{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Hagoon Jang"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15726"],"description":["to find out the lnc122(precursor of miR-122) role as an independent lncRNA, we designed the lnc122-/miR-122+ Huh7 cells with Lenti-CRISPRi_lnc122 + lenti-CAG-miR-122 combination. lenti-CRISPRi_lnc122 suppresses endogenous lnc122 as well as miR-122 but we add back the miR-122 ectopically."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - WT Huh7 cells and lnc122-/miR-122+ Huh7 cells were washed with cold PBS twice and then add Trizol reagent.","Growth Protocol - Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; GIBCO-BRL) with 2 mM L-glutamine, antibiotic/antimycotic and 10% FBS.","Sequencing - The library was sequenced on an Illumina partial lane Nova-seq to generate 2X150 paired-end reads (Novogene, USA), using Novaseq6000.","Sample Treatment - To generate dCas9-KRAB expressing Huh7 cell, we plated the 2 million Huh7 cells in 10cm and adding 200l of dCas9-KRAB lentivirus. Two days later, we select the cell using 50g/ml of blasticidin for 7 days. For generation of lnc122-/miR-122+ Huh7 cell lines, we performed combinational lentiviral transduction of sgSCR+shSCR and sglnc122#2+miR-122 in dCas9-KRAB expressed Huh7 cells. Two days later, we select the cell using 5g/ml of puromycin and 500g/ml of hygromycin for 7 days and check the gene expression","Nucleic Acid Extraction - RNA was extracted using Zymo Direct-zol RNA Miniprep Plus Kit with on-column DNase digestion (Zymo Research).","Library Construction - At least 100ng RNA was used to prepare the RNA-seq library using NEBNext rRNA Depletion Kit (E6310L, New England BioLabs) and TruSeq Stranded mRNA Library Prep Kit (Cat# 20020594, Illumina) for each sample following the manufacturer’s instruction."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - normalization using read per million (RPM), or deseq2 pipeline in R (software), and GSEA in R (fgsea package)","Sequence Alignment - We performed 4 biological replicate experiments for ctrl and lnc122-/miR-122+ Huh7 cells. Reads were aligned to hg19 (ENSEMBL transcripts) using STAR with default parameters (alignIntronMin 61 --alignIntronMax 265006) and sorted by samtools, the option is (-n). Quantification of aligned reads was carried out by HTseq count with parameters (-s reverse -m intersection-nonempty -r name -f bam). DESeq2 from R package was used for identifying differentially expressed gene. For GSEA, we used the fgsea (Fast Gene Set Enrichment Analysis) packages in R."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Hagoon Jang","Mark Kay"],"additional_accession":[]},"is_claimable":false,"name":"RNAsequencing of WT Huh7 cells and lnc122-/miR-122+ Huh7 cells","description":"to find out the lnc122(precursor of miR-122) role as an independent lncRNA, we designed the lnc122-/miR-122+ Huh7 cells with Lenti-CRISPRi_lnc122 + lenti-CAG-miR-122 combination. lenti-CRISPRi_lnc122 suppresses endogenous lnc122 as well as miR-122 but we add back the miR-122 ectopically.","dates":{"release":"2026-10-07T00:00:00Z","modification":"2026-10-07T01:00:43.86Z","creation":"2025-10-14T22:51:17.65Z"},"accession":"E-MTAB-15726","cross_references":{"ENA":["ERP182174"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}