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Sample GSM5261224 Query DataSets for GSM5261224
Status Public on Apr 30, 2023
Title MPP_b_BM
Sample type RNA
 
Source name Bone marrow
Organism Mus musculus
Characteristics cell type: Bone marrow MPP 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 Heckl3041
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 8.07247005
TC0100000018.mm.2 5.571512552
TC0100000021.mm.2 8.684734207
TC0100000022.mm.2 4.886540826
TC0100000023.mm.2 4.225122832
TC0100000027.mm.2 8.898649218
TC0100000038.mm.2 9.420701488
TC0100000039.mm.2 6.465240812
TC0100000041.mm.2 6.536269162
TC0100000044.mm.2 9.788035048
TC0100000045.mm.2 5.791684414
TC0100000048.mm.2 8.191747035
TC0100000055.mm.2 6.820075335
TC0100000056.mm.2 5.82401875
TC0100000064.mm.2 5.89156666
TC0100000071.mm.2 4.972872562
TC0100000082.mm.2 5.694316693
TC0100000092.mm.2 9.329783715
TC0100000097.mm.2 7.841755157
TC0100000101.mm.2 9.012775251

Total number of rows: 22203

Table truncated, full table size 648 Kbytes.




Supplementary file Size Download File type/resource
GSM5261224_Heckl3041_Clariom_S_Mouse_.CEL.gz 1.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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