|
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 |