|
| Status |
Public on Sep 18, 2023 |
| Title |
Pancreatic stellate cells, pH7.4, 120h, biol. replicate C |
| Sample type |
SRA |
| |
|
| Source name |
pancreas
|
| Organism |
Mus musculus |
| Characteristics |
tissue: pancreas
cell type: Pancreatic stellate cells
genotype: C57BL6/J WT
treatment: pH7.4
|
| Treatment protocol |
Medium of DMEM/Ham F12 was set to pH6.6 or pH7.4 using differential amount of sodium bicarbonate.
|
| Growth protocol |
Cells were grown in DMEM/Ham F12 1:1, supplemented with 10% FCS and 1% penicillin/streptomycin on plastic tissue culture dishes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The Rneasy Mini Kit was used to extract RNA from PSCs cultured 120 h at pHe6.6 or pHe7.4. Quality and quantity of isolated RNA were evaluated using the NanoDrop 2000. A total of 800 ng RNA was used per sample.
RNA libraries for RNA-seq were prepared using NEBNext RNA Ultra II directional library prep kit plus NEBNext Poly(A) enrichment kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
6_pH7_4_PSC_C_S66_R1
|
| Data processing |
Data processing and analysis was primarily carried out on the Galaxy platform (usegalaxy.eu)
Raw fastq files were aligned and mapped against the murine reference genome (mm10) with the HISAT2 v2.2.1 algorithm
Counts were subsequently extracted using featureCounts 2.0.1(53)
Differential expression of genes was analyzed using limma 3.50.1
Assembly: mm10
Supplementary files format and content: Excel file PSC_pH_RNAseq_counts includes raw count values for each Sample. Excel file PSC_pH_RNAseq_processed contains the DE output of limma 3.50.1 that was used to obtain study conclusions.
|
| |
|
| Submission date |
Jan 18, 2023 |
| Last update date |
Sep 18, 2023 |
| Contact name |
Zoltan Pethö |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Münster
|
| Department |
Physiology II
|
| Lab |
Cell Migration Lab
|
| Street address |
Robert-Koch Str. 27B
|
| City |
Münster |
| State/province |
NRW |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE223205 |
Acid-base homeostasis orchestrated by NHE1 defines the pancreatic stellate cell phenotype in pancreatic cancer |
|
| Relations |
| BioSample |
SAMN32784237 |
| SRA |
SRX19065429 |
