|
| Status |
Public on Jul 25, 2024 |
| Title |
Human Naïve CD4 DMSO Pretx 3Hr Stim Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
CLL Patient 01
|
| Organism |
Homo sapiens |
| Characteristics |
agent: DMSO
time point: 3Hr
cell type: CD4
tissue: Peripheral Blood
|
| Treatment protocol |
Cells were pre-incubated with 1 µM TAK-981 or DMSO (vehicle) for 1 hour and treated with 0.5 µg/mL αCD3/CD28 in the presence of the compound for 3 or 24 Hrs
|
| Growth protocol |
Peripheral blood mononuclear cells (PBMCs) were isolated using standard Ficoll-Hypaque technique (Amersham). Red blood cells were lysed using ACK buffer (Thermo Fisher Scientific). Naïve CD4+ T cells were FACS sorted by use of fluorescent antibodies in 2% FBS in PBS for 30 minutes on ice and subsequently washed. Naïve CD4+ T cells were then FACS-sorted by gating viable CD4+CD45RA+CD45RO- lymphocytes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the total RNA Kit I and Homogenizer Mini Columns (Omega Bio-Tek). cDNA was synthesized from 500 ng of RNA using the qScript cDNA Supermix (QuantaBio)
|
| Label |
biotin
|
| Label protocol |
3ng of total RNAf or each sample were amplified and biotin labelled using the Ovation RNA Amplification System V.2, and Encore Biotin Module (NuGEN Technologies) as per manufacturer recommendations
|
| |
|
| Hybridization protocol |
Labelled hybridization targets were mixed with hybridization solution containing hybridization controls (Applied Biosystems) according to NuGEN Technologies protocol and hybridized with the GeneChip Clariom S Human Array (Applied Biosystems)
|
| Scan protocol |
Arrays were scanned using the GeneChip Scanner 3000 7G.
|
| Description |
SST-RMA Expression value derived from Expression Console software; gene-level analysis
|
| Data processing |
Image processing was performed with GeneChip Command Console v. 3.1.1 and probe set summarization and CHP file generation was performed using Transcriptome Analysis Console v. 4.0 software. Expression values were determined from SST-RMA normalization.
|
| |
|
| Submission date |
Jul 25, 2022 |
| Last update date |
Jul 25, 2024 |
| Contact name |
Alexey V. Danilov |
| E-mail(s) |
adanilov@coh.org
|
| Organization name |
City of Hope National Medical Center
|
| Lab |
Danilov
|
| Street address |
1500 E Duarte Road
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL23159 |
| Series (1) |
| GSE209744 |
T cell intrinsic immunomodulatory effects of TAK-981 in chronic lymphocytic leukemia patient derived T cells |
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