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Sample GSM2865930 Query DataSets for GSM2865930
Status Public on Nov 28, 2017
Title 5753714054_G; T-PLL
Sample type RNA
 
Source name PATIENT_ID: P210_
Organism Homo sapiens
Characteristics cell type: T-PLL
sampleID: P210_
caseid: TP043
tcl1a: DIM
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_G
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 Since the official Illumina HumanHT-12 v4 Expression BeadChip annotation is outdated, we used the data mining tool biomaRt, version 75 of the Ensembl data base with R, version 3.1.0, and Bioconductor, version 2.10.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 4.86863509937134
ILMN_2055271 5.62844861769777
ILMN_1736007 4.49308787048971
ILMN_2383229 4.87262500531351
ILMN_1806310 4.94213890818703
ILMN_1779670 4.49171467167832
ILMN_1653355 4.59184584993027
ILMN_1717783 3.72062646119133
ILMN_1705025 4.7108065103283
ILMN_1814316 4.4111968983394
ILMN_2359168 3.98008284174145
ILMN_1731507 4.11366625683708
ILMN_1787689 4.63248305869218
ILMN_3241953 5.08160135377816
ILMN_1745607 4.61345325545138
ILMN_2136495 4.81419267346863
ILMN_1668111 5.15411236389039
ILMN_2295559 4.7112603392324
ILMN_1735045 4.23499354805557
ILMN_1680754 7.20124585375066

Total number of rows: 47293

Table truncated, full table size 1380 Kbytes.




Supplementary file Size Download File type/resource
GSM2865930_5753714054_G_Grn.idat.gz 1.6 Mb (ftp)(http) IDAT
Processed data included within Sample table

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