{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Ashwin Ajith"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15204"],"description":["To determine the molecular function of TREM1, we performed bulk RNA sequencing of FACS-purified CD133+EpCAM+ LCSLCs from Huh7 and HepG2, TREM1 KO, and control tumors."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - CD133+EpCAM+ control and TREM1 KO cells were sorted using FACS. Total RNA was isolated using Trizol reagent (5–596-026, Thermo Fisher Scientific) and purified using RNEasy mini kit (74104, Qiagen). The samples were submitted to Integrated Genomics Core Shared Resources at Augusta University (RRID: SCR_026483). Briefly RNA sequencing was carried out using an Illumina NovaSeq 6000, and filtered clean reads were mapped to a reference genome using hierarchical indexing for spliced alignment of transcripts 2 (HISAT2). Visualization of alignment results were verified using Integrative Genomics Viewer.  Differential expression analysis was performed using DESeq with Fold Change ≥1 and FDR < 0.05 set as screening criteria. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was used to identify the significantly affected pathways during TREM1 KO.","Sample Collection - Cells were harvested using trypsin-EDTA to ensure a single-cell suspension. Cells were washed by centrifugation at 1500 rpm for 5 minutes at 4°C and resuspended in ice-cold FACS buffer. Cell viability was confirmed to be above 90%. Fc block was performed by adding 100 µL of Fc block diluted in FACS buffer (1:50 ratio) to each sample, followed by incubation on ice for 20 minutes. Cells were stained with FITC anti-CD133 and APC anti-EpCAM antibodies diluted in FACS buffer at 4°C for 45 minutes in dark. Cells were washed three times by centrifugation at 1500 rpm for 5 minutes and resuspension in ice-cold FACS buffer. Cells were sorted using Invitrogen™ Bigfoot™ Cell Sorter (Thermo Fisher Scientific). Cells were sorted based on CD133 and EpCAM expression. Sorted cells were collected into appropriate collection tubes, and the purity of sorted populations was analyzed, aiming for at least 90% purity. Unstained, single-stained, and isotype controls were included for accurate gating.","Library Construction - Briefly RNA sequencing was carried out using an Illumina NovaSeq 6000, and filtered clean reads were mapped to a reference genome using hierarchical indexing for spliced alignment of transcripts 2 (HISAT2). Visualization of alignment results were verified using Integrative Genomics Viewer.  Differential expression analysis was performed using DESeq with Fold Change ≥1 and FDR < 0.05 set as screening criteria","Nucleic Acid Extraction - Total RNA was isolated using RNeasy Mini kit (74104, Qiagen)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw read count data were analyzed using iDEP (integrated Differential Expression and Pathway analysis, v0.X), a web-based platform that streamlines RNA-seq data processing and visualization. Genes with low expression were filtered out based on predefined thresholds (typically fewer than 10 total counts across all samples). Normalization was performed using the median-of-ratios method implemented in DESeq2, which accounts for differences in sequencing depth and RNA composition across samples. To stabilize variance and improve comparability across genes and samples, variance-stabilizing transformation (VST) was applied prior to visualization techniques such as hierarchical clustering, principal component analysis (PCA), and heatmap generation."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Ashwin Ajith"],"additional_accession":[]},"is_claimable":false,"name":"Bulk RNA-Seq of TREM1 deficient LCSLCs of Huh7 and Hepg2 cell lines","description":"To determine the molecular function of TREM1, we performed bulk RNA sequencing of FACS-purified CD133+EpCAM+ LCSLCs from Huh7 and HepG2, TREM1 KO, and control tumors.","dates":{"release":"2025-12-01T00:00:00Z","modification":"2025-12-01T02:01:49.368Z","creation":"2025-06-05T09:23:39.458Z"},"accession":"E-MTAB-15204","cross_references":{"ENA":["ERP173185"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}