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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
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
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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