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| Status |
Public on Jun 22, 2022 |
| Title |
Micorwell-seq datasets of Xenopus_kidney_COL17 |
| Sample type |
SRA |
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| Source name |
Xenopus_kidney_sample1
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| Organism |
Xenopus laevis |
| Characteristics |
strain: wild-type
age: one year elder
tissue: kidney
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissues or 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 |
HiSeq X Ten |
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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 merge (18bp); UMI:In read1, the bases 49-54 (6bp)
scRNA-seq reads were aligned to the Xenopus laevis J-strain 9.2 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: Xenopus laevis J-strain 9.2
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 |
Jan 31, 2022 |
| Last update date |
Jun 22, 2022 |
| Contact name |
Haide Chen |
| E-mail(s) |
hyde@zju.edu.cn
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| Organization name |
Zhejiang University
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| Street address |
866 Yuhangtang road
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| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL31294 |
| Series (1) |
| GSE195790 |
Cell landscape of Xenopus laevis at single-cell resolution |
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| Relations |
| BioSample |
SAMN25516216 |
| SRA |
SRX13995824 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5850503_Xenopus_kidney_COL17_dge.txt.gz |
11.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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