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| Status |
Public on Dec 03, 2018 |
| Title |
Sperm Donor Pool H3K9me3 ChIP-seq, rep1 |
| Sample type |
SRA |
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| Source name |
Sperm donor pool, H3K9me3 ChIP
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| Organism |
Homo sapiens |
| Characteristics |
cell type: sperm
chip antibody: anti-H3K9me3
antibody vendor: Active Motif
antibody catalog #: 39765
antibody lot #: 01609004
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| Growth protocol |
The four sperm donor samples were obtained from men of known fertility attending the University of Utah Andrology laboratory, consented for research. Samples were collected after 2-5 days abstinence, subjected to a density gradient to purify viable, motile, mature sperm, and pooled.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Histone isolation and chromatin immunoprecipitation experiments were performed with sperm pooled from four fertile donors as previously described (Hammoud et al., 2009). For each immunoprecipitation, 10 µL of antibody was coupled to 100 µL of Dynabeads (Invitrogen). Following the ChIP procedure and library preparation (Illumina TrueSeq DNA sample Preparation Protocol), DNA lengths corresponding to mononucleosomes (+ adapters) were gel purified and subjected to sequencing.
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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 |
8349X2
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| Data processing |
Basecalls were performed using CASAVA version 1.7.
Reads for H3K9me3 and H3.3 ChIP-seq were aligned using Novoalign V2.07.03 with parameters -rRandom -oSAM to an index containing the hg18 genome (UCSC), Lambda, PhiX, and Illumina Adapter sequences. Reads for H3K36me3, H3K4me1, H3K14ac, and H3K27ac ChIP-seq datasets were aligned with ELAND using the default parameters (Illumina).
Alignments were parsed using NovoalignParser (USeq) or ElandParser (USeq).
ChIP-seq data processing and analysis were performed as previously described in Hammoud et al., 2009. Briefly, differential enrichment between histone ChIP-seq datasets and mononucleosomal control datasets (from GSE15690) were determined with ScanSeqs (USeq), and statistically enriched peaks were called with EnrichedRegionMaker (USeq).
The GSM* numbers for the mononucleosomal controls used were GSM392708-GSM392713, GSM392717-GSM392720 plus approximately 5 million mapped filtered reads randomly subsampled from GSM392701-GSM392707, GSM392714-GSM392716.
The GSM* numbers for the mononucleosomal controls used were GSM392708-GSM392713, GSM392717-GSM392720 plus approximately 5 million mapped filtered reads randomly subsampled from GSM392701-GSM392707, GSM392714-GSM392716.
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text files contain ChIP-seq peaks. The files are linked to the Series record as supplementary files.
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| Submission date |
Aug 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew J Oler |
| E-mail(s) |
andrew.oler@nih.gov
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| Organization name |
NIAID/NIH
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| Department |
Bioinformatics and Computational Biosciences Branch (BCBB)
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| Lab |
Computational Biology Section
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| Street address |
31 Center Drive, Room 3B62E
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL9115 |
| Series (2) |
| GSE40195 |
Human Sperm Epigenomes and Transcriptomes Reveal Novel Features of Enhancers, Sex Chromosomes, piRNAs, Gametogenesis, and Inherited Small RNAs (ChIP-Seq) |
| GSE40196 |
Human Sperm Epigenomes and Transcriptomes Reveal Novel Features of Enhancers, Sex Chromosomes, piRNAs, Gametogenesis, and Inherited Small RNAs |
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| Relations |
| SRA |
SRX179244 |
| BioSample |
SAMN01120790 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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