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Sample GSM7100281 Query DataSets for GSM7100281
Status Public on Feb 27, 2024
Title breast_cancer_brain_metastasis_8
Sample type RNA
 
Source name breast_brain metastasis
Organism Homo sapiens
Characteristics tissue: breast cancer
metastatic site: brain
age at diagnosis: 48
Sex: female
histology: TNBC
smoking status: n.a
treatment after surgery of bm: Other
Extracted molecule total RNA
Extraction protocol Tissue sections of 5 μm were stained with hematoxylin and eosin (H&E), and examined by a pathologist. Total RNA was extracted from 10-12 sections of 10 μm thickness. RNA was stored in RNase/DNase-free water at -80°C. The nCounter® PanCancer IO 360™ Panel was used for NanoString targeted gene expression analysis. The total RNA was isolated from tumor tissue using the RNeasy® FFPE isolation kit (Qiagen, Hilden, Germany). The RNA quantity and quality were measured using the Agilent 2100 BioAnalyzer (Santa Clara, CA, USA), RNA degradation was calculated using percentages of fragments of 300-4000 nucleotides. The 300 ng of good quality RNA, with a maximum of 7 μL was used for hybridization with the panel probes for 17 hours at 65°C using a SimpliAmp Thermal Cycler (Applied Biosystems, Foster City, CA, USA).
Label NA
Label protocol n.a.
 
Hybridization protocol For each sample, 300 ng of good quality RNA, with a maximum of 7 μL was used for hybridization with the PanCancer IO 360™ probes for 17 hours at 67⁰C, following the manufacturing procedure (NanoString Technologies Inc., Seattle, WA, USA).
Scan protocol The nCounter FLEX platform was used and genes were counted by scanning 490 Fields-of-view (FOV).
Description BCBM 8
Data processing Data analysis was performed using the advanced analysis module (version 2.0) of nSolver software (version 4.0, NanoString Technology).
 
Submission date Mar 15, 2023
Last update date Feb 27, 2024
Contact name Shiva Najjary
E-mail(s) s.najjary@erasmusmc.nl
Organization name Erasmus University Medical Center
Street address Dr. Molewaterplein 40
City Rotterdam
ZIP/Postal code 3015 GD
Country Netherlands
 
Platform ID GPL32069
Series (1)
GSE227427 Tumor lineage-specific immune response in brain metastatic disease: opportunities for targeted immunotherapy regimen?

Data table header descriptions
ID_REF
VALUE Log2 transformed normalized expression

Data table
ID_REF VALUE
A2M 13.03050395
ACVR1C 4.943372653
ADAM12 8.433220614
ADGRE1 3.335690076
ADM 9.933476617
ADORA2A 6.788862704
AKT1 13.0802036
ALDOA 15.35645511
ALDOC 11.79629224
ANGPT1 5.920652577
ANGPT2 7.982291643
ANGPTL4 12.1856536
ANLN 10.73494257
APC 10.79082156
APH1B 6.954599909
API5 10.58226104
APLNR 9.284335417
APOE 12.46325458
APOL6 8.200760496
AQP9 5.030835494

Total number of rows: 754

Table truncated, full table size 13 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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