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Sample GSM2865927 Query DataSets for GSM2865927
Status Public on Nov 28, 2017
Title 5753714054_A; T-PLL
Sample type RNA
 
Source name PATIENT_ID: P119_
Organism Homo sapiens
Characteristics cell type: T-PLL
sampleID: P119_
caseid: TP034
tcl1a: POS
mtcp1: NA
os_diagnosis_to_last_fu: 912
os_treatment_to_last_fu: 906
os_scoring: DOD
pfs: 16
pfs_scoring: death; relapse or progression; primary treatment failure
wbc_diagn: NA
wbc_sample: 33
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
5753714054_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 Since the official Illumina HumanHT-12 v4 Expression BeadChip annotation is outdated, we used the data mining tool biomaRt, version 75 of the Ensembl data base with R, version 3.1.0, and Bioconductor, version 2.10.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

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
ILMN_1762337 5.64272078988593
ILMN_2055271 4.78236556681238
ILMN_1736007 4.63403314095479
ILMN_2383229 4.80674188634561
ILMN_1806310 4.83748827741761
ILMN_1779670 4.90190779861639
ILMN_1653355 4.62447673983375
ILMN_1717783 3.3451204469148
ILMN_1705025 5.66276274173297
ILMN_1814316 5.12201410797692
ILMN_2359168 4.72085274794811
ILMN_1731507 3.86166454158172
ILMN_1787689 4.50094149227753
ILMN_3241953 6.16019099122746
ILMN_1745607 4.64653054123062
ILMN_2136495 3.65980181971522
ILMN_1668111 4.09825937689819
ILMN_2295559 4.5263543689173
ILMN_1735045 4.04478307702928
ILMN_1680754 4.81897083607096

Total number of rows: 47293

Table truncated, full table size 1380 Kbytes.




Supplementary file Size Download File type/resource
GSM2865927_5753714054_A_Grn.idat.gz 1.6 Mb (ftp)(http) IDAT
Processed data included within Sample table

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