{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Christophe RACHEZ"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15194"],"description":["Expression profiling by high throughput sequencing in Bi-potential Murine Embryonic Liver cells (BMEL cells). Three clones (TKO1, TKO2, TKO3) of BMEL TKO cells invalidated for the expression of the three HP1 isoforms (Cbx1-/-; Cbx3-/-; Cbx5-/-), compared to three clones (Het1, Het32, Het35) of BMEL Het cells (Cbx1+/+; Cbx3+/+; Cbx5+/-) expressing HP1 as controls. Expression profiling was performed on total cell extracts, on cytosolic RNA and on chromatin-enriched RNA."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Library sequencing was performed by Novogene Co, Ltd, as Paired End 150 sequencing (30G raw data/sample).","Nucleic Acid Extraction - Total RNA was extracted out of nucleosol, chromatin, or total cells by guanidinium thiocyanate-phenol-chloroform extraction followed by proteinase K and Dnase I treatment.","Library Construction - Total RNA library preparation was performed by Novogene Co., Ltd, as a lncRNA sequencing service, including lncRNA directional library preparation with rRNA depletion (Ribo-Zero Magnetic Kit)","Sample Collection - Cytosolic and chromatin-enriched fractions were obtained by sequential lysis and centrifugation steps giving a cytosolic fraction, followed by nuclei lysis and centrifugation giving a nuclear soluble fraction and a chromatin pellet."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Bigwig files were generated from BAM files with bamCoverage (parameter: –normalizeUsing CPM) from Deeptools (v3.1.3).","Sequence Alignment - Mapping was carried out with STAR (v2.6.0b) (parameters: –outFilterMismatchNmax 1 – outSAMmultNmax 1 –outMultimapperOrder Random –outFilterMultimapNmax 30) on Mus musculus mm10 genome."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of total RNA"],"species":["Mus musculus"],"pubmed_authors":["Christophe RACHEZ"],"additional_accession":[]},"is_claimable":false,"name":"RNAseq of BMEL cell lines invalidated or not for the expression of the three HP1 isoforms (CBX1, CBX3, CBX5)","description":"Expression profiling by high throughput sequencing in Bi-potential Murine Embryonic Liver cells (BMEL cells). Three clones (TKO1, TKO2, TKO3) of BMEL TKO cells invalidated for the expression of the three HP1 isoforms (Cbx1-/-; Cbx3-/-; Cbx5-/-), compared to three clones (Het1, Het32, Het35) of BMEL Het cells (Cbx1+/+; Cbx3+/+; Cbx5+/-) expressing HP1 as controls. Expression profiling was performed on total cell extracts, on cytosolic RNA and on chromatin-enriched RNA.","dates":{"release":"2026-03-31T00:00:00Z","modification":"2026-03-31T01:03:47.056Z","creation":"2025-06-09T11:09:32.178Z"},"accession":"E-MTAB-15194","cross_references":{"ENA":["ERP173145"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}