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| Status |
Public on Jan 15, 2021 |
| Title |
23_Chromium_3p_v3_lymphocyte_cell line_mix |
| Sample type |
SRA |
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| Source name |
lymphocyte cell line mix
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| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell line: Jurkat, TALL104, EL4, IVA12 (1:1:1:1 mixture)
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| Extracted molecule |
total RNA |
| Extraction protocol |
cell suspensions were encapsulated in cell lysis buffer with the 10X Chromium
Libraries were constructed with the 10X Genomics 3' v2, v3 or 5' v1 kits.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
1:1:1:1 mixture of Jurkat, TALL104, EL4, IVA12 cells sequenced using the 10X Chromium 3' v3 kit targeting a capture of 6000 cells.
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| Data processing |
fastq files were downsampled using seqtk v1.3-r106
fastq files were processed with cellranger v3.0.2 for cell demultiplexing, read alignment and transcript counting
Genome_build: Data was aligned to a “cellRanger_1.2.0” reference composed of hg19 with Ensembl 82 and mm10 with Ensembl 84.
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx
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| Submission date |
Dec 23, 2020 |
| Last update date |
Jan 15, 2021 |
| Contact name |
Tracy Yamawaki |
| E-mail(s) |
tyamawak@amgen.com
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| Organization name |
AMGEN, INC.
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| Street address |
1120 VETERANS BLVD.
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| City |
SOUTH SAN FRANCISCO |
| State/province |
California |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platform ID |
GPL25526 |
| Series (2) |
| GSE163781 |
Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling [10x] |
| GSE163793 |
Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling |
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| Relations |
| BioSample |
SAMN17149090 |
| SRA |
SRX9725228 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4987148_23_barcodes.tsv.gz |
20.0 Mb |
(ftp)(http) |
TSV |
| GSM4987148_23_features.tsv.gz |
592.9 Kb |
(ftp)(http) |
TSV |
| GSM4987148_23_matrix.mtx.gz |
253.3 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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