|
| Status |
Public on Jun 07, 2011 |
| Title |
Columnar cells, donor 1 |
| Sample type |
SRA |
| |
|
| Source name |
Columnar cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: human nasal mucosa
cell type: Majority of columnar ciliated cells
rin number: 9.6
bank concentration (ng/µl): 208.9
|
| Treatment protocol |
Isolated HAECs were incubated with both mouse monoclonal anti-CD151-PE (6 µl/106 cells) and monoclonal mouse anti-TF-FITC antibodies (3 µl/106 cells).Bright basal cells (CD151+/TF+) and negative columnar cells (CD151-/TF-) were selected and sorted using the cell sorter’s purity option at a rate of 5,000 events per second. Sorted populations were reanalyzed (3 x 104 events recorded) for purity and viability.
|
| Growth protocol |
HAECs were dissociated from nasal polyps for cell sorting by FACSaria.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SREK was performed according to the manufacturer’s protocol (Ambion, Inc, Austin, TX).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB SOLiD System 2.0 |
| |
|
| Description |
Columnar ciliated cells
|
| Data processing |
Data analysis was performed using rna2map software provide by SOLiD™ Software Development Community (http://solidsoftwaretools.com/gf/). This tool allows to identifies reads as miRNAs among a reference set miRNAs: here xtr mirbase_v14. Parameters of identification has been set as follows: 1 color mismatch in the miRNAs seed (first 18 bases) and 2 color mismatchs in the extension step. Following identification of miRNAs, a normalization to 1000000 miRNAs count was performed. See supplementary series file for original (unrounded) counts and miRNA names.
|
| |
|
| Submission date |
Jun 04, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
|
| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
|
| Street address |
660 route des lucioles
|
| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
| |
|
| Platform ID |
GPL9138 |
| Series (2) |
| GSE22145 |
miRNAs high throughput sequencing profiling of basals cells and columnar cells |
| GSE22147 |
microRNAs-449 control vertebrate multi-ciliogenesis by repressing Notch signalling |
|
| Relations |
| SRA |
SRX021841 |
| BioSample |
SAMN00014626 |
