NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3291850 Query DataSets for GSM3291850
Status Public on Feb 27, 2019
Title MM at diagnosis, sample 18 [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(11;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-213
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
E-mail(s) luca.agnelli@istitutotumori.mi.it, luca.agnelli@gmail.com
Phone +390223903581
Organization name IRCCS Istituto Nazionale dei Tumori
Department Department of Advanced Diagnostics
Street address Venezian 1
City MILAN
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
Relations
BioSample SAMN09692199
SRA SRX4408709

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap