|
| Status |
Public on Apr 28, 2024 |
| Title |
cirrhotic liver, paired control, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: liver
disease: cirrhosis
time: 4hr
treatment: control
|
| Treatment protocol |
Laser-treated samples were ablated with a fractional CO2 laser. Untreated samples from the same liver were collected for paired controls
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were placed in RNAlater (Thermo Fisher Scientific) and stored at 4C overnight, then at -20C until ready to use. RNA extraction was performed using the RNeasy midi kit with proteinase K digestion and on-column DNase digestion according to manufacturer instructions (Qiagen, Hilden, Germany).
Libraries were prepared using NEBNext Ultra II (New England Biolabs, Ipswich, USA) with poly(A) selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw data quality was assessed with FastQC v0.11.9
Reads were trimmed with Cutadapt v3.4 and Trim Galore v0.6.7
Pseudo-alignment and transcript abundance estimation were performed with Salmon v1.5.2
Reads were imported to R with tximport and converted to gene-level data with the tx2gene option. Differential expression was calculated using DESeq2 v4.2.2
Assembly: rn6
Supplementary files format and content: tab-delimited text files include TPMs for each sample
|
| |
|
| Submission date |
Mar 28, 2023 |
| Last update date |
Apr 28, 2024 |
| Contact name |
Ben Leaker |
| E-mail(s) |
leakerb@mit.edu
|
| Organization name |
MIT
|
| Department |
HST
|
| Street address |
77 Massachusetts Avenue
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE228374 |
Increased susceptibility to ischemia causes exacerbated response to laser microinjuries in the cirrhotic liver |
|
| Relations |
| BioSample |
SAMN33952613 |
| SRA |
SRX19795815 |
