|
| Status |
Public on Sep 15, 2011 |
| Title |
FOXP1_ChIP-Seq_2 |
| Sample type |
SRA |
| |
|
| Source name |
H9 hESCs
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: FOXP1
chip antibody vendor: Abcam
chip antibody lot#: 958431
chip antibody catalog#: ab16645
cell type: H9 hESCs
|
| Growth protocol |
H9 hESCs were cultured under two different conditions (using feeder cells or Matrigel) to promote self-renewal. H9 ESCs were also cultured in micropatterned chambers of 200um2, 400um2 and 800um2 to control colony size, which previously has been shown induce differentiation along endoderm, mesoderm and neural-specified lineages, respectively
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction performed according to steps given by Schmidt et al. Methods 48 (2009) 240-248.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
ChIP against FOXP1 (both isoforms)
|
| Data processing |
ChIP-seq reads were aligned to the human hg19 genome assembly using Bowtie (Langmead et al., 2009) and peaks were called using QuEST (Valouev et al., 2008) with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
|
| |
|
| Submission date |
Jul 28, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Xinchen Wang |
| E-mail(s) |
xinchenw@mit.edu
|
| Organization name |
MIT
|
| Street address |
32 Vassar St, D514
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE30992 |
An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming |
| GSE31006 |
An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming [ChIP-Seq] |
|
| Relations |
| SRA |
SRX097581 |
| BioSample |
SAMN00718871 |
