NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1200339 Query DataSets for GSM1200339
Status Public on Sep 16, 2013
Title KLE2 N2 L3 Rep1 ChIPSeq
Sample type SRA
 
Source name whole worms
Organism Caenorhabditis elegans
Characteristics strain: N2
developmental stage: L3
matching input: Input_N2_L3_Rep1
antibody: KLE-2 SDQ3942 Rabbit polyclonal is against the antigen MTRNAPPGQESTDLAWLVTPAKDLVENFSIDVLKALAGYLEVIRQESEDTDNQVDAATTYRLFDFQRACRIIQGSCAVYGRKVDHVYELTISVVDLVENK May be available as part of modENCODE antibodies from Novus Biologicals "http://www.novusbio.com/"
Treatment protocol Larva were frozen in to "popcorn" by dripping into liquid nitrogen, and stored at -80C until extract preparation.
Growth protocol N2 L3 worms were obtained by growing synchronous culture in liquid media.
Extracted molecule genomic DNA
Extraction protocol Frozen Larva were broken into pieces using cryo-mixer mill, and crosslinked with 1% formaldehyde for 10 minutes. The worms were collected by centrifugation, were washed with and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of larva extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA were ligated to Illumina or home-made multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Basecalls were performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the WS220 genome assembly using bowtie version 0.12.7 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments.
Peaks were called using MACS version 1.4.141 with the following setting: input, genome size (-g ce), format (-f BAM), p-value (-p 1e-10 and -p 1e-5)
Genome coverage was estimated using MACS version 1.4.141 with the following setting: genome size (-g ce), format (-f BAM), output in wiggle format (-w), whole genome output (-S), resolution (--space=1)
Coverage per base was normalized to the genome-wide median coverage (excluding the mitochondrial chromosome). Final ChIP enrichment score per base was obtained by subtracting matching input coverage.
Replicates were merged by averaging coverage at each base position. To determine a set of final peaks per subunits, reads from the replicates were combined using the BEDTools utility mergeBam version 2.13.442, and MACS was used to call peaks (see above, p-value -p 1e-10). Only those peaks present in the majority of the individual replicates identified below p-value 1e-5 were included in the final peak set.
To get final peak sets representing condensinI-IDC and condensinII, we used a sliding window across the genome. Each base pair covered by at least two of the three non-SMC subunits (DPY-26, DPY-28, and CAPG-1 for condensinI-IDC, CAPG-2, HCP-6, and KLE-2 for condensinII) was included in the final peak set.
supplementary_files_format_and_content: Wig files were generated using MACS version 1.4.141, normalized according to the genome-wide mean coverage and the input subtracted. Scores represent the average coverage of each replicate at each base position.
supplementary_files_format_and_content: Bed files were generated by combining replicate reads and using MACS version 1.4.141 at two different p-values. Only peaks at the more stringend cut-off were inlcuded in the final set that were overlapping with the majority of peaks of each of the replicates at the less stringend p-value.
Genome_build: WS220
 
Submission date Aug 02, 2013
Last update date May 15, 2019
Contact name Sevinc Ercan
Organization name New York University
Department Biology
Street address 12 Waverly Place
City New York
State/province NY
ZIP/Postal code 10003
Country USA
 
Platform ID GPL13657
Series (1)
GSE45678 Genome-wide distribution of the three condensin complexes in C. elegans
Relations
BioSample SAMN02299577
SRA SRX330983

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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