|
| Status |
Public on Oct 01, 2022 |
| Title |
RNA_X1_cells_Proximal_polyadenylation sites_Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
X1 cells, Proximal peaks
|
| Organism |
Schmidtea mediterranea |
| Characteristics |
cell type: X1 (Stem cells)
strain: Sexual
|
| Treatment protocol |
No specific treatment was done to isolated RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We isolated mRNA through oligodT probes from different samples and used as input for the microarray experiment. Qiagen’s RNeasy minikit Cat#74106 was used.
|
| Label |
cy3
|
| Label protocol |
OligodT primer with T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis).Agilent’s Quick-Amp labeling Kit (p/n:5190-0442) was used for labelling
|
| |
|
| Hybridization protocol |
Agilent’s In situ Hybridzation kit 5190-6420 was used for hybridization
|
| Scan protocol |
The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 072436_D_F_20150113) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.Background detrend ( On(FeatNCRange, LoPass)), saturation value 65526.
|
| Description |
We isolated RNA from FACS sorted cells and gene expression analysis was done.
|
| Data processing |
The images were manually verified and found to be devoid of uneven hybridization, streaks, blobs and other artifacts. Hybridization across the slide was good based on number of feature that were “g is PosAndSignif” which indicates feature is positive and significantly above background.The microarray images were overall clean, uniform intensity and with very low background noise.
|
| |
|
| Submission date |
Feb 22, 2016 |
| Last update date |
Oct 01, 2022 |
| Contact name |
Dasaradhi Palakodeti |
| E-mail(s) |
dasaradhip@instem.res.in
|
| Phone |
+91 80 23666743
|
| Organization name |
inStem, NCBS
|
| Department |
TAS
|
| Lab |
Dr.Dasaradhi Palakodeti
|
| Street address |
GKVK Campus, Bellary road
|
| City |
Bangalore |
| State/province |
Karnataka |
| ZIP/Postal code |
560065 |
| Country |
India |
| |
|
| Platform ID |
GPL21495 |
| Series (2) |
| GSE78161 |
Genome-wide analysis of polyadenylation events in Schmidtea mediterranea (I) |
| GSE78503 |
Genome-wide analysis of polyadenylation events in Schmidtea mediterranea |
|
