 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 01, 2016 |
| Title |
TRIzol+MS2_pooled 1 |
| Sample type |
SRA |
| |
|
| Source name |
TRIzol+MS2_pooled_serum
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Serum
sample type: Orphan samples
sample type: DoD Serum Repository
sample type: small RNA
sample type: pooled serum samples
rna extraction method: TRIzol+MS2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Different extraction procedures such as TRIzol with and without carrier glycogen/yeast tRNA/bacteriophage MS2), miRNAeasy ,mirVANA and TRIzol with exosome precipitation using exoquick buffer.
Illumina Trueseq small RNA kit
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Reads were processed further for quality assessment, quality filtering, and adaptor trimming, and quality filtered again using a Phred quality score threshold of 20
The ligated adaptor sequences were trimmed, leaving a minimum overlap of five bases while allowing an error rate of 0.1 using CutAdapt 1.2.1
Using the short read aligner Bowtie 1.0.0 [27], filtered sequence reads were aligned to the Human reference genome assembly humanv37 from Ensembl and the best hits to the genome were identified using BEDtools 2.17
Small RNA species were annotated by mapping with the reference gene feature annotation table from the Ensembl database
Quantification/enrichment reads for miRNAs were first aligned to the Rfam RNA families database to filter other small RNA species, and then reads were mapped for small RNA annotation against reference.mature/precursor hg19_mature RNA sequences from the miRBase (miRbase 19)database .The miRNA read count matrix for each sample was generated using open source tools Picard 1.84
Genome_build: mirBASE19
Supplementary_files_format_and_content: miRNA count file
|
| |
|
| Submission date |
Apr 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Aarti Gautam |
| E-mail(s) |
aarti.gautam.civ@health.mil
|
| Phone |
301-619-7683
|
| Organization name |
WRAIR
|
| Department |
Medical Readiness Systems Biology
|
| Street address |
503 Robert Grant Avenue
|
| City |
Silver Spring |
| State/province |
MD |
| ZIP/Postal code |
20910 |
| Country |
USA |
| |
|
| Platform ID |
GPL15456 |
| Series (1) |
| GSE80274 |
Identification of extracellular miRNA in archived serum samples by next-generation sequencing from RNA extracted using multiple methods |
|
| Relations |
| BioSample |
SAMN04853040 |
| SRA |
SRX1704766 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
