|
| Status |
Public on Apr 16, 2024 |
| Title |
Tnfr1/2 KO 3 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
cell line: ex vivo
cell type: Ter119- CD45- CD326- CD31+
genotype: Tnfr1/2 KO/KO
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FACS sorting
mRNA was isolated from on average 50 ng total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s instructions. Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra II Directional RNA Library Prep, NEB). For ligation NEB Next Adapter for Illumina of the NEB Next Multiplex Oligos for Illumina Kit were used. After ligation, adapters were depleted by an XP bead purification (Beckman Coulter) adding the beads solution in a ratio of 0.9:1 to the samples. Unique dual indexing was done during the following PCR enrichment (14 cycles) using amplification primers carrying the same sequence for i7 and i5 index (Primer 1: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC NNNNNNNN ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, Primer 2: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After two more XP bead purifications (0.9:1), libraries were quantified using the Fragment Analyzer (Agilent). Libraries were sequenced on an Illumina NovaSeq 6000 in 100 bp paired-end mode with an average of 30 million fragments per library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
AW1-06004
|
| Data processing |
bcl2fastq2 2.20.0
Fragments were aligned to the mouse reference (GRCm39) with support of the Ensembl 104 gene annoation using the aligner gsnap (v2020-12-16) (-d GRCm39 --gunzip -A sam -t 12 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -n 1 -m 0.6 -s EnsemblGene-104.ss.GRCm39.iit -N 0)
Fragments per gene and samples were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl gene annotation using featureCounts (v2.0.1) (-a EnsemblGene-104.GRCm39.TR.gtf -s 2 -p -o genecount/bfx1909.GRCm39.e104.txt -Q 1 -T 8)
Assembly: GRCm39
Comma separated text file from FeatureCounts. Each columns is either the listing of gene characteristics or Samples and each row show the specific gene details / fragments per gene per sample
|
| |
|
| Submission date |
Sep 26, 2023 |
| Last update date |
Apr 16, 2024 |
| Contact name |
Rayk Behrendt |
| E-mail(s) |
behrendt@uni-bonn.de
|
| Phone |
+4922828751120
|
| Organization name |
Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn
|
| Department |
Nucleic Acid Immunity & Genome Defense
|
| Lab |
The 3ehrendt Lab
|
| Street address |
Venusberg-Campus 1
|
| City |
Bonn |
| State/province |
North Rhine-Westphalia |
| ZIP/Postal code |
53127 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE244062 |
Tissue-specific inflammation induced by constitutively active STING is mediated by enhanced TNF signaling |
|
| Relations |
| BioSample |
SAMN37551826 |
| SRA |
SRX21898626 |
