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| Status |
Public on Sep 10, 2009 |
| Title |
Transcriptomic analysis of human lung development |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
We decompose the genome-wide expression patterns in 38 embryonic human lung (53-154 days post conception/dpc) into their independent, dominant directions of transcriptomic sample variation in order togain global insight of the developing human lung transcriptome.The characteristic genes and their corresponding bio–ontologic attribute profile for the latter were identified. We noted the over–representation of lung specific attributes (e.g., surfactant proteins) traditionally associated with later developmental stages, and highly ranked attributes (e.g., chemokine–immunologic processes) not previously reported nor immediately apparent in an early lung development context. We defined the 3,223–gene union of the characteristic genes of the 3 most dominant sources of variation as the developing lung characteristic sub–transcriptome (DLCS). It may be regarded as the minimal gene set describing the essential biology of this process. The developing lung series in this transcriptomic variation perspectiveform a contiguous trajectory with critical time points that both correlate with the 2 traditional morphologic stages overlapping -154 dpc and suggest the existence of 2 novel phases within the pseudoglandular stage. To demonstrate that this characterization is robust, we showed that the model could be used to estimate the gestational age of independent human lung tissue samples with a median absolute error of 5 days, based on the DLCS of their lung profile alone. Repeating this procedure on the homologous transcriptome profiles of developing mouse lung 14–19 dpc, we were able to recover their correct developmental chronology.
Whole human fetal lung gene expression profiling from estimated gestational ages 53 to 154 days post conception.
Keywords: Whole lung gene expression profiling, lung development, human fetus.
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| |
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| Overall design |
Time series with biological replicates.
|
| |
|
| Contributor(s) |
Kho AT, Bhattacharya S, Tantisira KG |
| Citation(s) |
19815808, 24929828 |
| Submission date |
Jan 08, 2009 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Alvin T. Kho |
| E-mail(s) |
alvin_kho@hms.harvard.edu
|
| Phone |
617-919-2182
|
| Organization name |
Boston Children's Hospital
|
| Department |
Informatics Program
|
| Street address |
320 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
|
| Samples (38)
|
| GSM358631 |
Human fetal lung 76 dpc biological replicate 1 |
| GSM358632 |
Human fetal lung 110 dpc biological replicate 1 |
| GSM358633 |
Human fetal lung 63 dpc biological replicate 1 |
|
| Relations |
| BioProject |
PRJNA111513 |
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