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Sample GSM3291849 Query DataSets for GSM3291849
Status Public on Feb 27, 2019
Title MM at diagnosis, sample 17 [miRNA-Seq]
Sample type SRA
Source name Highly purified PCs from MM patient
Organism Homo sapiens
Characteristics tissue: Bone marrow plasma cells
molecular alteration: t(4;14)
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL).
Small RNA cDNA libraries (for transcripts <30nt) were built following standard Illumina Truseq® Small RNA protocol, starting from 2 micrograms of total RNA for each sample. BluePippin system was used for fragments selection within the range of 145-160 bp. RNA-seq was performed on Illumina HiSeq platform. A 50-cycle single-reads sequencing was run to generate the tags corresponding to small-RNAs
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
Description MM-206
Data processing base-calling Casava 1.9
read adapter trimming with FastxToolkit v0.0.13
reads longer than 30nt and with average quality less than 30 (Phred) were discarded
read alignment to genome and precursor sequences with Bowtie v1.1.0
read count was performed with custom scripts on miRBase v21 annotation and small RNAs predicted by the miR&moRe pipeline
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_data.txt
Supplementary_files_format_and_content: raw_variants.txt
Submission date Jul 19, 2018
Last update date Feb 27, 2019
Contact name Luca Agnelli
Phone +390223903581
Organization name IRCCS Istituto Nazionale dei Tumori
Department Department of Advanced Diagnostics
Street address Venezian 1
ZIP/Postal code 20133
Country Italy
Platform ID GPL11154
Series (2)
GSE117365 New and subgroup-specific miRNAs and miRNA-offset RNA unraveled by RNA-sequencing in multiple myeloma [miRNA-Seq]
GSE117366 New and subgroup-specific miRNAs and miRNA-offset RNA unraveled by RNA-sequencing in multiple myeloma
BioSample SAMN09692200
SRA SRX4408708

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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