|
| Status |
Public on Aug 27, 2016 |
| Title |
Heterozygous Stage5 Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole embryo
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: Cellular blastoderm
genotype: zen[7]/TM3, ftz-lacZ
embryonic stage: stage 5
|
| Treatment protocol |
zen[7] homozygous embryos were selected using a genotyping procedure described by Ghanim and White (2006). In our case, both the absence of lacZ specific band together with the presence of a control band (non-coding region of gene Dtg) were indicators of homozygous lethal embryos.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA extractions, extracts of homozygous (zen[7]) and heterozygous (zen[7]/TM3, ftz-lacZ) staged embryos, previously preserved in RNAWIZ reagent (N = 100) were pooled, then samples were carefully homogenized in a 1.5 mL Eppendorf tube on ice with the aid of RNAse-free polypropylene pellet pestle. After homogenization, RNA extraction was performed using standard protocols. RNA was quantified using Qubit RNA HS Assay Kit (Thermo Fisher) and the integrity was assayed in a Tape station 2200 (Agilent Technologies). Samples were treated with Turbo DNA-free DNase (Ambion) to remove contaminating DNA.
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.
Counts were extracted from BAM files using htseq-count
Genome_build: D. Melanogaster r6.04 (Flybase)
Supplementary_files_format_and_content: tab-delimited text files include counts each Sample.
|
| |
|
| Submission date |
Aug 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Christian E Hodar |
| E-mail(s) |
[email protected]
|
| 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 |
GPL13304 |
| Series (1) |
| GSE86114 |
Transcriptional profiling of zen homozygous and zen heterozygous Drosophila melanogaster embryos |
|
| Relations |
| Reanalyzed by |
GSM3281838 |
| BioSample |
SAMN05711880 |
| SRA |
SRX2056855 |
