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Sample GSM2518788 Query DataSets for GSM2518788
Status Public on May 03, 2017
Title bulk_mel1
Sample type SRA
 
Source name mRNAseq of whole embryo
Organism Drosophila melanogaster
Characteristics developmental stage: mixture stage 10 to 17 batch1
fixation: live, not fixed
cell type: dissociated cells
Growth protocol Egg lays occurred in 2 hour intervals after 3x 1 hour pre-lays; embryos were aged for 6 hours (D. melanogaster) at room temperature.
Extracted molecule polyA RNA
Extraction protocol Methanol-fixation was adapted from Stöckius et al. 2009 (Nat. Methods). To avoid cell clumping, 8 volumes (800 µl) of methanol p. a. (pre-chilled to -20˚C) were added drop-wise, while gently mixing or vortexing the cell suspension. Macosko et al. 2015 Cell; Online-Dropseq-Protocol-v.3.1.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description bulk transcriptomics
Data processing Cell and molecular barcodes were extracted from read1 and added as tags using Drop-seq tools v1.12. Sequenced reads were trimmed for polyA stretches, SMART adaptor sequences and low quality filtering using Drop-seq tools v1.12. Trimmed sequenced reads were mapped to hg38 and mm10 using STAR_2.4.0j. Mapped reads were sorted using samtools v1.2 and merged with cell and molecular barcodes using Drop-seq tools v1.12. Gene annotation tags were added and bead synthesis errors were detected and corrected using Drop-seq tools v1.12. Cumulative fraction of reads per cell was computed using Drop-seq tools v1.12, inflection point was computed using dropbead v.0.2. The digital gene expression matrices were computed using Drop-seq tools v1.12.
Genome_build: hg38, mm10
Supplementary_files_format_and_content: gene counts
clusters*.txt files generated using Seurat.
 
Submission date Mar 02, 2017
Last update date May 15, 2019
Contact name Nikos Karaiskos
E-mail(s) [email protected]
Organization name Max Delbrück Center for Molecular Medicine
Lab Systems Biology of Gene Regulatory Elements
Street address Hannoversche Str. 28
City Berlin
ZIP/Postal code 10115
Country Germany
 
Platform ID GPL19132
Series (1)
GSE89164 Cell fixation and preservation for droplet-based single cell transcriptomics
Relations
Reanalyzed by GSM3282951
BioSample SAMN06468911
SRA SRX2608938

Supplementary file Size Download File type/resource
GSM2518788_gene_counts_mel1.txt.gz 74.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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