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Sample GSM7805978 Query DataSets for GSM7805978
Status Public on Apr 16, 2024
Title SAVI Tnfr 1/2 KO 4
Sample type SRA
Source name lung
Organism Mus musculus
Characteristics tissue: lung
cell line: ex vivo
cell type: Ter119- CD45- CD326- CD31+
genotype: Tmem173 N154S KI/WT 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 AW1-06005
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 -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
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
BioSample SAMN37551821
SRA SRX21898631

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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