biostudies-arrayexpressZane KliesmeteMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15694To understand the effects of learning on expression in mouse striatum, we combined an automated operant conditioning chamber (OCC) setup with an efficient RNA-sequencing protocol. We compared 450 striatal expression profiles from 75 mice, e.g., the data contains 6 samples per mouse. Biopsies were taken from both hemispheres, three striatal regions (dorsoventral, dorsomedial, ventromedial striatum) at three learning stages (Early, Intermediate, Late). For each learning stage, there is the same number of samples from paired yoked control mice. There are also samples from control mice that were not kept in OCCs (Naive). The processed data can also be assessed and downloaded from here https://shiny.bio.lmu.de/Dopaloops/biostudies-arrayexpressSequencing - Two rounds of sequencing were done for two batches of learners and their respective controls. The first library was generated using Illumina NextSeq 2000 P2 flow cell with Read 1: 28 bp (barcode: 12 bp, UMI: 16 bp), Index 1 (i7): 8 bp; Read 2 (cDNA): 101bp. The second library contains Read 1: 40 bp (barcode: 24 bp, UMI: 16 bp), Index 1 (i7): 8 bp, Read 2 (cDNA): 47 bp.Nucleic Acid Extraction - Samples were placed inside of a RNAse-free Eppendorf tube (Dominique Dutscher, reference #033872) containing 200µL of buffer RLT Plus (Qiagen, reference #1053393), and immediately frozen on dry ice. All samples were transferred and kept at -80°C until shipment, which was done on dry ice.Library Construction - cDNA libraries for all samples were generated using the prime-seq protocol (Janjic et al. 2022).Sample Collection - All experimental procedures followed national and European guidelines and were approved by the institutional review boards (French Ministry of Higher Education, Research and Innovation; APAFiS Protocols no. 1418-2015120217347265 and 2021042017105235). Animals were group-housed in the animal facilities of the Paris Brain Institute in Tecniplast ventilated polycarbonate cages under positive pressure with hard-wood bedding in groups of up to six animals per cage with ad libitum food and water access. The temperature was maintained at 21–23 °C and the relative humidity at 55 ± 10% with a 12-h light/dark cycle (lights on/off at 8am and 8pm, respectively). Following ethical guidelines of animal experimentation on gender equity and the principle of the three Rs, we included both male and female adult mice (aged 5.50 ± 1.88 months). Operant conditioning was conducted in custom-modified experimental chambers (ENV-007CTX, Med Associates, Vermont, USA) as previously described23, in which each of the tested animals lives and performs the conditioning task 24/7 in an automated, self-initiated, self-paced manner. Seven such experimental operant chambers were operated in parallel in the same experimental room. Briefly, the rear wall of each chamber housed the feeder compartment (equipped with an infrared light beam to detect feeder entry crossing) and drinking water bottle holder, the front wall held two tactile screens, and a custom-made pair of black Plexiglas gates equipped with a pair of infrared (IR) beams. These beams allowed for tracking the locomotion of the mouse into or out of the area with the tactile screens. The chambers of the yoked controls were custom-built, plexiglass chambers as described in (Lamothe et al., 2023)24 and were located in the same experimental room as the operant conditioning chambers. The yoked control chambers contained ad libitum water access as well as the same woodchip bedding and cotton pad nesting material as the operant conditioning chambers and regular housing cages in the facilities. Precision reward pellets served as the sole nutrition during the entire experiment. The reward pellets (20 mg LabTabTM AIN-76A rodent precision pellets, TestDiet, Richmond, USA) are earned upon successful trials by the mice in the conditioning task (“learners”); yoked control mice, matched for sex, age and whenever possible also for litter, receive the exact same amount of food rewards as their matched pair undergoing actual conditioning. An additional group of naïve animals, which was never exposed to any behavioural task, served as a control for experimental treatment. To control for experimental factors, each learning mouse was paired with a matched animal of the same genotype, sex, and age as a yoked control (for e.g. change of the experimental room, social isolation, food consumption and quality). Learners and yoked controls were put into their according behavioural setup at the same time, and sacrificed at the same time, with the order of the dissection/tissue harvesting being randomized. The yoked controls received the exact same amount of precision food pellets as its learning partners during the past 24 hours in the mornings. Having reached respective criteria for early/intermediate/late learning stages, the brains of both learners and their paired yoked partners were rapidly dissected and collected during the morning of the following day. Naïve animals were directly taken from the group-housed home cages and their dissections were done at the same hours as the mice of the other groups. Before each dissection, all tools and surfaces were cleaned with RNAse decontamination solution (Fisher Scientific, reference #10180601). Concretely, animals were euthanized by cervical dislocation, rapidly dissected and their brains immediately collected and sliced (1mm thickness) using a 5-blade custom-made tool to rapidly obtain coronal slices of 1mm thickness at comparable levels across mice. All dissections were performed in a petri dish, which had been cleaned with RNAse decontamination solution beforehand. Brains were sprinkled with sterile saline to remove excess blood. All samples were collected by the same experienced researcher using 1mm2 biopsy punchers (pfm medical, reference #49101) to collect 1mm3 samples from each hemisphere of the three regions of interest: ventromedial striatum (AP = 0.10/ML = ±1.00/DV = 4.00), dorsomedial striatum (AP = 0.14/ML = ±1.50/DV = 2.10), and dorsolateral striatum (AP = 0.14/ML = ±2.50/DV = 2.50).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Genes that were expressed in at least 25% of the cells with an average of 3 counts or higher across samples from at least one striatal region were kept for the downstream analyses. This resulted in a count matrix containing 16,880 genes across 450 samples.Sequence Alignment - Fastq files were trimmed to remove the poly(A) tail using Cutadapt v1.12. The quality was assessed using fastqc v.0.11.8. zUMIs pipeline v.2.9.4d was used to process the data and generate a count matrix. Reads with a Phred quality score threshold of 20 for 3 BC bases and 4 UMI bases were filtered, mapped to the mouse genome (GRCm38) with the Gencode annotation (vM25) using STAR v.2.7.3a, and then counted using RSubread v.1.32.4.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 2000RNA-seq of coding RNAMus musculusMolecular signatures of the learning striatum during behavioral automatizationLousada E, Kliesmete Z, Janjic A, Briem E, Richter D, Wange LE, Burguière E, Enard W, Schreiweis CZane KliesmetefalseRNA-seq of learning and control mice (Mus musculus) striatum across three temporal phases of learningTo understand the effects of learning on expression in mouse striatum, we combined an automated operant conditioning chamber (OCC) setup with an efficient RNA-sequencing protocol. We compared 450 striatal expression profiles from 75 mice, e.g., the data contains 6 samples per mouse. Biopsies were taken from both hemispheres, three striatal regions (dorsoventral, dorsomedial, ventromedial striatum) at three learning stages (Early, Intermediate, Late). For each learning stage, there is the same number of samples from paired yoked control mice. There are also samples from control mice that were not kept in OCCs (Naive). The processed data can also be assessed and downloaded from here https://shiny.bio.lmu.de/Dopaloops/2025-10-25T00:00:00Z2026-05-27T17:38:24.046Z2025-10-10T13:13:43.595ZE-MTAB-15694ERP181356EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184