|
| Status |
Public on Sep 30, 2022 |
| Title |
Alveolar oragnoids_Dam-NKX2.1 [14556] |
| Sample type |
SRA |
| |
|
| Source name |
Human fetal lung
|
| Organism |
Homo sapiens |
| Characteristics |
sample id: 14556
developmetal age: 20 pcw
passage number: P6
|
| Treatment protocol |
200K of CD44+ cells sorted from pseudoglandular organoids, CD36+/CD44+ cells sorted from LinPOS organoids, or single cell dissociated alveolar organoids were infected with lentivirus habouring 'mNeonGreen-Dam (Dam only)' or 'mNeonGreen-Dam-NKX2.1' for 48 hours.
|
| Growth protocol |
Fetal lung tip organoids were cultured in self-renweing condition, or in alveolar differentiation medium containing DAPT, DCI, SB431542, and CHIR for 1 week
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted and processed as previously described (Marshall et al., 2016).
See method and Marshall et al., 2016
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Alveolar differentiation for day 7_Dam-NKX2.1
|
| Data processing |
Library strategy: DamID-seq
Illumina software used for conventional basecalling.
Reads were mapped to a bowtie2 indexed GRCh38 genome assembly (hg38), binned into 5’-GATC-3’ fragments.
NKX2-1 fusion samples were normalized against a paired Dam-only control derived from the same biological sample (RPM normalization, 300 bp bins)
Macs2 (v2.1.2) was used to call broad peaks for each NKX2-1 fusion and Dam-only pair using the bam files generated by the damidseq_pipeline.
Peaks were filtered to only those present in 2/3 replicates using bedtools (v2.26.0) and surpassing FDR<10-5
Genome_build: GRCh38 genome assembly (hg38)
Supplementary_files_format_and_content: A bigwig file (.bw format) for each NKX2-1 fusion samples normalized against a paired Dam-only control derived from the same biological sample
|
| |
|
| Submission date |
Nov 18, 2021 |
| Last update date |
Sep 30, 2022 |
| Contact name |
Kyungtae Lim |
| E-mail(s) |
kl492@cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
The Wellcome Trust/Cancer Research UK Gurdon Institute
|
| Lab |
Emma Rawlins' group
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE178529 |
Acquisition of alveolar fate and differentiation competence by human fetal lung epithelial progenitor cells |
| GSE189155 |
Targeted NKX2.1 DamID sequencing data from human fetal lung organoids recapitulating differential developmental features of human lung development |
|
| Relations |
| BioSample |
SAMN23286334 |
| SRA |
SRX13168023 |
