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Sample GSM1974929 Query DataSets for GSM1974929
Status Public on May 11, 2016
Title N2 control matched to FBF-1 3
Sample type SRA
 
Source name C. elegans with no FLAG tagged protein
Organism Caenorhabditis elegans
Characteristics protocol: with no FLAG tagged protein
Growth protocol iCLIP was performed on C. elegans grown to early adult phase, 25 hours after L4, on plates.
Extracted molecule total RNA
Extraction protocol Cells were lysed by ball milling, and libraries prepared by the iCLIP method.
iCLIP
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Data processing Library strategy: CLIP-Seq
PCR duplicates were removed using a random barcode.
The first 9 nucleotides of the read (the random barcode) were removed.
Reads were mapped to the C. Elegans WS235 genome using bowtie2 with the --local parameter or novoalign.
Reads with MAPQ below 20 were removed.
Peaks were called by custom CLIP-seq processing scripts or by the CIMS/CITS methods.
Genome_build: WS235
Supplementary_files_format_and_content: Processed data files are the number of reads mapped to each gene.
 
Submission date Dec 18, 2015
Last update date May 15, 2019
Contact name Douglas Porter
Organization name Stanford
Department Dermatology
Lab Khavari
Street address 269 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL13657
Series (1)
GSE76136 The genomic landscape of PUF binding in stem cells
Relations
BioSample SAMN04349936
SRA SRX1490802

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

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