biostudies-arrayexpressDong Hyun SeoHomo sapiensNot applicable in this studybcl2fastq (Illumina)Illumina Experiment ManagerStringTie v2.1.3b (for TPM calculation), R v4.3.2FastQC v0.11.7, Trimmomatic 0.38, HISAT2 v2.1.0, StringTie v2.1.3bhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15253RNA sequencing was performed on K1 papillary thyroid cancer (PTC) cells to investigate the biological function of TSC22D1 variant 2 overexpression. Cells were transfected with the TSC22D1 (NM_006022) Human Tagged ORF Clone, with three empty vector-transfected cells ((TSC22D1_0) serving as negative controls. Experimental groups included four replicates each of cells with low (TSC22D1_200) and high levels (TSC22D1_500) of TSC22D1 variant 2 overexpression. RNA integrity was confirmed for all samples using the Agilent TapeStation system, with RNA integrity numbers (RIN) exceeding 7.0.biostudies-arrayexpressSample Treatment - Transfection was performed using X-tremeGENE™ HP DNA Transfection Reagent (Roche, Cat# XTGHP-RO) according to the manufacturer’s protocol. The TSC22D1 (NM_006022) Human Tagged ORF Clone (Origene, Cat# RC223210) was transfected at two concentrations: 200 ng (low) and 500 ng (high). The pCMV6-Entry Mammalian Expression Vector (Origene, Cat# PS100001) was used as an empty vector control.Sample Collection - The K1 papillary thyroid cancer (PTC) cell line was seeded in a 10-cm dish and harvested 24 hours post-transfection. Cells were maintained at less than 80% confluency throughout the experiment.Library Construction - RNA libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit. mRNA was isolated with poly-T magnetic beads, fragmented, and converted to cDNA, followed by end repair, adapter ligation, and PCR enrichment.Sequencing - Indexed libraries were sequenced on an Illumina NovaSeq 6000 platform (2 × 100 bp paired-end). Raw reads were quality-checked with FastQC and trimmed using Trimmomatic.Nucleic Acid Extraction - Total RNA was extracted using TRIzol reagent. For tissue samples, frozen tissue was finely minced, ground under liquid nitrogen, and immediately homogenized in 1 mL TRIzol. Cell samples were lysed by pipetting in TRIzol, followed by 5 minutes of incubation at room temperature. Phase separation was performed by adding 250 µL chloroform (or 100 µL 1-bromo-3-chloropropane), vortexing, incubating for 10 minutes, and centrifuging at 12,000 rpm for 10 minutes at 4°C. The aqueous phase was transferred, mixed with 500 µL isopropanol, incubated, and centrifuged at 14,000 rpm for 20 minutes at 4°C to pellet RNA. The pellet was washed twice with 75% ethanol, air-dried, and resuspended in 15–30 µL DEPC-treated water. RNA purity was confirmed by spectrophotometry, with acceptable A260/A280 ratios near 1.8.Growth Protocol - Cells were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS) and Normocin® (InvivoGen, Cat# ant-nr-1). Transfection was performed 24 hours after seeding. Mycoplasma contamination was routinely tested using the Myco-Read™ Mycoplasma Detection Kit (PCR) (Biomax, Cat# SMD0172).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Cleaned reads were aligned to GRCh37 (hg19) using HISAT2 v2.1.0. Transcript assembly was performed using StringTie v2.1.3b. Gene expression was quantified in FPKM and raw counts.Data Transformation - Gene expression data were normalized using TPM (Transcripts Per Million) to account for sequencing depth and gene length. For downstream analysis, log2 transformation of TPM values (log2[TPM + 1]) was applied to stabilize variance and approximate normal distribution.UnknownTranscriptomicsGenomicsProteomicsNot applicable in this studyLiquid nitrogen freezer, surgical instrumentsIllumina NovaSeq 6000Benchtop centrifuge, vortex, NanoDrop or plate reader (for RiboGreen assay), TapeStation (Agilent)Thermal cycler (Bio-Rad C1000), Agilent 2100 Bioanalyzer, Qubit 4 FluorometerLinux server, HPC clusterRNA-seq of coding RNAHomo sapiensSunmi ParkJandee LeeDong Hyun SeoYoung Suk JofalseRNA-seq of K1 papillary thyroid cancer (PTC) cell with different TSC22D1 overexpression statusRNA sequencing was performed on K1 papillary thyroid cancer (PTC) cells to investigate the biological function of TSC22D1 variant 2 overexpression. Cells were transfected with the TSC22D1 (NM_006022) Human Tagged ORF Clone, with three empty vector-transfected cells ((TSC22D1_0) serving as negative controls. Experimental groups included four replicates each of cells with low (TSC22D1_200) and high levels (TSC22D1_500) of TSC22D1 variant 2 overexpression. RNA integrity was confirmed for all samples using the Agilent TapeStation system, with RNA integrity numbers (RIN) exceeding 7.0.2025-07-24T00:00:00Z2025-07-24T04:48:45.014Z2025-06-25T13:33:01.074ZE-MTAB-15253ERP174025EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969