|
| Status |
Public on May 16, 2010 |
| Title |
Donor 3 biological replicate b |
| Sample type |
SRA |
| |
|
| Source name |
Human sperm
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: sperm
|
| Treatment protocol |
Human spermatozoa were lysed in buffer I (0.3M Sucrose, 15mM Tris (pH 7.5), 60mM KCl, 15mM NaCl, 5mM MgCl2, 0.1mM EGTA, 0.5mM DTT) containing 0.5% deoxycholate and 0.25% NP-40 for 30 min on ice. Chromatin digestion was performed by micrococcal nuclease. Nucleosomal DNA was fractionated by polyacrylamide electroforesis. Control sample was prepared by sonication of human sperm chromatin that had been pretreated with detergents and DTT under the same conditions as used to generate mono-nucleosomal DNA by MNase treatment.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illumina's instructions. After adapter ligation library fragments of ~250 bp were band isolated from an agarose gel. The DNA was PCR amplified with Illumina primers for 18 cycles, purified and loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer 2 following the manufacturer's protocols.
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
MNase treated chromatin
|
| Data processing |
Thirty-six base pair reads were aligned to the hg18 human genome assembly using Bowtie allowing for up to 2 mismatches and reads with multiple hits to genome (up to 100) were assigned to all matching regions with a weight of one over the number of hits. Wiggle files showing the average coverage were generated in 300bp windows.
|
| |
|
| Submission date |
Jan 14, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Antoine Peters |
| E-mail(s) |
antoine.peters@fmi.ch
|
| Organization name |
Friedrich Miescher Institute for Biomedical Research (FMI)
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE19889 |
Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa (Illumina) |
| GSE19892 |
Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa |
|
| Relations |
| SRA |
SRX018538 |
| BioSample |
SAMN00010709 |
| Named Annotation |
GSM497194_283_2hMN.w300.wig.gz |
