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Sample GSM7152473 Query DataSets for GSM7152473
Status Public on Apr 10, 2023
Title G1E CTCF [2628]
Sample type SRA
 
Source name cell line
Organism Mus musculus
Characteristics cell type: G1E
strain: C57BL/6
chip antibody: CTCF
Growth protocol G1E and G1E-ER4 cells were grown in IMDM media + 15% FBS, kit ligand, and erythropoietin in a standard tissue culture incubator at 37°C with 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Lysates were prepared from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq samples were prepared by end repair, 3’ adenylation, and adaptor ligation using Illumina’s TruSeq ChIP-seq Sample Preparation Kit.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm10 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Filter blacklist regions from peaks, and convert the *peaks.xls file from MACs to broadpeak format (see UCSC Genome Browser for format specs)
Assembly: mm10
Supplementary files format and content: bigWigs, signal from MACS
 
Submission date Apr 06, 2023
Last update date Apr 11, 2023
Contact name Ross Hardison
E-mail(s) rch8@psu.edu
Organization name Pennsylvania State University
Street address 303 Wartik Lab
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platform ID GPL19057
Series (2)
GSE229100 Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes [mouse TFbs]
GSE229101 Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
Relations
BioSample SAMN34091135
SRA SRX19892449

Supplementary file Size Download File type/resource
GSM7152473_2628.mm10.bw 3.5 Gb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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