{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Dong Hyun Seo"],"organism":["Homo sapiens"],"software":["Not applicable in this study","bcl2fastq (Illumina)","Illumina Experiment Manager","StringTie v2.1.3b (for TPM calculation), R v4.3.2","FastQC v0.11.7, Trimmomatic 0.38, HISAT2 v2.1.0, StringTie v2.1.3b"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15253"],"description":["RNA 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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample 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)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence 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."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Not applicable in this study","Liquid nitrogen freezer, surgical instruments","Illumina NovaSeq 6000","Benchtop centrifuge, vortex, NanoDrop or plate reader (for RiboGreen assay), TapeStation (Agilent)","Thermal cycler (Bio-Rad C1000), Agilent 2100 Bioanalyzer, Qubit 4 Fluorometer","Linux server, HPC cluster"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Sunmi Park","Jandee Lee","Dong Hyun Seo","Young Suk Jo"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of K1 papillary thyroid cancer (PTC) cell with different TSC22D1 overexpression status","description":"RNA 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.","dates":{"release":"2025-07-24T00:00:00Z","modification":"2025-07-24T04:48:45.014Z","creation":"2025-06-25T13:33:01.074Z"},"accession":"E-MTAB-15253","cross_references":{"ENA":["ERP174025"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}