|
| Status |
Public on Jul 12, 2020 |
| Title |
Wild type_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Wild type_adult muscle precursors
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype/variation: P{1151-GAL4}; +;+
developmental stage: wandering third instar larva (25C)
tissue: Wing discs (notum and hinge, pouch was removed)
cell type: adult muscle precursors associated with the wing discs and epithelial cells of the presumptive hinge and notum
|
| Growth protocol |
Flies were kept at 25 °C in vials containing standard cornmeal- agar medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Third instar larva were collected, wing discs were dissected, pouch was manually removed using a microblade. Tissue was dissociated into single-cell suspension using a combination of Trypsin and Collagenase. Then Drop-seq was performed on the single cell suspension. Libraries were made and sequenced.
Nextera XT tagmentation using Illumina cat# FC-131-1096 (Drop-seq protocol)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Notum3
|
| 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 anlysis protocol described in Drop-seq cook-book (Macosko et al. 2015)(http://mccarrolllab.com/dropseq/) and used the Drop-seq_tools-1.13. We used STAR aligner to align the reads against Drosophila melanogaster genome version BDGP6 (From Ensembl) and corresponding gene modle 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
|
| |
|
| Submission date |
Oct 09, 2019 |
| Last update date |
Jul 13, 2020 |
| Contact name |
Elizaveta V Benevolenskaya |
| E-mail(s) |
[email protected]
|
| 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 |
GPL19132 |
| Series (1) |
| GSE138626 |
Single cell transcriptional profile of third instar larval wing discs in Drosophila using drop-seq (single cell RNA-seq) |
|
| Relations |
| BioSample |
SAMN12999627 |
| SRA |
SRX6968645 |
