|
| Status |
Public on Jul 25, 2019 |
| Title |
Gata2_SLC6ips_17787 |
| Sample type |
SRA |
| |
|
| Source name |
Human Induced Pluripotent Stem Cells (hiPSCs)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: iGATA2-hiPSC CL6
chip antibody: H-116: sc-9008, Santa Cruz
|
| Treatment protocol |
Doxycycline (Doxi) was added at a final concentration of 1 µg/ml to induce the expression of GATA2 transgene from days 2 to 7 of differentiation
|
| Growth protocol |
hiPSC lines were differentiated via embryoid body (EB) in serum-free condition cultures with the successive addition of BMP4 50 ng/ml (d0-d3), CHIR99021 3µM (d2-d3) and hematopoietic cytokines (d3-d15; SCF 300ng/ml, Flt3 300ng/ml, IL6 and IL3 10ng/ml) and maintained at 37 ºC in 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation assays were performed using ChIP-IT High Sensitive kit (Active Motif) following the manufacturer's instructions
Libraries were prepared according to Illumina instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Gata, replica #2, condition #1
|
| Data processing |
ChIPseq analysis: Alignment: Sequence reads were mapped to the Human genome (hg19) using BOWTIE (PubMed ID 19261174) with the option -m 1.
Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). ChIPseq profiles were produced by MACS in BedGraph format. Peaks were reported in BED format.
Genome_build: hg19
Supplementary_files_format_and_content: IgG_SLC9ips_17784.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Gata2_SLC9ips_17785.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: IgG_SLC6ips_17786.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Gata2_SLC6ips_17787.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Gata2_SLC6ebs_17788.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Gata2_SLC9ebs_17789.bedGraph (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: Gata2_SLC9ips_17785.bed (BED, signal enriched regions)
Supplementary_files_format_and_content: Gata2_SLC6ips_17787.bed (BED, signal enriched regions)
Supplementary_files_format_and_content: Gata2_SLC6ebs_17788.bed (BED, signal enriched regions)
Supplementary_files_format_and_content: Gata2_SLC9ebs_17789.bed (BED, signal enriched regions)
|
| |
|
| Submission date |
Dec 04, 2017 |
| Last update date |
Jul 25, 2019 |
| Contact name |
Enrique Blanco |
| E-mail(s) |
enrique.blanco@crg.eu
|
| Phone |
+34 93 316 01 00
|
| Organization name |
Center for Genomic Regulation (CRG)
|
| Department |
Gene Regulation, Stem Cells and Cancer
|
| Lab |
Epigenetic Events in Cancer (L. Di Croce's lab)
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE107639 |
Genome-wide mapping of GATA2 in human iPS |
|
| Relations |
| BioSample |
SAMN08128433 |
| SRA |
SRX3441733 |
