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Sample GSM5260619 Query DataSets for GSM5260619
Status Public on Apr 30, 2023
Title BRSST-Ezh2 rpl1
Sample type RNA
 
Source name Bone marrow
Organism Mus musculus
Characteristics tissue: Bone marrow
strain: C57Bl/6J
treatment: BRSST+sgEzh2
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 Heckl4001
Gene expression data from BM transplanted mice transduced with BRSST sgRNA +sgEzh2
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

Data table header descriptions
ID_REF
VALUE Normalized value

Data table
ID_REF VALUE
TC0100000014.mm.2 8.464196089
TC0100000018.mm.2 5.695469078
TC0100000021.mm.2 8.576804191
TC0100000022.mm.2 4.360411739
TC0100000023.mm.2 4.00703695
TC0100000027.mm.2 8.313506103
TC0100000038.mm.2 9.118878063
TC0100000039.mm.2 6.47051971
TC0100000041.mm.2 6.354959809
TC0100000044.mm.2 10.24339025
TC0100000045.mm.2 7.219741062
TC0100000048.mm.2 7.091799948
TC0100000055.mm.2 6.631143996
TC0100000056.mm.2 5.448126268
TC0100000064.mm.2 5.618576873
TC0100000071.mm.2 4.702909691
TC0100000082.mm.2 5.323697717
TC0100000092.mm.2 9.24718267
TC0100000097.mm.2 7.491398306
TC0100000101.mm.2 7.80620884

Total number of rows: 22203

Table truncated, full table size 649 Kbytes.




Supplementary file Size Download File type/resource
GSM5260619_Heckl4001_Clariom_S_Mouse_.CEL.gz 1.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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