|
Status |
Public on May 06, 2024 |
Title |
HIRH2 |
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 |
SAMN38207471 |
SRA |
SRX22488547 |