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Sample GSM5260622 Query DataSets for GSM5260622
Status Public on Apr 30, 2023
Title BRSST-Ezh2 rpl4
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 Heckl4004
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 8.751758635
TC0100000018.mm.2 5.949561368
TC0100000021.mm.2 9.2142101
TC0100000022.mm.2 4.351619351
TC0100000023.mm.2 3.968976277
TC0100000027.mm.2 8.883372472
TC0100000038.mm.2 8.761124454
TC0100000039.mm.2 6.555336312
TC0100000041.mm.2 5.887176443
TC0100000044.mm.2 10.36674496
TC0100000045.mm.2 6.664780761
TC0100000048.mm.2 7.425244888
TC0100000055.mm.2 6.106300359
TC0100000056.mm.2 5.463757356
TC0100000064.mm.2 5.264693173
TC0100000071.mm.2 4.451697332
TC0100000082.mm.2 4.744006916
TC0100000092.mm.2 9.853527729
TC0100000097.mm.2 7.840933538
TC0100000101.mm.2 8.142241685

Total number of rows: 22203

Table truncated, full table size 649 Kbytes.




Supplementary file Size Download File type/resource
GSM5260622_Heckl4004_Clariom_S_Mouse_.CEL.gz 1.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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