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Sample GSM4255729 Query DataSets for GSM4255729
Status Public on Jan 08, 2020
Title 1295 LSK CTCF
Sample type SRA
 
Source name bone marrow
Organism Mus musculus
Characteristics chip ab: CTCF (Millipore, 07-729, lot 2517762)
strain: C57BL6
developmental stage: adult
cell isolation markers: CD4-, CD8-, IL7Ra-, CD11b-, Ly6g-, CD45R-, Ter119-, cKit+, Sca1+
cell type: Lin-, Sca1+, cKit+
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and CTCF-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying TruSeq ChIP-seq Sample Preparation Kit. (Part# IP-202-1012). In brief, ChIP-enriched, fragmented DNA was subjected to end repair to generate blunt-end double stranded DNA, adenylation of 3’ ends, and adaptor ligation. Following ligation, SPRIselect (Beckman Coulter) beads were used at 0.9X and 0.6X for left and right side selection, respectively, to obtain an average library target size of ~300 bp. After size selection, fragments were amplified for 16 cycles, and PCR products were purified using Agencourt AMPureXP beads (Beckman Coulter).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiSeq
 
Data processing Illumina's bcl2fastq2 to generate fastq files
Mapping to reference genome 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)
UCSC's wigToBigWig to convert wiggle track
Genome_build: mm10
Supplementary_files_format_and_content: bigWig, signal from Macs
Supplementary_files_format_and_content: broadpeak, peaks from Macs
 
Submission date Jan 07, 2020
Last update date Oct 13, 2020
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 GPL16417
Series (2)
GSE143266 An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis [ChIP-seq]
GSE143271 An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis
Relations
Reanalyzed by GSM4831248
BioSample SAMN13750944
SRA SRX7517449

Supplementary file Size Download File type/resource
GSM4255729_1295.broadpeak.gz 282.9 Kb (ftp)(http) BROADPEAK
GSM4255729_1295.mm10.bw 4.6 Gb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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