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Sample GSM2865934 Query DataSets for GSM2865934
Status Public on Nov 28, 2017
Title 5753714054_D; CLL
Sample type RNA
 
Source name PATIENT_ID: P430_
Organism Homo sapiens
Characteristics cell type: CLL
sampleID: P430_
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
5753714054_D
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 Since the official Illumina HumanHT-12 v4 Expression BeadChip annotation is outdated, we used the data mining tool biomaRt, version 75 of the Ensembl data base with R, version 3.1.0, and Bioconductor, version 2.10.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 4.87273519210729
ILMN_2055271 5.83227579240782
ILMN_1736007 4.75449573873377
ILMN_2383229 5.20025386429226
ILMN_1806310 5.08020981555914
ILMN_1779670 4.76329427720507
ILMN_1653355 5.46542870237058
ILMN_1717783 4.02795521607927
ILMN_1705025 5.54900075705924
ILMN_1814316 4.74896597272235
ILMN_2359168 4.62866553934131
ILMN_1731507 3.94637583402267
ILMN_1787689 5.11443330429012
ILMN_3241953 5.26401995881162
ILMN_1745607 4.57368361609828
ILMN_2136495 4.1300814329469
ILMN_1668111 4.80276880042264
ILMN_2295559 5.44679411587984
ILMN_1735045 4.28580440418523
ILMN_1680754 6.10941747063376

Total number of rows: 47293

Table truncated, full table size 1380 Kbytes.




Supplementary file Size Download File type/resource
GSM2865934_5753714054_D_Grn.idat.gz 1.6 Mb (ftp)(http) IDAT
Processed data included within Sample table

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