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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 23, 2019 |
| Title |
SOX17day9rep2 |
| Sample type |
SRA |
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| Source name |
OG2MEF
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| Organism |
Mus musculus |
| Characteristics |
cell line: OG2MEF
cell type: reprogramming cells
day of reprogramming: Day9
genotype/variation: SOX17 WT
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| Growth protocol |
OG2MEF cells were transduced twice by pMX-Sox2, Klf4 along with OCT4, SOX17 or SOX17-V118M or GFP retroviruses produced using PlatE cells in DMEM + 10% FBS media supplemented with 1x NEAA and Glutamax. After second viral transduction, the medium was switched to mouse ESC media ((DMEM containing 4.5 g/L D-glucose, 15% FBS, 1% NEAA, 1% GlutaMAX, 1% Sodium Pyruvate, 0.5% penicillin/streptomycin, 1000 U/mL Leukemia inhibiting factor (LIF, prepared by the core facility of GIBH), 0.055 mM β-ME (beta mercaptoethanol) and 50 μg/mL Vitamin C).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TRIzol
TruSeq Nano RNA sample prep kit (Illumina) was used for library constructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
fastqc
The mouse transcriptome index was generated by RSEM with bowtie 2 and then the raw reads were aligned to the transcriptome index
Per-gene read counts were calculated using RSEM GC normalized using EDAseq
Genes with mean read counts over all traits and replicates of less than 20 were discarded leading to a final set of 15,130 genes
DESeq2 for differential gene expression
Genome_build: mm10
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| Submission date |
Jul 26, 2019 |
| Last update date |
Oct 23, 2019 |
| Contact name |
YOGESH SRIVASTAVA |
| E-mail(s) |
[email protected]
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| Phone |
15622320973
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| Organization name |
Guangzhou Institutes of Biomedicine and Health
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| Department |
Biochemistry and Molecular Biology
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| Lab |
Genome Regulation
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| Street address |
190 Kaiyuan Avenue
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510530 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE134930 |
Cancer-associated missense mutations enhance the pluripotency reprogramming activity of OCT4 and SOX17 |
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| Relations |
| BioSample |
SAMN12370142 |
| SRA |
SRX6597223 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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