|
| Status |
Public on Sep 12, 2013 |
| Title |
pse_1 |
| Sample type |
SRA |
| |
|
| Source name |
Blastoderm embryo
|
| Organism |
Drosophila pseudoobscura |
| Characteristics |
strain: Wild type
tissue: whole embryo
developmental stage: Blastoderm
genotype: wild type
|
| Growth protocol |
Blastoderm embryos
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using Trizol, according to manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Reads were mapped to the genomes using tophat {Trapnell:2009dp}. Refined annotations of D. yakuba, D. pseudoobscura and D. virilis were based on the reference annotations (Flybase releases 1.3, 2.22 and 1.2 respectively) and mRNA-seq data obtained from pools of embryos. The reference annotations and mapped reads were given as inputs to cufflinks (version 1.0.3) {Roberts:2011hw} with the options –g and ‘--3-overhang-tolerance 300’. Statistics on the new annotations are given in Table S4.
mRNA measurements were obtained as follows: reads from single-embryo mRNA-seq were mapped to the genome sequence using tophat and mRNA levels were estimated using cufflinks {Trapnell:2010kd} and refined annotations (except D. melanogaster samples for which the reference annotation was used).
Genome_build: Apr. 2006 assembly (Flybase Release 5) of the D. melanogaster genome, the February 2006 assembly (Flybase release 2) of the D.pseudoobscura genome and the February 2006 assembly (Flybase release 1) of the D.virilis genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Sep 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Mathilde PARIS |
| E-mail(s) |
thildeparis@gmail.com
|
| Organization name |
CNRS
|
| Department |
Institut de Genomique Fonctionnelle de Lyon
|
| Street address |
32-34 avenue Tony Garnier
|
| City |
Lyon |
| ZIP/Postal code |
69006 |
| Country |
France |
| |
|
| Platform ID |
GPL9958 |
| Series (2) |
| GSE50766 |
Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression (part 1) |
| GSE50773 |
Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression |
|
| Relations |
| BioSample |
SAMN02353788 |
| SRA |
SRX348446 |
