Fetal lung dataset - isoswitch report

The second dataset consists of 5 samples from human embryonic and fetal lung tissue. These samples are a subset of a larger study (20 samples) performed at Wellcome Sanger Institute (UK), and have been made available through a collaboration agreement with IPMC. Full details on this dataset are available at Sanger’s pre-print here.

The 5 samples available for this project were collected at 11 (1 sample), 15 (2 samples), and 20 (2 samples) weeks of gestation, and sequenced on both Illumina NextSeq (5’ assay) and Nanopore promethION, then processed by 10X Genomics Cell Ranger and SiCeLoRe (Lebrigand et al., 2020) pipelines, yielding gene- and isoform-level profiles for 12.803 cells.

The original cell type annotation provided by Sanger includes 124 cell types split across 9 compartments numbered C0 to C9 shown below:

Before running the isoform differential expression analysis cell clusters with less than 20 cells were filtered out.
Compartments C7 (Peripheral Nervous System), C8 (Mast cells), C9 (Hepatoblasts) are removed entirely.

The treemap below shows the composition of the resulting dataset after filtering:

Isoform switch reports

Three separate analyses were performed:

1- Between cell types inside each compartment

• Results C0: Fibroblast
• Results C1: Epithelial
• Results C2: Myeloid
• Results C3: Endothelial
  
• Results C4: T+NK+ILC
• Results C5: B cells
• Results C6: Ciliated

2- Between cell types across different compartments.

• Results cross-compartment

3- Between developmental stage for each cell type

• Results developmental stage