|
| Status |
Public on Oct 30, 2014 |
| Title |
Jurkat_K4_25%_R2 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral blood cells
|
| Organism |
Homo sapiens |
| Characteristics |
spike-in reference organism: Drosophila melanogaster
cell line: Jurkat
spike-in cell line: S2
chip antibody: H3K4me3
antibody manu.: Millipore
antibody catalog: 07-473
syros_id: 20140211_736
drug: DMSO / EPZ
spikein_mix_ratio: 2:1
duration: 4 days
concentration: 20 uM
|
| Treatment protocol |
Jurkat cells were treated with either DMSO or EPZ (Dot1L inhibitor), then collected individually and mixed according to the following composition by cell number: 75% DMSO to 25% EPZ.
|
| Growth protocol |
Jurkat cells were treated in RPMI, 10% FBS and 1% penstrep media with regular cell care maintenance. S2 cells were grown in SFX medium (Thermo/HyClone #SH30278.02) with 1% Penicillin/Streptomycin (Invitrogen #15140) at room temperature. S2 cells acquired from NCCC and crosslinked following Syros-specified conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Lysates were clarified from sonicated cells and target bound fragments were isolated with antibody.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sample 20140404_1216 was aligned to hg19 using Bowtie2 with default parameters
Sample 20131220_425 was aligned to dm3 using Bowtie2 with default parameters
All other samples were aligned to a combined hg19/dm3 genome and reads were separated into each organism post-alignment. See manuscript for details.
Supplementary_files_format_and_content: IGV compatible TDF files represent spike-in normalized (.spikein) counts for reads aligning to human (.hg19) or drosophila (.dm3). See manuscript for details. Except for 20140404_1216 and 20131220_425 which did not contain spike-in and were normalized using RPM.
|
| |
|
| Submission date |
Aug 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Eric Olson |
| Organization name |
Syros Pharmaceuticals
|
| Street address |
480 Arsenal Street
|
| City |
Watertown |
| State/province |
MA |
| ZIP/Postal code |
02472 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE60104 |
Global ChIP-seq Normalization Reveals Epigenome Modulations |
|
| Relations |
| BioSample |
SAMN02952085 |
| SRA |
SRX669612 |
