|
| Status |
Public on Jul 08, 2020 |
| Title |
DE_BRD3IP_rep2: BRD3 ChIP-seq H1 hESC differentiated to definitive endoderm for 4 days |
| Sample type |
SRA |
| |
|
| Source name |
BRD3 H1 human Embryonic stem cells (hESC)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: H1 human Embryonic stem cells (hESC)
state: Differentiated in RPMI, B27 supplement, and 50 ng/mL activin
|
| Treatment protocol |
hESCs were differentiated for 4 days in RPMI with B27 supplement in the presence of 50 ng/ml activin A (R&D Systems) as previously described (Daneshvar et al., 2016)
|
| Growth protocol |
H1 (WA01) cells (WiCell) were cultured in mTeSR1 (Stem Cell Technologies) in feeder-free conditions as described (Daneshvar et al, 2016).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
BRD3 ChIP was pefromed using an anti-BRD3 (Bethyl A302-368A)
ChIP-seq libraries were prepared according to instructions accompanying the NEBNext Ultra DNA Library Prep Kit for Illumina.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
The signal tracks of BRD3 ChIP of hESC differentiated at 4 hr after subtracting the background (WCE) (generated by MACS2)
|
| Data processing |
ChIP-seq data were mapped o human reference genome (hg38) by bowtie2. The mapped reads were processed using MACS2 to call peaks.
Genome_build: hg38
Supplementary_files_format_and_content: Mapped ChIP-seq reads were processed with MACS2.
|
| |
|
| Submission date |
Feb 16, 2019 |
| Last update date |
Jul 08, 2020 |
| Contact name |
Alan C. Mullen |
| E-mail(s) |
mullenlabmgh@gmail.com
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Department of Medicine
|
| Street address |
55 Fruit St.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02135 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE126661 |
lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation |
|
| Relations |
| BioSample |
SAMN10958784 |
| SRA |
SRX5385028 |
