.sga GM19098 - DNaseI DNaseI GSM778695
34 GSM778696.sga GM19099 - DNaseI DNaseI GSM778696
35 GSM778697.sga GM19101 - DNaseI DNaseI GSM778697
36 GSM778698.sga GM19114 - DNaseI DNaseI GSM778698
37 GSM778699.sga GM19116 - DNaseI DNaseI GSM778699
38 GSM778700.sga GM19119 - DNaseI DNaseI GSM778700
39 GSM778701.sga GM19127 - DNaseI DNaseI GSM778701
40 GSM778702.sga GM19130 - DNaseI DNaseI GSM778702
41 GSM778703.sga GM19131 - DNaseI DNaseI GSM778703
42 GSM778704.sga GM19137 - DNaseI DNaseI GSM778704
43 GSM778705.sga GM19138 - DNaseI DNaseI GSM778705
44 GSM778706.sga GM19140 - DNaseI DNaseI GSM778706
45 GSM778707.sga GM19141 - DNaseI DNaseI GSM778707
46 GSM778708.sga GM19143 - DNaseI DNaseI GSM778708
47 GSM778709.sga GM19144 - DNaseI DNaseI GSM778709
48 GSM778710.sga GM19147 - DNaseI DNaseI GSM778710
49 GSM778711.sga GM19152 - DNaseI DNaseI GSM778711
50 GSM778712.sga GM19153 - DNaseI DNaseI GSM778712
51 GSM778713.sga GM19159 - DNaseI DNaseI GSM778713
52 GSM778714.sga GM19160 - DNaseI DNaseI GSM778714
53 GSM778715.sga GM19171 - DNaseI DNaseI GSM778715
54 GSM778716.sga GM19190 - DNaseI DNaseI GSM778716
55 GSM778717.sga GM19192 - DNaseI DNaseI GSM778717
56 GSM778718.sga GM19193 - DNaseI DNaseI GSM778718
57 GSM778719.sga GM19200 - DNaseI DNaseI GSM778719
58 GSM778720.sga GM19201 - DNaseI DNaseI GSM778720
59 GSM778721.sga GM19203 - DNaseI DNaseI GSM778721
60 GSM778722.sga GM19204 - DNaseI DNaseI GSM778722
61 GSM778723.sga GM19206 - DNaseI DNaseI GSM778723
62 GSM778724.sga GM19207 - DNaseI DNaseI GSM778724
63 GSM778725.sga GM19209 - DNaseI DNaseI GSM778725
64 GSM778726.sga GM19210 - DNaseI DNaseI GSM778726
65 GSM778727.sga GM19222 - DNaseI DNaseI GSM778727
66 GSM778728.sga GM19223 - DNaseI DNaseI GSM778728
67 GSM778729.sga GM19225 - DNaseI DNaseI GSM778729
68 GSM778730.sga GM19238 - DNaseI DNaseI GSM778730
69 GSM778731.sga GM19239 - DNaseI DNaseI GSM778731
70 GSM778732.sga GM19257 - DNaseI DNaseI GSM778732

Technical Notes

Raw data was downloaded from NCBI SRA database (ID SRP007821) and mapped to hg19 genome using Bowtie aligner. The resulting SAM files were converted to BED using SAMtools and BEDtools. Final conversion to SGA files was done using ChIP-Seq.

References

Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, Pritchard JK
DNaseI sensitivity QTLs are a major determinant of human expression variation. Nature. 2012 Feb 5;482(7385):390-4. PubMed PMID: 22307276

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