Del Rosario 2015, H3K27ac profiles in multiple lymphoblastoid cell lines.

Description

ChIP-seq against H3K27ac in 57 human lymphoblastoid cell lines coming from a single population.
A single-ended sample and paired-ended samples are used as control.

Source

Samples

From Human Feb. 2009 (GRCh37/hg19) Assembly.

ChIP-seq data:

Filename Description Feature GEO-ID
1 GSM1420889.sga GM18486|H3K27ac|PairedEnd H3K27ac GSM1420889
2 GSM1420890.sga GM18498|H3K27ac|PairedEnd H3K27ac GSM1420890
3 GSM1420869.sga GM18499|H3K27ac|PairedEnd H3K27ac GSM1420869
4 GSM1420841.sga GM18502|H3K27ac|PairedEnd H3K27ac GSM1420841
5 GSM1420842.sga GM18504|H3K27ac|PairedEnd H3K27ac GSM1420842
6 GSM1420843.sga GM18507|H3K27ac|PairedEnd H3K27ac GSM1420843
7 GSM1420844.sga GM18508|H3K27ac|PairedEnd H3K27ac GSM1420844
8 GSM1420891.sga GM18510|H3K27ac|PairedEnd H3K27ac GSM1420891
9 GSM1420892.sga GM18511|H3K27ac|PairedEnd H3K27ac GSM1420892
10 GSM1420871.sga GM18516|H3K27ac|SingleEnd H3K27ac GSM1420871
11 GSM1420872.sga GM18517|H3K27ac|SingleEnd H3K27ac GSM1420872
12 GSM1420870.sga GM18519|H3K27ac|PairedEnd H3K27ac GSM1420870
13 GSM1420893.sga GM18520|H3K27ac|PairedEnd H3K27ac GSM1420893
14 GSM1420873.sga GM18522|H3K27ac|SingleEnd H3K27ac GSM1420873
15 GSM1420874.sga GM18523|H3K27ac|SingleEnd H3K27ac GSM1420874
16 GSM1420875.sga GM18852|H3K27ac|SingleEnd H3K27ac GSM1420875
17 GSM1420876.sga GM18853|H3K27ac|SingleEnd H3K27ac GSM1420876
18 GSM1420877.sga GM18855|H3K27ac|PairedEnd H3K27ac GSM1420877
19 GSM1420845.sga GM18856|H3K27ac|PairedEnd H3K27ac GSM1420845
20 GSM1420846.sga GM18861|H3K27ac|PairedEnd H3K27ac GSM1420846
21 GSM1420847.sga GM18862|H3K27ac|PairedEnd H3K27ac GSM1420847
22 GSM1420848.sga GM18870|H3K27ac|PairedEnd H3K27ac GSM1420848
23 GSM1420894.sga GM18909|H3K27ac|PairedEnd H3K27ac GSM1420894
24 GSM1420878.sga GM18912|H3K27ac|PairedEnd H3K27ac GSM1420878
25 GSM1420879.sga GM18913|H3K27ac|PairedEnd H3K27ac GSM1420879
26 GSM1420895.sga GM18916|H3K27ac|PairedEnd H3K27ac GSM1420895
27 GSM1420849.sga GM19093|H3K27ac|PairedEnd H3K27ac GSM1420849
28 GSM1420865.sga GM19098|H3K27ac|PairedEnd H3K27ac GSM1420865
29 GSM1420866.sga GM19099|H3K27ac|PairedEnd H3K27ac GSM1420866
30 GSM1420883.sga GM19101|H3K27ac|PairedEnd H3K27ac GSM1420883
31 GSM1420851.sga GM19102|H3K27ac|PairedEnd H3K27ac GSM1420851
32 GSM1420896.sga GM19114|H3K27ac|PairedEnd|rep1 H3K27ac GSM1420896
33 GSM1420898.sga GM19114|H3K27ac|PairedEnd|rep2 H3K27ac GSM1420898
34 GSM1420855.sga GM19116|H3K27ac|PairedEnd H3K27ac GSM1420855
35 GSM1420888.sga GM19119|H3K27ac|PairedEnd H3K27ac GSM1420888
36 GSM1420860.sga GM19127|H3K27ac|PairedEnd H3K27ac GSM1420860
37 GSM1420859.sga GM19128|H3K27ac|PairedEnd H3K27ac GSM1420859
38 GSM1420858.sga GM19130|H3K27ac|PairedEnd H3K27ac GSM1420858
39 GSM1420857.sga GM19131|H3K27ac|PairedEnd H3K27ac GSM1420857
40 GSM1420884.sga GM19137|H3K27ac|PairedEnd H3K27ac GSM1420884
41 GSM1420885.sga GM19138|H3K27ac|PairedEnd H3K27ac GSM1420885
42 GSM1420856.sga GM19140|H3K27ac|PairedEnd H3K27ac GSM1420856
43 GSM1420864.sga GM19143|H3K27ac|PairedEnd H3K27ac GSM1420864
44 GSM1420861.sga GM19144|H3K27ac|PairedEnd H3K27ac GSM1420861
45 GSM1420897.sga GM19147|H3K27ac|PairedEnd|rep1 H3K27ac GSM1420897
46 GSM1420899.sga GM19147|H3K27ac|PairedEnd|rep2 H3K27ac GSM1420899
47 GSM1420863.sga GM19152|H3K27ac|PairedEnd H3K27ac GSM1420863
48 GSM1420862.sga GM19153|H3K27ac|PairedEnd H3K27ac GSM1420862
49 GSM1420880.sga GM19159|H3K27ac|PairedEnd H3K27ac GSM1420880
50 GSM1420881.sga GM19160|H3K27ac|PairedEnd H3K27ac GSM1420881
51 GSM1420886.sga GM19171|H3K27ac|PairedEnd H3K27ac GSM1420886
52 GSM1420852.sga GM19172|H3K27ac|PairedEnd H3K27ac GSM1420852
53 GSM1420867.sga GM19193|H3K27ac|PairedEnd H3K27ac GSM1420867
54 GSM1420853.sga GM19200|H3K27ac|PairedEnd H3K27ac GSM1420853
55 GSM1420887.sga GM19201|H3K27ac|PairedEnd H3K27ac GSM1420887
56 GSM1420854.sga GM19209|H3K27ac|PairedEnd H3K27ac GSM1420854
57 GSM1420850.sga GM19210|H3K27ac|PairedEnd H3K27ac GSM1420850
58 GSM1420882.sga GM19222|H3K27ac|PairedEnd H3K27ac GSM1420882
59 GSM1420868.sga GM19239|H3K27ac|PairedEnd H3K27ac GSM1420868
60 GSM1420900.sga GM19147|Input|PairedEnded100bp Input GSM1420900
61 GSM1420902.sga GM19147|Input|PairedEnded50bp Input GSM1420902
62 GSM1420901.sga GM19147|Input|SingleEnded100bp Input GSM1420901

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.5.0) and mapped to the hg19 genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2).
For paired-ended data, the sga files provide the unoriented middle position of the fragments and for single-ended reads the starting or ending position of the reads.

References

Last update: 02 September 2017