|
| Status |
Public on Jan 28, 2022 |
| Title |
Sox2cre_batch3_sample_39 |
| Sample type |
RNA |
| |
|
| Source name |
sox2cre
|
| Organism |
Mus musculus |
| Characteristics |
batch: batch_3
localization: intracranial
localization details: brain, basal
age (weeks): 29
tumor classification: SHH
|
| 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 |
|
