|
| Status |
Public on Jan 01, 2014 |
| Title |
H3K4me3_RC04 ChIP seq |
| Sample type |
SRA |
| |
|
| Source name |
late embryos_H3K4me3 ChIP seq
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: JA1597
tissue: whole embryo
Stage: Late embryo
chip antibody: anti-H3K4me3
chip antibody vendor: Abcam
chip antibody cat.#: ab8580
|
| Treatment protocol |
Late embryos are frozen, ground and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and sonicated to an average size of 200bp using a Bioruptor. Extracts are then spun down and the soluble fraction is used for ChIP.
|
| Growth protocol |
About 2-7 million of adult worms are bleached to collect embryos. Late embryos were obtained by aging embryos 3.5 hrs at room teperature prior to flash freezing in liquid nitrogen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were made using the Truseq DNA sample prep kit (Illumina). 1-10ng of ChIP or 10ng of input are blunted (T4 polymerase), an A-overhang is added (Klenow), DNA is ligated to adaptors, amplified by PCR, and the library size-selected to a 250-400 bp range using Agencourt AMPure XP beads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
H3K4me3_RC04
|
| Data processing |
ChIP-seq reads were aligned to the WS220 assembly of the C. elegans genome using BWA (Li and Durbin, 2010) with default settings.
Data were normalized using BEADS algorithm (Cheung et al, 2011).
Signals were exported to bigWig tracks at native resolution.
Peaks ware called with MACS 2.0.10 using aligned files (BAM) as input.
Genome_build: WS220
We used 'Oct. 2010 (WS220/ce10)' reference genome assembly provided by USCS Genome Bioinformatics (http://hgdownload.soe.ucsc.edu/goldenPath/ce10/bigZips/)
The WormBase archive: http://ws220.wormbase.org/
Supplementary_files_format_and_content: bigWig track files were generated using BEADS pipeline in R; Scores represent BEADS normalized values;
Supplementary_files_format_and_content: Bed files represents the signal peaks called with MACS 2.0.10;
|
| |
|
| Submission date |
Aug 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Przemyslaw Aleksander Stempor |
| Organization name |
University of Cambridge
|
| Department |
The Gurdon Institute
|
| Lab |
Ahringer Lab
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| State/province |
United Kingdom |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE49870 |
HOT regions are CpG dense promoters in C. elegans and humans |
|
| Relations |
| BioSample |
SAMN02316835 |
| SRA |
SRX335104 |
