|
Status |
Public on Mar 28, 2017 |
Title |
polyA_plus_HEK_s4020_2 |
Sample type |
SRA |
|
|
Source name |
polyA_plus_HEK_s4020
|
Organism |
Homo sapiens |
Characteristics |
cell line: HEK293 condition: DHX9 knockdown with s4020
|
Treatment protocol |
5nM of Silencer Select siRNAs transfected with RNAiMAX
|
Growth protocol |
DMEM-Glutamax supplemented with sodium pyruvate, glucose and 10% FBS
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA with Zymo Quick RNA kit TruSeq Stranded mRNA Library Prep Kit (Illumina)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
Poly-A plus RNA
|
Data processing |
Read trimming for Illumina adapters using Cutadapt (v-1.8.1) Read mapping to genome using TopHat2 (v2.0.13) with bowtie2 (v2.2.3) Generating coverage signal tracks (bigWigs) from all mapped alignments using Samtools (v1.2) and DeepTools2 (v2.0.0) Genome_build: GRCh38 Supplementary_files_format_and_content: .bigWig files, containing coverage signals from TopHat alignments
|
|
|
Submission date |
Aug 03, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Asifa Akhtar |
E-mail(s) |
akhtarlab_data@ie-freiburg.mpg.de
|
Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
Department |
Chromatin Regulation
|
Lab |
Akhtar Lab
|
Street address |
Stuebeweg 51
|
City |
Freiburg |
ZIP/Postal code |
79108 |
Country |
Germany |
|
|
Platform ID |
GPL18573 |
Series (2) |
GSE85161 |
DHX9 suppresses spurious RNA processing defects originating from the Alu invasion of the human genome [RNA-Seq] |
GSE85164 |
DHX9 suppresses spurious RNA processing defects originating from the Alu invasion of the human genome |
|
Relations |
BioSample |
SAMN05509761 |
SRA |
SRX1998269 |