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Sample GSM4054743 Query DataSets for GSM4054743
Status Public on Sep 17, 2020
Title mmu_siSnrnp70_1
Sample type SRA
Source name Neurons
Organism Mus musculus
Characteristics cell type: ES cell derived neurons
strain: E14Tg2A.4
genotype: Snrnp70 KD1
Treatment protocol NFLAG-delGly, shRNA for Luciferase or shRNA for Snrnp70 were expressed in ES cell derived neurons by lentivirus system and cells were treated with DOX to induce expression of the exogenous protein or shRNA along with Geneticin to select the cells infected with virus.
Growth protocol Mouse embryonic stem cells (ES, E14Tg2A.4) were maintained in ES medium on gelatinized plates without feeder cells. Neuronal differentiation was performed as described previously (Wichterle et al., 2009). Cells were maintained into ADFNB+GDNF.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from neurons using Trizol reagent (Thermo).
Total RNA prepared as above was submitted to Novogene Co., Inc to prepare library using Eukaryotic directional mRNAseq kit (Illumina).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description Snrnp70 KD1
Data processing Obtained reads were mapped to the mouse genome (mm10) using HISAT2 version 2.1.0. with following parameters; --phred33 --rna-strandness RF -t --no-unal -p 4.
For gene count, HTseq-count (version 0.11.2) was used.
The gene count results of all samples obtained as above were combined into single file.
Genome_build: mm10
Supplementary_files_format_and_content: A text file contains read counts for genes for eight samples.
Submission date Aug 30, 2019
Last update date Sep 17, 2020
Contact name Tadashi Nakaya
Organization name International University of Health and Welfare
Department School of Pharmacy at Fukuoka
Street address 137-1 Enokizu
City Okawa
State/province Fukuoka
ZIP/Postal code 8318501
Country Japan
Platform ID GPL24247
Series (1)
GSE136663 Dissection of FUS domains involved in regulation of SnRNP70 gene expression
BioSample SAMN12661180
SRA SRX6779195

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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