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| Status |
Public on Apr 17, 2021 |
| Title |
TxT+GW4869_2 |
| Sample type |
SRA |
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| Source name |
Total lung
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| Organism |
Mus musculus |
| Characteristics |
tissue: Total lung
strain: C57BL/6
genotype: wild type
treatment: blast-wave induced thorax trauma + GW4869
age: 12 week-old
gender: male
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| Treatment protocol |
mice were subjected to blast-wave induced thorax trauma (TxT) under anesthesia. 10-15 minutes after the insult the sEV biogenesis inhibitor GW4869 (2µg/g body weight) or NaCl (vehicle) was injected intravenously.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from lung tissue using miRNAeasy mini kit (Qiagen)
RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
TG_2
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| Data processing |
Expression profiling libraries were sequenced on HiSeq 3000/4000 instruments (Illumina, San Diego, CA, USA) in 50-base-pair, single-end mode. Base calls, provided by the real-time analysis (RTA) software (Illumina, San Diego, CA, USA), were subsequently converted into multiplexed, unaligned BAM format before demultiplexing into sample-specific, unaligned BAM files. For raw data processing off the instruments, custom programs, based on Picard tools (https://broadinstitute.github.io/picard/), were used
NGS reads were mapped to the Genome Reference Consortium GRCm38 assembly via “Spliced Transcripts Alignment to a Reference” (STAR) utilising the “basic” Ensembl transcript annotation from version e99 (January 2020) as reference transcriptome. Since the mm10 assembly flavour of the UCSC Genome Browser was preferred for downstream data processing with Bioconductor packages for entirely technical reasons, Ensembl transcript annotation had to be adjusted to UCSC Genome Browser sequence region names. STAR was run with options suggested by the ENCODE project. Aligned NGS reads overlapping Ensembl transcript features were counted with the Bioconductor GenomicAlignments::summarizeOverlaps() function, taking into account that the Illumina TruSeq stranded mRNA protocol leads to sequencing of the second strand so that all reads needed inverting before counting. Transcript-level counts were aggregated to gene-level counts and the Bioconductor DESeq2 package was used to test for differential expression based on a model using the negative binomial distribution
Genome_build: GRCm38
Supplementary_files_format_and_content: TSV files, FPKMS all samples
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| Submission date |
Apr 16, 2021 |
| Last update date |
Apr 17, 2021 |
| Contact name |
Tim Eiseler |
| E-mail(s) |
tim.eiseler@uniklinik-ulm.de
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| Organization name |
Ulm University
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| Department |
Internal Medicine 1
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| Street address |
Albert-Einstein Allee 23
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| City |
Ulm |
| ZIP/Postal code |
89081 |
| Country |
Germany |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE172209 |
Whole transcriptome analysis of lung tissue from mice after thoraxtrauma with and without sEV biogenesis inhibitor GW4869 |
| GSE172212 |
Small extracellular vesicles propagate the inflammatory response after trauma. |
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| Relations |
| BioSample |
SAMN18754537 |
| SRA |
SRX10615328 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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