{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Leonardo Lupori"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16632"],"description":["Tlx3 neurons are a class of intratelencephalic neurons in the neocortex. By using a Cre mouse line, we can label two, only partially overlapping, cell populations depending on the time of labelling. We call these developmentally and adult labelled cells based on the fact that cells are tagged by crossing a Cre line with a reporter mouse line (tdTomato) or by injecting a Cre-dependent AAV in adult mice We aim to understand transcriptomic differences between developmentally labelled and adult labelled Tlx3 neurons."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Libraries were sequenced on an Illumina NovaSeq6000 using 112 cycles paired-end (2 × 56 bp). Demultiplexing was performed using bcl2fastq2 v2.20.","Nucleic Acid Extraction - RNA for bulk RNA-sequencing was purified with the Single Cell RNA Purification Kit (Norgen), and columns were treated with a Dnase to remove genomic DNA (Norgen). The isolation was performed according to the manufacturer’s instructions","Library Construction - mRNA-seq libraries were obtained using a SmartSeq2 approach using purified RNA as input.","Sample Collection - A portion of the mouse primary visual cortex was microdissected and a single cell suspension was created using progressively smaller fire-polished Pasteour pipettes. Cells were FACS sorted for fluorescence."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw gene counts were generated using the \\\"qCount\\\" function (QuasR) with GENCODE release M28 'basic gene annotation’ (\\\"gencode.vM28.annotation.gtf\\\" as TxDb object) as query, with default parameters except useRead=first and orientation=any. The count table was modified, by replacing the ensembl gene id with the gene symbol (if unique) or a combination of the gene symbol and the ensembl id (if the gene symbol was not unique) or keeping the ensembl id (for genes without a gene symbol) as the unique identifier.","Sequence Alignment - Initial RNA-sequencing analysis were conducted on a local Galaxy server (version 21.05) executing several R scripts (R version 4.4.1 and Bioconductor version 3.19): paired-end sequence reads were aligned to the human genome (GRCm39 primary assembly) using the \\\"qAlign\\\" function from the Bioconductor package QuasR version 1.44.0 with default parameters except for aligner = \\\"Rhisat2\\\", splicedAlignment=\\\"TRUE\\\", allowing only uniquely mapping reads."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Leonardo Lupori","Hans-Rudolf Hotz","Georg Keller"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq of developmentally- and adult-labeled Tlx3-Cre-positive neurons in the mouse primary visual cortex","description":"Tlx3 neurons are a class of intratelencephalic neurons in the neocortex. By using a Cre mouse line, we can label two, only partially overlapping, cell populations depending on the time of labelling. We call these developmentally and adult labelled cells based on the fact that cells are tagged by crossing a Cre line with a reporter mouse line (tdTomato) or by injecting a Cre-dependent AAV in adult mice We aim to understand transcriptomic differences between developmentally labelled and adult labelled Tlx3 neurons.","dates":{"release":"2026-06-19T00:00:00Z","modification":"2026-06-19T07:51:06.567Z","creation":"2026-02-10T20:48:01.839Z"},"accession":"E-MTAB-16632","cross_references":{"ENA":["ERP188965"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}