|
| Status |
Public on Apr 30, 2024 |
| Title |
Allogeneic treated ddH2O rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
skin
|
| Organism |
Mus musculus |
| Characteristics |
tissue: skin
genotype: Balb/c
treatment: ddH2O
|
| Treatment protocol |
To reflect the clinical situation with treatment only upon clinical signs of cGvHD, treatment was started 21 days after bone marrow transplantation and thus after the first clinically detectable manifestations of cGvHD in allogeneically transplanted mice. The outcome of treatment was analyzed seven weeks after transplantation. Antibodies were given i.p twice a week, with a first loading dose at 20 mg/kg and the following doses at 10 mg/kg. Nintedanib was given at 50 mg/kg p.o. daily.
|
| Growth protocol |
Recipient mice (BALB/c (H-2d)) with an age of 8 weeks received total body irradiation with 700 cGy. Six hours after irradiation, all BALB/c (H-2d) recipients received bone marrow from either BALB/c (H-2d) in a syngeneic or B10.D2 (H-2d) in an allogeneic transplantation manner.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 3mm-diameter area of skin using the Nucleo Spin RNA isolation kit (Macherey-Nagel).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Allo_H_3
|
| Data processing |
Reads were checked and filtered by FastQC and Trimmomatic
Reads were mapped to mouse genome (GRCm39) by Spliced Transcripts Alignment to a Reference (STAR)
Uniquely mapped reads were assigned to annotated genes using the “featureCounts” from R package “Rsubread” (version 1.22.2)
Assembly: GRCm39
Supplementary files format and content: text document containing raw counts all groups of sample
|
| |
|
| Submission date |
Feb 04, 2024 |
| Last update date |
Apr 30, 2024 |
| Contact name |
Jörg Distler |
| E-mail(s) |
[email protected]
|
| Organization name |
University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University
|
| Department |
Department of Rheumatology
|
| Lab |
Hiller Research Center
|
| Street address |
Merowingerplatz 1A
|
| City |
Düsseldorf |
| ZIP/Postal code |
40225 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE255031 |
Combined inhibition of IL-1, IL-33 and IL-36 signaling by targeting IL1RAP ameliorates skin and lung fibrosis in preclinical models of Systemic Sclerosis |
|
| Relations |
| BioSample |
SAMN39824635 |
| SRA |
SRX23531006 |
