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Sample GSM1973464 Query DataSets for GSM1973464
Status Public on Aug 25, 2016
Title 4C-seq-kit enhancer3
Sample type SRA
 
Source name expanded HSPCs sorted from mice
Organism Mus musculus
Characteristics cell type: hematopoietic stem and progenitor cells
protocol: expanded HSPCs, sorted
culture: 5 days in culture
primer set: Forward-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATC-BARCODE-ctaGGGTGAGGTAACAGATC; Reverse: CAAGCAGAAGACGGCATACGAcatattaggccatgcaaaat
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 enhancer 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 SAMN04338713
SRA SRX1484946

Supplementary file Size Download File type/resource
GSM1973464_B2-E2_TAACTC_FINAL_norm.wig.gz 5.3 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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