|
| Status |
Public on Jul 03, 2019 |
| Title |
D28_Chronic_rep4 |
| Sample type |
RNA |
| |
|
| Source name |
D28_Chronic
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: P14
cell type: T-cells
collection day: 28
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed by the company which also did the gene array. T cell lysates were provided frozen. Final disruption and homogenization of the cell lysates was achieved by using QIAshredder columns (Qiagen) after addition of RLT-buffer containing Beta-mercaptoethanol. Total RNA was then isolated using the RNeasy Mini Kit (Qiagen) following manufacturer's instructions. The principle of this kit is a silica membrane-based purification of total RNA. Final volume of the eluate was 40 ul. An aliquot of the total RNA samples was used to determine RNA concentration and purity on the NanoDrop ND-1000 spectral photometer (peqlab). The 2100 Bioanalyzer (Agilent Technologies) allows for analysis of total RNA samples by capillary electrophoresis. The RNA is separated according to fragment size, and results are returned as electropherograms and virtual gel images. An index for RNA quality, the so-called RIN (RNA integrity number), is derived from the electrophoretic profile. The RIN scale ranges from 1 to 10. A RIN of 10 denotes an excellent RNA quality, while a RIN value of 1 indicates massive degradation. For RIN calculation, the algorithm does not rely on the 28S/18S-rRNA ratio alone, but takes into account the entire electrophoretic profile (e.g. the fraction of short degraded RNA species). All samples were analyzed using RNA 6000 Pico LabChip Kits (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
performed by the company
|
| |
|
| Hybridization protocol |
Agilent mouse GE v2 Microarrays (4x44K) was used in combination with a one-color based hybridization protocol and was performed as described in the manufacturer’s instructions.
|
| Scan protocol |
Signals on the microarrays were detected using the Agilent DNA Microarray Scanner (Scan Control A.8.4.1 Software, Agilent Technologies)
|
| Description |
Gene expression profile
|
| Data processing |
Data were analyzed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1-107_Sep09 and Grid: 028005_D_F_20130207
GeneSpring GX12 (for Supp. Fig 1A) and GeneSpring GX13.0 (for Supp. Fig 1B) (Agilent Technologies) was used to normalize and analyze the raw data as well for quality control.
|
| |
|
| Submission date |
May 31, 2019 |
| Last update date |
Jul 03, 2019 |
| Contact name |
Dietmar Zehn |
| E-mail(s) |
dietmar.zehn@tum.de
|
| Phone |
+49 8161 71 3508
|
| Organization name |
Technical University of Munich
|
| Department |
Division of Animal Physiology and Immunology
|
| Street address |
Weihenstephaner Berg 3
|
| City |
Freising |
| ZIP/Postal code |
85354 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13912 |
| Series (2) |
| GSE131643 |
Tox reinforces the phenotype and longevity of exhausted T-cells in chronic viral infection |
| GSE132028 |
Tox reinforces the phenotype and longevity of exhausted T-cells in chronic viral infection [day28 acute vs chronic] |
|
