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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 17, 2017 |
| Title |
HEK Population |
| Sample type |
SRA |
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| Source name |
HEK Population
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| Organism |
Homo sapiens |
| Characteristics |
cell type: HEK293
exposure: NA
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| Extracted molecule |
total RNA |
| Extraction protocol |
[Seq-Well Protocol] Samples were processed as described in Gierahn et al. Nature Methods 2017.
Detailed Protocols at Nature Protocols Exchange DOI: 10.1038
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
STAR was used to align data to app
Aligned reads were collapsed to cell barcodes and UMIs using DropSeq Tools
See Sample_Processing_Pipeline.txt, for information regarding demultiplexing and alignment of each of the fastq files.
Digitial Gene Expression matrices were generated using DropSeq Tools
Genome_build: hg19/mm10 (Species Mixing1 and Species Mixing 2)
Genome_build: hg19 (PBMC, HEK, and MTB experiments)
Supplementary_files_format_and_content: [SpeciesMixing1_HumanUMI.txt] Filtered UMI DGE Matrix, Human Transcripts Across 250 Cells
Supplementary_files_format_and_content: [SpeciesMixing1_MouseUMI.txt] Filtered UMI DGE Matrix, Mouse Transcripts Across 250 Cells
Supplementary_files_format_and_content: [SpeciesMixing1_HumanReads.txt] Filtered Reads DGE Matrix, Human Reads Across 250 Cells
Supplementary_files_format_and_content: [SpeciesMixing1_MouseReads.txt] Filtered Reads DGE Matrix, Mouse Reads Across 250 Cells
Supplementary_files_format_and_content: [SpeciesMixing2_HumanUMI.txt] Filtered UMI DGE Matrix, Human Transcripts Across 331 Cells
Supplementary_files_format_and_content: [SpeciesMixing2_MouseUMI.txt] Filtered UMI DGE Matrix, Mouse Transcripts Across 331 Cells
Supplementary_files_format_and_content: [SpeciesMixing2_HumanReads.txt] Filtered Reads DGE Matrix, Human Reads Across 331 Cells
Supplementary_files_format_and_content: [SpeciesMixing2_MouseReads.txt] Filtered Reads DGE Matrix, Mouse Reads Across 331 Cells
Supplementary_files_format_and_content: [HEK_SingleCells.txt] Filtered UMI DGE Matrix, Human Transcripts Across 1453 Single HEK293 Cells
Supplementary_files_format_and_content: [HEK_Population.txt] Filtered UMI DGE Matrix, Bead-based Population RNA-Seq of 40,000 HEK293 Cells
Supplementary_files_format_and_content: [PBMC.txt] Filtered UMI DGE Matrix, 4296 PBMC Across 6713 Genes with cell type annotations
Supplementary_files_format_and_content: [MTB.txt] Filtered UMI DGE Matrix, 4638 Macrophages with cluster and exposure annotations
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| Submission date |
Feb 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Alex Shalek |
| Organization name |
Massachusetts Institute of Technology
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| Department |
Chemistry
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| Lab |
Shalek Lab
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| Street address |
77 Masachusetts Ave
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE92495 |
Seq-Well: A portable, low-cost platform for single-cell RNA-seq of low-input samples |
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| Relations |
| BioSample |
SAMN06328832 |
| SRA |
SRX2556658 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2486332_HEK_Population.txt.gz |
147.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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