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Sample GSM6965315 Query DataSets for GSM6965315
Status Public on Jan 29, 2023
Title Patient 20
Sample type RNA
 
Source name Medulloblastoma
Organism Homo sapiens
Characteristics age years: 26.2
dead status: 1
metastasis: No
gender: M
subgroup: SHH
Extracted molecule total RNA
Extraction protocol RNA isolation and quantification were performed using the RNeasy Mini Kit (Qiagen, Venlo, The Netherlands) and NanoDroPVR 2000 (Thermo Scientific, Waltham).
Label Capture and reporter probes
Label protocol Capture and reporter probes were used for 21 hours to label the mRNA.
 
Hybridization protocol All washing steps and the probe-mRNA complexes fixation into the cartridge were performed automatically in the prep station of the nCounter® PrepStation (NanoString). No post-process actions are needed since all the probes were already marked with specific color sequences.
Scan protocol The cartridges containing immobilized reporter complexes were transferred to nCounter® Digital Analyzer (NanoString) and analyzed using the PanCancer Immune Profiling Panel (NanoString Technologies, Inc., Seattle, WA)
Description Raw data has 88 medulloblastomas samples. Quality analysis revealed that only 80 of the 88 samples had good quality for posterior analysis. These 80 samples are the ones used in this dataset.
25-SHH
Data processing ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library
 
Submission date Jan 24, 2023
Last update date Jan 29, 2023
Contact name Rui Pedro Ferreira Marques
E-mail(s) pg45863@alunos.uminho.pt
Organization name School of Medicine, University of Minho
Department Life and Health Sciences Institute
Lab BiTCancer
Street address Campus de Gualtar
City Braga
ZIP/Postal code 4710-057
Country Portugal
 
Platform ID GPL32232
Series (1)
GSE223606 Nanostring analysis of medulloblastoma samples using the PanCancer Immune Profile Nanostring Panel

Data table header descriptions
ID_REF
VALUE Log2 normalized mRNA counts

Data table
ID_REF VALUE
A2M 9.72144729473017
ABCB1 6.72015049011172
ABL1 7.03583764502494
ADA 4.95876142200629
ADORA2A 4.60120941738821
AICDA 1.92313751227557
AIRE 4.35609691955168
AKT3 9.47926033011675
ALCAM 4.06064103602551
AMBP 3.50810001299673
AMICA1 5.50810001299673
ANP32B 8.37599647698939
ANXA1 7.20112225957534
APOE 8.15195620277145
APP 10.8952557306597
ARG1 2.18617191810937
ARG2 5.12477137344522
ATF1 6.39562528373832
ATF2 8.73306637799701
ATG10 5.06064103602551

Total number of rows: 730

Table truncated, full table size 16 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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