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Sample GSM4255731 Query DataSets for GSM4255731
Status Public on Jan 08, 2020
Title 183 MEP input
Sample type SRA
Source name bone marrow
Organism Mus musculus
Characteristics chip ab: none
strain: C57BL6
developmental stage: adult
cell isolation markers: CD4-, CD8-, IL7Ra-, CD11b-, Ly6g-, CD45R-, Ter119-, cKit+, Sca1-, CD34-, CD16/32-
cell type: megakaryocyte erythroid progenitor
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 HiSeq 2000
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 Jan 08, 2020
Contact name Ross Hardison
Organization name Pennsylvania State University
Street address 303 Wartik Lab
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
Platform ID GPL13112
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
BioSample SAMN13750942
SRA SRX7517451

Supplementary file Size Download File type/resource 3.4 Gb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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