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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 23, 2023 |
| Title |
ES_WT_Rep2 |
| Sample type |
SRA |
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| Source name |
Mouse Embryonic Stem Cells
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| Organism |
Mus musculus |
| Characteristics |
strain background: 129/Ola
genotype: Wild type (WT)
cell type: ES-E14
Stage: ESC
clone: WT
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| Growth protocol |
E14 mouse WT and mutant (Dnmt3a -/- and Dnmt3b -/-) ESCs were cultured in high-glucose DMEM (Euroclone) supplemented with 15% FBS (Millipore Corp., Billerica, MA, USA), 0.1 mmol/l nonessential amino acids (Invitrogen), 1 mmol/l sodium pyruvate (Invitrogen), 0.1 mmol/l β-mercaptoethanol, 1500 U/ml Leukemia Inhibitory Factor (LIF; Millipore), 25 U/ml penicillin, and 25 μg/ml streptomycin. For EpiSC induction, a single-cell suspension was seeded onto Geltrex (A1413202 GIBCO)-coated plates at a density of 10,000 cells cm-2 in N2B27 medium supplemented with 20ng/ml ActivinA (PHC9564 GIBCO) and 12 ng/ml bFGF (PHG0026 GIBCO). The cells were passaged 1:3 as small clumps using Collagenase IV (17104019 GIBCO). EpiSCs were collected for DNA and RNA analyses after 14 days of induction followed by daily medium changes. N2B27 medium is composed by 50% advanced DMEM/F12 (12634028 GIBCO) and 50% Neurobasal medium (21103049 GIBCO), supplemented with 0.5% N2 Supplement (17502048 GIBCO), 1% B27 Supplement (17504044 GIBCO), 0.033% BSA solution (A9647 SIGMA), 50 uM β-mercaptoethanol (M3148 Sigma), 2mM Glutamax (35050038 GIBCO), 100U/ml penicillin and 100 ug/ml streptomycin (DE17-602E LONZA). For Meso-endoderm directed lineage specific differentiation, EpiSCs were plated as small clumps onto Geltrex-coated plates in EpiSCs medium for 24 hours. The day after, medium was replaced with N2NB27 medium consisted of 50% advanced DMEM/F12 (12634028 GIBCO) and 50% Neurobasal medium (21103049 GIBCO), supplemented with 0.5% N2 Supplement (17502048 GIBCO), 1% B27 supplement minus Vitamin A (12587010 GIBCO) and 3 uM iGSK3β (CHIR99021 SIGMA). Cells were fed daily until the end of differentiation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by using TRIzol reagent (Invitrogen), according to manufacturer’s protocol.
Quantity and quality of the starting RNA were checked by Qubit and Bioanalyzer (Agilent). 1 μg of total RNA was subjected to poly(A) selection, and libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75 bp reads).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
NOT PROVIDED; REQUESTED
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: Tab-delimited text file of normalized read counts per gene/samples.
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| Submission date |
Mar 07, 2021 |
| Last update date |
Jan 23, 2023 |
| Contact name |
Andrea Lauria |
| E-mail(s) |
andrea.lauria@unito.it
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| Organization name |
University of Turin
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| Department |
Life Sciences and Systems Biology
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| Lab |
Functional Genomics, Epigenomics - S. Oliviero
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| Street address |
Via Accademia Albertina, 13
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| City |
Turin |
| ZIP/Postal code |
10123 |
| Country |
Italy |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE168412 |
DNMT3B supports meso-endoderm differentiation from mouse embryonic stem cells [RNA-seq] |
| GSE168415 |
DNMT3B supports meso-endoderm differentiation from mouse embryonic stem cells |
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| Relations |
| BioSample |
SAMN18201574 |
| SRA |
SRX10254338 |
| 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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