scRNA-seq 3’ gene expression version 3.1:

Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry) -User Guide -Library Prep -Single Cell Gene Expression -Official

 

scRNA-seq/Immune profiling (5’ chemistry) version 2:

Chromium Single Cell 5' Reagent Kits User Guide (v2 Chemistry Dual Index) -User Guide -Library Prep -Single Cell Immune Profiling -Official

 

scATAC-seq version 2:

Chromium Single Cell ATAC Reagent Kits User Guide (v2 Chemistry) -User Guide -Library Prep -Single Cell ATAC -Official

 

sc-Multiomics (ATAC + 3’ Gene Expression):

Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits User Guide -User Guide -Library Prep -Single Cell Multiome ATAC + Gene Exp. -Official

 

Spatial Transcriptomics:

Visium Spatial Gene Expression Reagent Kits User Guide -User Guide -Library Prep -Spatial Gene Expression -Official

Link to locally hosted sc 3’GEX Assay Scheme:

https://drive.google.com/file/d/10wv2M2L1YitmCKm5G-SPMUAV3_MP_J3F/view?usp=sharing

 

Link to locally hosted sc 5’GEX Assay Scheme:

https://drive.google.com/file/d/1GY40dQm6bOgmJb30T91rufB4eIVxctmh/view?usp=sharing

 

Link to locally hosted sc ATAC Assay Scheme:

https://drive.google.com/file/d/1kY4OHa8rUxEAoWLkFu_QlZnsNIVEHkeb/view?usp=sharing

 

Gene Expression Sample index plate: (At this time we use i7 indexes only for all gene expression libraries)

https://support.10xgenomics.com/single-cell-gene-expression/sequencing/doc/specifications-sample-index-sets-for-single-cell-3

 

ATAC-seq sample index plate:

https://support.10xgenomics.com/single-cell-atac/sequencing/doc/specifications-sample-index-sets-for-single-cell-atac

Seurat (R)

Scanpy (Python)

Single Cell Best Practices (Theis Lab, Interactive book by the authors of Scanpy detailing step-by-step analysis)

Introduction to single-cell RNA-seq data analysis in Python using scanpy (Dr. Maren Büttner, Postdoc at the ICB of the Helmholtz Munich, explains how to conduct analysis using scanpy in a 9-part YouTube series)

Guidelines for the computational analysis of single-cell RNA sequencing data

awesome-single-cell (software packages for single cell analysis)

Slides Webinar (Jon's Loupe Tutorial)

scrna-tools: catalogue of tools for analysing single-cell RNA seq data