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| Status |
Public on Nov 18, 2020 |
| Title |
CTCF iMk |
| Sample type |
SRA |
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| Source name |
iMk cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: bone marrow derived progenitor cells
facs cell isolation sort markers: CD4-, CD8-, IL7Ra-, CD11b-, Ly6g-, CD45R-, Ter119-, Sca1-, CD41+, CD61+, cKit-
strain: C57BL/6
chip antibody: Millipore 07-729
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| 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 ChIP-seq Sample Preparation Kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| 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)
S3norm version 1(https://github.com/guanjue/S3norm) and default parameters except -r max1
CLIMB 0.1.0 with dependent Julia package cgibbs.jl version 0.1.0. CLIMB was run at the default settings in all analyses.
Genome_build: mm10
Supplementary_files_format_and_content: bigwigs, normalized read counts
Supplementary_files_format_and_content: bed, CLIMB classes
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| Submission date |
Aug 12, 2020 |
| Last update date |
Nov 18, 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 |
GPL19057 |
| Series (1) |
| GSE156074 |
High dimensional association detection in large-scale genomic data |
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| Relations |
| Reanalyzed by |
GSM4831257 |
| BioSample |
SAMN15795877 |
| SRA |
SRX8929034 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4721996_climbCtcfSigMk.bw |
72.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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