|
| Status |
Public on Dec 02, 2019 |
| Title |
huh7_Norm |
| Sample type |
SRA |
| |
|
| Source name |
HuH-7 cultured cells, untreated control
|
| 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 |
SAMN04349947 |
| SRA |
SRX1490879 |
