|
| Status |
Public on Dec 25, 2013 |
| Title |
UtE-iPS-11.input |
| Sample type |
SRA |
| |
|
| Source name |
hiPSC
|
| Organism |
Homo sapiens |
| Characteristics |
line name: UtE-iPS-11
ip antibody: input
antibody source: NA
antibody lot: NA
|
| Growth protocol |
Human iPSCs were maintained on irradiated MEFs in 0222 medium (MED SHIROTORI CO., Ltd, Tokyo, Japan) supplemented with 10 ng/ml recombinant human basic fibroblast growth factor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed in ChIP buffer (50 mM Tris-HCl pH 7.9, 150 mM NaCl, 1% Triron X-100, 0.5% NP-40, 5 mM EDTA pH 8.0, 1 mM PMSF and protease inhibitor) and chromatin was sonicated to ~200 bp with a Diagenode Bioruptor
Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
mapped to hg19 with BOWTIE -m4 -v2
1nt resolution bedgraphs were generated with the BEDtools bamToBed and genomeCoverageBed utilities after extending each read to 200
coverage was normalized to FP10M (fragments per 10 million reads sequenced)
bigWig files were generated with bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: FP10M-normalized bigWigs
|
| |
|
| Submission date |
Jul 03, 2013 |
| Last update date |
Feb 04, 2022 |
| Contact name |
Roberto Bonasio |
| Organization name |
University of Pennsylvania
|
| Department |
Cell and Developmental Biology
|
| Lab |
Bonasio
|
| Street address |
3400 Civic Center Blvd - SCTR 9-111
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE48516 |
ChIP-seq in MEG3+ and MEG3- hIPSCs |
| GSE48518 |
Interactions between JARID2 and noncoding RNAs regulate PRC2 recruitment to chromatin |
|
| Relations |
| BioSample |
SAMN02225342 |
| SRA |
SRX317596 |
