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Sample GSM3017018 Query DataSets for GSM3017018
Status Public on Feb 13, 2019
Title NP_HuR knockdown 1
Sample type SRA
 
Source name Rat nucleus pulposus_HuR knockdown
Organism Rattus norvegicus
Characteristics strain background: Wistar
cell type: primary rat nucleus pulposus (NP) cells
genotype/variation: shHuR-transduced
culture condition: hypoxia (1% O2)
Treatment protocol Rat NP cells were transduced with lentivirally-delivered control (MISSION PLKO.1 non-target ShRNA, ShCTR) or HuR-specific (ShHuR) shRNA. 24 h before collection of total mRNA, cells were cultured under 1% O2 conditions.
Growth protocol Primary rat nucleus pulposus (NP) cells were dissected from Wistar rat spines, expanded from explant tissues, and maintained in DMEM containing 10% FBS and antibiotics
Extracted molecule total RNA
Extraction protocol Total mRNA was extracted using Qiagen RNeasy mini columns and treated with DNAse1
Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero GoldTotal RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples. Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold (RS-122-2301 and RS-122-2302). Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583). The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824). Individual libraries were normalized to 10 nM and equal volumes were pooled in preparation for Illumina sequence analysis.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description ShHuR 1
13657X4_S1_shHuR_Hx_normalized
Data processing HiSeq 50 Cycle Single-Read Sequencing version 4Sequencing libraries (25 pM) were chemically denatured and applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001). Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents.
Genome_build: Rn5 Ensembl annotations (Build 75)
Supplementary_files_format_and_content: File containing Gene identifiers, log2FC, adusted p value, and normalized reads
 
Submission date Feb 19, 2018
Last update date Feb 13, 2019
Contact name Makarand Risbud
E-mail(s) makarand.risbud@jefferson.edu
Phone (215) 955-1063
Organization name Thomas Jefferson University
Department Orthopaedic Surgery
Lab 511 College Bldg.
Street address 1015 Walnut St.
City Philadelphia
State/province PA
ZIP/Postal code 19107
Country USA
 
Platform ID GPL18694
Series (1)
GSE110804 RNA sequencing reveals RNA binding protein HuR/ELAVL1 regulates extracellular matrix gene expression in nucleus pulposus cells of the intervertebral disc
Relations
BioSample SAMN08564451
SRA SRX3721470

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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