5k Human PBMCs, 3' v3.1, Chromium Controller

This dataset is part of the Alternative transcript isoform detection with single cell and spatial resolution Application Note. The Chromium library input files, Cell Ranger output files, and Oxford Nanopore library FASTQ files are provided.

Human peripheral blood mononuclear cells (PBMCs) were extracted from fresh whole peripheral blood samples obtained from StemExpress. PBMCs were isolated using SepMate density centrifugation methods as previously described (CG000392).

3' Single Cell Gene Expression Library

Libraries were generated from ~8,000 cells (5,140 cells recovered) as described in the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index) (CG000315 Rev B) using the Controller and sequenced on an Illumina NovaSeq 6000 to a read depth of approximately 35,000 mean reads per cell.

Paired-end, dual indexing

• Read 1: 28 cycles (16 bp barcode, 12 bp UMI)
• i5 index: 10 cycles (sample index)
• i7 index: 10 cycles (sample index)
• Read 2: 90 cycles (transcript)

Oxford Nanopore Technologies Library

Oxford Nanopore cDNA libraries were prepared starting from full-length, 10x barcoded cDNA using the PCR-cDNA Sequencing Kit per the manufacturer’s protocol, "Single-cell transcriptomics with cDNA prepared using 10X Genomics".

Each long-read sequencing library was loaded onto an individual PromethION Flow Cell. Libraries were sequenced for 72 hours and base calling was performed using MinKNOW’s Super Accurate Base Calling mode (MinKNOW software version 22.03.04).

This dataset is licensed under the Creative Commons Attribution license.