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| Status |
Public on Aug 31, 2023 |
| Title |
HS360-Day0-rep5 [1-d0-1] |
| Sample type |
genomic |
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| Source name |
HS360, day 0, hESCs undifferentiated
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| Organism |
Homo sapiens |
| Characteristics |
gender: male
cell type: hESCs
treatment: Day 0 control
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| Treatment protocol |
In brief, at Day 0 HS360 hESCs grown in E8 were collected with Accutase and seeded in Geltrex precoated 12 well dishes. Single-cell suspensions were transferred to E8 medium containing 10 µM Rock inhibitor and at Day 1, the culture medium was switched to neural induction medium (NIM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2). During days 2 to 6, media were changed daily and the LSX combo (LDN-193189, SB431542, XAV939) was added fresh to NIM. Cells were collected at Day 7 for passaging into the self patterning phase, counted and seeded on 12 well plates sequentially precoated with polyornithine (PO), fibronectin (F) and Geltrex. At Day 7 the Stage II neural self-patterning (NSPM) medium (Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 1% B27) was supplemented with 10 µM Rock inhibitor. Culture medium was changed daily till day 13. At Day 13, cells were collected for passaging into the maturation phase, counted and seeded on precoated PO+F+Geltrex 12 well dishes and Stage III Neural maturation medium (NMM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 0.5% B27, 10 ng/ml FGF2, 10 ng/ml EGF) was changed daily till Day 20, where cells were collected. For cells that were exposed to either 100 or 200 μM paracetamol, fresh media with paracetamol was added every day from Day 1 until collection day (Day 7 or Day 20)
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| Growth protocol |
Human embryonic stem cells HS360 (Karolinska Institutet, Sweden, RRID:CVCL_C202) were maintained in Essential 8™ Medium, in feeder-free conditions on Geltrex™ Matrix solution pre-coated culture plates.Culture media were replaced daily and cells were routinely passaged at 75-85% confluency using 0.5 mM EDTA in ratios between 1:3 to 1:6.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cultured cells using Norgen RNA/DNA purification kit according to the manufacturer's instructions
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| Label |
Cy3, Cy5
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| Label protocol |
Standard Illumina Protocol
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| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip v-1-0_B3 using standard Illumina protocol
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| Scan protocol |
Arrays were imaged using Illumina iScan System using standard recommended Illumina scanner settings
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| Description |
Day 0", "male", "hESCs", "control
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| Data processing |
R software, Minfi package v 1.36.0m Background correction was performed using NOOB method and β values were normalized using functional normalization. Probes with detection p values >0.01 (n = 12538) and cross-reactive probes (n = 42844) were removed, resulting in a final data set consisting of 810477
Normalized Average Beta (functional normalization)
Unmethylated and methylated signal intensities
"rgSet_paracetamol.Rdata". Minfi object with all data except SNP probes, removed due to data sensitivity.
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| Submission date |
Dec 03, 2022 |
| Last update date |
Aug 31, 2023 |
| Contact name |
Ragnhild Eskeland |
| E-mail(s) |
ragnhild.eskeland@medisin.uio.no
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| Phone |
(+47) 22 85 14 57
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| Organization name |
University of Oslo
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| Department |
Institute of Basic Medical Sciences
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| Lab |
Chromatin Biology
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| Street address |
Sognsvannsveien 9
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| City |
Oslo |
| ZIP/Postal code |
0371 |
| Country |
Norway |
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| Platform ID |
GPL21145 |
| Series (2) |
| GSE220023 |
Epigenome analysis of hESCs undergoing neuronal differentiation in presence or absence of paracetamol [MethylationEPIC BeadChip] |
| GSE220027 |
Multi-omics analysis of paracetamol exposure identifies dysregulated genes involved in neurotoxicity and neuronal differentiation of human embryonic stem cells |
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| Supplementary data files not provided |
| Processed data are available on Series record |
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