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| Status |
Public on Jun 16, 2021 |
| Title |
pPDCN3839DAPIB030419 |
| Sample type |
SRA |
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| Source name |
Human Caudate nucleus
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Caudate nucleus
Sex: Male
age: 59
pmi: 15.8
disease: Ctrl
status: Ctrl
Cause of death: Colon cancer, cholangiocarcinoma
facs classification: Negative
10x version: V3
genome build: hg19
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Please see: https://www.protocols.io/view/frozen-tissue-nuclei-extraction-for-10xv3-snseq-bi62khge
10X Chromium Single Cell 3' (V3), manufacturer's protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Homo_bcd.tsv.gz
Homo_features.tsv.gz
Homo_matrix.tsv.gz
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| Data processing |
Sequencing was performed on either Illumina NovaSeq6000 or Illumina NextSeq
All sequencing reads from substantia nigra samples were demultiplexed and aligned to their respective animal genomes using Drop-Seq Tools
Digital gene expression matrices for all substantia nigra samples were generated from Drop-Seq Tools after alignment with the following genomes per species: human (hg19), rat (Rnor_6.0), macaque (Mmul_10), Tree shrew (tupBel1)
Digital gene expression matrices for all caudate samples were demultiplexed and aligned to hg38_premrna using CellRanger v3. Digital gene expression matrices were generated using CellRanger v3
Digital gene expression matrices were aggregated on a per individual or species basis and analyzed using Seurat v2.3.4, rliger v1.0.0, and Harmony
Genome_build: hg19, hg38
Genome_build: Rnor_6.0
Genome_build: Mmul_10
Genome_build: tupBel1
Supplementary_files_format_and_content: digital gene expression matrix (sparse format): matrix market format, rows = genes/transcripts, columns = barcodes/cells
Supplementary_files_format_and_content: barcodes.txt: names of barcodes/cells for corresponding DGE matrix file
Supplementary_files_format_and_content: genes.txt: names of transcripts/genes for corresponding DGE matrix file
Supplementary_files_format_and_content: Each species (human; rat; macaque; tree shrew) were aggregated into a combined species' matrix
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| Submission date |
Jun 15, 2021 |
| Last update date |
Jun 16, 2021 |
| Contact name |
Evan Macosko |
| E-mail(s) |
emacosko@broadinstitute.org
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| Organization name |
Broad Institute
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| Street address |
75 Ames St, Broad Institute
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE178265 |
A molecular census of midbrain dopaminergic neurons in Parkinsons disease |
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| Relations |
| BioSample |
SAMN19715168 |
| Supplementary data files not provided |
| Processed data are available on Series record |
| Raw data not provided for this record |
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