|
| Status |
Public on Oct 17, 2021 |
| Title |
JLMG_LowCell_400k |
| Sample type |
SRA |
| |
|
| Source name |
THP1
|
| Organism |
Homo sapiens |
| Characteristics |
cancer: Acute Myeloid Leukemia
chip antibody: H3K27Ac (Abcam, Catalog 4729)
syros chip-seq protocol: SOP (low-cell)
syros_id: 20150616_3412
|
| Growth protocol |
THP1 cells were purchased from ATCC and cultured according to vendor’s instruction at 37°C in 5% CO2 and in a humidified incubator.
|
| 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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Aligned to hg19 using bowtie2-2.0.5/bowtie2 with configuration -p 4 --sensitive
ChIP-seq reads were aligned to the hg19 genome assembly
Genome_build: hg19
Supplementary_files_format_and_content: TDF files(s) represent counts of aligned reads within 1 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1
|
| |
|
| Submission date |
Oct 17, 2018 |
| Last update date |
Oct 17, 2021 |
| 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 (2) |
| GSE121430 |
SY-1365, a covalent, first in-class CDK7 inhibitor for cancer treatment (ChIP-Seq) |
| GSE121431 |
SY-1365, a covalent, first in-class CDK7 inhibitor for cancer treatment |
|
| Relations |
| BioSample |
SAMN10254777 |
| SRA |
SRX4901064 |
