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| Status |
Public on Jan 01, 2021 |
| Title |
samples in 3DCS day05 Donor1 |
| Sample type |
SRA |
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| Source name |
normal peripheral blood
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| Organism |
Homo sapiens |
| Characteristics |
time point: day 05
tissue: PBMCs
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| Treatment protocol |
Nonmobilized peripheral blood-derived cells were culture in 3DCS plus the factors as SCF, FLT3L, TPO, and IL3. Single-cell RNA sequencing samples were collected at four time points: day 0, day 5, day 10 and day 14.
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| Growth protocol |
Nonmobilized peripheral blood-derived cells were cultured in 3DCS and collected at day 0, day 5, day 10 and day 14 followed by single cell sequencing analysis.
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| Extracted molecule |
total RNA |
| Extraction protocol |
ScRNA-seq RNA were generated from the 10X Chromium Single Cell 3` Reagent Kits v3 according to the manufacturer’s protocol (10x Genomics).
ScRNA-seq libraries were generated from the 10X Chromium Single Cell 3` Reagent Kits v3 according to the manufacturer’s protocol (10x Genomics). Libraries were sequenced on the Illumina Hiseq X10 platform according to the manufacturer’s instructions (Illumina).
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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 |
Each scRNA-seq sample data was separately demultiplexed, aligned to the human genome (version GRCh38), and calculated unique molecular identifier (UMI) were estimated using the Cellranger toolkit (Version 3.0.0, 10X Genomics), with default parameters. Cells with fewer than 200 detected genes, or 20,000 detected transcripts, or total mitochondrial gene expression exceeding 20% were excluded from the analysis. Genes expressed in less than 3 cells were also removed.
Ten UMI matrices from two donors at four time points were designed as replication batches, and data integration were performed into a single Seurat objects with the R package Seurat (v3.0.0). The data was normalized with the NormalizeData function in Seurat using a scale factor of 10000. Anchors were identified using FindIntegrationAnchors.
Downstream analysis as principal component analysis (PCA), SNN graph building (FindNeighbors), and data feature scaling (ScaleData) were performed.
Genome_build: GRCh38 - 10x reference
Supplementary_files_format_and_content: csv-delimited table of the aggregated UMI count matrix
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| Submission date |
Jun 28, 2020 |
| Last update date |
Jan 03, 2021 |
| Contact name |
xu yu lin |
| Organization name |
zhejiang university
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| Department |
medicine school
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| Lab |
hematopoietic cell research
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| Street address |
yuhangtang road 388
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| City |
hanghzou |
| State/province |
zhejiang province |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE153421 |
3D Polypeptide Facilitates the Expansion of Rare, Circulating Peripheral Blood Hematopoietic Stem/Progenitor Cells with Repopulating Capabilities |
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| Relations |
| BioSample |
SAMN15395075 |
| SRA |
SRX8627650 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4644046_donor1_d05.csv.gz |
9.6 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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