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Sample GSM8588619 Query DataSets for GSM8588619
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

Supplementary file Size Download File type/resource
GSM8588619_CMC_Scores_adult_brain_rep2.tsv.gz 262.4 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA

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