|
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.
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|
|
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 |