|
| Status |
Public on Jul 15, 2012 |
| Title |
D8.2 (endogenous DGCR8 IP) |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
rna associated: endogenous (D8) DGCR8
|
| Growth protocol |
HEK293T cells were grown in standard conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs (20-100nt long) associated to DGCR8 were phenol extracted and ethanol precipitated. Libraries were prepared from these RNAs using the Illumina Small RNA kit (v1.5)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Read were processed with MIRO (http://seq.crg.es/main/bin/view/Home/MiroPipeline) to remove reads containing Ns and with a sequence complexity below 0.5. We also removed PCR duplicates.
HITS-CLIP reads were aligned using bowtie v0.11.3 with parameters --best -v2 -a to an index file containg hg18 genome, Ensembl54 transcripts and lincRNA from Ensembl59 mapped to hg18. Initially, all reads are mapped to the index file. After the mapping, all those reads that could not be mapped are trimmed 1 base at the 3’ end of the read and mapped again to the index file. This procedure is repeated until the reads have a minimum length of 21nt. For further analyses, only uniquely mapped reads to the genome were used.
Reads mapped to the same strand were clustered according to their position in the reference sequence to generate clusters. To identify significant clusters we applied a modified false discovery rate (mFDR) using Pyicos. Only significant clusters (pval < 0.01) were kept.
Clusters overlapping Genomic and Centromeric Gaps (hg18 Gap Track from UCSC) and Satellites (hg18 repeat masked track from UCSC) were discarded.
Genome_build: hg18
Supplementary_files_format_and_content: bedGraph files. Each of the files contains all the significant clusters identified for a sample in a strand (+ or -). The score given represents the amount of reads in a position.
|
| |
|
| Submission date |
Jul 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Mireya Plass |
| E-mail(s) |
mireya.plassportulas@mdc-berlin.de
|
| Organization name |
MDC-Berlin
|
| Street address |
Robert-Rössle Str. 10
|
| City |
Copenhagen |
| ZIP/Postal code |
13092 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE39086 |
DGCR8 HITS-CLIP reveals novel functions for the Microprocessor (CLIP-seq) |
|
| Relations |
| SRA |
SRX157657 |
| BioSample |
SAMN01085589 |
