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| Status |
Public on Mar 13, 2020 |
| Title |
mouse_FetalStomach_1 (For supplementing the Mouse Cell Atlas data) |
| Sample type |
SRA |
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| Source name |
mouse_FetalStomach_1
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| Organism |
Mus musculus |
| Characteristics |
developmental stage: Fetal
Sex: Female
tissue: Stomach
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| Extracted molecule |
total 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 |
Microwell-seq analysis
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| Data processing |
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.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 Mus_musculus.GRCm38.88 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 based on UMI counts.The cellbarcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.
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| Submission date |
Mar 13, 2020 |
| Last update date |
Mar 14, 2020 |
| 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 |
GPL21273 |
| Series (1) |
| GSE134355 |
Construction of A Human Cell Landscape by Single-cell mRNA-seq |
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| Relations |
| BioSample |
SAMN14372177 |
| SRA |
SRX7906597 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4409681_mouse_FetalStomach_1_dge.txt.gz |
6.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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