|
| Status |
Public on Jul 30, 2014 |
| Title |
iPSC_MED1_ChipSeq |
| Sample type |
SRA |
| |
|
| Source name |
iPSC
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: Med1/TRAP220
antibody catalog number: Bethyl A300-793A
cell type: NGFP iPSC
young_id: 02282013_D1T3YACXX_8.GCCAAT
|
| Growth protocol |
V6.5 (C57BL/6-129) and SHBcT4 murine ES cell lines and Nanog-GFP OSKM#2 iPSCs were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates. Colonies 23 and 44 were grown under typical ES conditions plus 2ug/ml doxycycline. Oct4-GFP OSKM#2 and #4 and Oct4-GFP SNEL#3 and #4 were grown under ESC naive 2i condition without feeder. MEFs were grown in DMEM supplemented with 10%FBS, Glutamine and P/S.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Library construction protocol: Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Chromatin IP against iPSC_MED1
barcode: GCCAAT
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files: For all samples, reads were aligned with bowtie 0.12.9 to the mm9 genome. Aligned sequences were processed with MACS 1.4.2 with parameters -w -S --space=50 --keep-dup=auto -p 1e-9. Counts were normalized to reads per million.
|
| |
|
| Submission date |
Jul 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE59569 |
The developmental potential of iPSCs is greatly influenced by the selection of the reprogramming factors |
|
| Relations |
| BioSample |
SAMN02927215 |
| SRA |
SRX657141 |
