{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["RGCC Central Europe GmbH"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16838"],"description":["The behavior of cancer cells strongly relies on the properties of the extracellular microenvironment. The aim was to compare the whole transcriptome of three non-invasive cancer cell lines, HCT-116, A549 and T-47D, embedded in collagen I matrices in a time-dependent manner to standard two-dimensional cell culture. For this purpose, human cancer cell lines (HCT-116, A549 and T-47D) were cultured in their recommended media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37 °C, 5% CO₂ and 95% humidity. Cells were regularly tested negative for mycoplasma and authenticated by STR analysis. For 2D culture, cells were grown to 70–90% confluency and RNA was isolated. For 3D culture, single cells were embedded in 2.5 mg/mL collagen I matrices, which was polymerized at 37 "],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Cells were lysed and matrices were dissolved using 1 mL QIAzol Reagent (Qiagen). 200 µL chloroform (Roth) per mL QIAzol were added, followed by homogenization of the suspension and centrifugation at 4°C, 12000 x g for 15 min. The aqueous phase was merged with 1 volume cold isopropanol (Roth) and RNA was precipitated at - 20°C for 3 days. Precipitated RNA was pelleted at 4°C, washed three times with ice cold 75% ethanol (ITW Reagents). Afterwards, the pellet was dried and dissolved in RNase-free H2O.","Library Construction - For library preparation, 100 ng of total RNA was used per sample whenever available. Samples T47D_d3_n1 (59 ng), A549_d3_n2 (89 ng), T47D_d3_n3Nr26 (81 ng), and A549_d3_n3 (67 ng) were processed using the maximum available input. Libraries were prepared using the KAPA RNA HyperPrep with RiboErase (HMR) kit together with KAPA Globin Depletion Hybridization Oligos (Roche) according to the manufacturer’s instructions.","Sequencing - Libraries were sequenced on an Illumina NovaSeq 6000 system in 101-bp paired-end mode, yielding between 32 and 53 million paired-end reads per sample with Q30 values ≥ 91.33% across samples.","Sample Collection - For 2D culture, cells were seeded in TC-treated culture flasks (Corning) and grown upon reaching 70 to 90% confluency. Cells were washed twice with pre-warmed Dulbecco´s phosphate-buffered saline (DPBS, Capricorn).  For 3D cultured cells, Coll I matrices were transferred to an empty well, washed twice with DPBS.","Growth Protocol - The human cell lines HCT-116 (colon carcinoma, ECACC 91091005), A549 (non-small cell lung cancer, ECACC 86012804), and T-47D (breast carcinoma, DSMZ ACC 739) were cultivated as recommended in McCoy’s 5A, F-12K, and RPMI, respectively. Each medium was supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin. Cell cultivation and all incubation steps were performed at 37°C, 5% CO2 and 95% humidity. Unless otherwise stated, cell culture medium and consumables were used from Life Technologies. Cell lines were regularly tested negative for mycoplasma contamination by PCR (Takara Bio; Transgen Biotech) and authentication was confirmed by STR analysis (Eurofins).   For the 3D cultivation of single cells embedded in Coll I matrices, cells were carefully resus"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Demultiplexing was performed with bcl2fastq v2.20, and adapter trimming was carried out using Skewer v0.2.2. Downstream bioinformatics analyses were conducted using an in-house Nextflow v25.04.7 pipeline. Reads were aligned to the human reference genome GRCh38 (Ensembl release 110) using HISAT2 v2.2.1 with the parameter --rna-strandness FR. Resulting BAM files were sorted and indexed with SAMtools v1.20. Transcript-level quantification was performed using HTSeq-count v2.0.9 with the following parameters: -s yes -t exon -m intersection-strict --nonunique=fraction, using the corresponding GRCh38 (Ensembl release 110) GTF annotation. All further analyses were performed in R (v4.5.2). Raw transcript-level counts were aggregated to gene-level counts by summation. Genes wit"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Adaptation to 3D collagen I microenvironment induces transcriptional reprogramming with impact on non-coding RNA expression of non-invasive cancer cell lines"],"pubmed_authors":["Theresa Wießner-Kroh, Stefanie Hübschmann, Gudrun Marquardt Jennifer Szczesny, Miriam Faxel, Stefan Rubner and Ioannis Papasotiriou","RGCC Central Europe GmbH"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of human cancer cell lines HCT116, T47D and A549 in 3D collagen I microenvironments compared to 2D cell culture","description":"The behavior of cancer cells strongly relies on the properties of the extracellular microenvironment. The aim was to compare the whole transcriptome of three non-invasive cancer cell lines, HCT-116, A549 and T-47D, embedded in collagen I matrices in a time-dependent manner to standard two-dimensional cell culture. For this purpose, human cancer cell lines (HCT-116, A549 and T-47D) were cultured in their recommended media supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37 °C, 5% CO₂ and 95% humidity. Cells were regularly tested negative for mycoplasma and authenticated by STR analysis. For 2D culture, cells were grown to 70–90% confluency and RNA was isolated. For 3D culture, single cells were embedded in 2.5 mg/mL collagen I matrices, which was polymerized at 37 ","dates":{"release":"2026-07-31T00:00:00Z","modification":"2026-07-31T13:12:34.629Z","creation":"2026-03-31T11:31:47.487Z"},"accession":"E-MTAB-16838","cross_references":{"ENA":["ERP191623"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}