|
| Status |
Public on Aug 04, 2016 |
| Title |
CB rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole embryo
|
| Organism |
Musca domestica |
| Characteristics |
developmental stage: Cellular blastoderm
|
| Extracted molecule |
total RNA |
| Extraction protocol |
100 embryos of each stage were flash frozen on liquid N2 and RNA was extracted using Tri-reagent. Remain DNA was digested with Ambion Turbo DNAse and purified using the RNA cleanup protocol from the RNAeasy Mini Kit (Quiagen)
Transcriptome sequencing was performed at the Duke Center for Genomic and Computational Biology in a Hiseq2000 platform (Illumina) with a 100 bp pair end library and 200 bp insert size
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Reads were received already filtered by quality and mapped using STAR alignment using M. domestica Aabys strain genomic scaffold sequences (VectorBase) as reference.
Counts were extracted from BAM files using htseq-count
Genome_build: MdomA1.1
Supplementary_files_format_and_content: tab-delimited text files include counts each Sample.
|
| |
|
| Submission date |
Aug 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Christian E Hodar |
| E-mail(s) |
chodar@inta.uchile.cl
|
| Phone |
+56922978532
|
| Organization name |
Universidad de Chile
|
| Department |
INTA
|
| Lab |
Bioinformatics and Genexpression
|
| Street address |
Av. El Libano 5524
|
| City |
Santiago |
| State/province |
Santiago |
| ZIP/Postal code |
7830490 |
| Country |
Chile |
| |
|
| Platform ID |
GPL15805 |
| Series (1) |
| GSE85160 |
Early developmental transcriptome of Musca domestica. |
|
| Relations |
| BioSample |
SAMN05509753 |
| SRA |
SRX1998274 |
