|
Status |
Public on Apr 28, 2024 |
Title |
healthy liver, laser treated, rep1 |
Sample type |
SRA |
|
|
Source name |
liver
|
Organism |
Rattus norvegicus |
Characteristics |
tissue: liver disease: healthy time: 4hr treatment: fractional laser
|
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 |
SAMN33952626 |
SRA |
SRX19795802 |