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| Status |
Public on Sep 26, 2016 |
| Title |
697 H3K27ac ChIP-seq |
| Sample type |
SRA |
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| Source name |
697 cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: 697
cell type: B-ALL
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| Treatment protocol |
The ChIP-protocol has been adapted from previous studies (Lee et al. 2006). In brief, 100*106 cells were cross-linked with 1,1% formaldehyde (Sigma-Aldrich, F1635) at room temperature for 10 min and the cross-linking reaction was quenched with glycine (125 mM final concentration, Sigma-Aldrich, G-8790). Nuclei were isolated and chromatin was purified by chemical lysis. Next, the purified chromatin was fragmented to 200-300 bp fragments by sonication (Covaris, S220, Focused-ultrasonicator). Chromatin immunoprecipitation was performed by incubation of the chromatin fraction overnight with 100 ul of protein-A coated beads (Thermo-Scientific, catalog number 53139) and 10 μg of H3K27ac-specific antibody (Abcam, ab4729). The next day, beads were washed to remove non-specific binding events and enriched chromatin fragments were eluted from the beads, followed by reverse cross-linking by incubation at 65°C overnight.
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| Growth protocol |
Cells were grown in RPMI supplemented with 10% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified by phenol/chloroform extraction, assisted by phase lock gel tubes (5Prime).
TruSeq
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Aligned to hg19 using bowtie2, default settings, mapq>4
peak calling using macs2 with input DNA as control
Genome_build: hg19
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| Submission date |
Apr 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Farzaneh Ghazavi |
| E-mail(s) |
farzaneh.ghazavi@ugent.be
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| Organization name |
Gent university hospital
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| Department |
Center of medical genetics
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| Street address |
De Pintelaan 185
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| City |
Ghent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE79870 |
H3K27ac ChIP-Seq in REH and 697 |
| GSE79873 |
Unique long non-coding RNA expression signature in ETV6/RUNX1-driven B-cell precursor acute lymphoblastic leukemia |
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| Relations |
| BioSample |
SAMN04605045 |
| SRA |
SRX1677199 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2107712_697_H3K27ac_peaks.txt.gz |
2.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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