|
| Status |
Public on Jan 12, 2023 |
| Title |
Mixed species - 80K rpcc saturation curve comparison |
| Sample type |
SRA |
| |
|
| Source name |
HEK393T / NIH-3T3
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
strain: HEK393T / NIH-3T3
|
| Treatment protocol |
Cells were grown to a confluence of ~70% and treated with TrypLE Express with Phenol red (ThermoFisher #12605010) for 3 minutes, quenched with an equal volume of growth medium, and centrifuged at 5 min at 200 x g. The supernatant was removed, and the cells resuspended in 1X DPBS without calcium or magnesium. Cells were diluted to their final concentration in 1X DPBS with 0.04% BSA and mixed evenly to create a 50:50 Human:Mouse mixture.
|
| Growth protocol |
human HEK 293T cells (ATCC # CRL-3216) were grown in DMEM (ThermoFisher #11995073) supplemented with 10% FBS (ThermoFisher #A3840001) and 1% Penicillin-Streptomycin-Glutamine (ThermoFisher #10378016). Murine NIH/3T3 cells (ATCC # CRL-1658) were grown in DMEM (ThermoFisher #11995073) supplemented with 10% bovine calf serum (ATCC # 30-2030) and 1% Penicillin-Streptomycin-Glutamine.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
PIP-seq single cell library prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
JI20220520_FR_5
Species mixing experiment
|
| Data processing |
The samples are downsampled using seqtk, aligned to a combined human (GRCh38.p13) + mouse (GRCm38.p6) transcriptome index with Salmon and quantified with alevin v1.2.0
Assembly: GRCh38.p13 + GRCm38.p6
Supplementary files format and content: Filtered matrices are zipped folders of 3 files: (1) sparse matrix, (2) barcodes file, (3) genes file. Raw data are gzipped fastqs, with 2 per sample.
|
| |
|
| Submission date |
Oct 07, 2022 |
| Last update date |
Jan 14, 2023 |
| Contact name |
Iain Christopher Clark |
| Organization name |
University of California, Berkeley
|
| Street address |
374 Stanley Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL30202 |
| Series (2) |
| GSE202919 |
Microfluidics-free single-cell genomics with templated emulsification |
| GSE215062 |
Cross-Platform Comparison |
|
| Relations |
| BioSample |
SAMN31210096 |
| SRA |
SRX17829951 |
