|
| Status |
Public on Feb 27, 2014 |
| Title |
Mouse pachytene spermatocytes, biological rep 1, chip I |
| Sample type |
RNA |
| |
|
| Source name |
Mouse pachytene spermatocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: Balb/c
gender: male
age: 60 days
cell type: pachytene spermatocytes
|
| Treatment protocol |
Testes from mice at different ages were harvested and decapsulated. Isolated seminiferous tubules were enzymatic digested and mechanically dissociated to single cells, and undergone differential plating for 2 hours to eliminate Sertoli cells. Cells at different developmental stages were isolated by a preivously described method (Bellvé AR, et al. J Cell Biol 1977; 74:68-85). The purities of three isolated cell types were all above 90%.
|
| Growth protocol |
Balb/c mice were on a 12-hour light-dark cycle in a pathogen-free animal facility.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
15 micrograms of total RNA was extracted for each biological replicate. RNA quality was validated with Bioanalyzer 2100 (Agilent). mRNA was enriched with RiboMinus Human/Mouse Transcriptome Isolation Kit according to manufacturer's protocol.
|
| Label |
Biotin
|
| Label protocol |
cDNA was synthesized with GeneChip WT Amplified Double-Stranded cDNA Synthesis Kit and amplified with GeneChip WT cDNA Amplification Kit. Amplified double-stranded cDNA was labeled with GeneChip WT Double-Strand DNA Terminal Labeling Kit according to manufacturer's guideline.
|
| |
|
| Hybridization protocol |
Purified biotin-labelled cDNA was hybrided to the microarray gene for 16 hours at 45C with 60 rpm rotation on Affymetrix Mouse Tiling 1.1R Array Set (14 GeneChips per set). GeneChips were washed and stained in the Afymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G and the images were obtained by the Affymetrix GeneChip Operating Software (GCOS).
|
| Description |
Spcy_I.bar
Affymetrix Mouse Tiling 1.1R Array Set
|
| Data processing |
Expression data were analyzed with Affymetrix Tiling Analysis Software (TAS) and library files BPMAP files version 35 (available from Affymetrix website http://www.affymetrix.com/)
A BAR file was created for each triplicate.
The resulting BAR files were generated by the Affymetrix TAS using probe analysis parameters: Bandwidth = 75, Test type = One side Upper, Intensities = PM/MM
|
| |
|
| Submission date |
Feb 26, 2014 |
| Last update date |
Feb 27, 2014 |
| Contact name |
Tin-Lap Lee |
| Phone |
+852 39434436
|
| Organization name |
The Chinese University of Hong Kong
|
| Department |
School of Biomedical Sciences
|
| Street address |
Area 39
|
| City |
Shatin |
| ZIP/Postal code |
00000 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL13202 |
| Series (1) |
| GSE55381 |
Whole transcription data for mouse spermatogonial cells |
|
