|
| Status |
Public on May 11, 2016 |
| Title |
FBF-1 CLIP-seq 2 |
| Sample type |
SRA |
| |
|
| Source name |
C. elegans bearing a 3xFLAG tagged FBF-1 integrated as a single copy
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
protocol: 3xFLAG tagged FBF-1 integrated as a single copy
|
| 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 |
SAMN04349929 |
| SRA |
SRX1490795 |
