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| Status |
Public on Jun 20, 2024 |
| Title |
BCD-Ket (#9949) |
| Sample type |
SRA |
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| Source name |
Brain (PFC)
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: PFC
age: 13 weeks old
genotype: wild type
treatment: BCD-Ket
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| Extracted molecule |
total RNA |
| Extraction protocol |
Brains were harvested, and the prefrontal cortices were rapidly dissected and transferred into ice-cold Hibernate A/B27 medium (60 ml Hibernate A medium with 1ml B27 and 0.15 ml Glutamax). The tissues were enzymatically dissociated into single cell suspension, and the cells were captured with the 10X Chromium platform (10X Genomics, Pleasanton, CA).
Reverse transcription, cDNA amplification and library construction were performed according to the manufacturer’s instructions and used for sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
9949-1
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| Data processing |
The sequencing data were processed using the Cell ranger software to demultiplex the samples, generate FASTQ files, align the reads to mm9 genome and generate feature-barcode matrices. The filtered featured matrices were individually analyzed using Seurat R package (v3.1.1) and submitted to quality control (gene count per cell, percent of mitochondrial transcripts).
Genome_build: mm9
Supplementary_files_format_and_content: filtered_feature_bc_matrix folder (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)
Supplementary_files_format_and_content: raw_feature_bc_matrix
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| Submission date |
Dec 15, 2021 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Andiara Espindola de Freitas |
| E-mail(s) |
andiaraef@gmail.com
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| Phone |
858-281-3373
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| Organization name |
UC San Diego (UCSD)
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| Department |
Biological Sciences
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| Lab |
Zou Lab
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| Street address |
Gilman Drive
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| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92121-2460 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE191016 |
Planar cell polarity proteins mediate ketamine-induced restoration of glutamatergic synapses in prefrontal cortical neurons in a mouse model for chronic stress |
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| Relations |
| BioSample |
SAMN24248067 |
| SRA |
SRX13456804 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5737567_9949-1_filtered_feature_bc_matrix.tar.gz |
12.2 Mb |
(ftp)(http) |
TAR |
| GSM5737567_9949-1_raw_feature_bc_matrix.tar.gz |
62.8 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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