|
| Status |
Public on Nov 12, 2024 |
| Title |
EBV(-) B cell line, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
B cell line from EBV(-) diffuse large B cell lymphoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: B cell line from EBV(-) diffuse large B cell lymphoma
|
| Growth protocol |
All cell lines were cultured in RPMI-1640 (Cytiva) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS; Corning) and 1% (v/v) Glutamax (Gibco) at 37°C with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested from healthy cell cultures in the log-phase of growth, washed in ice-cold phosphate-buffered saline, and immediately stored at -80°C for later use. Total RNA was isolated from cell pellets using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. RNA was eluted in the supplied RNase-free water. Total RNA was checked for quality and integrity using a BioAnalyzer (Agilent).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Samples were hybridised to Clariom™ S Assays, human (Affymetrix/Applied Biosystems™) using the GeneChip™ Hybridization, Wash, and Stain Kit (Affymetrix).
|
| Scan protocol |
GeneChips were scanned using the GeneArray Scanner 3000 (Affymetrix).
|
| Description |
Gene expression data from B cell line from EBV(-) diffuse large B cell lymphoma
|
| Data processing |
Background reduction and quantile normalization were first carried out on CEL files using the Signal Space Transformation-Robust Multi-array Average (SST-RMA) method from Transcriptome Analysis Software v4.0 (Applied Biosystems). The SST-RMA method includes GC Correction Version 4 (GC4) background reduction and SST intensity normalization.
|
| |
|
| Submission date |
Oct 16, 2024 |
| Last update date |
Nov 12, 2024 |
| Contact name |
Jiaying Toh |
| Organization name |
Stanford University
|
| Street address |
1201 Welch Road
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL23159 |
| Series (2) |
| GSE279598 |
Integrated multi-modal analysis reveals tumor and immune characteristics that distinguish Epstein-Barr virus-positive and -negative B cell post-transplant lymphoproliferative disorders [Affymetrix] |
| GSE279991 |
Integrated multi-modal analysis reveals tumor and immune characteristics that distinguish Epstein-Barr virus-positive and -negative B cell post-transplant lymphoproliferative disorders |
|
