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Sample GSM2258987 Query DataSets for GSM2258987
Status Public on Mar 28, 2017
Title polyA_minus_HEK_s4019_3
Sample type SRA
 
Source name polyA_minus_HEK_s4019
Organism Homo sapiens
Characteristics cell line: HEK293
condition: DHX9 knockdown with s4019
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 SAMN05509759
SRA SRX1998254

Supplementary file Size Download File type/resource
GSM2258987_polyA_minus_HEK_s4019_3.bigWig 77.1 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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