|
| Status |
Public on Jan 22, 2019 |
| Title |
polyA-mRNA_BtzKD_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
S2R+cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2R+
cell type: Embryonic
genotype/variation: knock-downed for Btz
|
| Treatment protocol |
For knock down experiments, dsRNA was synthesized overnight at 37 °C using Hi-Scribe T7 transcription kit (NEB, Cat No- E2040). dsRNA was transfected in S2R+ cells by serum starvation for 6 hours. The treatment was repeated three times and cells were harvested 7 days after the first treatment
|
| Growth protocol |
Drosophila S2R+ cells were cultured in Schneider Cell’s Medium (GIBCO, Cat No -) supplemented with 10% FBS and 2% Penicillin/Streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted from cells using Trizol reagent, following the manufacturer’s protocol
Libraries of strand-specific RNA-seq were constructed using Illumina TruSeq Kit, following the manufacturer’s protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
strand specific mRNA Seq
Btz_KD_2_S6
|
| Data processing |
The data was sequenced on a HiSeq2500 in a rapid run with a readlength of 71 bp paired end (HiSeq Rapid SBS/Cluster Kit v2) or on a NextSeq500 with 42bp paired end. Demultiplexing and fastq file conversion was done using blc2fastq v. 1.8.4 (HiSeq2500) or blc2fastq v2.19 (NextSeq500)
Mapping was performed suing STAR (v. 2.5.1b) against ensembl release 84 of BDGP6.
UCSC compatible library normalised bigwig tracks were produced using samtools version 1.2, ucsc tools (bedGraphToBigWig from 04-11-2012) and bedtools (v. 2.25.0) and custom scripts
Counts per gene were derived using htseq count (v.0.6.1p1)
Genome_build: BDGP6
Supplementary_files_format_and_content: UCSC compatible library size normalised bigwig tracks and readcounts per gene
|
| |
|
| Submission date |
Nov 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jean-Yves Roignant |
| Organization name |
Institute of molecular Biology
|
| Lab |
Roignant
|
| Street address |
Ackermannweg 4
|
| City |
Mainz |
| ZIP/Postal code |
55128 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19132 |
| Series (2) |
| GSE92389 |
Promoter-proximal pausing mediated by the exon junction complex regulates splicing |
| GSE106909 |
RNA Sequencing of Btz knockdown [Promoter-proximal pausing mediated by the exon junction complex regulates splicing] |
|
| Relations |
| BioSample |
SAMN08027417 |
| SRA |
SRX3393702 |
