NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3629772 Query DataSets for GSM3629772
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

Supplementary file Size Download File type/resource
GSM3629772_E4B_GTCCGC.ReadsPerGene.out.tab.gz 96.6 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap