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Sample GSM4697076 Query DataSets for GSM4697076
Status Public on Aug 13, 2020
Title EFL1.lin36::eGFP.rep1
Sample type SRA
 
Source name EFL1.lin36::eGFP.whole worm
Organism Caenorhabditis elegans
Characteristics strain: lin-36::eGFP (we30)
developmental stage: starved L1
growth temperature: 25°C
tissue: whole worm
chip antibody: EFL1
sample id: AA1000
Growth protocol Starved L1 animals were collected by bleaching synchronized adults grown in liquid culture using standard S-basal medium with HB101 E. coli at 20°C. Following bleaching, eggs were hatched at 25°C in M9 and starved L1s were sucrose floated and collected 20-22 hours following hatching by flash freezing in liquid nitrogen.
Extracted molecule genomic DNA
Extraction protocol Frozen starved L1 worms were ground to a powder, which was incubated in 1.5 mM EGS (Pierce 21565) in PBS for 8 minutes, followed by the addition of formaldehyde to a final concentration of 1%, and incubated for a further 8 minutes. The fixation was quenched for 5 minutes by the addition of 0.125 M glycine. Fixed tissue was washed 2X with PBS with protease inhibitors (Roche EDTA-free protease inhibitor cocktail tablets 05056489001) and once in FA buffer (50 mM Hepes pH7.5, 1 mM EDTA, 1% TritonX-100, 0.1% sodium deoxycholate, and 150 mM NaCl) with protease inhibitors (FA+), then resuspended in 1 ml FA+ buffer per 1 ml of ground worm powder. The extract was sonicated to an average size of ~250 base pairs using a Bioruptor Pico (Diagenode), and 10-20 ug of DNA was used per ChIP reaction.
ChIP DNA is blunt ended, A-tailed, ligated to adaptors, amplified by PCR, then size selected using AMPure beads. Illumina TruSeq adaptors and barcodes were used.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Description EFL1.lin36::eGFP.rep1.AA1000
Data processing ChIP-seq reads were aligned to a concatenated ce11+cb3 assembly of the C. elegans and C. briggsae genomes using BWA v. 0.7.7 with default settings (BWA-backtrack algorithm) (Li and Durbin, 2010).
The SAMtools v. 0.1.19 ‘view’ utility (Li et al., 2009) was used to convert the alignments to BAM format. Normalized mapq10 ChIP-seq coverage tracks were generated using the BEADS algorithm (Cheung et al., 2011).
Genome_build: ce11 + cb3 (concatenated)
Supplementary_files_format_and_content: BEADS-normalized genome-wide linear read coverage (from reads with MAPQ value >= 10)
 
Submission date Jul 27, 2020
Last update date Aug 13, 2020
Contact name Francesco Nicola Carelli
E-mail(s) fr.carelli@gmail.com
Organization name University of Cambridge
Lab Julie Ahringer
Street address Henry Wellcome Building of Cancer and Developmental Biology, Tennis Court Road
City Cambridge
ZIP/Postal code CB2 1QN
Country United Kingdom
 
Platform ID GPL18730
Series (2)
GSE155189 DREAM represses distinct targets by cooperating with different THAP domain proteins [CHIP-seq]
GSE155191 DREAM represses distinct targets by cooperating with different THAP domain proteins
Relations
BioSample SAMN15651192
SRA SRX8832089

Supplementary file Size Download File type/resource
GSM4697076_EFL1.lin36_eGFP.rep1.AA1000.BEADSQ10NU_linear.bw 195.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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