|
| Status |
Public on Dec 21, 2022 |
| Title |
fetal pancreas pool_2_121419_PCW_HTO library |
| Sample type |
SRA |
| |
|
| Source name |
human fetal pancreas
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreas
developmental stage: 12, 14 and 19 PCW
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Human fetal pancreases were dissociated into single cells by collagenase and trypsin/EDTA treatment. Each batch contains 3 samples from different gestational stages which were stained with oligonucleotide-conjugated antibodies from BioLegend and pooled
Single cell mRNA and antibody (HTO) libraries were prepared according to the manufacturer’s protocol and paired-end sequencing was carried out on an Illumina NextSeq 2000, except for batch 15, 18 and 20 PCW batch which was sequenced on a HiSeq 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Totalseq B HTO library of of single cells from 3 fetal pancreases at 12, 14 and 19 PCW
|
| Data processing |
Generation of FASTQ files and alignment of raw sequencing reads were carried out using CellRanger (version 6.0.0, 10x Genomics).
Raw sequence data from HTO libraries were processed using CITE-Seq-Count, version 1.4.5
Genome_build: hg38
Supplementary_files_format_and_content: csv files contain de-hashing result of the pooled samples into their indvidual gestation age
Supplementary_files_format_and_content: final_matrix.csv.gz is a five-column filtered gene-count-matrix file from Cellranger output contatining 10x Genomics cellular barcode, feature ID, feature name, feature type and UMI count
|
| |
|
| Submission date |
Feb 20, 2022 |
| Last update date |
Dec 21, 2022 |
| Contact name |
Oladapo Edward Olaniru |
| E-mail(s) |
oladapo.e.olaniru@kcl.ac.uk
|
| Organization name |
King's College London
|
| Department |
Department of Diabetes
|
| Lab |
Shanta Persuad Lab
|
| Street address |
Hodgkin building, Guy's campus
|
| City |
London |
| ZIP/Postal code |
SE1 1UL |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE197064 |
Single cell transcriptomic and spatial landscapes of the developing human pancreas |
|
| Relations |
| BioSample |
SAMN26102580 |
| SRA |
SRX14232455 |
