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Sample GSM2257960 Query DataSets for GSM2257960
Status Public on Aug 03, 2016
Title A549_shNT_rep2
Sample type SRA
 
Source name human A549_shNT
Organism Homo sapiens
Characteristics cell type: lung cancer cell line
cell line: A549
Treatment protocol Human lung cancer cell line A549 cells were infected with shNT or shIno80, and total RNA was extracted 4 days after infection. The RNA was submitted to RNA-Seq subsequently.
Growth protocol A549 cells were obtained from ATCC, and cultured in DMEM supplemented with 10% fetal bovine serum (FBS).
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from cells using the GeneJet RNA purification kit (Thermo Scientific)
For RNA-seq, One microgram total RNA was used for sequencing library generation using the Truseq RNA Library Prep Kit V2 (Illumina) according to the manufacturer’s instructions. Truseq RNA Library Prep Kit V2 (Illumina)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Gene expression 4 days after transfection
Data processing Aligned with TopHat2 version 2.0.4 with the following parameters: -g 10
FPKM measurements obtained using CuffLinks version 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: text file with FPKM: 1st column = RefSeq ID, 2nd column = fragments per kilobase of exon per million mapped reads (FPKM value)
 
Submission date Aug 02, 2016
Last update date May 15, 2019
Contact name Li Wang
Organization name NIH
Street address 111 T.W. Alexander Dr
City Durham
ZIP/Postal code 27709
Country USA
 
Platform ID GPL18573
Series (2)
GSE85118 INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer [RNA-seq]
GSE85119 INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer
Relations
BioSample SAMN05505548
SRA SRX1996511

Supplementary file Size Download File type/resource
GSM2257960_A549_shNT_rep2_FPKM.txt.gz 283.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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