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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 01, 2013 |
| Title |
Jmjd2c_KD_Spt5 |
| Sample type |
SRA |
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| Source name |
Jmjd2c KD mESCs
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| Organism |
Mus musculus |
| Characteristics |
strain: 129S4/Svjae
phenotype: agouti
gender: male
cell type: ESC
genotype/variation: Jmjd2c shRNA KD
chip antibody: Spt5 (H-300) (sc-28678), Santa Cruz Biotechnology
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| Treatment protocol |
mESCs were crosslinked with 1% formaldehyde, reaction was quenched by 0.125M glycine, trypsinized, sonicated in SDS Chip buffer, followed by incubation with 5µg of antibodies overnight. Protein A or G beads were added to ChIP reactions to immunoprecipitate chromatin. Beads were washed several times, de-crosslinked at 65ºC overnight, followed by RNase and Proteinase K treatment to collect ChIP-ed DNA, which was ready for library preparation. For bioChIP reactions, streptavidin beads (Dynabeads MyOne Streptavidin T1- Invitrogen) were used for the precipitation of chromatin, and 2% SDS was applied for first washing step. All other steps were same as conventional ChIP protocol.
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| Growth protocol |
mESCs were grown in standard mouse ES cells media with LIF
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
[Illumina] Purified ChIP DNA was measured in Qubit (Invitrogen). 2-10ng of purified ChIP DNA was used to prepare sequencing libraries, using NEB next generation ChIP sequencing Kit and Illumina ChIP seq kit according to the manufacturer's instructions.
[Helicos] ChIP DNA was processed for 3' polyA tailing, followed by 3'ddATP-blocking. Processing samples by ligation, amplification and size selection are not required by Helicos sequencing.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Jmjd2c shRNA KD in mESCs
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| Data processing |
Basecalls performed using Solexa pipeline for data generated by HiSeq 2000 or Helicos pipeline for data generated by Helicos Heliscope.
Sequencing reads were aligned to mouse genome assembly mm9 using Illumina software pipeline (data generated by HiSeq 2000) or Helisphere (data generated by Helicos).
Only ChIP-seq reads that aligned to exactly one location in the reference mouse genome (mm9) were retained for downstream data analysis.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the window was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by HiSeq 2000.
Genome_build: mm9
Supplementary_files_format_and_content: Mapped read bed file (reporting the coordinates of aligned reads) which were converted from BAM files by using BAMtools; wig file which contain the read densities normalized by sequencing depth; and peak bed file which were outputed by MACs (reporting the coordinates of peaks called by MACS).
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| Submission date |
Jan 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhen Shao |
| E-mail(s) |
shaozhen@picb.ac.cn
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| Organization name |
Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences
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| Lab |
Zhen Shao
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| Street address |
320 Yueyang Road
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| City |
Shanghai |
| ZIP/Postal code |
230031 |
| Country |
China |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE43229 |
Combinatorial role of Jmjd2b and Jmjd2c in mESCs identity |
| GSE43231 |
Combinatorial role of Jmjd2b and Jmjd2c in mESC identity |
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| Relations |
| SRA |
SRX213834 |
| BioSample |
SAMN01881909 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1059037_Spt5_2cKD_6_19_12.bed.gz |
217.8 Mb |
(ftp)(http) |
BED |
| GSM1059037_Spt5_2cKD_binsize_200_stepsize_50_fixedstep_rpkm.wig.gz |
15.9 Mb |
(ftp)(http) |
WIG |
| GSM1059037_Spt5_2cKD_pd10_peaks.bed.gz |
429.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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