|
| Status |
Public on Jan 15, 2021 |
| Title |
29_iCELL8_3pDEUMI_lymphocyte_cell line_mix |
| Sample type |
SRA |
| |
|
| Source name |
lymphocyte cell line mix
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell line: Jurkat, TALL104, EL4, IVA12 (1:1:1:1 mixture)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cell suspensions were processed using the iCELL8 cx system to isolate and identify single cells and perform RT and cDNA amplification.
Libraries were constructed with the Takara iCELL8 3'DE kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
1:1:1:1 mixture of Jurkat, TALL104, EL4, IVA12 cells sequenced using the DropSeq method with encapsulation with the iCELL8 cx system using a modified 3'DE protocol processing 1465 wells
|
| Data processing |
fastq files were downsampled using seqtk v1.3-r106
Cell barcode extraction and transcript counting was peformed using the mappa v0.9 pipeline (read counts) or Drop-seq_Tools v2.3.0 and PicardTools v2.18.14 (UMI counts).
Genome_build: Data was aligned to a “cellRanger_1.2.0” referenced composed of hg19 with Ensembl 82 and mm10 with Ensembl 84 using STAR v2.7.0b (read counts) or STAR v2.4.2a (UMI counts).
Supplementary_files_format_and_content: count_genematrix, UMIcount_genematrix
|
| |
|
| Submission date |
Dec 23, 2020 |
| Last update date |
Jan 15, 2021 |
| Contact name |
Tracy Yamawaki |
| E-mail(s) |
tyamawak@amgen.com
|
| Organization name |
AMGEN, INC.
|
| Street address |
1120 VETERANS BLVD.
|
| City |
SOUTH SAN FRANCISCO |
| State/province |
California |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL24625 |
| Series (2) |
| GSE163792 |
Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling [icell8] |
| GSE163793 |
Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling |
|
| Relations |
| BioSample |
SAMN17149439 |
| SRA |
SRX9725828 |
