{"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-17225"],"description":["Intensive usage of cancer cell lines as cellular model system in cancer research caused the generation of variant subtypes during the last decades.  This study focused on the human leukemic THP-1 cell line as a monocyte model. THP-1 cells from two different depositors were differentiated into various immune states. Additionally primary immune cells were differentiated into various immune states in order to be a comparative dataset."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - RNA was isolated from cultivated THP-1 cells, primary monocytes and respective M0, M1 and M2 differentiation states.","Nucleic Acid Extraction - RNA was isolated via RNeasy Mini kit (Qiagen) with an additional on-column DNase I (Qiagen) digest according to the manufacturer’s instructions.","Nucleic Acid Extraction - Cells were lysed 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. Libraries were prepared using the Corall RiboCop (HMR/Globin) (Lexogen) according to the manufacturer’s instructions.","Growth Protocol - THP-1 cells were purchased from German Collection of Microorganism and Cell Cultures (DSMZ, Braunschweig Germany) and European Collection of Authenticated Cell Cultures (ECACC, Salisbury United Kingdom). Cells were maintained in RPMI 1640 medium (Thermo Fisher Scientific, 42401042) supplemented with 10 % heat-inactivated fetal bovine serum (Thermo Fisher Scientific, A5256801), 1 % (v/v) penicillin/streptomycin (Thermo Fisher Scientific,15140122), 1 % (v/v) L-glutamine (Thermo Fisher Scientific, 25030024), 1 % (v/v) sodium pyruvate (Thermo Fisher Scientific, 11360039) and 0.01 % (v/v) ß-mercaptoethanol (Thermo Fisher Scientific, 31350010). Cells were cultured at 37 °C and 5 % CO2 in a humid environment. Mycoplasma tests were regularly performed during cultivation using Tra","Growth Protocol - RNA was isolated from primary monocytes, isolated from fresh Leukopaks from healthy adult donors purchased from Grifols Bio Supplies Inc. First, peripheral blood mononuclear cells (PBMCs) were isolated using the StraightFrom Leukopak PBMC Isolation Kit (Miltenyi, 130-123-456) in combination with the MultiMACS-Cell24-Separator-Plus. Monocytes were isolated with a positive selection using CD14 MicroBeads (Miltenyi, 130-050-201) and were differentiated using a standard protocol from Promocell. Here, cells were seeded at 120,000 cells/cm² in an appropriate cell culture flask with Monocyte Attachment media (Promocell, C-28051). Cells were incubated at 37 °C and 5 % CO2 in a humid environment for 1.5 h. For further differentiation, media was changed to M1 macrophage generation ","Sequencing - Libraries were sequenced on an Illumina NovaSeq X Plus system in paired-end mode, yielding between 28 and 50 million paired-end reads per sample with Q30 values ≥ 95% across samples."],"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 X"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Comparison of THP-1 subtypes reveals differences on transcriptomic and protein expression level throughout their immunological differentiation"],"pubmed_authors":["RGCC Central Europe GmbH","Sabine Klatt, Gudrun Marquardt, Miriam Faxel, Stefan Rubner and Ioannis Papasotiriou"],"additional_accession":[]},"is_claimable":false,"name":"RNAseq of differentiation states of primary monocytes and THP-1 cells (from two depositors)","description":"Intensive usage of cancer cell lines as cellular model system in cancer research caused the generation of variant subtypes during the last decades.  This study focused on the human leukemic THP-1 cell line as a monocyte model. THP-1 cells from two different depositors were differentiated into various immune states. Additionally primary immune cells were differentiated into various immune states in order to be a comparative dataset.","dates":{"release":"2026-07-24T00:00:00Z","modification":"2026-07-24T07:03:00.241Z","creation":"2026-06-25T14:10:04.819Z"},"accession":"E-MTAB-17225","cross_references":{"ENA":["ERP195727"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}