|
| Status |
Public on Jun 01, 2014 |
| Title |
Diffuse large B cell lymphoma biopsy, patient 2089 |
| Sample type |
SRA |
| |
|
| Source name |
GC-derived lymphomas
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Diffuse large B cell lymphoma bioptic tissue
|
| Treatment protocol |
The frozen tissue was homogeneized in Trizol reagent.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol Reagent (Invitrogen) following the manufacturer's indications. The small RNA fraction was enriched by flashPAGE fractionation (Ambion).
small RNA libraries were generated using the SOLiD Small RNA Expression Kit (Applied Biosystems).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Data processing |
Sequenced reads were trimmed for adapter sequence, then mapped to miRBase 19 precursors using bowtie-0.12.7 with parameters –color --col-keepends -f --all --maqerr 400 --seedmms 2 --norc –seedlen 20
Custom software to remove poorly matched reads and then assemble reads into clusters
Clusters were trimmed to give a core region mapped by the majority of reads in a cluster
Consensus sequences were formed from the most abundant bases at each position in each cluster
Consensus clusters were overlapped with miRBase 19 mature sequences to annotate
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files including normalized miRNA expression for each sample
|
| |
|
| Submission date |
Mar 31, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Riccardo Dalla-Favera |
| E-mail(s) |
rd10@cumc.columbia.edu
|
| Organization name |
Columbia University
|
| Street address |
1130 St Nicholas Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL9442 |
| Series (1) |
| GSE56354 |
Small-RNA expression in normal and malignant mature B cells |
|
| Relations |
| BioSample |
SAMN02712106 |
| SRA |
SRX504139 |
