|
| Status |
Public on Dec 02, 2019 |
| Title |
cells_mmu_hepa_Proton |
| Sample type |
SRA |
| |
|
| Source name |
primary hepatocytes
|
| Organism |
Mus musculus |
| Characteristics |
origin: cultured primary hepatocytes
treatment: untreated control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with Norgen total RNA purification kit (Norgen Biotek Corp., Canada), small RNAs were enriched using Ion Total RNA-Seq Kit v2 (Life Technologies)
small RNA libraries were prepared with Ion Total RNA-Seq Kit v2 according to the kit manual
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Basecalls performed using Ion Torrent Suite, default parameters
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 mature miRNA assembly (release 21) using Shrimp2 version 2.2.3 with default parameters
Aligned RNA-seq reads were counted using custom Python script
Read counts from PGM and Proton were combined
Genome_build: mmu mature miRNA (release 21) from mirbase.org
Supplementary_files_format_and_content: Tab-delimited text files were generated using custom Python script; Scores represent number of aligned sequence fragments per gene
|
| |
|
| Submission date |
Feb 03, 2016 |
| 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 |
GPL18635 |
| Series (1) |
| GSE77554 |
Next-gen sequencing for miRNA content of exosomes and hepatocytes in mice with acetaminophen toxicity |
|
| Relations |
| BioSample |
SAMN04455452 |
| SRA |
SRX1559806 |
