|
| Status |
Public on May 06, 2024 |
| Title |
Chip1D3 |
| Sample type |
SRA |
| |
|
| Source name |
Human pancreatic islet cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human pancreatic islet cell
genotype: primary cells from 2 human donors
medium: pancreatic islet media (PIMS, Prodo Laboratories)
time point: 24 hour culture
|
| Treatment protocol |
Single cells were dissociated with TrypLE for ~15-30 minutes, washed with PBS, stained with Calcein-AM/propidium iodide, and sorted onto nanoSPLITS chips using a cellenONE cell sorter.
|
| Growth protocol |
Human pancreatic islets from two human donors (Prodo Laboratories) were acquired and cultured for 24 hr in pancreatic islet media (PIMS, Prodo Laboratories).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was acquired through nanoSPLITS. RNA quality and quantity were analysed with a RNA6000 Nano Assay using the Agilent 2100 Bioanalyzer (Agilent Technologies).
For RNA‐Seq, The TruSeq stranded mRNA (cat#20020594) was used to generate cDNA library for illumina NextSeq550 platform according to the manufacture protocol. Single-read sequencing of the cDNA libraries with a read length of 150 was performed with NextSeq 500 Sequencing System using NextSeq 500/550 High Output v2 kit 150 cycles (cat#20024907).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Data quality was assessed with fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Read-trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/).
Reads were aligned to the mouse genome using STAR (https://github.com/alexdobin/STAR).
BAM file outputs were mapped to genes using htseq‐count (Anders et al., 2015) using default settings.
Assembly: human genome GRCh38
Supplementary files format and content: .txt files represent number of raw read counts mapping to each gene
|
| |
|
| Submission date |
Nov 11, 2023 |
| Last update date |
May 06, 2024 |
| Contact name |
James Michael Fulcher |
| E-mail(s) |
james.fulcher@pnnl.gov
|
| Organization name |
Pacific Northwest National Laboratory
|
| Department |
Environmental Molecular Sciences Laboratory
|
| Street address |
902 Battelle Blvd
|
| City |
Richland |
| State/province |
Washington |
| ZIP/Postal code |
99354 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE247519 |
Multimodal measurement of the transcriptome and proteome in single cells using nanoSPLITS |
|
| Relations |
| BioSample |
SAMN38207530 |
| SRA |
SRX22488404 |
