|
| Status |
Public on Jan 07, 2015 |
| Title |
SMARTseq2 - 2.5x dilution - 1% |
| Sample type |
SRA |
| |
|
| Source name |
Pooled embryos 0-4hrs
|
| Organisms |
Drosophila melanogaster; Drosophila virilis |
| Characteristics |
fraction d. virilis: 1%
library prep protocol: SMARTseq v2 - Tagmentation volume 1/2.5
input rna volume: 1ng
|
| Growth protocol |
Standard conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol extraction of pools of whole embryos
Illumina TruSeq mRNA Unstranded
Epicentre TotalScript: oligo(dT) Primed
Clontech Low Volume Library Construction Kit
SMARTseq v2
SMARTseq v2 - Tagmentation volume 1/2.5
SMARTseq v2 - Tagmentation volume 1/5
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
CASAVA v1.8
STAR --runMode genomeGenerate --sjdbGTFfile dmel_dvir.gtf
STAR --outSAMstrandField intronMotif --outReadsUnmapped Fastx
htseq-count --idattr='gene_name' --stranded=no --order=pos
Genome_build: D. virilis r1.2
Genome_build: D. melanogaster r5.54
|
| |
|
| Submission date |
Jan 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Acuña Combs |
| E-mail(s) |
pcombs@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Biology
|
| Lab |
Hunter Fraser
|
| Street address |
Gilbert Rm 309, 371 Serra Mall
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL19602 |
| Series (1) |
| GSE64673 |
Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols |
|
| Relations |
| Reanalyzed by |
GSM3287698 |
| BioSample |
SAMN03275773 |
| SRA |
SRX831222 |
