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Sample GSM1326218 Query DataSets for GSM1326218
Status Public on May 22, 2014
Title Control_IgG, replicate1
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 1
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 SAMN02640208
SRA SRX469457

Supplementary file Size Download File type/resource
GSM1326218_control_IgG_rep1_density.wig.gz 106.9 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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