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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 19, 2023 |
| Title |
mouse neuron, rep6 |
| Sample type |
SRA |
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| Source name |
cortex
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| Organism |
Mus musculus |
| Characteristics |
genotype: C57/BL6
tissue: cortex
condition: primary culture
cell type: neuron
harvest method: pipette
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| Growth protocol |
For cultured astrocytes and neurons, a 3-month old male mouse was anaesthetized with halothane, euthanized by thoracotomy, then subjected to cardiac perfusion with 5 ml PBS followed by 20 ml PBS/4% paraformaldehyde. For sliced interneurons, we used standard brain slice preparation technology (see GSE135060).
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| Extracted molecule |
total RNA |
| Extraction protocol |
For cultured astrocytes and neurons, the brain was removed and post fixed at 4 °C for 16 hr., then rinsed in PBS and sectioned in the coronal plane at 100 μm on a vibratome (Leica VT-1000s). Sections including the hippocampus were then subjected to immunofluorescence labeling with chicken anti-MAP2 antisera (1:1000;Ab 5392; Abcam) followed by Alexa 488 conjugated goat anti-chicken secondary antibody (1:400;ab150169; Abcam). For sliced interneurons, mice were quickly anesthetized in 2% isoflurane, and decapitated. Brains were removed and laced into ice cold artificial cerebrospinal fluid (ACSF). Slices were cut by vibratome (Leica VT1000 S, Leica Biosystems, Wetzlar, Germany) under ice cold ACSF supplied with Carbogen (5% CO2 in 95% oxygen), then were stored in storage ACSF on room temperature in a chamber and permanently supplied by Carbogen for 1 hour before recording. Three hundred µm slices were cut from a mouse brain so that we were able to collect cells from different layers from the prefrontal cortex (PFC). Individual cells were collected by patch-clamp pipette.
For cultured astrocytes and neurons,Illumina TruSeq Nano DNA Library Preparation Kit was used with modifications. All of the second round PCR amplified double-stranded DNA was used as input. After converting DNA fragment into blunt ends with End Repair Mix, base “A” was added; sequence adapters were ligated. DNA inserts were amplified with PCR and sequenced by NextSeq 500. For sliced interneurons, libraries were made with Illumina TruSeq Stranded kit (RS-122-2101/2) and sequenced by Illumina HiSeq 2500.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
mouse neuron
MouseBrainRNAExonCnts.csv.gz
MouseBrainRNAIntronCnts.csv.gz
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| Data processing |
Base calls and demultiplexed using bcl2fastq v2.17. Reads were preprocessed by SCAP-T Next Generation Sequencing pipeline (https://github.com/safisher/ngs) using STAR v2.4.0 (Dobin et al. 2013).
Uniquely mapped reads were used for gene quantification using VERSE v0.1.4 with parameters "-s 1 -z 3 --nonemptyModified" (Zhu et al. 2016, doi:https://doi.org/10.1101/053306).
Assembly: mm10
Supplementary files format and content: csv files containing mouse brain single-cell raw exonic or intronic counts
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| Submission date |
May 04, 2023 |
| Last update date |
May 02, 2024 |
| Contact name |
Junhyong Kim |
| Organization name |
University of Pennsylvania
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| Department |
Biology
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| Lab |
Junhyong Kim
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| Street address |
433 S University Avenue
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE231725 |
Single-cell RNA-seq of astrocytes and neurons from primary culture of the mouse brain and of acute slice of interneurons from Patch-clamp pipette [RNA-seq mouse brain] |
| GSE232216 |
Light-Assisted Single-Stranded Open-Chromatin Analysis in K562 and Spatially Localized Neuronal Single Cells |
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| Relations |
| BioSample |
SAMN34590371 |
| SRA |
SRX20228549 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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