|
| Status |
Public on Aug 10, 2016 |
| Title |
KW2309-L4440-1Ama-2-CHIP |
| Sample type |
SRA |
| |
|
| Source name |
mixed stage early embryos
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
range of embryonic cell stages: 1cell to 350 cell stage
strain: KW2309
genotype/variation: control
chip antibody: anti-AMA-1 (Novus Biological, Cat# 38520002)
|
| Treatment protocol |
Collected embryos were fixed with 2% formaldehyde for 22min on rotator. Samples were sonicated using a Bioruptor sonicator at high setting for 40min (40sec on/ 20sec off).
|
| Growth protocol |
Synchronized L1s were grown on 15cm peptone rich plates seeded with NA22 bacteria for 72hrs, then adult worms were treated with standard bleaching solution to collect early embryos in utero
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA Pol II-DNA complexes were isolated using AMA-1 antibody from prepared lysates.
DNA CHIP-seq library is prepared as described in Bowmen et al (doi:10.1186/1471-2164-14-466)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
AMA1.Peak.calls.txt
|
| Data processing |
bowtie 1.0.1 was run with the -m 2 option to map the Illumina reads to the genome version ws220
MACS2 was run on the bowtie output with the -bdg option to obtain degraph signal track files
MACS2 was run with the -broad peak call option and a significance cutoff of 0.01 to optain AMA-1 peak calls for each AMA-1 ChIP-seq replicate
Genes were called enriched for AMA-1 if a peak overlapped at least 250 bp (or 45% the length of the gene, whatever is smaller) with the body of the gene.
Genes needed to be called enriched for AMA-1 in both replicates of a condition to be called enriched for that condition.
Genome_build: ws220 (ce10)
Supplementary_files_format_and_content: bedgraph signal track files and txt file with genes that were called enriched for AMA-1 in L4440 and/or sig-7 RNAi.
|
| |
|
| Submission date |
Aug 10, 2016 |
| Last update date |
May 15, 2019 |
| 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) |
| GSE85441 |
Comparison of RNA Pol II localization in the genomes of sig-7 (RNAi) vs WT C. elegans early stage embryos |
| GSE85445 |
HTS comparison of sig-7 (RNAi) vs WT C. elegans early stage embryos |
|
| Relations |
| BioSample |
SAMN05559047 |
| SRA |
SRX2011723 |
