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| Status |
Public on Jul 08, 2022 |
| Title |
Microwell-seq datasets of Drosophila_D16_2 |
| Sample type |
SRA |
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| Source name |
D16_2
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: w1118
age: 16 day after laying eggs
tissue: whole organism
Sex: Female
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissue dissociation and single-cell lysate
Library preparations were performed with the Microwell-seq protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
D16_2
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| Data processing |
Base call files were performed with Illumina bcl2fastq.
Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode: in read1, the bases 1-6, 22-27, 43-48 are merged (18bp); UMI: in read1, the bases 49-54 (6bp).
scRNA-seq reads were aligned to the Drosophila melanogaster BDGP6.28 genome assembly using STAR (version 2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix (DGE) based on UMI counts. The cell barcode is tagged with XC, the UMI is tagged with XM, and the gene is tagged with GE.
Genome_build: Drosophila melanogaster BDGP6.28
Supplementary_files_format_and_content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMI counts, with genes as rows and cells as columns.
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| Submission date |
Jun 14, 2021 |
| Last update date |
Jul 08, 2022 |
| Contact name |
Guoji Guo |
| Organization name |
Center for Stem Cell and Regenerative Medicine
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| Department |
Zhejiang University School of Medicine
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| Street address |
Yuhangtang street 866
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| City |
Hanzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL23702 |
| Series (2) |
| GSE178149 |
Construction the adult Drosophila cell atlas at single cell resolution |
| GSE178151 |
Construction of the whole animal at a single cell resolution |
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| Relations |
| BioSample |
SAMN19696737 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5380989_D16_2_dge.txt.gz |
8.8 Mb |
(ftp)(http) |
TXT |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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