|
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.
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|
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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
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|
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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 |