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| Status |
Public on Oct 28, 2022 |
| Title |
Teratoma_H9_6, scRNAseq, Microwell-seq |
| Sample type |
SRA |
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| Source name |
NA
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| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
tissue: NA
cell line: NA
strain: NOD/SCID
age: 14-16 weeks
Sex: female
treatment: NA
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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 single cell |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
Microwell-seq_scRNA-seq
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| Data processing |
The original FASTQ files were converted to BAM format firstly with Drop-seq_tools-1.12, which was used for the subsequent processing except for barcode correction and alignment. The cell barcodes were extracted and tagged with XC in the offered BAM files, and the unique molecular identifiers (UMIs) were tagged with XM. Three 6bp barcodes ware combined to identify a single cell. Reads with the quality of cell barcodes or UMIs less than 10 were tagged with XQ and removed afterwards. Next, the PolyATrimmer was used to trim ployA. Before alignment, the known barcode sequences involved in the library construction were utilized for cell barcode correction, allowing one mismatch in each 6bp barcode.
STAR (version 2.5.2a) was used for reads alignment in single-end mode. The teratoma data were aligned to a merged hg19-mm10 reference genome, the ESCs data were aligned to GRCh38, and the mouse data were mapped to mm10. Then the aligned BAM files were sorted by query names and were merged with the unaligned BAM files, in order to recover the XC and XM tags that were lost after the alignment. The TagReadWithGeneExon function was employed to recognize the reads that were mapped to the exonic regions of genes. Finally, the top 20,000 cell barcodes ranked by reads number were used to generate the digital expression matrices in each sample or each technical repeat. For teratoma data that mix human cells with mouse cells, the aligned BAM files should be divided into human.bam and mouse.bam before generating the digital expression matrices.
Assembly: Teratoma: A merged hg19-mm10 reference genome; ESCs: GRCh38; Mouse: mm10
Supplementary files format and content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMIs counts, with genes as rows and cells as columns.
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| Submission date |
Oct 21, 2022 |
| Last update date |
Oct 29, 2022 |
| Contact name |
Xiaoping Han |
| E-mail(s) |
xhan@zju.edu.cn
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| Organization name |
Zhejiang University School of Medicine
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| Department |
Center for Stem Cell and Regenerative Medicine
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| Lab |
Xiaoping Han Lab
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| Street address |
Yuhangtang Road 866
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310012 |
| Country |
China |
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| Platform ID |
GPL26363 |
| Series (2) |
| GSE216324 |
Characterization of human pluripotent stem cell differentiation by single-cell dual-omics analyses (scRNA-seq) |
| GSE216325 |
Characterization of human pluripotent stem cell differentiation by single-cell dual-omics analyses |
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| Relations |
| BioSample |
SAMN31407865 |
| SRA |
SRX17989130 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6668805_H9_6_raw_count_human.txt.gz |
10.6 Mb |
(ftp)(http) |
TXT |
| GSM6668805_Ter_mouse_mH9_6_raw_count.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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