|
| Status |
Public on Sep 30, 2022 |
| Title |
14404_folded_P2_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Human fetal lung
|
| Organism |
Homo sapiens |
| Characteristics |
sample id: 14404
developmetal age: 19 pcw
passage number: P2
tissue: Human fetal lung
cell type: LinPOS organoids
cell type: Folded
|
| Treatment protocol |
After complete removal of Matrigel, TripLE (Thermo Fisher Scientific, 12605010) were treated to dissociate organoids into single cells.
|
| Growth protocol |
Fetal lung tip organoids were cultured in Matrigel in self-renweing (SN) culture medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested from lung organoids using Rneasy Kit (Quiagen, 74004) and Illumina TruSeq RNA Sample Prep Kit (Illumina, 20020594) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
LinPOS organoids RNA-seq
|
| Data processing |
Illumina 1.9 software used for conventional basecalling.
Reads were trimmed using TrimGalore v0.4.1.
Reads were mapped using STAR v2.5.2a.
Number of reads that map to genomic features is calculated using HTSeq v0.6.0. Reads with a mapping quality less than 10, or those that map to multiple loci or to overlapping gene regions are discarded to avoid ambiguity and false positives.
PCA plots and heatmaps are based on normalised and rlog transformed counts obtained with DESeq2 version 1.14.1 (R version 3.4.1). Differential Gene Expression Analysis was done using the counted reads and the R package edgeR version 3.16.5 (R version 3.4.1), for the 3 pairwise comparisons.
Genome_build: Ensembl Homo_sapiens.GRCh38 (release 92)
Supplementary_files_format_and_content: A text file (csv format) includes FPKM values for each sample
|
| |
|
| Submission date |
Jun 21, 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 |
GPL20301 |
| Series (2) |
| GSE178528 |
Transcriptomic data from cultured human fetal lung tip-derived organoids at different stages of lung development |
| GSE178529 |
Acquisition of alveolar fate and differentiation competence by human fetal lung epithelial progenitor cells |
|
| Relations |
| BioSample |
SAMN19792069 |
| SRA |
SRX11187504 |
