NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1320329 Query DataSets for GSM1320329
Status Public on Apr 08, 2014
Title WT_input_FCL_rep2_(20130920_1_2_6)
Sample type SRA
 
Source name crosslinked chromatin
Organism Caenorhabditis elegans
Characteristics age: embryos
strain: N2
genotype: WT
Extracted molecule genomic DNA
Extraction protocol N2 wildtype embryonic nuclei were subjected to MNase treatment for 2 minutes and soluble chromatin was formaldehyde crosslinked (FCL) and solubilized by sonication. Replicate 2.
MNase_ChIP_Seq_protocol.rtf
 
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina HiSeq 2500
 
Data processing 1. We used Novoalign (2.08.01 - Mar 14 2012) 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. 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.
 
Submission date Feb 03, 2014
Last update date May 15, 2019
Contact name Jorja Henikoff
E-mail(s) jorja@fhcrc.org
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 GPL18245
Series (1)
GSE44412 Holocentromeres are dispersed point centromeres localized at transcription factor hotspots
Relations
BioSample SAMN02615853
SRA SRX461558

Supplementary file Size Download File type/resource
GSM1320329_WT_input_FCL_rep2.bed.gz 104.4 Mb (ftp)(http) BED
GSM1320329_WT_input_FCL_rep2.bedgraph.gz 77.2 Mb (ftp)(http) BEDGRAPH
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