|
| Status |
Public on May 27, 2015 |
| Title |
RNA-seq replicate 2 (Control for iCLIP rep2) |
| Sample type |
SRA |
| |
|
| Source name |
Schneider 2 (S2) cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
rt primer with random barcode / index: X33NNTTAANNNAGATCGGAAGAGCGTCGTGGATCCTGAACCGC
random barcode: NNNNN Random Barcode at the read beginning
|
| Growth protocol |
S2 cells were growth at 26C in Schneider's Drosophila Medium containing 10% heat inactivated fetal bovine serum, 100U/ml Penicillin and 100ug/ml Streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 5x107 S2 cells using the standard TRI Reagent protocol (Sigma Aldrich). Poly(A) RNA was enriched from 100ug total RNA using Poly(A)Purist MAG kit (Ambion) according to manufacturer’s specifications. Poly(A) RNA was fragmented using MgCl2. The rest of the library preparation was performed as described in (Konig et al, 2011) with PCR amplification using 17 cycles.
See individual experiment
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Cytoplamic mRNA
|
| Data processing |
Base-calling was performed with CASAVA-1.8.2
Reads were demultiplexed using their fixed barcodes
Reads were trimmed at the 3'end to remove adapter sequences and low-quality sequences using custom python scripts. Reads shorter than 18nt were discarded.
Duplicated reads were collapsed using random barcodes to discriminate between identical sequences.
Reads were mapped to the Drosophila genome (dm3) + exon junction index (ensembl72) using BWA-PSSM with parameters -n 0.04 -l 1024-m 400 -P 0.99. PAR-iCLIP experiments were mapped modeling C>T conversions that arise due to the use of 4SU assuming a 12.5% conversion rate.
Confidently mapped reads with a posterior probability > 0.99 were further clustered according to their genomic positions.
Genome_build: dm3
Supplementary_files_format_and_content: Bedgraph files containing the read clusters
Supplementary_files_format_and_content: Plain text file containing the counts per gene, fold changes and p-values as calculated by DESeq
|
| |
|
| Submission date |
Nov 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Mireya Plass |
| E-mail(s) |
[email protected]
|
| Organization name |
MDC-Berlin
|
| Street address |
Robert-Rössle Str. 10
|
| City |
Copenhagen |
| ZIP/Postal code |
13092 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE62997 |
Drosophila Imp iCLIP identifies an RNA assemblage co-ordinating F-actin formation |
|
| Relations |
| Reanalyzed by |
GSM3287518 |
| BioSample |
SAMN03164257 |
| SRA |
SRX751578 |
