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Sample GSM5737371 Query DataSets for GSM5737371
Status Public on Sep 19, 2022
Title siNTRK2_Sen_2
Sample type SRA
 
Source name siNTRK2_Sen_2
Organism Homo sapiens
Characteristics cell line: WI-38
cell type: fibroblasts
treatment: siNTRK2
condition: Etoposide-induced senescence (8 days)
Treatment protocol Cells were transfected with RNAiMAX (Invitrogen) following the manufacturer’s instructions. Briefly, cells at 50% confluency were transfected with ON-TARGETplus SMARTPool (Dharmacon) non-targeting siCtrl (Catalog ID: D-001810-10-05), siNTrk2 (Catalog ID: L-003160-00-0005), or siBDNF (Catalog ID: L-017626-00-0005) siRNAs at a final concentration of 25 nM.
Growth protocol Human WI-38 (Coriell Institute) cells were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Gibco), Penn/Strep (Gibco), Sodium Pyruvate (Gibco), and non-essential amino acids (Gibco) in a 5% CO2 incubator. Cells were maintained at low population doubling levels (PDL), between PDL15 and PDL25. Etoposide was added to the media as indicated every three days; control conditions included equivalent concentrations of vehicle (DMSO).
Extracted molecule total RNA
Extraction protocol RNA was extracted with RLT buffer (Qiagen) and purified using the QIAcube system (Qiagen) through the RNeasy plus method. The quality and quantity of RNA were checked using Agilent RNA 6000 nano kit on the Agilent Bioanalyzer.
125ng of high quality of RNA was used for sequencing library prep using Illumina TruSeq Stranded mRNA Library prep kit according to manufacturer’s protocol (Illumina, San Diego, CA). The quality and quantity of sequencing libraries were checked using Agilent DNA 1000 Screen Tape on the Agilent Tapestation.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description siNTRK2-transfected WI-38 cells were cultured for 8 days in 50 µM etoposide-containing media.
mRNA
Data processing BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to human genome hg19 Ensembl v82 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to create gene counts from the samples.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_geneCOUNT.txt: Tab-delimited text files containing counts.
 
Submission date Dec 15, 2021
Last update date Sep 19, 2022
Contact name Supriyo De
Organization name NIA-IRP, NIH
Department Laboratory of Genetics and Genomics
Lab Computational Biology & Genomics Core
Street address 251 Bayview Blvd
City Baltimore
State/province Maryland
ZIP/Postal code 21224
Country USA
 
Platform ID GPL24676
Series (2)
GSE190998 A BDNF-TrkB autocrine loop enhances senescent cell viability [RNA-seq]
GSE202951 A BDNF-TrkB autocrine loop enhances senescent cell viability
Relations
BioSample SAMN24103704
SRA SRX13440102

Supplementary file Size Download File type/resource
GSM5737371_8_SiNTRK2_Sen_2_S17_geneCOUNT.txt.gz 203.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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