|
| Status |
Public on Mar 28, 2017 |
| Title |
polyA_minus_HEK_s4020_1 |
| Sample type |
SRA |
| |
|
| Source name |
polyA_minus_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 minus RNA
Ribo-Zero Treated after mRNA depletion
|
| 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 |
SAMN05509764 |
| SRA |
SRX1998256 |
