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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 01, 2012 |
| Title |
RenLab-CTCF-spleen |
| Sample type |
SRA |
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| Source name |
Mouse spleen
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
chip antibody: CTCF
chip antibody details: Kim et al., 2007
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| Treatment protocol |
None
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| Growth protocol |
Adult liver, kidney, bone marrow, lung, heart, cortex, cerebellum, spleen were dissected from 8-week old male C57Bl/6 mice (Charles River). Mouse embryonic fibroblast (MEF) MEF cells were derived from E13.5 C57Bl/6 mouse embryos and genotyping was performed to select male MEF cells used for this study. mESC line Bruce4 was maintained on mitomycin C-inactivated MEF feeder layers in DME containing 15% fetal calf serum, leukemia inhibiting factor, penicillin/streptomycin, L-glutamine and non-essential amino acids. All ES cells were passaged on 0.2 % gelatin twice to deplete feeder cells before harvest for experiments.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
CTCF IP
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| Data processing |
RenLab-CTCF-spleen-DM406.bam: Alignment to mm9 using Bowtie software with a seed length of 25 bases and up to 2 mismatches. Only sequences mapping to exactly one location were kept. If multiple sequences aligned to the same location, all but one of the sequences were discarded.
RenLab-CTCF-spleen-DM431.bam: Alignment to mm9 using Bowtie software with a seed length of 25 bases and up to 2 mismatches. Only sequences mapping to exactly one location were kept. If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq: Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.
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| Submission date |
May 11, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Bing Ren |
| E-mail(s) |
biren@ucsd.edu
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| Organization name |
University of California, San Diego
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| Street address |
9500 Gilman Drive
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE29184 |
A draft map of cis-regulatory sequences in the mouse genome |
| GSE29218 |
A draft map of cis-regulatory sequences in the mouse genome [ChIP-Seq] |
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| Relations |
| SRA |
SRX062978 |
| BioSample |
SAMN00618923 |
| Named Annotation |
GSM722990_RenLab-CTCF-spleen.bigwig |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM722990_RenLab-CTCF-spleen-DM406.bam |
528.0 Mb |
(ftp)(http) |
BAM |
| GSM722990_RenLab-CTCF-spleen-DM431.bam |
553.0 Mb |
(ftp)(http) |
BAM |
| GSM722990_RenLab-CTCF-spleen.bigwig |
52.0 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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