|
Status |
Public on Nov 28, 2024 |
Title |
CMC_adult_brain_treated_rep2 |
Sample type |
SRA |
|
|
Source name |
Brain
|
Organism |
Mus musculus |
Characteristics |
tissue: Brain 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 |
SAMN44405684 |
SRA |
SRX26475817 |