|
| 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 |
| 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 |
SAMN09692200 |
| SRA |
SRX4408708 |
