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Sample GSM1973459 Query DataSets for GSM1973459
Status Public on Aug 25, 2016
Title 4C-seq-kit Promoter1
Sample type SRA
 
Source name enriched c-kit cells from mice
Organism Mus musculus
Characteristics cell type: hematopoietic stem and progenitor cells
protocol: enriched c-kit cells
primer set: Forward-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCT-BARCODE-CTCCCACCTTACTCCAGATC ; Reverse-CAAGCAGAAGACGGCATACGATGAACAGCAAAAGTGTTGAG
Extracted molecule genomic DNA
Extraction protocol Cells were washed with PBS and crosslinked with 2% of formaledehyde for 10 minutes
Library was prepared according to previously published protocols (Rocha PP, Micsinai M, Kim JR, Hewitt SL, Souza PP, Trimarchi T, Strino F, Parisi F, Kluger Y, Skok JA. 2012. Close proximity to Igh is a contributing factor to AID-mediated translocations. Mol Cell 47: 873-885.)
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description 4C analysis from promoter view point
Data processing library strategy: 4C-Seq
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.0.17
Counts and wig files were normalized with DeSeq
Genome_build: mm9
Supplementary_files_format_and_content: Normalized wigs
Supplementary_files_format_and_content: csv files reporting normalized counts
 
Submission date Dec 16, 2015
Last update date May 15, 2019
Contact name Beatriz Aranda-Orgilles
Organization name NYU School of Medicine
Street address 522 First Avenue
City New York
ZIP/Postal code 10016
Country USA
 
Platform ID GPL17021
Series (2)
GSE76054 4C-seq analysis of the c-Kit locus
GSE76055 Regulation of enhancer dynamics by MED12
Relations
BioSample SAMN04338708
SRA SRX1484941

Supplementary file Size Download File type/resource
GSM1973459_5-Promoter_TCTGAT_FINAL_norm.wig.gz 13.9 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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