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Sample GSM5747347 Query DataSets for GSM5747347
Status Public on Dec 12, 2022
Title Early-onset B-cell lymphoma case 7
Sample type genomic
 
Channel 1
Source name Early-onset precursor B-cell lymphoma by the irradiation of gamma-rays at 7 weeks of age
Organism Mus musculus
Characteristics strain: B6C3F1
gender: Female
treatment: irradiation of gamma-rays at 7 weeks of age
disease state: Early-onset precursor B-cell lymphoma
tissue: B-cell lymphoma
Treatment protocol Mice were left untreated or were subjected to whole-body irradiated with gamma-rays (4 Gy) or X-rays (3.8 Gy) at 1 or 7 weeks of age.
Growth protocol Mice were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 3°C) and humidity (50 ± 10%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet and sterilized water ad libitum.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA of B-cell lymphomas and normal normal ears were extarcted by AllPrep DNA/RNA/Protein Mini Kit and DNeasy Blood & Tissue Kit (Qiagen), respectively.
Label Cy5
Label protocol Labeling reactions with cyanine 5-UTP and cyanine 3-UTP were performed according to the Agilent SureTag DNA labeling kit (Agilent Technologies, Santa Clara, CA, USA).
 
Channel 2
Source name Normal ear
Organism Mus musculus
Characteristics strain: B6C3F1
gender: Female
tissue: Ear skin
Treatment protocol Mice were left untreated or were subjected to whole-body irradiated with gamma-rays (4 Gy) or X-rays (3.8 Gy) at 1 or 7 weeks of age.
Growth protocol Mice were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 3°C) and humidity (50 ± 10%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet and sterilized water ad libitum.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA of B-cell lymphomas and normal normal ears were extarcted by AllPrep DNA/RNA/Protein Mini Kit and DNeasy Blood & Tissue Kit (Qiagen), respectively.
Label Cy3
Label protocol Labeling reactions with cyanine 5-UTP and cyanine 3-UTP were performed according to the Agilent SureTag DNA labeling kit (Agilent Technologies, Santa Clara, CA, USA).
 
 
Hybridization protocol Slides were hybridised in 1X Agilent Blocking Agent/Hi-RPM Buffer for 24 hours at 67°C in a rotating hybridization oven, then washed with the Agilent Oligo aCGH Buffer 1 and Buffer 2 in an ozone-depleted hood.
Scan protocol Scanned on an Agilent microarray scanner.
Description Early-pBL7
Data processing Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).
 
Submission date Dec 22, 2021
Last update date Dec 14, 2022
Contact name Kazuhiro DAINO
E-mail(s) daino.kazuhiro@qst.go.jp
Organization name National Institutes for Quantum and Radiological Science and Technology
Street address 4-9-1 Anagawa, Inage-ku
City Chiba
ZIP/Postal code 263-8555
Country Japan
 
Platform ID GPL19767
Series (1)
GSE192455 Genomic DNA copy number alterations of mouse B-cell lymphomas induced by ionizing radiation

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (Cy5/Cy3)

Data table
ID_REF VALUE
A_67_P04000012 0.4287809
A_67_P04000058 0.69054186
A_67_P00000082 0.43134883
A_67_P00000133 -0.088083096
A_67_P00000185 0.42705807
A_67_P04000400 0.31686896
A_67_P04000501 0.15273564
A_67_P04000664 -0.77907854
A_67_P04000834 0.008750686
A_67_P00000662 0.12669246
A_67_P04001017 0.028840521
A_67_P04001131 -0.324922
A_67_P04001245 0.43847093
A_67_P04001347 -0.015229827
A_67_P04001449 -0.16490452
A_67_P04001560 0.37872994
A_67_P00001198 -0.23464192
A_67_P00001289 -0.049557537
A_67_P00001369 0.4870226
A_67_P00001423 0.32526755

Total number of rows: 52202

Table truncated, full table size 1278 Kbytes.




Supplementary file Size Download File type/resource
GSM5747347_Early-pBL7.txt.gz 6.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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