|
| Status |
Public on Oct 20, 2017 |
| Title |
CLIP_AGO2_siSFPQ_LET7_2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse stem cell
|
| Organism |
Mus musculus |
| Characteristics |
hits-clip antibody: 2D4 clone from Wako Chemicals
cell type: P19 cell
condition: Ago2 HITS-CLIP in SFPQ knockdown in let-7a transfection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was recovered from the nitrocellulose using Proteinase K treatment followed by phenol–chloroform extraction and ethanol precipitation. Isolated RNA were subjected to small RNA libraries preparation (New England Biolabs), following the manufacturer’s instructions.
cDNA products were then subjected to PCR amplification for 20–24 cycles and size-fractionated on columns. PCR products representing cDNA inserts of 20–50 nts were recovered and subject to sequencing on a Ion Proton™ System for Next-Generation Sequencing
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Reads were trimmed with the program cutadapt and reads shorter than 15 nt were discarded
filtering versus mouse ribosomal RNA with bowtie2
Mapping of reads onto mouse genome mm10 was performed with STAR, than bowtie2
Genome_build: mm10
Supplementary_files_format_and_content: differential peaks were identified with dCLIP software. Peaks from differential CLIP were compared calculating the Jaccard index. In the excel files are reported Ago2 peaks dismissed or recruited in absence of Sfpq, Sfpq peak,s Ago2 peaks and Ago2+let-7a peaks.
|
| |
|
| Submission date |
Oct 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Silvia Bottini |
| E-mail(s) |
silvia.bottini@unice.fr
|
| Organization name |
C3m
|
| Street address |
299, chemin de la ginestiere
|
| City |
Nice |
| ZIP/Postal code |
06200 |
| Country |
France |
| |
|
| Platform ID |
GPL18635 |
| Series (2) |
| GSE89027 |
Post-transcriptional Gene Silencing Mediated by microRNAs is Controlled by Nucleoplasmic Sfpq [HITS-CLIP] |
| GSE89033 |
Post-transcriptional Gene Silencing Mediated by microRNAs is Controlled by Nucleoplasmic Sfpq |
|
| Relations |
| BioSample |
SAMN05933419 |
| SRA |
SRX2256206 |
