|
| Status |
Public on Jun 12, 2017 |
| Title |
Stk40 knockout E14.5 mouse fetal liver cells, biological rep2 |
| 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 |
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