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Sample GSM2494312 Query DataSets for GSM2494312
Status Public on Jun 12, 2017
Title Stk40 knockout E14.5 mouse fetal liver cells, biological rep1
Sample type RNA
 
Source name E14.5 mouse fetal liver cell
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: fetal liver
genotype: Stk40 KO
age: E14.5
Treatment protocol Stk40 heterozygous (Het) mice were maintained in a C57BL/6J background under specific pathogen-free conditions. Heterozygotes were mated for timed pregenancy. Fetal livers were collected from E14.5 embryos.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the TRIzol reagent (Invitrogen) in accordance with the manufacturer’s instructions. Quality and integrity of the total RNA isolated was assessed on the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).
Label biotin
Label protocol Total RNA (1 μg) is first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction is carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.
 
Hybridization protocol The biotinylated cRNA targets are cleaned up, fragmented, and hybridized to the Affymetrix mouse 430 2.0 array.
Scan protocol Hybridized chips were scanned using Affymetrix genechip scanner 3000
Description Gene expression data from fetal liver cells of E14.5 KO embryos.
Data processing MAS 5.0 algorithm was used to calculate the transcript concentration from mouse genome 430 2.0 chip. For data processing, first, all the probesets with negative values in all samples were removed; second, probesets with values inconsistent in each group (wild type or knockout) were also removed; third, Values less than 0.1 were set to 0.1 for further analysis. Differentially expressed genes were defined by a fold change of two.
 
Submission date Feb 17, 2017
Last update date Jun 12, 2017
Contact name Ying Jin
E-mail(s) yjin@sibs.ac.cn
Organization name Shanghai JiaoTong University
Department School of Medicine
Lab Laboratory of Molecular Developmental Biology
Street address 280 South Chongqing Road, Bldg 5, Rm 206
City Shanghai
ZIP/Postal code 210025
Country China
 
Platform ID GPL1261
Series (1)
GSE95017 Deletion of Stk40 impairs definitive erythropoiesis in the mouse fetal liver

Data table header descriptions
ID_REF
VALUE normalized signal

Data table
ID_REF VALUE
AFFX-TrpnX-M_at -14.35
AFFX-TrpnX-5_at 3.6
AFFX-TrpnX-3_at 37
AFFX-TransRecMur/X57349_M_at 79.4
AFFX-TransRecMur/X57349_5_at 91.95
AFFX-TransRecMur/X57349_3_at 289.25
AFFX-ThrX-M_at 63.35
AFFX-ThrX-5_at 36.5
AFFX-ThrX-3_at 140.7
AFFX-r2-P1-cre-5_at 7243.90909
AFFX-r2-P1-cre-3_at 8284.63636
AFFX-r2-Ec-bioD-5_at 2654
AFFX-r2-Ec-bioD-3_at 3096.63636
AFFX-r2-Ec-bioC-5_at 628.27273
AFFX-r2-Ec-bioC-3_at 778.45455
AFFX-r2-Ec-bioB-M_at 322.63636
AFFX-r2-Ec-bioB-5_at 198.45455
AFFX-r2-Ec-bioB-3_at 309.90909
AFFX-r2-Bs-thr-M_s_at 120.09091
AFFX-r2-Bs-thr-5_s_at 84

Total number of rows: 45101

Table truncated, full table size 895 Kbytes.




Supplementary file Size Download File type/resource
GSM2494312_SBCG2009051_FL_KO14.5A.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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