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Sample GSM4648537 Query DataSets for GSM4648537
Status Public on Jul 02, 2020
Title control shRNA-1
Sample type SRA
 
Source name cortex
Organism Rattus norvegicus
Characteristics strain: Sprague Dawley Rat
cell type: rat primary cortical neuron
treatment: infected control shRNA lentivirus
Treatment protocol Lentiviruses of pSicoR-Ef1a-mCh-Puro vector carrying Trank1-shRNA#1, Trank1-shRNA#2 or empty were generated according to the manufacturer’s protocol. Rat neurons were infected at 14-15 days in vitro (DIV) with Trank1-shRNAs or control shRNA.
Growth protocol Dissociated cortical neurons were prepared from infant Sprague Dawley rats at E18 days of gestation. In brief, cortices were dissected, trypsinized and gently triturated into single cell suspension. Neurons in this suspension were then counted, and seeded at a density of 1×106 viable cells/well in 6 well culture-plates pre-coated with poly-D-lysine (10 μg ml−1) for at least 12 hours at 37 °C. Cultures were maintained at 37 °C with 5% CO2, supplemented with Neurobasal medium with 2% B27 (Invitrogen) and 2.0 mM glutamax.
Extracted molecule total RNA
Extraction protocol Total RNAs from infected neurons were purified by TRIzol reagent according to the manufactor’s instruction.
For RNA-Seq, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Trimmomatic v0.32 were used to examine the sequencing quality and trim reads.
Clean paired-end reads were aligned to the reference genome using Hisat2.
We quantified gene-level expression using featureCounts.FPKM (fragments per kilobase of exon per million fragments mapped) was calculated to measure gene-level expression according to the formula: FPKM=F×103/L×106/N, where F was the number of the fragments assigned to the gene annotation, L was the length of gene and N was the total number of mapped fragments.
Genome_build: Rnor6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date Jul 01, 2020
Last update date Jul 02, 2020
Contact name Ming Li
E-mail(s) limingkiz@mail.kiz.ac.cn
Organization name Kunming Institute of Zoology, Chinese Academy of Sciences
Street address NO 32 Jiao-Chang Donglu
City Kunming
State/province Yunnan
ZIP/Postal code 650223
Country China
 
Platform ID GPL14844
Series (1)
GSE153638 RNA-seq analysis of rat neurons treated with shRNA-mediated Trank1 knockdown
Relations
BioSample SAMN15417059
SRA SRX8647148

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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