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| Status |
Public on Nov 09, 2014 |
| Title |
C_H3K4me3_3659 |
| Sample type |
SRA |
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| Source name |
lymphoblastoid cell line
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| Organism |
Pan troglodytes |
| Characteristics |
cell line: lymphoblastoid
antibody: H3K4me3 antibody (4 ug, Abcam ab8580)
Sex: Female
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| Growth protocol |
cell line source: LCLs from chimpanzee and rhesus macaque individuals were obtained from New Iberia Research Center (University of Louisiana at Lafayette), and New England Primate Research Center (NEPRC, Harvard Medical School)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was extracted using protocol described in Cain et al. 2011, except that for some samples, chromatin was sheared with a Covaris S2 (settings: 40 minutes, duty cycle 20%, intensity 8, 200 cycles/burst, 500uL at a time in 12 x 24mm tubes).
Prepared Illumina sequencing libraries as described by the ENCODE Project Consortium (2011), starting with 20 uL of ChIP output or 4 ng of pooled input sample.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
H3K4me3 ChIP-seq for Chimpanzee Individual 3659 S003659
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| Data processing |
Basecalls by Illumina CASAVA 1.7.0
Mapped reads to panTro3 and rheMac2 using BWA 0.5.9, allowing up to 2 mismatches per read (-n 2), and excluding gapped alignments (-o 0)
Discarded reads that were assigned with a quality score less than 10 or were duplicates
For Chip-Seq, MACS version 1.4.1 was used to identify sharp peaks of enrichment for H3K4me1, H3K4me3, H3K27ac, and Pol II; RSEG version 0.4.4 was used to classify enrichment of broad genomic regions of enrichment for H3K27me3
For RNA-seq, reads mapped to orthologous exons are counted and summed at gene level
For Chip-Seq, a two-step procedure is used to classify the enriched regions/peaks for each mark
Genome_build: panTro3 and rheMac2 (and hg19 for H_input)
Supplementary_files_format_and_content: bed file format; for ChipSeq they contain peaks and enriched regions identified for each marker; for RNA-seq, they contain number of reads mapped to each gene
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| Submission date |
Aug 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiang Zhou |
| E-mail(s) |
xzhousph@umich.edu
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| Phone |
734-764-7067
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| Organization name |
UNIVERSITY OF MICHIGAN
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| Department |
Biostatistics
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| Street address |
1415 Washington Heights
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platform ID |
GPL9378 |
| Series (1) |
| GSE60269 |
Epigenetic modifications are associated with inter-species gene expression variation in primates |
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| Relations |
| BioSample |
SAMN02979462 |
| SRA |
SRX673198 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1468870_C_H3K4me3_3659.bed.gz |
658.9 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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