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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jan 08, 2020 |
Title |
1295 LSK CTCF |
Sample type |
SRA |
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Source name |
bone marrow
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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+
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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).
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina MiSeq |
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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
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Submission date |
Jan 07, 2020 |
Last update date |
Oct 13, 2020 |
Contact name |
Ross Hardison |
E-mail(s) |
rch8@psu.edu
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Organization name |
Pennsylvania State University
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Street address |
303 Wartik Lab
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City |
University Park |
State/province |
PA |
ZIP/Postal code |
16802 |
Country |
USA |
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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 |
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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 Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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