|
| Status |
Public on Nov 05, 2015 |
| Title |
control #2 |
| Sample type |
RNA |
| |
|
| Source name |
CD3e-/- primary thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
tissue: Thymus
genotype: CD3e-/-
age: 3 week old
|
| Treatment protocol |
Untreated 3 week-old mice were use to obtain thymocytes.
|
| Growth protocol |
Thymus from 3 week-old mice were dissected out and kept in PBS 2% fetal bovine serum until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted and purified using Qiagen RNeasy Mini Kit (P/N 741104) and resuspended in 5 ml of RNase free water at a concentration of 0.05 mg/ul.
|
| Label |
biotin
|
| Label protocol |
The extract was labelled using the GeneChip Eukaryotic Small Sample Target Labelling protocol (Affymetrix).
|
| |
|
| Hybridization protocol |
Hybridization to the probe array Mouse Genome 430A 2.0 (Affymetrix) was performed by the Ottawa Genome Center.
|
| Scan protocol |
Scanning performed by the Ottawa Genome Center.
|
| Data processing |
Normalization and summarization were performed using Bioconductor packages in the R environment, according to the following pipeline: (i) probesets were summarized and normalized using the RMA procedure implemented in the Affy package [115]; (ii) absent/present probesets were detected using the MAS5 implementation of the Affy package, and probesets deemed absent in both conditions (Cd3ε-/- and Cd3ε-/-SCLtgLMO1tg) were removed from downstream analysis; and (iii) detection of differentially expressed genes was carried out using the Rank Products package.
Differentialy expressed genes between Cd3ε-/- and Cd3ε-/-SCLtgLMO1tg thymocytes that show a significant change (adjusted p-val <0.05) were subsequently selected based on published association with self-renewal.
|
| |
|
| Submission date |
Nov 04, 2015 |
| Last update date |
Aug 08, 2021 |
| Contact name |
mathieu tremblay |
| E-mail(s) |
[email protected]
|
| Organization name |
Université de Montréal/IRIC
|
| Street address |
2950 Chemin de Polytechnique, pav marcelle-coutu 1432
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
h3t 1j4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL339 |
| Series (1) |
| GSE74659 |
SCL and LMO1 reprogram thymocytes into self-renewing cells. |
|
