|
| Status |
Public on Sep 10, 2014 |
| Title |
HITS CLIP replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
bovine retina HITS CLIP replicate 2
|
| Organism |
Bos taurus |
| Characteristics |
strain: Mixed
tissue: Retina
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Eyes were enucleated and retinas were dissected, triturated to clusters of cells, and subjected to in vivo protein-RNA crosslinking (3X 400mJ/cm2)
Argonaute HITS-CLIP library preparation was performed according to Chi et. al (2)
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
retinal mRNA (co-purifying with Argonaute Proteins
|
| Data processing |
Base-calling was performed using the Illumina pipeline software Casava 1.8.1
reads were mapped to bovine genome release bosTau7 using GSNAP with 2 mismatches allowed
enrichment in HITS-CLIP target mRNAs was analyzed using MACS program by considering corresponding bovine retina transcriptome samples as the control. High confidence miRNA target sites were defined as peaks with a P-value for enrichment less than 1 * 10-20 present in all three biological replicates (defined as having a summit within 100bp). The genes wherein the identified miRNA target sites are found were annotated by hand using the UCSC genome browser.
Genome_build: bostau7
Supplementary_files_format_and_content: xlsx file showing regions of the bovine genome with highly statistically significant enrichment in HITS-CLIP reads vs. transcriptome reads and their annotation
|
| |
|
| Submission date |
Jul 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Sundermeier |
| E-mail(s) |
trs7@case.edu
|
| Organization name |
Case Western Reserve University
|
| Department |
Pharmacology
|
| Lab |
Palczewski
|
| Street address |
2109 Adelbert Road/W317
|
| City |
Cleveland |
| State/province |
OHIO |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL17875 |
| Series (2) |
| GSE59909 |
Argonaute HITS-CLIP to identify miRNA target sites in the bovine retina |
| GSE59912 |
HITS-CLIP and RNA-Seq of bovine retina |
|
| Relations |
| BioSample |
SAMN02947216 |
| SRA |
SRX666270 |
