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Sample GSM2084566 Query DataSets for GSM2084566
Status Public on Jun 10, 2016
Title H460 Control biological replicate 3
Sample type SRA
 
Source name H460 cells
Organism Homo sapiens
Characteristics cell type: non-small-cell lung cancer cell line
cell line: H460
Treatment protocol Transfected with control or NGFR siRNA
Growth protocol Cells were cultured in DMEM plus 10% FBS
Extracted molecule total RNA
Extraction protocol QIAGEN RNeasy mini Kit
Ribo-depletion: Ambion RiboMinus Eukaryote System v2
Library Preparation: Ion Total RNA-Seq Kit v2
Template Preparation: Ion PI Hi-Q Template OT2 200 Kit
Sequencing: Ion PI Hi-Q Sequencing 200 Kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Data processing Align RNA-Seq reads with STAR
Align unmapped reads from Step 1 with bowtie2
Sort sam files
Merge bam files
Use SAMMatev2.6.1 to generate read counts and wiggle (coverage) files
Perform differential expression testing using EBSeq (100 iterations)
Genome_build: hg38
Supplementary_files_format_and_content: xlsx files including ensembl gene ID, gene name, read counts
 
Submission date Mar 09, 2016
Last update date May 15, 2019
Contact name HUA LU
E-mail(s) hlu2@tulane.edu
Organization name TULANE UNIVERSITY
Department Biochemistry and Molecular Biology
Street address 1430 Tulane Ave
City New Orleans
State/province LA
ZIP/Postal code 70112
Country USA
 
Platform ID GPL17303
Series (1)
GSE79051 RNA sequencing analysis of NGFR ablation in both p53-positive and negative non-small-cell lung cancer cell lines
Relations
BioSample SAMN04543855
SRA SRX1622128

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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