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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 05, 2024 |
| Title |
iMAC,scRNAseq |
| Sample type |
SRA |
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| Source name |
macrophage
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| Organism |
Homo sapiens |
| Characteristics |
cell type: macrophage
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| Extracted molecule |
total RNA |
| Extraction protocol |
The matrigel was gently removed by pipetting and spinning down liver organoids, and the organoids were then washed with co-culture media. Organoids were chopped into pieces and collected. Organoid fragments were repeatedly incubated and pipetted following TrypLE addition, and washed with co-culture media to make single cells. Following LUNA-fl cell counting, libraries for scRNA-seq were created in a 10x Chromium platform.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, single cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
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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 |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/5.0/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Apr 13, 2023 |
| Last update date |
May 05, 2024 |
| Contact name |
Dayeon Gil |
| E-mail(s) |
gilje@korea.kr
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| Phone |
+82-43-249-2527
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| Organization name |
Korea national institute of health
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| Department |
Division of intractable disease research
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| Street address |
202 Osongsaengmyung 2-ro, Heungdeok-gu
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| City |
Cheongju-si |
| State/province |
Chungcheongbuk-do |
| ZIP/Postal code |
28160 |
| Country |
South Korea |
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| Platform ID |
GPL20795 |
| Series (2) |
| GSE229608 |
Multicellular liver organoid model for recapitulating hepatitis C virus infection and non-alcoholic fatty liver disease progression [scRNA-Seq] |
| GSE229609 |
Multicellular liver organoid model for recapitulating hepatitis C virus infection and non-alcoholic fatty liver disease progression |
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| Relations |
| BioSample |
SAMN34164605 |
| SRA |
SRX19951146 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7166275_iMAC_barcodes.tsv.gz |
23.4 Kb |
(ftp)(http) |
TSV |
| GSM7166275_iMAC_features.tsv.gz |
302.7 Kb |
(ftp)(http) |
TSV |
| GSM7166275_iMAC_matrix.mtx.gz |
26.4 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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