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Sample GSM6209525 Query DataSets for GSM6209525
Status Public on Aug 17, 2022
Title CTH-44
Sample type RNA
Source name Unsorted Peripheral Blood Cells
Organism Homo sapiens
Characteristics disease state: T-ALL
cell type: Unsorted Peripheral Blood Cells
chromothripsis status: negative
phenotype: non-ETP
Extracted molecule total RNA
Extraction protocol RNA was extracted from bone marrow or peripheral blood samples using a QIAamp RNA Blood Mini Kit (Qiagen) at a QIAcube automated station
Label biotin
Label protocol GeneChip® WT PLUS Reagent Kit (Affymetrix Applied Biosystem Microarray, Thermo Fisher, Milan, Italy) was used to generates amplified and biotinylated sense-strand DNA targets from total RNA; it uses a reverse transcription priming method that primes the entire length of RNA. Amplified cDNA was quantified, fragmented, marked, and prepared for hybridization from the GeneChip® Clariom S Human Array (Thermo Fisher Scientific) for expression level measurement
Hybridization protocol Hybridization of the microarrays was performed in a GeneChip® Hybridization Oven 645 (Affymetrix/Thermo Fisher Scientific). GeneChips were washed and stained
Scan protocol Arrays were scanned using the GeneChip Scanner 3000 (Affymetrix Applied Biosystem Microarray, Thermo Fisher, Milan, Italy)
Data processing Primary data analysis was performed with Transcriptome Analysis Console software version 4.0 (TAC Differentially expressed RNA were estimated by fold-change filtering combined with Student’s t-test. Transcripts with fold change in expression ≥ ±2.0 and FDR<0.05 were considered significantly differentially expressed. Hierarchical clustering was performed to show the distinguishing genes expression pattern among samples
Submission date Jun 01, 2022
Last update date Aug 17, 2022
Contact name Cristina Mecucci
Phone +39 075 5783808
Organization name University of Perugia
Department Department of Medicine, Hematology and Bone Marrow Transplantation Unit
Lab Laboratory of Cytogenetics and Molecular Genetics
Street address Piazzale Menghini n.9
City Perugia
ZIP/Postal code 06132
Country Italy
Platform ID GPL23159
Series (2)
GSE205265 Chromothripsis is a frequent event and underlies typical genetic changes in early T-cell precursor lymphoblastic leukemia in adults [gene expression]
GSE205270 Chromothripsis is a frequent event and underlies typical genetic changes in early T-cell precursor lymphoblastic leukemia in adults

Data table header descriptions

Data table
AFFX-BkGr-GC03_st 7.02711 0.741723
AFFX-BkGr-GC04_st 7.02348 0.906337
AFFX-BkGr-GC05_st 7.08306 0.942686
AFFX-BkGr-GC06_st 6.78873 0.945992
AFFX-BkGr-GC07_st 6.32835 0.930666
AFFX-BkGr-GC08_st 4.12597 0.925635
AFFX-BkGr-GC09_st 3.70766 0.904315
AFFX-BkGr-GC10_st 3.55156 0.877856
AFFX-BkGr-GC11_st 3.376 0.835632
AFFX-BkGr-GC12_st 3.3118 0.764146
AFFX-BkGr-GC13_st 3.11275 0.783823
AFFX-BkGr-GC14_st 3.00367 0.754693
AFFX-BkGr-GC15_st 3.018 0.752118
AFFX-BkGr-GC16_st 3.26887 0.727108
AFFX-BkGr-GC17_st 3.32556 0.708104
AFFX-BkGr-GC18_st 3.71678 0.665378
AFFX-BkGr-GC19_st 6.66147 0.588418
AFFX-BkGr-GC20_st 6.68999 0.587642
AFFX-BkGr-GC21_st 6.75184 0.583473
AFFX-BkGr-GC22_st 6.83964 0.58475

Total number of rows: 24351

Table truncated, full table size 898 Kbytes.

Supplementary file Size Download File type/resource
GSM6209525_CTH-44_Clariom_S_Human_.CEL.gz 1.1 Mb (ftp)(http) CEL
GSM6209525_CTH-44_Clariom_S_Human_.sst-rma-gene-full.chp.gz 270.8 Kb (ftp)(http) CHP
Processed data included within Sample table

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