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Sample GSM5261220 Query DataSets for GSM5261220
Status Public on Apr 30, 2023
Title ST_a_BM
Sample type RNA
 
Source name Bone marrow
Organism Mus musculus
Characteristics cell type: Bone marrow ST-HSC cells
developmental stage: Adult
strain: C57Bl/6J
Growth protocol Fetal liver cells were isolated from e13.5 embryos. Bone marrow was isolated from mice 3 to 12 months old.
Extracted molecule total RNA
Extraction protocol RNeasy Micro Kit (Qiagen No. 74004).
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 Heckl3037
Gene expression data from BM transplanted mice transduced with +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)
GSE173158 Expression data of freshly isolated and sorted HSC populations from murine fetal liver or adult bone marrow [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 8.047556041
TC0100000018.mm.2 6.21390968
TC0100000021.mm.2 8.721093533
TC0100000022.mm.2 5.058833274
TC0100000023.mm.2 4.540086051
TC0100000027.mm.2 9.049568002
TC0100000038.mm.2 9.642887879
TC0100000039.mm.2 7.165852942
TC0100000041.mm.2 7.005508124
TC0100000044.mm.2 9.497393786
TC0100000045.mm.2 5.712516188
TC0100000048.mm.2 7.450549974
TC0100000055.mm.2 7.038355775
TC0100000056.mm.2 5.842602956
TC0100000064.mm.2 5.900668158
TC0100000071.mm.2 5.117454462
TC0100000082.mm.2 5.740332802
TC0100000092.mm.2 8.699751888
TC0100000097.mm.2 7.871298763
TC0100000101.mm.2 8.767763765

Total number of rows: 22203

Table truncated, full table size 649 Kbytes.




Supplementary file Size Download File type/resource
GSM5261220_Heckl3037_Clariom_S_Mouse_.CEL.gz 1.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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