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| Status |
Public on Jun 17, 2019 |
| Title |
SKIN_HV2 |
| Sample type |
SRA |
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| Source name |
Skin biopsy from HV2
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| Organism |
Homo sapiens |
| Characteristics |
disease diagnosis: Healthy
tissue: Skin
manipulation: Freshly isolated
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were prepared using 10X Genomics Chromium 5' kit and 3' kit (v2).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
SKIN_HV2
Healthy volunteer
Single-cell RNA-Seq
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| Data processing |
CellRanger (10X Genomics) pipelines were used for demultiplexing base calls into Fastq, filtering, barcode counting and filtering, UMI counting and alignment with reference human genome GRCh38.
The quality control, normalization, linear regression of number of UMIs and scaling were performed using Seurat (v2.3.4).
Two different groups (disease vs. healthy volunteers, pre- vs. post-treatment) were aligned using canonical correlation analysis by Seurat package (v2.3.4).
Genome_build: GRCh38
Supplementary_files_format_and_content: *.h5: Filtered gene expression matrices with cells identified as cell barcodes and the values representing gene UMI counts.
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| Submission date |
Jun 16, 2019 |
| Last update date |
Jun 18, 2019 |
| Contact name |
Doyoung Kim |
| E-mail(s) |
dykim@yuhs.ac
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| Organization name |
Yonsei University College of Medicine
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| Department |
Dermatology
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| Street address |
50-1 Yonsei-ro Seodaemun-gu
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| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE132802 |
Single-cell RNA-sequencing of skin, fresh blood, and cultured peripheral blood mononuclear cells from a patient with drug-induced hypersensitivity syndrome and healthy volunteers |
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| Relations |
| BioSample |
SAMN12070442 |
| SRA |
SRX6075370 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3892579_SKIN_HV2_filtered_gene_bc_matrices_h5.h5 |
13.5 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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