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Sample GSM1974952 Query DataSets for GSM1974952
Status Public on Dec 02, 2019
Title huh7_A5
Sample type SRA
 
Source name HuH-7 cultured cells, arsenic 5 ┬ÁM
Organism Homo sapiens
Characteristics cell line: Huh-7
cell type: human hepatocellular carcinoma
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with mirVana kit followed by ribosomal RNA removal with RiboMinus kit (both Ambion),
RNA libraries were prepared with Ion Total RNA-Seq Kit v2 (Life Technologies) according to the kit manual
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Data processing Basecalls performed using Ion Torrent Suite version 4.2.1 with following configuration; BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1
Raw RNA-seq reads were trimmed using fastq_quality_trimmer version 0.0.14 with default parameters
Trimmed RNA-seq reads were aligned to the GRCh37 genome assembly using Tophat version 2.0.13 with default parameters
Aligned RNA-seq reads were counted using htseq-count version 0.6.1 with default parameters
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files were generated using htseq-count; Scores represent number of aligned sequence fragments per gene
 
Submission date Dec 18, 2015
Last update date Dec 02, 2019
Contact name Sanjeev Gupta
E-mail(s) sanjeev.gupta@einsteinmed.org
Organization name Albert Einstein College of Medicine
Department Medicine
Street address 1300 Morris Park Ave.
City Bronx
State/province NY
ZIP/Postal code 10461
Country USA
 
Platform ID GPL17303
Series (1)
GSE76139 Next-gen sequencing for transcriptomic differences in HuH-7 human hepatocellular carcinoma cell line models of hepatotoxicity
Relations
BioSample SAMN04349953
SRA SRX1490885

Supplementary file Size Download File type/resource
GSM1974952_A5_count.txt.gz 193.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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