This is a folder containing information of the human fetal lung leukocyte atlas
The manuscript can be found on here. The high-resolution supplementary figures can be found in this repository.
Data can be browsed and downloaded from CZI CellxGene and our local website
Raw sequencing data of primary human fetal lungs
Raw sequencing data of human fetal lung organoids
genotyping
| File | GenotypeID | SubmissionID | HDBR ID | Maternal or Fetal? | Corresponding scRNAseq Sample ID | Age of Fetus | Gender of Fetus: M/F |
|---|---|---|---|---|---|---|---|
| uclSamples.vcf | Sample73 | JB_1 | 15503 | Fetal | FL17-C and FL18 | 9 pcw | M |
| uclSamples.vcf | Sample74 | JB_2 | 15404 | Fetal | FL17-C | 9 pcw | F |
| uclSamples.vcf | Sample75 | JB_3 | 14944 | Maternal | FL14 | 9 pcw | F |
| uclSamples.vcf | Sample76 | JB_4 | 15404 | Maternal | FL17-C | 9 pcw | F |
| uclSamples.vcf | Sample77 | JB_5 | 15246 | Maternal | FL6 and FL7-C | 20 pcw | M |
| uclSamples.vcf | Sample78 | JB_6 | 15332 | Maternal | FL16-C | 12 pcw | M |
| uclSamples.vcf | Sample79 | JB_7 | 14732 | Maternal | FL1 and FL15-C | 12 pcw | M |
| uclSamples.vcf | Sample80 | JB_8 | 14776 | Maternal | FL5 and FL15-C | 12 pcw | F |
| uclSamples.vcf | Sample95 | JB_9 | 15084 | Maternal | FL13 | 8 pcw | M |
| jbID.vcf Part I | JB1 | JB1 | 14706 | Fetal | FL2 | 20 pcw | F |
| jbID.vcf Part I | JB2 | JB2 | 14732 | Fetal | FL1 and FL15-C | 12 pcw | M |
| jbID.vcf Part I | JB3 | JB3 | 14774 | Fetal | FL6 and FL7-C | 20 pcw | F |
| jbID.vcf Part I | JB4 | JB4 | 14776 | Fetal | FL5 and FL15-C | 12 pcw | F |
| jbID.vcf Part I | JB6 | JB6 | 14787 | Fetal | FL8 and FL15-C | 20 pcw | M |
| jbID.vcf Part I | JB7 | JB7 | 14794 | Fetal | FL4 and FL15-C | 12 pcw | F |
| jbID.vcf Part I | JB9 | JB9 | 14806 | Fetal | FL3 and FL15-C | 20 pcw | F |
| jbID.vcf Part I | JB10 | JB10 | 14815 | Fetal | FL10 and FL11 | 12 pcw | M |
| jbID.vcf Part I | JB11 | JB11 | 15024 | Fetal | FL9 and FL15-C | 20 pcw | F |
| jbID.vcf Part I | JB12 | JB12 | 15084 | Fetal | FL13 | CS23 | M |
| jbID.vcf Part I | JB13 | JB13 | 15246 | Fetal | FL6 and FL7-C | 20 pcw | M |
| jbID.vcf Part I | JB14 | JB14 | 14944 | Fetal | FL14 | 9 pcw | F |
| jbID.vcf Part I | JB15 | JB15 | 15111 | Fetal | FL12 | 9 pcw | M |
| jbID.vcf Part I | JB16 | JB16 | 14969 | Fetal | FL13 | 8 pcw | F |
| jbID.vcf Part I | JB17 | JB17 | 15332 | Fetal | FL16-C | 12 pcw | M |
| jbID.vcf Part I | JB18 | JB18 | 15383 | Fetal | FL16-C | 20 pcw | M |
scripts
Script to do multi-library donor-demultiplexing based on genetics
Sometimes we may have multiple libraries sharing donors. Pooling them may increase the sample size (number of cells) for each donor and improve demultiplexing results. This script adds artificial "library" barcodes to the bam files of each library, merges them, and runs souporcell demultiplexing. The results will show both library IDs and donor IDs for each cell.