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Sample GSM3073180 Query DataSets for GSM3073180
Status Public on Jun 26, 2018
Title MRE_KO1_3T9_8h
Sample type SRA
 
Source name 3T9 fibroblast
Organism Mus musculus
Characteristics "serpine1_3utr": miR-30_MRE_deleted_clone1
cell line: 3T9 fibroblast
time: 8h
treatment: Serum-Stimulated MRE-KO1 cells at 8 hours
Growth protocol cells were kept in absence of serum for 72 hours to induce quiescence (0h samples). Then, cells were stimulated with serum at collected at different time-points (8hrs and 12hrs)
Extracted molecule total RNA
Extraction protocol Total RNA was isolated through the miRNeasy mini kit (Qiagen).
1000 nanograms of total RNA were used to prepare RNA libraries following the Illumina TruSeq Library Preparation Kit instructions
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description GEO_fghini_3T9_serum_RNAseq_TPM.xls
Data processing FASTQ data of the total RNA sequencing experiment were aligned using TopHat 2.0.6 with default parameters
Read Counts were obtained for each gene using FeatureCounts
Raw Read Counts were normalized to TPM (transcript per million)
Genome_build: mm9
Supplementary_files_format_and_content: Excel Spreadsheet containing TPM for each gene
 
Submission date Apr 01, 2018
Last update date Jun 26, 2018
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 GPL24247
Series (2)
GSE104650 Endogenous transcripts control miRNA levels and activity in mammalian cells by a target-dependent miRNA degradation mechanism
GSE112578 Endogenous transcripts control miRNA levels and activity in mammalian cells by a target-dependent miRNA degradation mechanism [RNA-Seq_2]
Relations
BioSample SAMN08828588
SRA SRX3870955

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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