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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 01, 2020 |
| Title |
GSK3_KO_ESC_DMSO_SL_rep2 |
| Sample type |
SRA |
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| Source name |
mouse embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cells
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| Treatment protocol |
ESCs cultured in SL or 2iL were treated with 100 nM JQ1 or DMSO, Cells were harvested 60 hours post treatment.
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| Growth protocol |
ESCs in SL medium were cultured in DMEM/high glucose containing 15% FBS, GlutaMax, nonessential amino acids, sodium pyruvate, β-mercaptoethanol, and 1,000 U/ml LIF on mitomycin-C treated mouse embryonic fibroblasts (MEFs), and they were split onto 0.2% gelatin pre-coated plates prior to the experiment. ESCs in 2iL medium were cultured in a 1:1 mix of DMEM/F12 and Neurobasal medium, with N2 and B27 supplements, GlutaMax, nonessential amino acids, sodium pyruvate, β-mercaptoethanol, 1,000 U/ml LIF, 3 μM, and 1 μM PD0325901 on 0.2% gelatin pre-coated plates
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were isolated using the TRIzol™ Reagent (ThermoFisher Scientific, 15596026).
A total amount of 1 μg RNA per sample was used as input material for the library preparation. The sequencing libraries were generated using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina® following the manufacturer's recommendations.
Libraries were sequenced on a NovaSeq 6000 sequencer according to the manufacturer’s instructions with 6 Gbase PE150 reads.
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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 |
Illumina bcl2fastq2.17 software was used for base-calling.
For RNA-seq gene expression quantification, data were first aligned with STAR (v2.5.2) and quantified according to GENCODE vM15 in a RSEM-based pipeline.
Differentially expressed genes were determined by DESeq2 (v 1.18.1) and were defined as absolute fold change > 2, q value < 0.1. Functional annotation was further performed by ClusterProfiler (v3.6.0).
Genome_build: mm10
Supplementary_files_format_and_content: Count tables generated by RSEM are attached as supplementary files.
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| Submission date |
Nov 13, 2019 |
| Last update date |
Jul 02, 2020 |
| Contact name |
Yiwei Lai |
| E-mail(s) |
[email protected]
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| Organization name |
Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences
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| Department |
South China Institute for Stem Cell Biology and Regenerative Medicine Key Laboratory of Regenerative Biology, CAS
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| Lab |
Miguel
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| Street address |
190 Kai Yuan Avenue, Science Park
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510530 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE123691 |
β-catenin safeguards the ground state of pluripotency by strengthening the robustness of the transcriptional apparatus [RNA-seq] |
| GSE123692 |
β-catenin safeguards the ground state of pluripotency by strengthening the robustness of the transcriptional apparatus |
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| Relations |
| BioSample |
SAMN13279909 |
| SRA |
SRX7135433 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4159465_GSK3_KO_ESC_DMSO_SL_rep2.count_table.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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