|
| Status |
Public on Jul 23, 2018 |
| Title |
Oocyte input, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Ovulated but unfertilized oocytes collected from feminized worms
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain and genotype: CF512 rrf-3(b26); fem-1(hc17ts)
purity of sample: > 95%
chip antibody: none
xchromosome: autosome ratio: X:A=1:1
|
| Growth protocol |
Synchronized L1 larvae from CF512 were plated on 40-60 High Growth (HG) plates seeded with E. coli OP50 and grown for ~55 hr at 15oC until worms reached late L3 stage. Worms were then up-shifted to 25oC for 24-36 hr to feminize them. ~1 million feminized adults were washed from the plates, and densely packed worms were transferred to a 15 cm petri dish on ice. Worms were chopped with a razor blade for 5 min until oocytes were liberated. Oocytes and carcass fragments were poured over a 45-micron mesh. Oocytes passed through the mesh, while carcass fragments remained above the mesh. The flow-through was filtered through a 20-micron mesh to collect oocytes above the mesh, while smaller debris went through the mesh.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Oocyte chromatin was crosslinked in 2.2% formaldehyde for 5 min, sonicated with a tip sonicator, and digested with micrococcal nuclease.
Oocyte libraries were prepared with the NEBNext Ultra DNA library Prep Kit (NEB) following the manufacturers' instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Solubilized nucleosomes (histone-DNA complexes) were used as input.
|
| Data processing |
Raw sequence reads from the Illumina HiSeq (50 bp single-end read sequencing for ChIP-seq) were mapped to the C. elegans genome (Wormbase version WS220) using Bowtie with default settings.
MACS2 was used to call peaks and to create bedgraph files with the following settings: -g ce --bdg --keep-dup=auto --broad --broad-cutoff=0.01 --nomodel --extsize=250.
Custom scripts were used to scale bedgraph files to 10 million total autosomal reads (to account for different X:A ratios of oocytes and embryo samples compared to sperm samples) and converted to bigwig using the bedGraphToBigWig UCSC Genome Browser tool.
Genome_build: WS220
Supplementary_files_format_and_content: bigWig containing scaled read coverage
|
| |
|
| Submission date |
Jun 12, 2018 |
| Last update date |
Jul 24, 2018 |
| Contact name |
Susan Strome |
| E-mail(s) |
sstrome@ucsc.edu
|
| Organization name |
UC Santa Cruz
|
| Department |
MCD Biology
|
| Street address |
1156 High St
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platform ID |
GPL13657 |
| Series (2) |
| GSE115704 |
Distribution of histone modifications across the genome in C. elegans sperm vs. oocytes vs. early embryos |
| GSE115709 |
Epigenome of C. elegans sperm, oocytes, and early embryos (MNase-seq, ChIP-seq, RNA-seq) |
|
| Relations |
| BioSample |
SAMN09402997 |
| SRA |
SRX4200543 |
