Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 24
Release date: Mar 28 2017
Last update date: Nov 29 2018
Access: Public
Genes: DHX9
Taxon: Homo sapiens, Mus musculus
Dataset link DHX9 suppresses spurious RNA processing defects originating from the Alu invasion of the human genome [RNA-Seq]

Experimental Protocol


We perfomed knockdown of human RNA heliase-A (also known as DHX9 ) in HEK293 cells using 2 different siRNAs, followed by polyA-plus and polyA-minus RNA sequencing. siRNAs used: control: silencer select siRNA control #2 (https://www.thermofisher.com/order/catalog/product/4390846) DHX9 KD_1: s4019 (http://www.ncbi.nlm.nih.gov/probe/16735410) chr1: 182860161-182860180 (hg38) DHX9 KD_2: s4020 (http://www.ncbi.nlm.nih.gov/probe/16735422) chr1: 182858158-182858177 (hg38) siRNA were used at a final concentration of 5nM, transfected to HEK293 cells with RNAiMAX. Total RNA was isolated 3d after transfection. For polyA(+) samples, TruSeq library prep protocol was used (starting with ~1µg total RNA) For polyA(-) samples, we depleted polyA(+) RNA from total RNA with oligo-dT(+) beads, twice. The rest was first ribodepleted with RiboZero kit, which then went through the TruSeq protocol. Sequencing parameters : 150x2 bp reads, full run of the NextSeq500 machine.

Repositories


GEO

GSE85161

ENA

SRP080966

BioProject

PRJNA336449

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Contact


Asifa Akhtar