|
| Status |
Public on May 13, 2012 |
| Title |
Naïve_Donor2 |
| Sample type |
RNA |
| |
|
| Source name |
peripheral naïve T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lymphocytes
|
| Treatment protocol |
Naïve T cells were in vitro differentiated to Th1 with IL-12 and anti-IFNgamma for 7 days. CD161-CCR6- and CD161+CCR6+ memory T cells were in vitro expanded with IL-1b and IL-23 for 7 days.
|
| Growth protocol |
Human PBMDs were isolated by Ficoll separation, and then FACS-sorted to naïve and CD161-CCR6-, CD161+CCR6+ CD4 T cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation was done with Qiagen Rneasy Kit according to manufacturer's manual.
|
| Label |
biotin
|
| Label protocol |
High quality total RNA is subjected to the Ambion Whole Transcript Expression Kit where their patented primer is used to prime for mRNA and coding RNA’s only. The RNAs that have been primed are then amplified to create cDNA and which is used in in vitro transcription to create cRNA. The cRNA is cleaned using Ambion’s bead purification that comes within the WT Expression kit and quantitated. 10ug of amplified cRNA is placed into a reaction with a random primer and then onto to generate a second cycle of 1st strand sense direction cDNA. The cDNA is purified using the Ambion bead cleanup as described previously and quantitated. 5.5ug of sscDNA is then enzymatically fragmented using ADP and UDG using the Affymetrix Terminal Labeling kit and ran on the Agilent bioanalyzer to ensure proper transcript size. The fragmented material is then labeled using TdT and then placed into a hybridization cocktail.
|
| |
|
| Hybridization protocol |
Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned.
|
| Scan protocol |
The images are analyzed using Affymetrix Command Console Viewer and metric analyses are carried out according to the instructions provided by Affymetrix using the Affymetrix Expression Console.
|
| Description |
SAMPLE 2
Gene expression data from human naïve T cells
|
| Data processing |
The data was RMA normalized using Partek Genomics suite.
|
| |
|
| Submission date |
Oct 11, 2011 |
| Last update date |
Sep 01, 2016 |
| Contact name |
Wei Zhang |
| E-mail(s) |
wei.zhang.wz73@yale.edu
|
| Phone |
203-737-1354
|
| Fax |
203-785-7273
|
| Organization name |
Yale School of Medicine
|
| Lab |
Zhang
|
| Street address |
333 cedar st., P.O. Box 208019
|
| City |
New Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06405 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE32901 |
Expression data for effector T cells |
|
| Relations |
| Reanalyzed by |
GSE86357 |
