NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM979033 Query DataSets for GSM979033
Status Public on Aug 01, 2012
Title H4K20me1 ChIP-seq of set-4 mutant, rep1
Sample type SRA
 
Source name L3 larvae, set-4 mutant, H4K20me1 ChIP
Organism Caenorhabditis elegans
Characteristics genotype: set-4(n4600)
tissue: whole body
developmental stage: L3 larvae
chip antibody: anti-H4K20me1
chip antibody vendor: Abcam
antibody catalog#: ab9051
antibody lot#: 602259
Treatment protocol Worms are frozen, ground and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue is washed, 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 worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. The next day when larvae reach the L3 stage, they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection, DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.
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 is 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 AA015
Data processing ChIP-seq reads were aligned to the WS190 assembly of the C. elegans genome using BWA (Li and Durbin, 2010 (PMID 20080505)) with default settings.
Data were normalized using BEADS (Cheung et al., 2011 (PMID 21646344)). BEADS scores were converted to log2, and then the datasets were z-scored.
Signals were averaged in 50bp windows and wig files were generated.
Genome_build: WS190
Supplementary_files_format_and_content: Wig files were generated using the BEADS pipeline in R. Scores represent log2-transformed BEADS scores (single experiments). The wig file for the mean of AA015 and AA016 was generated by z-scoring the average of the single log2 scores.
 
Submission date Jul 31, 2012
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)
GSE39789 H4K20me1 contributes to downregulation of X-linked genes for Caenorhabditis elegans dosage compensation
Relations
SRA SRX172526
BioSample SAMN01096297
Named Annotation GSM979033_H4K20me1_ab9051_AC1_F_set4_L3_NORM_log2_25bp_AA015_F0f00539.wig.gz
Named Annotation GSM979033_Mean_AA015+AA016_H4K20me1_ab9051_AC1+AC2__F_set4_L3_norm_log2zsc_50bp.wig.gz

Supplementary file Size Download File type/resource
GSM979033_H4K20me1_ab9051_AC1_F_set4_L3_NORM_log2_25bp_AA015_F0f00539.wig.gz 13.4 Mb (ftp)(http) WIG
GSM979033_Mean_AA015+AA016_H4K20me1_ab9051_AC1+AC2__F_set4_L3_norm_log2zsc_50bp.wig.gz 7.0 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap