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Status |
Public on Jul 01, 2012 |
Title |
RenLab-H3K4me1-spleen (Illumina GA IIx) |
Sample type |
SRA |
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Source name |
Mouse spleen
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Organism |
Mus musculus |
Characteristics |
strain: C57Bl/6 chip antibody: H3K4me1 chip antibody details: Abcam, ab8895
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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 Genome Analyzer IIx |
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Description |
H3K4me1 IP
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Data processing |
RenLab-H3K4me1-spleen-DM378.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 |
GPL11002 |
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 |
SRX062979 |
BioSample |
SAMN00618924 |
Named Annotation |
GSM722991_RenLab-H3K4me1-spleen.bigwig |
Supplementary file |
Size |
Download |
File type/resource |
GSM722991_RenLab-H3K4me1-spleen-DM378.bam |
390.9 Mb |
(ftp)(http) |
BAM |
GSM722991_RenLab-H3K4me1-spleen.bigwig |
60.2 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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