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Sample GSM6209498 Query DataSets for GSM6209498
Status Public on Aug 17, 2022
Title CTH-17
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 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 8.49879 0.76867
AFFX-BkGr-GC04_st 7.13447 0.840794
AFFX-BkGr-GC05_st 7.12955 0.912597
AFFX-BkGr-GC06_st 6.72992 0.921659
AFFX-BkGr-GC07_st 6.4371 0.930767
AFFX-BkGr-GC08_st 4.43113 0.924139
AFFX-BkGr-GC09_st 4.0767 0.898802
AFFX-BkGr-GC10_st 3.78856 0.875202
AFFX-BkGr-GC11_st 3.64173 0.838707
AFFX-BkGr-GC12_st 3.51587 0.792416
AFFX-BkGr-GC13_st 3.30702 0.799143
AFFX-BkGr-GC14_st 3.18287 0.774185
AFFX-BkGr-GC15_st 3.14109 0.770321
AFFX-BkGr-GC16_st 3.42214 0.734997
AFFX-BkGr-GC17_st 3.49839 0.709523
AFFX-BkGr-GC18_st 3.87363 0.674069
AFFX-BkGr-GC19_st 6.67934 0.596972
AFFX-BkGr-GC20_st 6.71984 0.595446
AFFX-BkGr-GC21_st 6.77486 0.590457
AFFX-BkGr-GC22_st 6.82237 0.589252

Total number of rows: 24351

Table truncated, full table size 893 Kbytes.

Supplementary file Size Download File type/resource
GSM6209498_CTH-17_Clariom_S_Human_.CEL.gz 1.1 Mb (ftp)(http) CEL
GSM6209498_CTH-17_Clariom_S_Human_.sst-rma-gene-full.chp.gz 270.5 Kb (ftp)(http) CHP
Processed data included within Sample table

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