|
| Status |
Public on Jan 24, 2024 |
| Title |
LSECs; iron citrate-injected mouse, rep. 2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
cell line: LSECs
cell type: FAC-sorted LSECs (CD45-dim, STAB2-high, CD146-high)
genotype: wild type
treatment: intravenous injection with iron citrate (150 ug) for 5 hours
|
| Treatment protocol |
n/a
|
| Growth protocol |
n/a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from sorted LSECs was extracted using TRIzol™ LS Reagent (ThermoScientific, #10296028) according to the manufacturer’s instructions with an additional step of RNA precipitation with glycogen (ThermoScientific, #R0551).
Library was prepared using Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit according to the manufacturer’s protocol (Thermo Fisher Scientific)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
female Balb/c mouse
|
| Data processing |
The raw reads were processed with Ion Torrent RNASEQAnalysis pipeline (Torrent Suite version 5.0.4)
htseq-count, version 0.6.0, default parameters
DESeq2, version 1.18.1, normalization
Assembly: AmpliSeq Mouse Transcriptome v1
Supplementary files format and content: htseq normalized count
|
| |
|
| Submission date |
Jun 23, 2023 |
| Last update date |
Jan 24, 2024 |
| Contact name |
Michal Mikula |
| E-mail(s) |
mikula.michal@gmail.com
|
| Phone |
+48225462655
|
| Organization name |
Maria Skłodowska-Curie National Research Institute of Oncology
|
| Department |
Experimental Oncology
|
| Lab |
Cancer Metabolism
|
| Street address |
Roentgena 5
|
| City |
Warsaw |
| ZIP/Postal code |
02781 |
| Country |
Poland |
| |
|
| Platform ID |
GPL18635 |
| Series (2) |
| GSE235692 |
NRF2-independent iron-triggered signaling via MAPK p38-ETS1 regulates LSEC Bmp6 mRNA expression [I] |
| GSE235976 |
NRF2-independent iron-triggered signaling via MAPK p38-ETS1 regulates LSEC Bmp6 mRNA expression |
|
| Relations |
| BioSample |
SAMN35881682 |
| SRA |
SRX20765466 |
