{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Shirin Sharghi"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of total RNA"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17716"],"description":["A gene sequencing analysis of caudate putamen tissue of Fmr1-KO mice in comparison to wild-type mice was performed to identify new pre-clinical tissue biomarkers that might be relevant in Fragile X-Syndrome."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Growth Protocol - Five male C57BL/6J (B6; #:000664) and five male B6.129P2-Fmr1tm1Cgr/J (Fmr1-KO; #:003025) were purchased from Jackson Laboratory, Bar Habor, ME, USA (18). Based on vendors information, homozygous female Fmr1-KO mice were bred with hemizygous Fmr1-KO mice to receive homozygous male Fmr1-KO mice (35). All mice were 6 weeks old at arrival. Animals were housed in groups of 3-5 mice per cage and kept in individually ventilated cages under a 12:12 h dark-light cycle with a temperature of 21 ± 1°C at 40 to 70% humidity at the AAALAC-accredited animal facility of Scantox Neuro GmbH. Dried pelleted standard rodent chow (Altromin®, Lage, Germany) and water were provided ad libitum. All animal procedures were conducted in accordance with the Austrian Animal Welfare Act and were appr","Sample Treatment - no treatment was performed","Library Construction - Sequencing-ready libraries were produced using a QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina with 500 ng of total RNA from each left CPu as input. Standard procedures were followed as outlined in the respective User Guide (version 113UG227V0110). Quality of the libraries was determined with Agilent 5300 Fragment Analyzer High Sensitivity NGS Fragment Kit on DNF-474-33 - HS NGS Fragment 1-6 000bp method mode. Concentrations of obtained libraries were quantified using a Qubit dsDNA HS assay (Thermo Fisher). A sequencing-ready pool of indexed libraries was prepared in equimolar ratio according to these quantifications. The Quant Seq 3` method for library preparation was used as mRNAs are not fragmented before reverse transcription from the 3’ end. Thus, only one ","Sequencing - Sequencing of total RNA from each left CPu was performed on an Illumina NextSeq 2 000 system with a NextSeq 1 000/2 000 P3 Reagent Kit (100 cycles) by Lexogen GmbH, Vienna, Austria.[","Sample Collection - At 7 weeks of age, animals were deeply anesthetized by intraperitoneal injection of 600 mg/kg pentobarbital. Blood was collected via cardiac puncture, stored in EDTA tubes (MiniCollect® K2EDTA potassium ethylenediaminetetraacetic acid) and processed to plasma by centrifugation at 1 000 x g for 15 min at 4°C.  The brain was removed and hemisected. From the left hemisphere, caudate putamen tissue was collected in RNA-later solution (Thermo Fisher, Invitrogen), kept at 4°C overnight, and sent to Lexogen GmbH (Vienna, Austria) on dry ice for RNA extraction and RNA sequencing. The right hemisphere was fixed by immersion in 4% paraformaldehyde in phosphate buffer (pH = 7.4) overnight at 4°C. The right hemisphere was then transferred to 15% sucrose in phosphate buffered saline","Nucleic Acid Extraction - Total RNA was extracted by Lexogen GmbH using SPLIT RNA Extraction Kit, Lexogen (PN: 008.48) according to the manufacturer’s guidelines. In brief, tissue was homogenized in 400 µl isolation buffer. Acidic buffer and acidic phenol were added to efficiently separate the genomic DNA. Chloroform was added and phases were cleanly separated using Phase Lock Gel tubes. Further, RNA was purified from the trace amount of phenol and fractionated on a silica column. RNase inhibitor and Enzymatics (PN: Y9240) were added to each sample after elution in 30 µl elution buffer (10 mM Tris-HCl pH 7.0). RNA quantity was measured by UV-Vis spectrophotometry (NanoDrop2000c, Thermo Fisher), RNA integrity was assessed with Agilent 5300 Fragment Analyzer Standard Sensitivity Kit on DNF-4"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Shirin Sharghi"],"additional_accession":[]},"is_claimable":false,"name":"Gene Expression Analysis of Fmr1-KO Mouse Caudate Putamen as a Model of Fragile X-Syndrome Compared to Wild-Type Mouse","description":"A gene sequencing analysis of caudate putamen tissue of Fmr1-KO mice in comparison to wild-type mice was performed to identify new pre-clinical tissue biomarkers that might be relevant in Fragile X-Syndrome.","dates":{"release":"2026-09-25T00:00:00Z","modification":"2026-10-02T14:23:00.505Z","creation":"2026-10-02T14:22:45.101Z"},"accession":"E-MTAB-17716","cross_references":{"ENA":["ERP207349"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0003789","EFO_0005518","EFO_0004184","EFO_0003969"]}}