|
| Status |
Public on May 22, 2014 |
| Title |
Control_IgG, replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
hASC_Control_IgG
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Adipose stromal cell (ASC) adipocyte
time (relative to induction): 12 days
chip antibody: rabbit IgG
chip antibody vendor: Santa Cruz Biotechnology
chip antibody cat.#: sc-2027
|
| Growth protocol |
The isolation procedure and culture/differentiation conditions have been described previously (PMID:23393180; 15492368).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested and nuclear fractions were enriched by a brief sonication in lysis buffer . Then protein-DNA complexes were isolated with antibody.
ChIP-sequencing libraries were prepared using NEBnext chip-seq library Prep master mix set (New England Biolabs, USA) from 5 ng of anti-EBF1 and anti-IgG ChIP DNA according to manufacturer's protocol.The concentration of the library was determined by Nanodrop spectrophotometer (Thermo Fisher Scientific Inc.) and 10 pmol of the DNA was applied for one flow-cell lane.samples were indexed with DNA barcodes and 3 different samples were multiplexed in one library and sequenced using Illumina HiSeq 2000 (single 36 bp reads). Barcode for IgG sample is ATTT and for EBF1 sample is GCCT in replicate 1 In replicate2, barcode for IgG sample is ACAT and for EBF1 sample is TAAT .
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 3
|
| Data processing |
Basecalls performed using Casava 1.4
Fastq files were split by barcode.
Reads were aligned to the human genome (hg19) using BWA 0.5.0
peaks were called by two different approaches, MACS 1.4 and Homer , using default settings. Regions that were detected by both methods were considered as the binding regions
Genome_build: hg19
|
| |
|
| Submission date |
Feb 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
hui Gao |
| E-mail(s) |
hui.gao@ki.se
|
| Organization name |
Karolinska Institutet
|
| Department |
Department of Biosciences and Nutrition
|
| Street address |
Novum
|
| City |
Huddinge |
| ZIP/Postal code |
14183 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE54889 |
Early B-cell Factor 1 Regulates Adipocyte Morphology and Lipolysis in White Adipose Tissue [ChIP-seq] |
| GSE54890 |
Early B-cell Factor 1 Regulates Adipocyte Morphology and Lipolysis in White Adipose Tissue |
|
| Relations |
| BioSample |
SAMN02640211 |
| SRA |
SRX469459 |
