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Sample GSM5687670 Query DataSets for GSM5687670
Status Public on Jan 28, 2022
Title rosa26cre_batch2_sample_20
Sample type RNA
 
Source name rosa26cre
Organism Mus musculus
Characteristics batch: batch_2
localization: intracranial
localization details: brain, trigeminal
age (weeks): 23
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 5.66917059190429
17200003 5.53780005559543
17200005 3.37854028403186
17200007 4.31826344212728
17200009 5.78255013985652
17200011 3.60156739361739
17200013 4.49198037650152
17200015 5.78719172950143
17200017 3.01704619334199
17200019 3.46737025583342
17200021 4.60270137784131
17200023 5.56300613542626
17200025 4.74671646441261
17200027 4.98035470025483
17200029 3.54322634006229
17200031 3.2035075404784
17200033 1.99737297127642
17200035 2.23650363685877
17200037 5.39742732931222
17200039 3.15670820815405

Total number of rows: 41345

Table truncated, full table size 1045 Kbytes.




Supplementary file Size Download File type/resource
GSM5687670_P159_11_Rosini_822.CEL.gz 8.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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