|
| Status |
Public on Apr 15, 2013 |
| Title |
AT cell D0 (AT2) 5626686051_F |
| Sample type |
RNA |
| |
|
| Source name |
Alveolar Epithelial type 2 (AT2 cell)
|
| Organism |
Homo sapiens |
| Characteristics |
time: D0
cell type: AT cell (AT2)
Sex: female
age (y): 49
smoker: non-smoker
cod: Anoxia
|
| Treatment protocol |
Differentiating in culture over time, no extra treatments added.
|
| Growth protocol |
Remnant human transplant lungs were obtained in compliance with Institutional Review Board-approved protocols for the use of human source material in research (HS-07-00660) and processed within 3 days of death. Lung tissue was processed as previously described (Ballard et al., 2010) with inclusion of anti-EpCAM conjugated beads to select for epithelial cells. Cells were plated in 50:50 [DMEM High glucose media (GIBCO 21063): DMEM-F12 (Sigma D6421)]. Differentiation into AT1-like cells was verified by measuring SFTPC and AQP5 expression.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the Illustra TriplePrep Kit (GE LifeSciences, Piscataway, NJ).
|
| Label |
biotin
|
| Label protocol |
IlluminaTotalPrep RNA kit
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
BeadStudio was used to convert images to raw signal data.
|
| Description |
AT cell D0 (AT2)
|
| Data processing |
Using R (version 2.11.1), normalization was performed with VSN using LUMI (Du et al., 2008) to allow for a large number of significantly differentially expressed genes. Statistical analyses were performed using LIMMA (Smyth, 2004). The most variant probes were selected and a linear regression model was fitted over the time-course of differentiation. Technical replicates were removed, and T-tests were performed between Day 0 samples and Day 8 samples. P-values were controlled for false-discovery using the Benjamini-Hochberg (BH) correction (Benjamini & Hochberg, 1995).
|
| |
|
| Submission date |
Jun 07, 2012 |
| Last update date |
Jul 17, 2023 |
| Contact name |
Crystal N Marconett |
| E-mail(s) |
[email protected], [email protected]
|
| Phone |
626-218-4357
|
| Organization name |
City of Hope
|
| Department |
Integrative Translational Sciences
|
| Lab |
Crystal Marconett
|
| Street address |
1500 E Duarte Rd
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE38569 |
Integrated transcriptomic and epigenomic analysis of primary human lung cell differentiation (Human) |
| GSE38571 |
Integrated transcriptomic and epigenomic analysis of primary human lung cell differentiation |
|
