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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 15, 2014 |
| Title |
Chromatin-IP of K4Me3 in Dcr KO |
| Sample type |
SRA |
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| Source name |
Dcr Knockout mouse embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cells
strain: 129S4/SvJae
ChIP: antiH3K4me3 Abcam (Cat #: ab8580, Lot #: GR87168-1)
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| Growth protocol |
Feeder-free WT, 3 lines of Dcr KO mESCs, cMycf/f and cMyc-/- were generated and maintained on gelatin as described previously (Calabrese et. al., PNAS, 2007).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq libraries are prepared using protocols outlined by O'Geen et. al. (O'Geen et. al., Methods Mol Biol, 2011).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
ChIP library of K4Me3
embryonic stem cells
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| Data processing |
RNA-seq reads were aligned to the mouse genome (mm9) with tophat and uniquely mapped reads were assembled into transcripts with cufflink. Transcripts were annotated by comparing them to databases of known coding genes, lncRNAs, pseudogenes, rRNAs and repeats. lncRNAs were annotated by comparing them to existing annotations. Transcripts that did not match to anything known were termed unannotated. Since our sequencing and analysis protocols selected for poly-adenylated, and non-repetitive reads, we discarded reads that mapped to rRNAs and repeats. DESeq was used to normalize reads between samples, and log fold change of each transcript between WT and Dcr KO cells was calculated. FDR ≤ 0.05 was used to decide if a transcript was significantly up or down-regulated.
ChIP-seq reads were mapped to mouse genome (mm9) with bowtie allowing no mismatch.
Genome_build: mm9 from UCSC
Supplementary_files_format_and_content: The processed .exp.txt files contain tab-separated columns, the first column is the transcript ID, and the remaining columns represent normalized reads in respective mESCs. The processed .bedgraph files contain mapped reads of ChIP-seq libraries.
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| Submission date |
Feb 25, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Kun Qu |
| E-mail(s) |
kqu@stanford.edu
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| Organization name |
Stanford University
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| Department |
Dermatology
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| Lab |
Howard Chang
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| Street address |
269 Campus Dr. CCSR 2150
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE55338 |
Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs |
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| Relations |
| BioSample |
SAMN02664715 |
| SRA |
SRX475945 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1334369_chipseq_KO_K4Me3.bedgraph.gz |
78.1 Mb |
(ftp)(http) |
BEDGRAPH |
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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