|
| Status |
Public on Aug 05, 2016 |
| Title |
Kasumi-3_GATA2_N1 |
| Sample type |
SRA |
| |
|
| Source name |
Kasumi-3 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Kasumi-3
|
| Treatment protocol |
Samples containing 3 x 10^6 cells were crosslinked with 1% formaldehyde for 10 min. Crosslinking reaction was extinguished by adding glycine to 125 mM. Lysates were immunoprecipitated with rabbit polyclonal anti-GATA-2 antibody.
|
| Growth protocol |
Kasumi-3 cells were maintained in RPMI 1640 medium (Invitrogen/Thermo Fisher Scientific, Waltham, MA, USA) containing 1% penicillin-streptomycin and 20% fetal bovine serum (FBS).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-Seq was performed by Peggy J. Farnham at University of Southern California. Immunoprecipitated DNA was processed into Illumina libraries using standard procedures, and libraries were sequenced on Illumina GenomeAnalyzer Iix.
Immunoprecipitated DNA was processed into Illumina libraries using standard procedures.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
GATA-2 ChIP-seq in a human AML cell line
untreated cells
|
| Data processing |
Sequence reads were aligned to the genome using the Eland alignment program.
Data was scored using Sole-Search based on sequence reads (length ~30 bps) that align uniquely to human genome (build hg19 ). From the mapped tags, a signal map of ChIP DNA fragments (average fragment length ~ 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome.
Peaks were called using Sole-search (false-discovery rate, 0.0001; α value 0.001) with sequenced Kasumi-3 input DNA as background.
Genome_build: hg19
Supplementary_files_format_and_content: sgr files were generated using Sole-search
|
| |
|
| Submission date |
Jul 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kyle Hewitt |
| E-mail(s) |
KJHEWITT@WISC.EDU
|
| Organization name |
University of Wisconsin
|
| Street address |
1111 Highland Ave.
|
| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE84782 |
GATA-2 occupancy in Kasumi-3 cell line |
|
| Relations |
| BioSample |
SAMN05437877 |
| SRA |
SRX1974321 |
