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| Status |
Public on Jul 08, 2022 |
| Title |
Microwell-seq datasets of Zebrafish_3m_COL64 |
| Sample type |
SRA |
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| Source name |
Zebrafish_3m_sample3
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| Organism |
Danio rerio |
| Characteristics |
strain: AB
age: 3 month (90 day)
tissue: whole organism
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Whole-body single-cell dissociation and 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 |
DNBSEQ-T7 |
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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. For raw file 1-5 in each COL, cellbarcode: in read1, the bases 1-6, 22-27, 43-48 are merged (18bp); UMI: in read1, the bases 49-54 (6bp). For raw file 6 in each COL, cellbarcode: in read1, the bases 1-6, 7-12, 13-18 are merged (18bp); UMI: in read1, the bases 19-24 (6bp).
scRNA-seq reads were aligned to the Danio rerio GRCz11 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: Danio rerio GRCz11
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 25, 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 |
GPL30277 |
| Series (2) |
| GSE178150 |
Construction the larval and adult zebrafish cell atlas at single cell resolution |
| GSE178151 |
Construction of the whole animal at a single cell resolution |
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| Relations |
| SRA |
SRX11229465 |
| BioSample |
SAMN19897714 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5400025_Zebrafish_3m_COL64_dge.txt.gz |
13.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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