NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4704965 Query DataSets for GSM4704965
Status Public on Aug 20, 2020
Title RNA-seq in A549 cells after control siRNA treatment for double knockdown samples rep2
Sample type SRA
 
Source name A549 lung adenocarcinoma cell line
Organism Homo sapiens
Characteristics sirna: siControl
cell line: A549
Treatment protocol siRNA knockdown was performed in triplicate on A549 cells using 100 nM of ON-TARGETplus siRNA oglionucleotides for human MYBL2 (# L-010444-00-005, Dharmacon - Horizon Discovery, UK) and FOXM1 (# L-009762-00-005, Dharmacon - Horizon Discovery, UK) , or non-targeting control (# D-001810-10-05, Dharmacon - Horizon Discovery, UK) mixed with 5X siRNA buffer (# B-002000-UB-100, Horizon Discovery, UK) and transfected using DharmaFECT 1 Transfection reagent (# T-2001-01, Horizon Discovery, UK). Cells were transfected, cultured for 24 hours, and transfected again with the same concentration of siRNA, then were incubated for an additional 24 hours
Growth protocol Human lung adenocarcinoma A549 cells (ATCC # CRL-185) were grown at 37oC with 5% CO2 in RPMI 1640 (#10-040-CV, Corning, NY, USA) supplemented with 10% FBS (#FBS-500, X&Y Cell Culture, MI, USA) and 100 units/ml of penicillin/streptomycin (formulated by Norris Comprehensive Cancer Center Media Core, CA, USA).
Extracted molecule total RNA
Extraction protocol For RNA sequencing, RNA was extracted using the Aurum Total RNA Mini Kit (# 7326820, Bio-Rad, CA, USA). cDNA was synthesized using an iScript cDNA Synthesis Kit (# 1708891, Bio-Rad, CA, USA).
RNA-seq was performed after siRNA knockdown using libraries created by MedGenome (Foster City, CA), and sequenced using 100bp paired-end reads on an Illumina NovaSeq 6000 by MedGenome (Foster City, CA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing RNA-seq reads were aligned to the human reference genome hg38 using the Genomic Data Commons Bioinformatics mRNA analysis pipeline (https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/). In brief, the two-pass alignment method was performed using STAR v2.6.0a using settings as specified by the pipeline. Read counts were generated for GENCODE v22 genes using the htseq-count function from HTSeq v0.11.1
Genome_build: hg38
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files contain read counts for GENCODE v22-annotated genes
 
Submission date Jul 31, 2020
Last update date Aug 21, 2020
Contact name Daniel James Mullen
E-mail(s) dmullen@usc.edu
Organization name University of Southern California
Department Biochemistry and Molecular Medicine, Surgery
Lab Offringa
Street address 1441 Eastlake Ave., Room NTT 6420
City Los Angeles
State/province CA
ZIP/Postal code 90089
Country USA
 
Platform ID GPL24676
Series (1)
GSE143145 TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma
Relations
BioSample SAMN15685340
SRA SRX8858005

Supplementary file Size Download File type/resource
GSM4704965_A549-NC2-2_readcounts.txt.gz 242.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap