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Sample GSM5261213 Query DataSets for GSM5261213
Status Public on Apr 30, 2023
Title LT-HSC_a_FL
Sample type RNA
 
Source name Fetal liver
Organism Mus musculus
Characteristics cell type: Fetal liver LT-HSC cells
developmental stage: E13.5
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 Heckl3030
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)
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 7.943012204
TC0100000018.mm.2 6.155040198
TC0100000021.mm.2 9.230354898
TC0100000022.mm.2 4.941144877
TC0100000023.mm.2 4.434113622
TC0100000027.mm.2 8.493572865
TC0100000038.mm.2 9.757227546
TC0100000039.mm.2 7.330046493
TC0100000041.mm.2 6.610336858
TC0100000044.mm.2 8.168501921
TC0100000045.mm.2 5.614121098
TC0100000048.mm.2 7.581289518
TC0100000055.mm.2 7.000580979
TC0100000056.mm.2 6.3645507
TC0100000064.mm.2 5.834786065
TC0100000071.mm.2 5.096672239
TC0100000082.mm.2 5.49132858
TC0100000092.mm.2 8.978784889
TC0100000097.mm.2 8.257116983
TC0100000101.mm.2 8.989873323

Total number of rows: 22203

Table truncated, full table size 648 Kbytes.




Supplementary file Size Download File type/resource
GSM5261213_Heckl3030B_Clariom_S_Mouse_.CEL.gz 1.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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