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Status |
Public on Sep 14, 2020 |
Title |
Control replicate 4 |
Sample type |
SRA |
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Source name |
Third instar brain
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Organism |
Drosophila melanogaster |
Characteristics |
tissue: brain developmental stage: wandering third instar larvae genotype: repo>+
|
Extracted molecule |
total RNA |
Extraction protocol |
Third instar brains from control and repo>AmaRNAi were dissociated into single cells using a combination of Trypsin and Collagenase. We then performed Drop-seq on the single cell suspension. Nextera XT tagmentation using Illumina cat# FC-131-1096 (Drop-seq protocol).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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|
Description |
BC4 Single cell RNA Single cell RNA-seq was performed using Drop-seq.
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Data processing |
Illumina Casava1.7 software used for basecalling. Illumina paired end raw FastQ file were processed for read alignment and gene expression. Drop-seq single-cell data was analyzed using the data analysis protocol described in Drop-seq cook-book (Macosko et al. 2015)(http://mccarrolllab.com/dropseq/) and used the Drop-seq_tools-2.3.0. We used STAR aligner to align the reads against Drosophila melanogaster genome version BDGP6 (from Ensembl) and corresponding gene model is extracted from Ensembl version 90. Quality of read and mapping were checked using the program FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Digital Gene Expression (DGE) data obtained from an aligned library is done using the Dropseq program DigitalExpression (integrated in Drop-seq_tools-1.13). Number of cells that were extracted from aligned BAM file is based on knee plot which extracts the number of reads per cell, then plot the cumulative distribution of reads and select the “knee” of the distribution. Genome_build: BDGP6 Supplementary_files_format_and_content: Tab-delimited text file. Gene expression (as count) of each gene for each extracted cell.
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Submission date |
Mar 29, 2020 |
Last update date |
Sep 22, 2020 |
Contact name |
Elizaveta V Benevolenskaya |
E-mail(s) |
evb@uic.edu
|
Phone |
312-413-8947
|
Organization name |
University of Illinois at Chicago
|
Department |
Biochemistry and Molecular Genetics
|
Street address |
900 S. Ashland Ave.
|
City |
Chicago |
State/province |
IL |
ZIP/Postal code |
60607 |
Country |
USA |
|
|
Platform ID |
GPL25244 |
Series (1) |
GSE147688 |
Profiling the repo>+ (control) and repo>AmaRNAi knockdown third instar Drosophila brains using Drop-seq (single cell RNA-seq) |
|
Relations |
BioSample |
SAMN14482433 |
SRA |
SRX8022399 |