|
| Status |
Public on Mar 23, 2017 |
| Title |
HiC_hESC |
| Sample type |
SRA |
| |
|
| Source name |
Human Embryonic Stem Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9 ESC
cell type: Human Embryonic Stem Cells
|
| Growth protocol |
Human ESC (H9/WA09; obtained from WiCell) were cultured at 37°C in 5% CO2 in air in Pluripro media and matrix (Cell Guidance Systems). ESC were routinely verified as mycoplasma-free using a PCR-based assay. ESC were differentiated into NEC using a previously described protocol (Rada-Iglesias, A. Nature 470, 279–283 (2011)) and samples were harvested on day 7.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted as described in Wilson, N.K. et al., Blood 127, e12–e23 (2016).
Hi-C and PCHi-C libraries were generated as described in Wilson, N.K. et al., Blood 127, e12–e23 (2016). For PCHi-C, ligation products containing promoter sequences were captured using a custom-made RNA capture bait system (SureSelect Target Enrichment, Agilent Technologies) designed as previously described in Mifsud, B. et al. Nat. Genet. 47, 598–606 (2015), and containing 37,608 biotinylated RNAs targeting 22,076 HindIII restriction fragment ends. Libraries were paired-end sequenced on an Illumina HiSeq 1000 machine at the Babraham Institute Sequencing Facility.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Library strategy: Hi-C-seq
Standard Illumina base-calling pipeline.
PCHi-C/Hi-C reads were mapped and filtered with HiCUP (v0.4.2) and Bowtie(v1.0.0). Significant interactions were called with CHiCAGO(v0.1.4). RNA-Seq mapping was performed with TopHat (v2.0.8b).
Genome_build: Hg19
Supplementary_files_format_and_content: Hi-C interaction file (Tabix format); RNA-Seq raw counts per gene
|
| |
|
| Submission date |
Sep 12, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Steven William Wingett |
| E-mail(s) |
steven.wingett@mrc-lmb.cam.ac.uk
|
| Organization name |
MRC Laboratory of Molecular Biology
|
| Department |
Cell Biology
|
| Street address |
Francis Crick Avenue, Cambridge Biomedical Campus
|
| City |
Cambridge |
| State/province |
Cambs |
| ZIP/Postal code |
CB2 0QH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE86821 |
Global rewiring of cis-regulatory units upon lineage commitment of human embryonic stem cells |
|
| Relations |
| BioSample |
SAMN05762671 |
| SRA |
SRX2159278 |
