|
| Status |
Public on Jan 15, 2021 |
| Title |
12_ddSEQ_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 encapsulated in cell lysis buffer with the BioRad ddSEQ.
Libraries were constructed with the SureCell WTA 3′ Library Prep 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 ddSEQ kit using a cell concentration of 2500 cells/ul.
|
| Data processing |
fastq files were downsampled using seqtk v1.3-r106
cell barcodes were extracted using ddSeeker v0.9.0
Transcript counting was peformed using Drop-seq_Tools v2.3.0 and PicardTools v2.18.14.
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 v2.4.2a.
Supplementary_files_format_and_content: DigitalExpressionTable.txt
|
| |
|
| 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) |
| GSE163788 |
Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling [ddSEQ] |
| GSE163793 |
Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling |
|
| Relations |
| BioSample |
SAMN17149432 |
| SRA |
SRX9725815 |
