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| Status |
Public on Jun 18, 2024 |
| Title |
FGF replicate 2 |
| Sample type |
SRA |
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| Source name |
delta cell-containing islet organoids
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| Organism |
Homo sapiens |
| Characteristics |
tissue: delta cell-containing islet organoids
treatment: FGF2+7
cell type: islet cells
cell line: H1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, S7D14 cell clusters were dispersed with TrpLE. Single cells with more than 85% viability were adjusted to 1,000 cells per μL. Approximately 16,000 cells were added to each channel of a 10X loading chip and then approximately 10,000 cells were captured.
Single-cell libraries were constructed using the Single Cell 3 Library & Gel Bead Kit v.3 according to the manufacturer's instructions (10X Genomics)120. Briefly, S7D14 cell clusters were dispersed with TrpLE. Single cells with more than 85% viability were adjusted to 1,000 cells per μL. Approximately 16,000 cells were added to each channel of a 10X loading chip and then approximately 10,000 cells were captured. The captured cells were divided into Gel Beads in Emulsion (GEMs) and lysed, and the isolated RNA was reverse transcribed, barcoded, and amplified.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x genomics
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| Data processing |
Raw FASTAQ files were processed using the Cell Ranger pipeline (v4.0.0) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references) with the default options
To filter out low quality cells, only cells expressing more than 200 genes (defined as genes detected in at least 3 cells) and less than 20% mitochondrial genes were selected. Datasets were integrated based on 'anchors' identified between datasets (nfeatures=2000, normalization.method='SCT') before performing linear dimension reduction by principal component (PC) analysis. The top 30 PCs were used in a Uniform Manifold Approximation and Projection (UMAP) dimensionality reduction.
Assembly: GRCh38
Supplementary files format and content: Matrix files and Tab-separated values files
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| Submission date |
Jun 13, 2024 |
| Last update date |
Jun 18, 2024 |
| Contact name |
LIHUA CHEN |
| E-mail(s) |
chen_lihua@gzlab.ac.cn
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| Phone |
086-13724864235
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| Organization name |
Guangzhou Laboratory
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| Street address |
Guangzhou International Bioland
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510000 |
| Country |
China |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE269764 |
Directed differentiation of pancreatic δ cells from human pluripotent stem cells |
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| Relations |
| BioSample |
SAMN41817523 |
| SRA |
SRX24911529 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8326529_barcodes2.tsv.gz |
51.0 Kb |
(ftp)(http) |
TSV |
| GSM8326529_features2.tsv.gz |
297.6 Kb |
(ftp)(http) |
TSV |
| GSM8326529_matrix2.mtx.gz |
150.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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