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Sample GSM5320127 Query DataSets for GSM5320127
Status Public on May 18, 2021
Title Neuron Brg1-SA, Basal - rep1
Sample type SRA
 
Source name Neuron
Organism Mus musculus
Characteristics genotype: Brg1-SA
cell type: primary cortical neurons
treatment: Basal level of KCl
Treatment protocol For depolarization, the cultures were pretreated with TTX (1 µM) and APV (100 µM) to inhibit spontaneous activation on 5 div and 50 mM KCl was added to the cultures for 1 h on 6 div.
Growth protocol Primary cortical neurons were culture from E16.5 mouse embryo. Dissociated cortical neurons were plated on poly-L-ornithine- and fibronectin-coated wells. Culture media contained neurobasal plus with B27 plus supplement (Gibco).
Extracted molecule total RNA
Extraction protocol Total RNA were expreact with TRIZOL and cleaned with a Qiagen RNeasy Kit.
RNA-seq libraries were prepared using the Illumina RNA-Seq Preparation Kit and sequenced at the University of Texas Southwestern Sequencing Core Facility.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
Description SA1_con
Data processing Kallisto (version 0.43.1) was used to quantify gene expression with GENCODE annotation M15 for GRCm38.
The parameter used in Kallisto is "--bias"
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: The columns in Kallisto output are isoform_id, length, effective-length, estimated_read_count, TPM.
 
Submission date May 17, 2021
Last update date May 18, 2021
Contact name Zhenyu Xuan
E-mail(s) zhenyu.xuan@utdallas.edu
Phone 972-883-2518
Organization name UT Dallas
Street address 800 West Campbell
City Richardson
State/province TX
ZIP/Postal code 75080
Country USA
 
Platform ID GPL28457
Series (2)
GSE174584 BRG1 S1382 phosphorylation regulates neuronal activity-dependent gene activation [RNA-seq_B]
GSE174585 BRG1 role in neuronal activity
Relations
BioSample SAMN19235185
SRA SRX10913955

Supplementary file Size Download File type/resource
GSM5320127_SA1_con_abundance.tsv.gz 4.1 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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