|
| Status |
Public on Aug 26, 2010 |
| Title |
Plasma B cells (PC137) |
| Sample type |
SRA |
| |
|
| Source name |
Lymphoid organ
|
| Organism |
Homo sapiens |
| Characteristics |
b cell type: Plasma cell (FACS sorted primary human)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA (typically 5ug) from each sample was run on denaturing polyacrylamide-urea gels. The 18-30 nucleotide RNAs were excised from the gel, reverse transcribed, and ligated to sequencing adaptors on the 5’ and 3’ ends. The resulting cDNA library was PCR-amplified for 15 cycles and gel purified on 6% acrylamide gel. The gel-purified amplicon quality and quantity were analyzed on a 6% acrylamide gel relative to oligonucleotides of known concentration and size. 120 μl of 1-4 pM library were loaded on to the Illumina cluster station, where DNA molecules were attached to high-density universal adaptors in the flow cells and amplified. The DNA clusters generated via this process were sequenced with sequencing-by-synthesis technology, where successive high-resolution images were captured of the four-color fluorescence excitation dependent on the base incorporated during each cycle.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
size fractionated small RNA
|
| Data processing |
Sequence mapped to the genome, flanking sequence retrieved and biogenesis characteristics of miRNA checked.
The supplementary *_seq.txt file is an intermediate data file that was used to map the sequences to the reference genome.
|
| |
|
| Submission date |
Mar 13, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Dereje D. Jima |
| E-mail(s) |
ddjima2014@gmail.com
|
| Phone |
9195155932
|
| Organization name |
North Carolina State University
|
| Department |
Center for Human Health and the Environment (CHHE) and Bioinformatics Research Center (BRC)
|
| Street address |
850 Campus Drive
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE15229 |
Massively Parallel Sequencing Identifies the MicroRNA Transcriptome of Normal and Malignant Human B cells |
| GSE22898 |
Deep Sequencing of the Small RNA Transcriptome of Normal and Malignant Human B cells Identifies Hundreds of Novel MicroRNAs |
|
| Relations |
| SRA |
SRX003948 |
| BioSample |
SAMN02197837 |
