|
| Status |
Public on Nov 12, 2021 |
| Title |
WPMC isolated from heterozygous Stat1 mouse (control to Stat1KO) [WPMC_Stat1het_2] |
| Sample type |
SRA |
| |
|
| Source name |
white pulp mesenchymal cell
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Stat1-heterozygous
strain: Stat1tm1.2Mmul_heterozygous
cell type: WPMC
|
| Treatment protocol |
Samples represent biological replicates sorted from pooled splenic preparations from 2 three-months-old male per replicate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were directly FACS-sorted into RLT+ lysis buffer (Qiagen), containing 10 µl/ml β-mercaptoethanol (Roth). Total RNA was extracted with the RNeasy Plus Micro kit (Qiagen) according to manufacturer’s instructions.
cDNA conversion was carried out using the SMART‑Seq v4 Ultra Low Input RNA Kit (Takara Clontech Laboratories) according to manufacturer’s instructions, followed by PCR product purification with Agencourt AMPure XP magnetic beads (Beckman Coulter). Libraries were prepared with the Nextera XT DNA Library Prep Kit (Illumina) employing enzymatic tagmentation and simultaneous adapter ligation before subsequent indexing and fragment amplification. PCR product clean-up and size selection was performed with the Agencourt AMPure XP magnetic beads. RNA and cDNA quality and content, as well as the correct sizing of cDNA library fragments was verified using the Agilent Technologies 2100 Bioanalyzer profiles and Qubit measurements after each step.
Libraries were pooled and sequenced at the genome analytics facility of the Helmholtz Centre for Infection Research on Illumina HiSeq2500 using 50 bp single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ex vivo isolated cells
Stat1 deficiency comparison
|
| Data processing |
Read quality of sequenced libraries was evaluated with FastQC. Sequencing reads were aligned to the reference mouse genome assembly GRCm38 using STAR, and aligned reads to annotated genes were quantified with htseq-count.
Raw read counts were converted to RPKM (reads per kilobase of exon length per million mapped reads) values. Protein-coding genes with with at least 20 reads in at least two replicates were included in the analysis.
The calculated read counts were further processed with DESeq2 for quantification of differential gene expression[]. Unless not otherwise mentioned genes were considered as differentially expressed at log2(foldchange) > 0.8 and an adjusted p-Value of < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM/FPKM, fold-change matrices for each replicate.
|
| |
|
| Submission date |
Aug 13, 2020 |
| Last update date |
Nov 12, 2021 |
| Contact name |
Joern Pezoldt |
| E-mail(s) |
jorn.pezoldt@epfl.ch
|
| Phone |
0041766040171
|
| Organization name |
EPFL
|
| Department |
SV
|
| Lab |
Laboratory Systems Biology and Genetics
|
| Street address |
Station 19, SV 3818.A
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE156162 |
Single-cell transcriptional profiling of splenic fibroblasts reveals subset-specific innate immune signatures in homeostasis and during viral infection |
|
| Relations |
| BioSample |
SAMN15808877 |
| SRA |
SRX8939649 |
