|
| Status |
Public on Nov 30, 2021 |
| Title |
Group I - 1 |
| Sample type |
SRA |
| |
|
| Source name |
liver tissue
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
age: 46
tissue: liver
|
| Treatment protocol |
RNA extraction, DNA digestion, ribosomal RNA depletion and library construction
|
| Growth protocol |
life human lever tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rneasy kit Qiagen for RNA extraction
Strand Specific RNA
2x 30 million reads per sample (2 x 50 nucleotides)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
AL10
|
| Data processing |
Samples were sequenced using the 50 nt paired-end. Each sample produced 2 fastQ files and were screened for Illumina adapters and primers with the program fastq-mcf. Afterwards, filtered reads were aligned to the human genome GRCh38 using the program STAR.
The program Samtools was used to transform SAM files into BAM files and reads were sorted according the position of the alignments, based on their coordinates on each chromosome. The total number of reads per gene for each sample was generated. All samples were merged in a single table for downstream analysis using the packages uuid, stringr, parallel and data.table from R.
Genome_build: Homo_sapiens.GRCh38.97.gtf
Supplementary_files_format_and_content: count data
|
| |
|
| Submission date |
Sep 10, 2021 |
| Last update date |
Dec 01, 2021 |
| Contact name |
Ramiro Vichez-Vargas |
| E-mail(s) |
ramiro.vilchez@med.ovgu.de
|
| Phone |
+493916724713
|
| Organization name |
Otto-von-Guericke-Universität Magdeburg
|
| Department |
Gastroenterology, Hepatology and infectious diseases
|
| Lab |
Molecular Gastroenterology and Microbiota-associated Diseases
|
| Street address |
Leipzigerstr. 44
|
| City |
Magdeburg |
| State/province |
Saxony Anhalt |
| ZIP/Postal code |
39120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE183915 |
Transcriptome-Wide Analysis of Human Liver Reveals Age-Related Differences in the Expression of Select Functional Gene Clusters and Evidence for a PPP1R10-Governed ‘Aging Cascade’. |
|
| Relations |
| BioSample |
SAMN21386167 |
| SRA |
SRX12134672 |
