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Sample GSM2803941 Query DataSets for GSM2803941
Status Public on Jun 26, 2018
Title Parental cells_1
Sample type SRA
 
Source name 3T9 FIBROBLAST
Organism Mus musculus
Characteristics genotype/variation: miR-30_MRE_WT
cell line: 3T9
cell type: fibroblast
Growth protocol cells were grown in complete medium (10% FBS)
Extracted molecule total RNA
Extraction protocol Total RNA, including small species, was isolated through the miRNeasy mini kit (Qiagen).
1000 nanograms of total RNA were used to prepare Small RNA libraries following the Illumina TruSeqTM Small RNA kit instructions
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
 
Description small RNA sequecing Illumina
Data processing FASTQ data were trimmed using cutadapt-1.9.1; then trimmed data was aligned to custom sequence libraries listing all isoforms of small RNA molecules by using Bowtie with --best and -v 0 switches and saved in .map output format.
Isomirage software was used to count the number of occurrences in the .map file of each isoform listed in the .genome file
Raw counts were finally normalized using CPM (copies-per-million)
Genome_build: mm9
Supplementary_files_format_and_content: Excel Spreadsheet containing the raw counts of miRNA, including miRNA isoforms
 
Submission date Oct 04, 2017
Last update date May 15, 2019
Contact name Francesco Nicassio
E-mail(s) francesco.nicassio@iit.it
Organization name Istituto Italiano di Tecnologia
Department Center for genomic science
Street address Via Adamello 16
City Milano
ZIP/Postal code 20139
Country Italy
 
Platform ID GPL13112
Series (2)
GSE104598 Endogenous transcripts control miRNA levels and activity in mammalian cells by a target-dependent miRNA degradation mechanism [miRNA-Seq]
GSE104650 Endogenous transcripts control miRNA levels and activity in mammalian cells by a target-dependent miRNA degradation mechanism
Relations
BioSample SAMN07737768
SRA SRX3243598

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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