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Sample GSM6209494 Query DataSets for GSM6209494
Status Public on Aug 17, 2022
Title CTH-13
Sample type RNA
 
Source name Unsorted Bone Marrow Cells
Organism Homo sapiens
Characteristics disease state: T-ALL
cell type: Unsorted Bone Marrow Cells
chromothripsis status: negative
phenotype: immature
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 4.0.2.15). 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
E-mail(s) cristina.mecucci@unipg.it
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
ID_REF
VALUE RMA
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
AFFX-BkGr-GC03_st 6.58359 0.799974
AFFX-BkGr-GC04_st 7.08482 0.932435
AFFX-BkGr-GC05_st 7.2204 0.982542
AFFX-BkGr-GC06_st 6.86216 0.985388
AFFX-BkGr-GC07_st 6.50258 0.987463
AFFX-BkGr-GC08_st 4.30737 0.973076
AFFX-BkGr-GC09_st 3.71816 0.965135
AFFX-BkGr-GC10_st 3.39904 0.93706
AFFX-BkGr-GC11_st 3.16494 0.90862
AFFX-BkGr-GC12_st 3.14825 0.832812
AFFX-BkGr-GC13_st 3.09138 0.849277
AFFX-BkGr-GC14_st 3.13101 0.806844
AFFX-BkGr-GC15_st 3.17006 0.787431
AFFX-BkGr-GC16_st 3.46012 0.763051
AFFX-BkGr-GC17_st 3.51427 0.732982
AFFX-BkGr-GC18_st 3.95087 0.703725
AFFX-BkGr-GC19_st 6.72183 0.626036
AFFX-BkGr-GC20_st 6.7482 0.626698
AFFX-BkGr-GC21_st 6.77553 0.617219
AFFX-BkGr-GC22_st 6.81803 0.613773

Total number of rows: 24351

Table truncated, full table size 899 Kbytes.




Supplementary file Size Download File type/resource
GSM6209494_CTH-13_Clariom_S_Human_.CEL.gz 1.0 Mb (ftp)(http) CEL
GSM6209494_CTH-13_Clariom_S_Human_.sst-rma-gene-full.chp.gz 270.0 Kb (ftp)(http) CHP
Processed data included within Sample table

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