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Sample GSM5687660 Query DataSets for GSM5687660
Status Public on Jan 28, 2022
Title Sox2cre_batch2_sample_10
Sample type RNA
 
Source name sox2cre
Organism Mus musculus
Characteristics batch: batch_2
localization: intracranial
localization details: brain, basal
age (weeks): 34
tumor classification: MYC
Extracted molecule total RNA
Extraction protocol Fresh tumor tissues were isolated and fresh frozen. Afterwards, total RNA was extracted using RNeasy Mini Kit (Quiagen) following the manufacturer’s suggested protocol. Genomic DNA was removed using a gDNA eraser step.
Label Biotin
Label protocol The Affymetrix GeneChip Whole Transcript (WT) PLUS Reagent Kit Protocol was used for the preparation of biotinylated sense-strand single-stranded cDNA from 200ng of total RNA, followed by an enzymatic fragmentation and terminal labeling with biotin.
 
Hybridization protocol 3.8 µg fragmented and labeled sense-strand single-stranded cDNA were hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST arrays for 16 h at 45 °C and 60 rpm in an Affymetrix GeneChip hybridization oven 640.
Scan protocol GeneChips were washed and stained in an Affymetrix GeneChip Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G System. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.1.3 software.
Data processing The .CEL files were read into R (version 3.5.1) using the package oligo. Data normalization was performed per batch, with the RMA algorithm. Samples from the three batches were then combined and batch effect was corrected using the ComBat function from the sva package.
 
Submission date Nov 12, 2021
Last update date Jan 28, 2022
Contact name Kornelius Kerl
E-mail(s) kornelius.kerl@ukmuenster.de
Organization name University Children's Hospital Münster
Department Department of Pediatric Hematology and Oncology
Street address Albert-Schweitzer-Campus 1
City Münster
ZIP/Postal code 48149
Country Germany
 
Platform ID GPL16570
Series (2)
GSE188654 Primordial germ cells identified as one potential cell of origin of MYC rhabdoid tumors
GSE188817 Primordial germ cells identified as one potential cell of origin of MYC rhabdoid tumors

Data table header descriptions
ID_REF
VALUE log2 gene level RMA signal intensity

Data table
ID_REF VALUE
17200001 5.72941594918998
17200003 5.63769664524646
17200005 4.44202844417353
17200007 4.61521908988724
17200009 5.50224038653607
17200011 4.32838854089718
17200013 5.0313323880388
17200015 5.02296494947396
17200017 3.08041521235634
17200019 3.46697542693481
17200021 4.93269214860713
17200023 4.94736859302616
17200025 5.15507164747799
17200027 4.66666287415333
17200029 4.03088050296074
17200031 2.90509885210256
17200033 3.24517325369793
17200035 2.38554605236618
17200037 5.11980625605972
17200039 2.85924662732409

Total number of rows: 41345

Table truncated, full table size 1045 Kbytes.




Supplementary file Size Download File type/resource
GSM5687660_P159_01_SoxiniD3_97.CEL.gz 8.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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