{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Yihang Shen"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15381"],"description":["Our previous study (Environ Pollut. 2023;323:121307) has indicated that Glucose-dependent insulinotropic polypeptide receptor (GIPR) is down-regulated in periodontal ligament stem cells (PDLSCs) by cigarette and E-cig. In the current study, ChIP-seq was conducted to study the genome-wide occupancies of phosphorylated CREB (p-CREB), p-STAT, p-ERK and TCF4 in PDLSCs treated with GIPR agonist (GIPRA) (Pro3) GIP (0.5 nM, 24 h, Cat. No. HY-P3584, MCE, China) and ERK1/2 inhibitor SCH772984 (0.5 μM, 24 h, HY-50846, MCE) compared to normal PDLSCs."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Sequencing was performed on a NovaSeq 6000 platform with 150 bp paired-end reads","Nucleic Acid Extraction - 5 × 10^7 PDLSCs were cross-linked with 1% formaldehyde at room temperature for 10 min, and the reaction was quenched with 0.125 M glycine. Chromatin was isolated and sheared to an average size of 200-500 bp under the condition (Power, high intensity; Cycle, 30 s On/30 s Off for 30 cycles; Temperature, 4 °C) using a Bioruptor Pico Sonication Device (Cat. No. B01080010, Hologic Diagenode, Belgium). Immunoprecipitation was carried out overnight at 4 °C using 1 μg IP grade antibodies against p-CREB1 (Cat. No. 81871-1-RR, Proteintech), p-ERK1/2 (Thr202/Tyr204), p-STAT3 (Ser727) (same with Western blot), TCF4 (Cat. No. 22337-1-AP, Proteintech). Next day, the immune complex were added 30 μL Pierce Protein A/G magnetic beads (Cat. No. 88802, Thermo Fisher Scientific) slurry after vortex, and washed, eluted, and reverse cross-linked, followed by DNA purification using a VAHTS Universal Plus DNA Library Prep Kit V4 (Cat. No. ND801-01, Vazyme).","Library Construction - ChIP and input DNA were used to prepare sequencing libraries with a NEBNext Ultra II RNA Library Prep Kit for Illumina","Sample Collection - Human periodontal ligament (PDL) tissues were obtained from five healthy orthodontic donors with informed consent. Immediately after extraction, the teeth were rinsed thoroughly with sterile phosphate-buffered saline (PBS) containing 100 U/mL penicillin and 100 μg/mL streptomycin (Cat. No. 15140122, Thermo Fisher Scientific, USA) to remove blood and debris. PDL tissues were carefully scraped from the middle third of the root surface using a sterile scalpel under aseptic conditions to minimize contamination from gingival and pulp tissues. PDLSCs were primarily cultured within α-MEM supplemented with 15% fetal bovine serum (Thermo Fisher Scientific), and 1 × GlutaMAX (Cat. No. 35050061, Thermo Fisher Scientific).The culture medium for inflammatory PDLSCs were additionally supplemented with 10 ng/mL recombinant human FGF-2 (Cat. No. ab9596, Abcam, USA)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw ChIP-seq reads were first subjected to quality control using FastQC, and adapter sequences were trimmed using Cutadapt. High-quality reads were then aligned to the reference genome (e.g., mm10 for mouse or hg38 for human) using Bowtie2 or BWA with default parameters. PCR duplicates were removed using Picard tools or SAMtools to minimize amplification bias. Normalization of ChIP-seq signal was performed using reads per kilobase per million mapped reads (RPKM) or counts per million (CPM) to account for sequencing depth and gene length, as appropriate for peak-based or gene-based analyses. Genome-wide ChIP-seq signal tracks were generated using deepTools with normalization to either 1x genome coverage (RPGC, reads per genomic content) or CPM for visualization in genome browsers. Input control samples were processed in parallel, and fold enrichment or log2 ratio (ChIP/Input) was calculated to identify true enrichment regions. Data transformation methods such as log2 transformation or Z-score scaling were applied to normalized signal intensities for heatmaps, clustering, or correlation analyses. All computational analyses were performed in a standardized pipeline using tools such as deepTools, MACS2, and custom R scripts."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["ChIP-seq"],"species":["Homo sapiens"],"pubmed_authors":["Yihang Shen"],"additional_accession":[]},"is_claimable":false,"name":"Genome-wide occupancies of multiple transcription activators in PDLSCs induced by GIPRA","description":"Our previous study (Environ Pollut. 2023;323:121307) has indicated that Glucose-dependent insulinotropic polypeptide receptor (GIPR) is down-regulated in periodontal ligament stem cells (PDLSCs) by cigarette and E-cig. In the current study, ChIP-seq was conducted to study the genome-wide occupancies of phosphorylated CREB (p-CREB), p-STAT, p-ERK and TCF4 in PDLSCs treated with GIPR agonist (GIPRA) (Pro3) GIP (0.5 nM, 24 h, Cat. No. HY-P3584, MCE, China) and ERK1/2 inhibitor SCH772984 (0.5 μM, 24 h, HY-50846, MCE) compared to normal PDLSCs.","dates":{"release":"2025-08-06T00:00:00Z","modification":"2025-07-21T13:23:34.284Z","creation":"2025-07-21T13:23:34.284Z"},"accession":"E-MTAB-15381","cross_references":{"ENA":["ERP177001"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002692","EFO_0005518","EFO_0003816","EFO_0004184"]}}