|
| Status |
Public on May 22, 2024 |
| Title |
LX-2_siControl_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
LX-2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LX-2
cell type: Hepatic Stellate Cells
treatment: siControl
|
| Treatment protocol |
LX-2 cells were transfected with siControl or siOGT at 20 nM for 72 h using JetPrime® (Polyplus transfection) (3 biological replicates)
|
| Growth protocol |
LX-2 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, GibcoTM) supplemented with 5% fetal bovine serum (FBS, Deutscher).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
LX-2 total RNA was harvested using Nucleospin® RNA 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 human genome (hg38) 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 GRCh38.84
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: hg38
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 ; "sign_siOGT_control_genes_with_Batch_all.csv" 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 |
GPL29480 |
| Series (2) |
| GSE243105 |
Transcriptome of human LX-2 hepatic stellate cells transfected with siRNA directed against OGT |
| GSE243107 |
O-GlcNAcylation controls pro-fibrotic transcriptional regulatory signaling in hepatic stellate cells |
|
| Relations |
| BioSample |
SAMN37385239 |
| SRA |
SRX21769725 |
