|
| Status |
Public on May 22, 2024 |
| Title |
pMF-HSC_C57Bl6/J_Control_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Primary myofibroblastic hepatic stellate cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Primary myofibroblastic hepatic stellate cell
treatment: DMSO
|
| Treatment protocol |
Primary mouse myofibroblastic HSCs (pMF-HSCs at 7 d of culture) were treated with vehicle (DMSO) or OSMI-1 at 50 µM for 24 h (4 biological replictates)
|
| Growth protocol |
Mice were housed in standard cages in a temperature-controlled room (22-24°C) with 12 hours (h) light-dark cycles and provided with water and standard diet ad libitum. Mice were allowed to acclimate for at least 1 week (wk) prior to any experiment. Quiescent primary mouse HSCs were isolated from WT C57BL/6J mice (male, 15-18 wks old, Charles River) according to the protocol described in Bobowski-Gerard et al. (2022) and underwent spontaneous activation into myofibroblastic HSCs (MF-HSCs) upon regular in vitro cell culture for 7 days in Dulbecco’s Modified Eagle Medium (DMEM, GibcoTM) supplemented with 5% fetal bovine serum (FBS, Deutscher).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
pMF-HSC total RNA was harvested using Nucleospin® RNA Plus XS kit (Macherey-Nagel).
RNA libraries for RNA-seq were prepared with DNBSEQ stranded mRNA library after oligo dT based enrichment
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke
Mapping of reads to the mouse genome was achieved using Bowtie2 (v2.3.5.1; parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200) using the GENCODE annotation GRCm39
Read counting was then performed using the RNA‑Seq by Expectation Maximization (RSEM, v1.3.1; parameters: -p 8 --forward-prob 0 --paired-end)
Normalization and differential gene expression analyses were performed using DESeq2 (v1.36.0). Genes with low expression (total read counts below 10) were removed and treatment and control samples from the same replicate were paired for differential expression analysis.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include Ensembl IDs and count values for each Sample
Supplementary files format and content: Matrix table include normalized abundance measurements (output from DESeq2 ; "OSMI1vsCtrl.complete.txt" file)
|
| |
|
| Submission date |
Sep 13, 2023 |
| Last update date |
May 22, 2024 |
| Contact name |
Jérôme Eeckhoute |
| E-mail(s) |
jerome.eeckhoute@inserm.fr
|
| Organization name |
CNRS
|
| Lab |
INSERM UMR 1011, Université Lille-Nord de France
|
| Street address |
Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc
|
| City |
Lille |
| ZIP/Postal code |
59045 |
| Country |
France |
| |
|
| Platform ID |
GPL28330 |
| Series (2) |
| GSE243106 |
Transcriptome of activated mouse primary hepatic stellate cells treated with the OGT inhibitor OSMI-1 |
| GSE243107 |
O-GlcNAcylation controls pro-fibrotic transcriptional regulatory signaling in hepatic stellate cells |
|
| Relations |
| BioSample |
SAMN37384962 |
| SRA |
SRX21768246 |
