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| Status |
Public on Aug 20, 2020 |
| Title |
RNA-seq in A549 cells after control siRNA treatment for double knockdown samples rep1 |
| Sample type |
SRA |
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| Source name |
A549 lung adenocarcinoma cell line
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| Organism |
Homo sapiens |
| Characteristics |
sirna: siControl
cell line: A549
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| 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
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| 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).
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Jul 31, 2020 |
| Last update date |
Aug 21, 2020 |
| Contact name |
Daniel James Mullen |
| E-mail(s) |
dmullen@usc.edu
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| Organization name |
University of Southern California
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| Department |
Biochemistry and Molecular Medicine, Surgery
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| Lab |
Offringa
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| Street address |
1441 Eastlake Ave., Room NTT 6420
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE143145 |
TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma |
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| Relations |
| BioSample |
SAMN15685341 |
| SRA |
SRX8858004 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4704964_A549-NC2-1_readcounts.txt.gz |
240.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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