|
| Status |
Public on Sep 18, 2023 |
| Title |
Tg_BBLN_right_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
right ventricular heart specimen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: right ventricular heart specimen
strain: FVB/N-TgMHCBBLN
Sex: male
genotype: BBLN
age: 3-4 months
|
| Growth protocol |
After weaning at an age of 3-4 weeks, Tg-BBLN mice and non-transgenic FVB/N control mice were housed until the end of the observation period at an age of 3-4 months in groups of 2-4 mice under SPF conditions with a 12 h dark cycle in individually ventilated cages. All the mice had free access to food and water and were fed a standard rodent diet.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Right and left ventricular heart specimens were dissected from total hearts isolated from euthanized, male Tg-BBLN mice and non-transgenic FVB/N mice (age: 3-4 months). Dissected heart specimens were rapidly frozen in liquid nitrogen. For RNA isolation, right and left heart specimens were pulverized under liquid nitrogen, and total RNA was isolated with the RNeasy midi kit (Qiagen).
RNA libraries were prepared for transcriptome sequencing by GATC Biotech AG, an Eurofins Genomics Company, using standard Illumina protocols in frame of the INVIEW Transcriptome Discover protocol. For library preparation, mRNA was fragmented, and random hexamer-primed cDNA synthesis was performed. Illumina paired-end read sequencing (2 x 150 bp) with guaranteed 30 million reads per sample was performed by the Genome Sequencer Illumina HiSeq, in the sequence mode HiSeq 4000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Tg_BBLN_right_rep2 (TPM)
|
| Data processing |
Trimmed RNA-Seq reads in FASTQ format were generated by GATC Biotech AG. RNA-Seq reads in FASTQ format were imported into the program CLC Genomics workbench 20 version 20.0.4 (QIAGEN Bioinformatics, QIAGEN Aarhus A/S) and aligned to the reference genome (Mouse GRCm39) in frame of the RNA Sequencing Workflow of CLC Genomics workbench 20.
The trimmed RNA-Seq reads in FASTQ format were mapped to the reference genome (Mouse GRCm39) in frame of the RNA Sequencing Workflow of CLC Genomics workbench 20. The following mapping settings were used: Mismatch count: 2; Insertion cost: 3; Deletion cost: 3; Length fraction: 0.8; Similarity fraction: 0.8; Maximum number of hits for a read: 10; Expression value: TPM. Gene and transcript annotations of the reference genome were added to the mapped reads. With these settings, read tracks and reports were generated. The processed data files show transcripts per million (TPM) for every transcript and every sample.
Assembly: Mouse GRCm39
Supplementary files format and content: Tab-separated text (txt) files show TPM values of each sample and transcript. The following tab-separated columns are presented in the processed data files: Name; Chromosome; Region; TPM; Gene name; Transcript length; Exons; Gene ID; Transcript ID; ENSEMBL; Biotype.
Supplementary files format and content: The matrix table shows TPM values of every transcript and every sample. The following tab-separated columns are included in the matrix table (Matrix_table_right_left_heart.txt): Name; Chromosome; Region; Gene name; Transcript length; Exons; Gene ID; Transcript ID; ENSEMBL; Biotype; TPM values of 16 samples.
|
| |
|
| Submission date |
Aug 16, 2023 |
| Last update date |
Sep 18, 2023 |
| Contact name |
Ursula Quitterer |
| E-mail(s) |
ursula.quitterer@pharma.ethz.ch
|
| Phone |
+41-446329801
|
| Organization name |
ETH Zurich
|
| Department |
Molecular Pharmacology
|
| Street address |
Winterthurerstrasse 190
|
| City |
Zurich |
| ZIP/Postal code |
CH-8057 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE241022 |
Cardiac transcriptome analysis of right and left ventricular heart specimens of BBLN-transgenic mice by NGS |
|
| Relations |
| BioSample |
SAMN37008904 |
| SRA |
SRX21384610 |
