Skip to content

5. Running Test Data

Isolation protocol: CG000392 RevA: Isolation of Leukocytes, Bone Marrow and Peripheral Blood Mononuclear Cells for Single Cell RNA Sequencing - Whole Blood Lysis for Granuloctyes track. Whole transcriptome/Gene Expression libraries were generated as described in the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) User Guide (CG000204 Rev D). TUTORIAL: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/tutorials/neutrophils SOURCE: https://www.10xgenomics.com/resources/datasets/whole-blood-rbc-lysis-for-pbmcs-neutrophils-granulocytes-3-3-1-standard

WB_1

  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L001_I1_001.fastq.gz
  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L001_I2_001.fastq.gz
  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L001_R1_001.fastq.gz
  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L001_R2_001.fastq.gz

WB_2

  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L002_I1_001.fastq.gz
  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L002_I2_001.fastq.gz
  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L002_R1_001.fastq.gz
  • WB_Lysis_Granulocytes_3p_Introns_8kCells_S1_L002_R2_001.fastq.gz

WB_3 and WB_4 are copies

  • WB_1 → WB_3
  • WB_2 → WB_4

samples were then subsampled with a set seed

  • WB_1 → sample1,sample2 → s100
  • WB_2 → sample3,sample4 → s101
  • WB_3 → sample5,sample6 → s102
  • WB_4 → sample7,sample8 → s103

grouping tests should be

  • group1,group2
  • group3,group4
  • group1+group3,group2+group4