|
| Status |
Public on Feb 17, 2023 |
| Title |
marmoset iPSC, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
iPSC
|
| Organism |
Callithrix jacchus |
| Characteristics |
tissue: iPSC
cell type: iPSC
Sex: Male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To minimize the contamination with feeder cells, >30 colonies of cjiPSCs cultured on feeder layer were randomly picked under an inverted microscope. Aggregates were rinsed with PBS twice and dissociated into single cells with 0.1% trypsin/EDTA treatment for 15 min at 37°C with periodic pipetting. Cells were loaded into chromium microfluidic chips with the Chromium Next GEM Single Cell 3ʼReagent Kit (v3.1 chemistry) and then used to generate single-cell gel bead emulsions (GEMs) using the Chromium Controller (10× Genomics) according to the manufacturer’s protocol. GEM-RT was performed in a C1000 Touch Thermal Cycler with 96-Deep Well Reaction Module (Bio-Rad). All subsequent cDNA amplification and library construction steps were performed according to the manufacturer’s protocol. Libraries were sequenced using a 2 × 150 paired-end sequencing protocol on an Illumina HiSeq 4000 or NovaSeq 6000 instrument.
10X genomics
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v.6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: calJac4
Supplementary files format and content: h5 files of raw counts tables
Supplementary files format and content: tar.gz files of velocity counts tables
|
| |
|
| Submission date |
Nov 16, 2022 |
| Last update date |
Feb 17, 2023 |
| Contact name |
keren cheng |
| E-mail(s) |
keren.cheng@outlook.com
|
| Organization name |
Zhejiang University
|
| Department |
School of Medicine
|
| Street address |
1575 chouzhou bei road
|
| City |
Yiwu |
| State/province |
Zhejiang |
| ZIP/Postal code |
320000 |
| Country |
China |
| |
|
| Platform ID |
GPL17712 |
| Series (2) |
| GSE210576 |
Efficient generation of marmoset primordial germ cell-like cells using induced pluripotent stem cells |
| GSE218108 |
Efficient generation of marmoset primordial germ cell-like cells using induced pluripotent stem cells [scRNA-Seq 2] |
|
| Relations |
| BioSample |
SAMN31757327 |
| SRA |
SRX18286093 |
