ERC000011
ENA-CHECKLIST
2023-12-11T00:33:11Z
ENA-FIRST-PUBLIC
2023-12-11T00:33:11Z
ENA-LAST-UPDATE
SAMEA113542151
External Id
THE UNIVERSITY OF TOKYO
INSDC center name
2023-12-11T00:33:11Z
INSDC first public
2023-12-11T00:33:11Z
INSDC last update
public
INSDC status
ERS15538568
SRA accession
E-MTAB-12988:Sample 4: DNA barcodes of micro-beads in ID-coded droplets (without cells)
Submitter Id
ArrayExpress
broker name
synthetic construct
cell_line
Protocols: Micro-particles functionalized both by DNA barcodes and fluorescent molecules were synthesized and used for the study. Synthetic DNA oligonucleotides bearing barcodes sequences provided in protocol 13 were used in the study. DNA-barcoded microbeads were resuspended in a buffer containing 0.75% (w/v) agarose (Sigma Aldrich, ultra-low gelling temperature). Monodisperse droplets were generated by flowing the beads suspension and HFE7500 oil supplemented with 2% 008-fluorosurfactant (RAN Biotechnologies) into a droplet generation chip. After droplet generation, water-in-oil hydrogel droplets were cooled at 4 °C at 500 rpm shaking. To the droplets, medium-based buffer solution and perfluoro octanol (final volume: 20% in oil, v/v) were slowly added, and hydrogel droplets were extracted into the aqueous layer, which was further washed with 20% perfluorooctanol in HFE7200, and hexane supplemented with Span 80. The resulting hydrogel droplets were firstly subjected to microscopic imaging and then “single-droplet” sequencing, where the whole nucleic acid components in a hydrogel droplet were processed as single-cell components in the droplet-based single-cell RNA sequencing library preparation. Cell lysis and RNA extraction using polyT-functionalized DNA-barcoded beads for droplet-based single cell RNA sequencing (drop-seq) Reverse transcription and cDNA preparation using polyT-functionalized DNA-barcoded beads for droplet-based single cell RNA sequencing (drop-seq)
description
DNA barcoding
library construction
synthetic construct
organism
synthetic construct
organism
synthetic construct
scientific_name
Sample 4: DNA barcodes of micro-beads in ID-coded droplets (without cells)
title