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Sample GSM2267042 Query DataSets for GSM2267042
Status Public on Aug 10, 2016
Title KW2309-L4440-1Ama-1-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
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
BioSample SAMN05559040
SRA SRX2011722

Supplementary file Size Download File type/resource
GSM2267042_AMA1_KW2309.L4440_r1.bedgraph.gz 113.7 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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