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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 04, 2020 |
| Title |
Std-2 |
| Sample type |
SRA |
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| Source name |
C57BL6/J WT mESC_Std
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL6/J
cell type: Embryonic stem cell
culture condition: standard (Std) medium
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| Growth protocol |
WT mESCs derived from inbred mouse (Bruce 4 C57BL/6J, male, EMD Millipore, Billerica, MA) were cultured on either LN511 coated dish under either Std (StemSure D-MEM [Wako Pure Chemicals, Osaka, Japan], 15% of fetal bovine serum, 0.1 mM β-mercaptoethanol, 1x MEM nonessential amino acids [Wako Pure Chemicals], a 2 mM L-alanyl-L-glutamine solution [Wako Pure Chemicals], 1000 U/mL LIF [Wako Pure Chemicals], 20 mg/ mL gentamicin [Wako Pure Chemicals]), 2i (Std + 1 µM PD0325901 [CS-0062, Chem Scene], 3 µM CHIR99021 [034-23103, Wako Pure Chemicals]) or PD-MK (Std medium + 1 µM PD0325901 [CS-0062, Chem Scene], 4 µM MK-2206 2HCl [S1078, Selleck Chemicals, Houston TX]) medium.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from either Std/LN511, 2i/LN511 or PDMK/LN511 conditioned cells at 70% confluency in a well of a 6-well plate using RNeasy Plus Mini (Qiagen).
Bulk RNA-Seq was performed by CEL-Seq2 method (Hashimshony et al., 2016) with total RNA amounts were used the range of 30-60 ng.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
Std-2_cs2_sample_0005
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| Data processing |
All reads were aligned to the reference genome (GRCm38) using HISAT (v.2.1.0)
The software HTSeq (Anders et al., 2015) was used in calculating gene-wise unique molecular identifier (UMI) counts which were converted into transcript counts after collision probability correction (Grün et al., 2014)
Genome_build: mm10
Supplementary_files_format_and_content: umi_counts.txt includes read count data for each sample.
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| Submission date |
Jun 12, 2019 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Itoshi NIKAIDO |
| E-mail(s) |
[email protected]
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| Organization name |
RIKEN
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| Department |
Center for Biosystems Dynamics Research
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| Lab |
Laboratory for Bioinformatics Research
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| Street address |
2-1 Hirosawa
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| City |
Wako |
| State/province |
Saitama |
| ZIP/Postal code |
351-0198 |
| Country |
Japan |
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| Platform ID |
GPL18480 |
| Series (2) |
| GSE132592 |
RNA-seq analysis of mouse embryonic stem cells cultured in medium containing MEK and Akt inhibitors |
| GSE132593 |
Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells |
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| Relations |
| BioSample |
SAMN12037639 |
| SRA |
SRX6047939 |
| 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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