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| Status |
Public on Jul 19, 2023 |
| Title |
S2GOTTFR2 |
| Sample type |
SRA |
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| Source name |
S2GOTTFR2
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| Organism |
Mus musculus |
| Characteristics |
cell line: S2GOTTFR2
cell type: old fibroblasts
genotype: no_TF
age: 2.5-year-old
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| Growth protocol |
MEFs isolated from E13.5 embryos and tail tip fibroblasts isolated from old mice we cultured in MEF medium (DMEM high glucose supplemented with 10% FBS, 1x NEAA, 1x Glutamax and 1x P/S). Mouse fibroblasts were transduced with M2rtTA lentivirus and Dox-inducible lentiviruses of transcription factors in MEF medium. 24 hours after transduction, the medium was switched to reprogramming medium. The medium switch day was defined as day 0 of reprogramming and cells were further cultured with media change every other day. For mouse iNSC reprogramming, cells were cultured in mNSC medium (DMEM/F-12 medium supplemented with 1x N2, 1x B27, 1x Glutamax, 10 ng/mL bFGF, 10 ng/mL EGF). 1 μg/mL Dox was added for 18 days. Mouse iNSC colonies were picked at day 20 and further expanded in Matrigel-coated plates in mNSC medium.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) of cells was isolated using Quick-DNA Microprep Kit (Zymo, #D3021) following the user guide and quantified using a Nanodrop One spectrophotometer (Thermo Scientific).
The gDNA was digested using MspI, followed by end repair, and dA-tailing. The adapter ligation was performed by using adapters with all cytosines being methylated. After size selection, DNA fragments were bisulfite treated. After the bisulfite conversion, unmethylated cytosines were converted to U and further to T after PCR amplification, while methylated cytosines remained unchanged. After PCR amplification, the libraries were checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina NovaSeq 6000 platform using 150 bp paired-end sequencing.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
RRBS raw reads were trimmed with Trim Galore (version 0.6.6, -rrbs) followed by alignment to the mouse genome (GRCm38/mm10) using Bismark (version 0.23.1).
Then Bismark coverage files were generated from the deduplicated bam files using Bismark Methylation Extractor (–gzip –bedGraph).
Assembly: mm10
Supplementary files format and content: Bismark Coverage files in a GZIP compressed format (*.bismark.cov.gz).
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| Submission date |
Feb 14, 2023 |
| Last update date |
Jul 19, 2023 |
| Contact name |
Mingxi WENG |
| E-mail(s) |
mingxi@connect.hku.hk
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| Phone |
55326522
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| Organization name |
School of Biomedical Sciences, The University of Hong Kong
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| Street address |
L408A, Laboratory Block, 21 Sassoon Road, Pokfulam, Hong Kong
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| City |
Hong Kong |
| State/province |
Not Applicable |
| ZIP/Postal code |
000000 |
| Country |
Hong Kong |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE195556 |
An engineered Sox17 induces somatic to neural stem cell fate transition independently from pluripotency reprogramming |
| GSE225305 |
An engineered Sox17 induces somatic to neural stem cell fate transition independently from pluripotency reprogramming [RRBS] |
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| Relations |
| BioSample |
SAMN33294021 |
| SRA |
SRX19367681 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7043853_S2GOTTFR2_bismark_bt2_pe.bismark.cov.gz |
23.9 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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