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| Status |
Public on Jan 30, 2020 |
| Title |
CN_1b (10x) |
| Sample type |
SRA |
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| Source name |
Caudate (a mixture from all four organisms)
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| Organisms |
Macaca mulatta; Pan paniscus; Pan troglodytes; Homo sapiens |
| Characteristics |
tissue: brain
tissue region: Caudate
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Nuclear RNA from frozen tissue samples was extracted according to Nuc-Seq protocol
Library was constructed according to manufacturers protocol (10x Genomics, Chomium single-cell)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics Single Cell Expression Experiment
CN_H_barcodes.tsv
CN_H_genes.tsv
CN_H_matrix.mtx
CN_C_barcodes.tsv
CN_C_genes.tsv
CN_C_matrix.mtx
CN_B_barcodes.tsv
CN_B_genes.tsv
CN_B_matrix.mtx
CN_M_barcodes.tsv
CN_M_genes.tsv
CN_M_matrix.mtx
CN_species.txt
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| Data processing |
R1 read is technical; R2 is biological. Barcode position in R1 is 1-16bp; UMI - 17-26bp.
The Cell Ranger v2.2.0 pipeline was used to process data generated using the 10x Chromium platform. Using Cell Ranger, the reads were converted to fastq format, processed, filtered, and then the aligned reads were generated. This pipeline was used with a custom reference genome (genome.fa). The custom reference genome was created using Cell Ranger pipeline by concatenating the sequences of hg38, panTro5, panPan2 and rheMac8 genomes.
To assign each cell to species, we used custom scripts. First, the table was normalized for the total number of UMIs per species, to balance the mappability differences arising due to the evolutionary differences between the primate species. Then, a cell was assigned to a particular species if >50% of its UMIs were mapped to this species. The threshold of 50% was chosen based on the distribution of maximal proportions of UMI mapped to one species per cell. Cells, which could not be assigned to species unambiguously, were discarded.
Genome_build: hg38; panTro5; panPan2; rheMac8
Supplementary_files_format_and_content: 10x Digital Gene Expression matrix, gene list, barcode list and the list of filtered cells
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| Submission date |
Mar 04, 2019 |
| Last update date |
Nov 01, 2022 |
| Contact name |
Ilia Kurochkin |
| E-mail(s) |
ilia.kurochkin@med.lu.se
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| Organization name |
Lund University
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| Street address |
BMC A12, Sölvegatan 17
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| City |
Lund |
| State/province |
Skane |
| ZIP/Postal code |
221 84 |
| Country |
Sweden |
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| Platform ID |
GPL26248 |
| Series (1) |
| GSE127774 |
Transcriptome map of the human brain at the single-cell resolution |
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| Relations |
| BioSample |
SAMN11049913 |
| SRA |
SRX5459890 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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