|
| Status |
Public on Jun 28, 2019 |
| Title |
E4B_rnaseq |
| Sample type |
SRA |
| |
|
| Source name |
Embryo
|
| Organism |
Drosophila melanogaster |
| Characteristics |
Stage: Stage 8
tissue: embryo
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq on individual embryos was described previously in Scacchetti et al. 2018. Briefly, embryos were hand-picked from collection plates and soaked in a drop of Voltalef 10 S halocarbon oil (Lehman and Voss Co.). Stages were determined by morphological features under stereomicroscope. Embryos were smashed with a needle into 200 µl lysis buffer (Agencourt RNAdvance Tissue kit, Beckman Coulter, Cat. No. A32645) and 10 μl 1:100 ERCC Spike-in RNA mix was added (Ambion, Cat. No. 4456740). RNA was extracted from the lysate following the manufacturers protocol with volume adjustment.
Ribosomal RNA was depleted using rRNA depletion kit (human/mouse/rat) (New Englands Biolab, Cat. No. E6310). Directional (except 8 embryos non-directional) libraries were prepared using NEBnext Ultra RNA Library Prep kit for Illumina (New Englands Biolab, Cat. No. E7530S) following the recommended protocol. In total 54 embryos from 8 stages were sequenced on an Illumina HiSeq1500 instrument in paired-end mode
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Paired-end RNA-seq reads were aligned to the reference genome (dmel release 6) using STAR (version 2.5.3a) with the parameter --outFilterMultimapNmax 1.
Genic reads were counted using STAR --quantMode GeneCounts and the Flybase GTF annotation (dmel-all-r6.17).
Genome_build: dm6
Supplementary_files_format_and_content: TAB: genic read counts.
|
| |
|
| Submission date |
Feb 26, 2019 |
| Last update date |
Jun 28, 2019 |
| Contact name |
Tamas Schauer |
| E-mail(s) |
[email protected]
|
| Organization name |
Helmholtz Zentrum München
|
| Department |
Institute of Epigenetics and Stem Cells
|
| Street address |
Feodor-Lynen-Straße 21
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19951 |
| Series (2) |
| GSE127176 |
Progressive dosage compensation during Drosophila embryogenesis is reflected by gene arrangement on the X chromosome [RNA-seq] |
| GSE127177 |
Progressive dosage compensation during Drosophila embryogenesis is reflected by gene arrangement on the X chromosome |
|
| Relations |
| BioSample |
SAMN11020325 |
| SRA |
SRX5431078 |
