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Sample GSM1089278 Query DataSets for GSM1089278
Status Public on Apr 08, 2014
Title knl2_CenH3_(20120223_3)
Sample type SRA
Source name ChIPed chromatin
Organism Caenorhabditis elegans
Characteristics tissue: embryo
genetic background: N2
genotype: WT
chip antibody: cenH3
knockdown: knl2
Extracted molecule genomic DNA
Extraction protocol KNL-2 depleted (knl-2(RNAi),knl2) embryonic nuclei were subjected to MNase treatment for 2 minutes and soluble chromatin was purified by needle extraction followed by ChIP with anti-cenH3 (CENP-A, HCP-3) antibody. KNL-2 was depleted by RNAi by feeding N2 worms on bacteria expressing dsRNA, so the depletion is entirely post-transcriptional.
see MNase_ChIP_Seq_protocol
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Description ChIPed chromatin
age:embryos, backgroun strain:N2, mutant:WT, RNAi:knl2, antibody:anti-cenH3
Data processing 1. We used Novoalign (2.07.00 - Aug 5 2010) to map paired-end 25bp reads to release WS220 (Feb 2011) of the C. elegans genomic sequence obtained from WormBase. If a read was mapped to multiple locations, one location was picked at random (Supplementary file .bam) 2. We extracted properly paired reads mapped only to C. elegans (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group.
Genome_build: WS220
Supplementary_files_format_and_content: bam, wig, and bed
Submission date Feb 27, 2013
Last update date May 15, 2019
Contact name Jorja Henikoff
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
Platform ID GPL13657
Series (1)
GSE44412 Holocentromeres are dispersed point centromeres localized at transcription factor hotspots
SRA SRX246038
BioSample SAMN01931893

Supplementary file Size Download File type/resource
GSM1089278_knl2_CenH3_20120223_3.bam 759.8 Mb (ftp)(http) BAM
GSM1089278_knl2_CenH3_20120223_3.bed.gz 37.8 Mb (ftp)(http) BED
GSM1089278_knl2_CenH3_20120223_3.wig.gz 72.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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