characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-06-05T20:20:10Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-06-05T20:20:10Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA110472396
characteristics.characteristic: External Id
characteristics.text: Maastricht University
characteristics.characteristic: INSDC center name
characteristics.text: 2023-06-05T20:20:10Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-06-05T20:20:10Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS12570416
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-12078:Nthyori_DMSO_3_poly(A)
characteristics.characteristic: Submitter Id
characteristics.text: 35
characteristics.unit: year
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: Nthy-ori 3-1
characteristics.characteristic: cell_line
characteristics.text: epithelial cell
characteristics.characteristic: cell_type
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: The human epithelial follicular cell line Nthy-ori 3-1 was seeded at a density of 40,000 cells/cm^2 in a 6-well plate exposed for 24 hours in triplicate to 1 μM or 10 μM benzo[a]pyrene (BAP) (B-1760, Sigma) dissolved in DMSO (1029521000, Merck) (final concentration of DMSO 0.5%). Six 0.5% DMSO solvent controls were also included. The medium used for cell culture was RPMI 1640 Medium, GlutaMAX™ Supplement (61870036, Gibco) supplemented with 10% FBS and 100 U mL-1 Penicillin-Streptomycin (15140122, Gibco). Enriched thyroid follicles were exposed to DMSO 0.5% for 24 hours (5 biological replicates). The medium used was DMEM (31966021, Gibco) supplemented with 15% FBS, vitamin C (50 μg mL-1) (A4544, Sigma), nonessential amino acids (0.1 mM) (11140035, Gibco), sodium pyruvate (1 mM) (11360039, Gibco), penicillin and streptomycin (50 U mL-1) (15140122, Gibco), 2-mercaptoethanol (0.1 mM) (31350010, Gibco), 8-Br-cAMP (10 µM) and TGF-βRI inhibitor SB431542 (10 µM) (1614, Tocris). At the end of the exposure time, cells were collected in 1.5 mL Eppendorf tubes and washed once with PBS. They were then lysed in QIAzol Lysis Reagent (79306, Qiagen). Murine thyroid organoids were derived from recombinant embryonic stem cell line (A2LoxNkx2-1-Pax8). Total RNA was extracted using the Direct-zol RNA miniprep (R2051, Zymo Research) for Nthy-ori 3-1 cells. Total RNA was extracted using the miRNAeasy Micro Kit (217084, Qiagen) for the thyroid follicles. All prepared libraries were quantified on a Qubit 2.0 Fluorometer (ThermoFisher) and quality control checked on the 2200 TapeStation System (Agilent) or BioAnalyzer 2100 expert (Agilent). 50 ng of total RNA isolated from Nthy-ori 3-1 samples were used as input for the NEXTFLEX® Combo-Seq™ mRNA/miRNA Kit (NOVA-5139-53, PerkinElmer). All RIN (RNA Integrity Number) values were 8 or higher. To deplete tRNA fragments and Y RNA fragments during the library preparation, the NEXTFLEX® tRNA/YRNA Blocker was used following the manufacturer’s instruction. We performed 13 PCR cycles during library preparation. 20 ng of total RNA isolated from thyroid organoids samples were used as input for the NEXTFLEX® Combo-Seq™ mRNA/miRNA Kit (NOVA-5139-53, PerkinElmer). All RIN (RNA Integrity Number) values were 8 or higher. To deplete tRNA fragments and Y RNA fragments during the library preparation, the NEXTFLEX® tRNA/YRNA Blocker was used following the manufacturer’s instruction. We performed 16 PCR cycles during library preparation. Poly(A) libraries were prepared on an automated system (Zephyr G3® NGS) with the NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 (NOVA-5198-02, PerkinElmer) using 1 μg of total RNA extracted from Nthy-ori 3-1 samples and performing 10 PCR cycles. NEXTFLEX® Poly(A) Beads 2.0 (NOVA-512992, PerkinElmer) and NEXTFLEX® Unique Dual Index Barcodes (NOVA-512923, PerkinElmer) were used during the library preparation. Small RNA libraries were prepared manually with the NEXTFLEX® Small RNA-Seq Kit v3 (NOVA-5132, PerkinElmer) from 100 ng of total input Nthy-ori 3-1 RNA and performing 18 PCR cycles.
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: normal
characteristics.characteristic: disease
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.characteristic: growth condition
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: thyroid gland
characteristics.characteristic: organism part
characteristics.characteristic: progenitor cell type
characteristics.text: 3
characteristics.characteristic: replicate
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.characteristic: sex
characteristics.text: Nthyori_DMSO_3_poly(A)
characteristics.characteristic: title