title: del7_SSO648_rep1
organism: Homo sapiens
description: Protocols: Cells were washed in PBS and harvested for RNA extraction after 48 hours following SSO transfection. Cells were cultured at 37°C, 5% CO2, in RPMI-1640 medium (Sigma Aldrich, United Kingdom) supplemented with fetal bovine serum (10%), L-glutamine (4 mM), and penicillin (100 U/ml)/streptomycin (100 µg/ml). CRISPR-edited HepG2 cells were transfected with splice-switching antisense oligonucleotides (SSO); RNA oligonucleotides with 2'-O-methyl modifications and phosphorothioate backbones (LGC Biosearch Technologies, Denmark), at 20 nM final concentrations. Cells were transfected with a non-targeting control SSO (5'-AUGUUCUAUGAAAUUCACAGUGUUG-3') or SSO 2 targeting a pseudoexon sequence in PCCA intron 14 (5'-GCUCAAUAUGCUACUGCCAUGCUUG-3'). SSO transfection was performed at the time of cell seeding (200,000 cells/well in 12-well plates; 3.5 cm2/well) using Lipofectamine RNAiMAX Transfection Reagent (Invitrogen, CA, USA) and harvested for RNA extraction after 48 hours. Gene editing was performed using the Alt-R CRISPR-Cas12a (Cpf1) system (Integrated DNA Technologies, IA, USA) for homology-directed repair in HepG2 cells. Cas12a:crRNA (5'-UAAUUUCUACUCUUGUAGAUAGGACAUAAACUGAUGUUCUAUG-3') ribonucleoprotein was co-transfected with a 75 nt single-stranded DNA donor template of the PCCA c.1285-1416A>G sequence variant (¬¬¬-37/+37 nt) using Lipofectamine CRISPRMAX Transfection Reagent (Invitrogen, CA, USA). Cell cultures were expanded from single cell colonies and genotypes were verified by Sanger sequencing: HepG2 PCCA MUT cells functionally hemizygous for PCCA c.1285-1416A>G with a large complex deletion on the other allele (spanning from intron 12 to intron 14), HepG2 PCCA Del7 cells homozygous for PCCA c.1285-1411delTAGAACA, and HepG2 PCCA WT with no editing introduced in the PCCA gene. Total RNA was extracted from cells using TRIzol Reagent (Ambion, CA, USA) by phase separation with chloroform and precipitation in isopropanol. RNA purity was estimated on a NanoDrop 2000c spectrophotometer, and RNA integrity was estimated on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano Kit (Agilent Technologies, CA, USA). RNA with a 260/280 absorbance ratio >1.8 and RNA integrity number (RIN) >8.0 was used for library preparation. Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, MA, USA) with rRNA depletion. Size estimation of the amplified cDNA libraries was performed on an Agilent 2100 Bioanalyzer using the DNA 1000 Kit (Agilent Technologies, CA, USA), and concentrations were estimated by qPCR using the KAPA Library Quantification Kit (Roche, South Africa).
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2023-12-10T12:45:01Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2023-12-10T12:45:01Z
attributes.tag: External Id
attributes.value: SAMEA114639712
attributes.tag: INSDC center name
attributes.value: Department of Biochemistry and Molecular Biology University of Southern Denmark
attributes.tag: INSDC first public
attributes.value: 2023-12-10T12:45:01Z
attributes.tag: INSDC last update
attributes.value: 2023-12-10T12:45:01Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-13549:del7_SSO648_rep1
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell_line
attributes.value: HepG2
attributes.tag: cell_type
attributes.value: hepatocyte
attributes.tag: collection date
attributes.value: not collected
attributes.tag: common name
attributes.value: human
attributes.tag: developmental stage
attributes.value: juvenile
attributes.tag: disease
attributes.value: hepatocellular carcinoma
attributes.tag: genotype
attributes.value: PCCA c.1285-1411delTAGAACA (homozygous)
attributes.tag: geographic location (country and/or sea)
attributes.value: not collected
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism part
attributes.value: liver
attributes.tag: sample name
attributes.value: E-MTAB-13549:del7_SSO648_rep1
attributes.tag: scientific_name
attributes.value: Homo sapiens