|
| Status |
Public on Apr 30, 2023 |
| Title |
BRSST-Luc rpl1 |
| Sample type |
RNA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone marrow
strain: C57Bl/6J
treatment: BRSST+sgLuc
|
| Growth protocol |
1-4x10^4 LSK cells from Cas9 knockin mice were transduced with the given sgRNA combinations and transplanted after 24 h into irradiated (7 Gy) C57Bl/6J mice. Complete BM was harvested after presenting with signs of leukemia or after 6 month.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Zymo RNA Micro Kit (Zymo Research No. R1050).
|
| Label |
biotin
|
| Label protocol |
cRNA was prepared according to the standard Affymetrix protocol from 2 ng total RNA (GeneChIP Pico Reagent Kit , Affymetrix). 10 cycles were used for Pre IVT-PCR.
|
| |
|
| Hybridization protocol |
Cartridge Array Hybridization was performed according to standard Affymetrix protocols (Affymetrix Pico Kit User Guide (P/N 703262) for Array Plate Hybridization).
|
| Scan protocol |
Arrays were scanned using the Affymetrix GCS3000 Scanner (Software GCOS 1.2).
|
| Description |
Heckl4005
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgLuc
|
| Data processing |
The data were analyzed using R 3.5.01 and Bioconductor2. Raw files (.cel) were read in using the function “read.celfiles” from the R package “oligo”. Quality control was performed by inspection of the RLE (Relative Log Expression ) plots and NUSE (normalized unscaled standard error) plots after fitting a Probe Level Model to the raw intensity data by using the function “fitProbeLevelModel” from the package “oligo”. The Raw data was background corrected, quantile-normalized, and log2-transformed using the function “rma” from the ”oligo” package.
|
| |
|
| Submission date |
Apr 22, 2021 |
| Last update date |
Apr 30, 2023 |
| Contact name |
Dorit Borchert |
| E-mail(s) |
Borchert.Dorit@mh-hannover.de
|
| Organization name |
Hannover Medical School
|
| Department |
Pediatric Hematology and Oncology
|
| Street address |
Carl-Neuberg-Str. 1
|
| City |
Hannover |
| ZIP/Postal code |
30625 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23038 |
| Series (2) |
| GSE173135 |
Expression data from murine BM Tx transduced with BRSST gRNA +/- sgEzh2 [array] |
| GSE173497 |
Oncofetal gene reactivation drives EZH2-mutant myeloid leukemia pathogenesis |
|
