|
| Status |
Public on Nov 28, 2017 |
| Title |
5753714093_A; Naive_T-cells |
| Sample type |
RNA |
| |
|
| Source name |
PATIENT_ID: 5850naive
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Naive_T-cells
sampleID: 5850naive
caseid: NA
tcl1a: NA
mtcp1: NA
os_diagnosis_to_last_fu: NA
os_treatment_to_last_fu: NA
os_scoring: NA
pfs: NA
pfs_scoring: NA
wbc_diagn: NA
wbc_sample: NA
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
GEP of human T-PLL cells. Sample preparation: PBMCs isolated from T-PLL patients (>95% purity of T-cells) and CD3+ T-cells isolated from PB of healthy donors (see paragraph 2 for detailed descriptions on cell purification) were submitted to RNA isolation using the mirVana kit (Invitrogen). GEP analyses were conducted using Illumina HumanHT‑12 v4 BeadChip arrays according to manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
Standard Illumina protocol
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
NA
5753714093_A
|
| Data processing |
Bioinformatics: We used the Illumina proprietary software GenomeStudio v1 to background-correct and to initially annotate the probes of the HumanHT-12 v4 Expression BeadChip. We filtered samples and genes by detection p-values and fluorescence intensities for at least 2/3 hits (p<0.05) to reduce false calls. Batch-effects were corrected by the ComBat method which uses an empiric Bayesian model framework. For literature references to bioinformatics methods and algorithms see Supplementary Table2). Since the official Illumina HumanHT-12 v4 Expression BeadChip annotation is outdated, we used the data mining tool biomaRt, version 75 of the Ensembl data base with R, version 3.1.0, and Bioconductor, version 2.10.
T-PLLs (n=70) and normal controls (CD3+ T-cells from 10 healthy donors) were grouped and tested separately for differential expression using the Student’s t-test on log-transformed fluorescence values (normally distributed). Fold-changes (fc) were calculated on the fluorescence values without logarithmic transformation. False discovery rates (FDRs) were calculated using the R package “qvalue”. Hierarchical clustering was carried out using the R package gplots, version 2.15.0 (distance function: euclidean; clustering: complete linkage).
|
| |
|
| Submission date |
Nov 27, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Giuliano Crispatzu |
| Organization name |
University of Cologne (UoC), Germany
|
| Department |
CECAD
|
| Street address |
Joseph-Stelzmann-Straße 26
|
| City |
Cologne |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE107397 |
The molecular basis of T-PLL is an actionable perturbation of TCL1/ATM- and epigenetically instructed damage responses [human gene expression array] |
| GSE107513 |
The molecular basis of T-PLL is an actionable perturbation of TCL1/ATM- and epigenetically instructed damage responses |
|
