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| Status |
Public on Aug 31, 2023 |
| Title |
AT2_3_L |
| Sample type |
SRA |
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| Source name |
Fetal lung
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Fetal lung
cell line: AT2 organoid
cell type: 17 post-conception week
genotype: Passage 12
treatment: AT2 medium
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| Growth protocol |
Cultured in alveolar type 2 differentiation medium (AT2 medium): Advanced DMEM/F12 supplemented with 1x GlutaMax, 1 mM HEPES and Penicillin/Streptomycin, 1X B27 supplement (without Vitamin A), 1X N2 supplement, 1.25 mM N-acetylcysteine, 50 nM Dexamethasone, 0.1 mM 8-Bromoadenosine 3’5’-cyclic monophosphate (cAMP), 0.1 mM 3-Isobutyl-1-methylxanthine (IBMX), 50 μM DAPT, 100 ng/ml recombinant human FGF7, 3 μM CHIR99021, 10 μM A83-01, and 10 μM Y-27632. Medium was replaced every 2 days and cultures maintained for 2 weeks until the initial AT2 organoid colonies formed in the matrigel droplet. Organoids were typically passaged at a 1 to 3 ratio weekly by gently breaking into small fragments.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries of four biological lines of AT2 organoids at early (P1,4,6,7) and late (P12,13,16,17) passage were generated using an RNeasy kit (Qiagen, 74004) including the optional DNAse digestion step.
The quality of the RNA libraries was validated on Agilent 2200 Tapestation before sequencing on an Illumina NovaSeq 6000 at Novogene (novogene.com). RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
AT2_16392_L
AT2_merged.gene_counts_length_scaled.tsv
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| Data processing |
Raw RNA sequencing data was run by a bioinformatics pipeline, nf-core/rnaseq
According to the nf-core/rnaseq pipleline: Merge re-sequenced FastQ files (cat); Sub-sample FastQ files and auto-infer strandedness (fq, Salmon); Read QC (FastQC); UMI extraction (UMI-tools); Adapter and quality trimming (Trim Galore); Removal of genome contaminants (BBSplit); Removal of ribosomal RNA (SortMeRNA); Alignment and quantification; Sort and index alignments (SAMtools); UMI-based deduplication (UMI-tools); Duplicate read marking (picard MarkDuplicates); Transcript assembly and quantification (StringTie); Create bigWig coverage files (BEDTools, bedGraphToBigWig); Extensive quality control; Pseudo-alignment and quantification (Salmon); Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks (MultiQC, R)
A comparison between the RNA sequencing data of AT2 organoids and publicly available data of fetal organoid types and other alveolar cell types was performed: fetal early tip progenitor organoids GSM5393370 and GSM5393371; fetal late tip progenitor organoids6 GSM5393372 and GSM5393373; PSC-iAT2s7 GSM5578511, GSM5578512 and GSM5578513; cultured adult AT2 cells7 GSM5578508, GSM5578509 and GSM5578510; freshly isolated adult AT2 cells8 GSM2537127, GSM2537128 and GSM2537129
A list of differentially expressed genes was extracted using the counted reads and R package edgeR10 version 3.40.2.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Expression matrix in tsv format.
Supplementary files format and content: Genes are represented in NCBI official gene symbols.
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| Submission date |
Jul 14, 2023 |
| Last update date |
Aug 31, 2023 |
| Contact name |
Kyungtae Lim |
| E-mail(s) |
kl492@cam.ac.uk, ktlim492@korea.ac.kr
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| Organization name |
University of Cambridge
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| Department |
Gurdon Institute
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| Lab |
Emma Rawlins
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| Street address |
Tennis Court Road
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| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE237359 |
A novel human fetal lung-derived alveolar organoid model reveals mechanisms of surfactant protein C maturation relevant to interstitial lung disease |
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| Relations |
| BioSample |
SAMN36449116 |
| SRA |
SRX21022193 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7610406_AT2_3_L.forward.bigWig |
83.7 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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