characteristics.text: 2025-12-01
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: Georgia Cancer Center, Augusta University
characteristics.characteristic: INSDC center name
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS24832312
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-15204:Sample 10
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: HuH-7
characteristics.characteristic: cell line
characteristics.text: HCC
characteristics.characteristic: cell type
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: 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. Total RNA was isolated using RNeasy Mini kit (74104, Qiagen).  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
characteristics.characteristic: description
characteristics.text: Cripsr Control
characteristics.characteristic: genetic modification
characteristics.text: Huh7 Control
characteristics.characteristic: genotype
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: liver
characteristics.characteristic: organism part
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: Sample 10
characteristics.characteristic: title