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| Status |
Public on Oct 11, 2018 |
| Title |
mES_H3K27me3_ChIPSeq |
| Sample type |
SRA |
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| Source name |
mouse embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: mouse embryonic stem cells
cell type: E14
strain: 129/Ola
genotype: wild type
age: Passage 15
chip antibody: anti-H3K27me3 (Active motif, #39157)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Unfixed cells were lysed and treated with Micrococcal nuclease. Libraries were prepared using ThruPLEX-FD or ThruPLEX DNA-seq kit (Rubicon Genomics)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
MACS_peak_annotation_ES.xlsx
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| Data processing |
For ChIP-seq analysis, the replicate was concatenated and mapped using Bowtie2 at default setting.
ChIP-seq peaks were called using MACS14 against the input control data. The parameter set used in MACS14 was as follows: H3K4me3 (Band width 300, Pvalue cutoff 1e-05, the nearby regions to calculate dynamic lambda 1000-10000) and H3K27me3 (Band width 2900, Pvalue cutoff 1e-04 (mES and MM(Cited1)) or 1e-03 (UB), the nearby regions to calculate dynamic lambda 1000-20000).
Peaks were annotated with overlapping genes using AnnotateGenomicRegions ( https://sourceforge.net/projects/annotatelocus/files/webarchive/JSFversion/AnnotateGenomicRegions.war/download)
For RNA-seq analysis, all sequencing reads were mapped using Tophat at default setting.
Aligned RNA-seq reads were further analyzed using Cufflinks, Cuffmerge, and Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: BED files with called peaks on sample records and peak annotation files on series record.
RNA-seq: text file with FPKM
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| Submission date |
Aug 15, 2018 |
| Last update date |
Oct 11, 2018 |
| Contact name |
Masaki Nishikawa |
| E-mail(s) |
masakiwestriver@gmail.com
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| Organization name |
UCLA / VA
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| Lab |
Yanagawa
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| Street address |
16111 Plummer st
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| City |
North Hills |
| State/province |
CA |
| ZIP/Postal code |
91343 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE118607 |
Comprehensive analysis of chromatin signature and transcriptome in nephron progenitor cells |
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| Relations |
| BioSample |
SAMN09839551 |
| SRA |
SRX4557397 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3334222_ES201_202_peaks.bed.gz |
178.4 Kb |
(ftp)(http) |
BED |
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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