|
| Status |
Public on Sep 13, 2017 |
| Title |
embryonic LG, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
minimum 10 embryonic E18 murine LGs pooled together
|
| Organism |
Mus musculus |
| Characteristics |
strain: ICR
tissue: lacrimal gland, epithelial and mesenchymal compartments
developmental stage: E18 embryos
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Mice were kept in a pathogen-free animal facility until sample collection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA was performed with RNeasy microkit (Qiagen), according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays P/N 703262 Rev. 1
|
| |
|
| Hybridization protocol |
GeneChip® Expression Wash, Stain and Scan User Manual For Cartridge Arrays, P/N 702731 Rev. 3, Affymetrix
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000
|
| Description |
manually dissected out LG, epithelial and mesenchymal compartments
|
| Data processing |
The data-analysis consisted of data pre-processing, quality analysis and detection of statistically differentially expressed genes between the sample groups. The .CEL files [2] of each of the six arrays were loaded into the Affymetrix Expression Console software [3]. They were processed with two different analysis methods [4]: * Gene level SST-RMA (Signal Space Transformation - Robust Multichip Analysis), includes background reduction and SST intensity normalization to produce the gene expression difference results * Exon level SST-Alt Splicing - includes additionally the extraction of all exon, exon-exon splice junction and transcript isoform expression changes These results can be found from the .CHP files [5] included in the project folder. The file names indicate which method has been used. These files in turn are used with the Affymetrix Transcriptome Analysis Console (TAC) Software [6] to produce the differential expression tables and charts. [7] REFERENCES [1] MTA 1.0 - http://www.affymetrix.com/catalog/prod870009/AFFY/Mouse+Transcriptome+Assay+1.0 [2] CEL file format - http://media.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html [3] Affymetrix Expression Console Software - http://www.affymetrix.com/estore/browse/level_seven_software_products_only.jsp?productId=131414 [4] Affymetrix Expression Console Software Manual - http://media.affymetrix.com/support/downloads/manuals/expression_console_userguide.pdf [5] CHP file format - http://dept.stat.lsa.umich.edu/~kshedden/Courses/Stat545/Notes/AffxFileFormats/chp.html [6] Affymetrix Transcriptome Analysis Console (TAC) Software - http://www.affymetrix.com/estore/browse/level_seven_software_products_only.jsp?categoryIdClicked=&productId=prod760001&navAction=jump [7] Affymetrix Transcriptome Analysis Console (TAC) Software Manual - http://media.affymetrix.com/support/downloads/manuals/tac_user_manual.pdf
|
| |
|
| Submission date |
Sep 12, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Frederic Michon |
| E-mail(s) |
[email protected]
|
| Organization name |
Inserm
|
| Department |
Institute for Neurosciences of Montpellier
|
| Lab |
Eye
|
| Street address |
80, rue Augustin Fliche
|
| City |
Montpellier |
| ZIP/Postal code |
34000 |
| Country |
France |
| |
|
| Platform ID |
GPL20775 |
| Series (1) |
| GSE103743 |
Comparison of embryonic samples (E18) vs. adult (34 weeks old) lacrimal gland transcriptome |
|
