|
| Status |
Public on Jan 20, 2023 |
| Title |
hDPSCs, Nutlin-3 |
| Sample type |
SRA |
| |
|
| Source name |
hDPSCs
|
| Organism |
Homo sapiens |
| Characteristics |
agent: Nutlin-3
cell type: hDPSCs
treatment: osteogenic differentiation
time: Day 7
|
| Treatment protocol |
To detect the osteogenic differentiation capability of hDPSCs, they were cultured in 50 μg/mL ascorbic acid (Sigma-Aldrich) and 10 mM β-glycerophosphate (Sigma-Aldrich) in DMEM containing 10% FBS and 1% penicillin-streptomycin.
|
| Growth protocol |
Human dental pulp-derived mesenchymal stromal cells (hDPSCs) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C °C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Prepare cells using LUNA-FL™ Automated Fluorescence Cell Counter (logos biosystems). Resuspend nuclei in transposition reaction mix. Incubate the transposition reaction for 30min at 37°C. Immediately following transposition, purify using a Qiagen MinElute PCR purification Kit.
Amplify transposed DNA fragment using Nextera DNA Flex kit. The purified libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA) and qualified using Bioanalyzer (Agilent technologies).
bulk ATAC-seq
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trim Galore version 0.5.0 was used to remove adapter sequences. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Trimmed reads were aligned to human genome (GRCh38) using Bowtie2 version 2.3.4.1 parameter set --maxins 5000 --very-sensitive --no-discordant --no-mixed --no-unal --mm. Duplicate reads were removed using MarkDuplicates in Picard version 1.118.
Peaks were called in the aligned sequence data using a model-based analysis of ATAC-seq MACS2 version 2.1.1. The following parameters were used: macs2 callpeak --bdg --nolambda --keep-dup all --broad. Among the called peaks, the peaks overlapping with ENCODE blacklisted regions were removed.
ChIPseeker version 1.20.0 a bioconductor package within R version 3.6.0 to facilitate batch annotation of enriched peaks.
Assembly: GRCh38
Supplementary files format and content: bigWig, bedGraph
|
| |
|
| Submission date |
Nov 04, 2022 |
| Last update date |
Jan 20, 2023 |
| Contact name |
SoYoung Park |
| E-mail(s) |
sypark1004@snu.ac.kr
|
| Phone |
01051590787
|
| Organization name |
Seoul National University
|
| Street address |
Seoul, Republic of Korea,, 1 Gwanak-ro, Gwanak-gu, Seoul, 86-509
|
| City |
Seoul |
| State/province |
Korea,Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE217264 |
Targeting class A GPCRs for hard tissue regeneration [ATAC-seq] |
| GSE217437 |
Targeting class A GPCRs for hard tissue regeneration |
|
| Relations |
| BioSample |
SAMN31605495 |
| SRA |
SRX18169396 |
