|
| Status |
Public on Nov 28, 2024 |
| Title |
CMC_adult_liver_treated_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
genotype: WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol.
cDNAlibraries were done following ONT instruction manuals.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Data processing |
Basecalling using Guppy.
Demultiplexing using Guppy.
Mapping using graphmap.
Assembly: Mouse and human rRNA fasta.
Supplementary files format and content: CMC scores for the nanoCMC sequencing (they are calculated by comparing the treated vs untreated sample, that is why there is only one processed file per 2 raw files), as well as the EpiNano outputs for the rest of the cDNA runs; they contain the values for mismatches, insertions and deletions per site for all cytosolic rRNA molecules, which we used to infer the presence/absence of modifications and SNPs.
|
| |
|
| Submission date |
Oct 23, 2024 |
| Last update date |
Nov 28, 2024 |
| Contact name |
Ivan Milenkovic |
| E-mail(s) |
[email protected]
|
| Organization name |
Centre for Genomic Regulation
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| State/province |
Catalonia |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL24973 |
| Series (1) |
| GSE280137 |
cDNA sequencing of rRNA from mouse tissues and human matched normal-tumor samples. |
|
| Relations |
| BioSample |
SAMN44405680 |
| SRA |
SRX26475821 |
