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| Status |
Public on Jan 12, 2022 |
| Title |
PFC WT Bulk RNA-Seq Sample1 |
| Sample type |
SRA |
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| Source name |
PFC
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N
tissue: PFC
Sex: male
age: 8-10 weeks
treatment: None
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| Growth protocol |
Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee
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| Extracted molecule |
total RNA |
| Extraction protocol |
For Foxp2+ neuron-specific RNA-Seq, Foxp2-Cre or Foxp2-Cre/Setd1a+/- mice were euthanized by inhalation of CO2. Brains were rapidly removed and the prefrontal cortex was dissected and immediately frozen with dry ice and then stored at −80 °C until processing for nuclear isolation. Frozen brain samples were homogenized in 1 ml ice-cold homogenization buffer [320 mM sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH7.6, 0.1 mM EDTA, 0.1% NP40, 0.1 mM PMSF, 1 mM β-mercaptoethanol, 1% BSA, 1:250 RNasin Plus RNase Inhibitor (Clontech)] using a 1 ml Dounce homogenizer (Wheaton); 20 times with pestle A, followed by 20 times with pestle B. After 10 min on ice, the homogenate was filtered with 40 μm cell strainer (Fisher) and added 1 ml dilution buffer [50% OptiPrep density gradient medium (Sigma), 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.6, 0.1 mM PMSF, 1 mM β-mercaptoethanol] and mixed thoroughly with pipette. Loaded 0.5 ml lysate on the top of 0.5 ml 29% iso-osmolar OptiPrep solution (in PBS) in a 1.5 ml centrifuge tube and centrifuged at 6000×g for 10 min at 4 °C. After removing the supernatant, the nuclei were resuspended in wash buffer [2.5 mM MgCl2, 1% BSA in PBS, 1:500 RNasin Plus RNase Inhibitor (Clontech)] for FACS. The GFP+ nuclei were directly sorted into Trizol (Thermo Fisher) with Sony SH800 sorter. The RNA was extracted with Direct-zol RNA Microprep Kits (Zymo) and store at −80 °C upon use.
The RNA-seq library were constructed with Smart-seq V4 reagents following the manufacturer's protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Raw reads were first preprocessed to remove low quality reads and adaptor sequences using Trimgalore (v0.4.5) (https://github.com/FelixKrueger/TrimGalore) with the parameter “--paired” for paired-end samples. Reads were mapped to the reference genome was performed with STAR (v.2.7.3a) (PMID: 23104886) software. Gene level quantification was done using RSEM (v.1.3.0) (PMID: 21816040). Differential gene expression were performed using the R/Bioconductor package edgeR (3.28.0) (PMID: 19910308).
Bigwig files were generated using deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
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| Submission date |
Jul 28, 2021 |
| Last update date |
Jan 13, 2022 |
| Contact name |
Mohamed Nadhir Djekidel |
| E-mail(s) |
djek.nad@gmail.com
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| Organization name |
Sidra Medicine
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| Department |
Translational Medicine Department
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| Lab |
Maternal and Child Health Division
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| Street address |
Gharafa
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| City |
Doha |
| State/province |
Doha |
| ZIP/Postal code |
26999 |
| Country |
Qatar |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE181024 |
Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis [bulk RNA-seq] |
| GSE181027 |
Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis |
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| Relations |
| BioSample |
SAMN20457281 |
| SRA |
SRX11583704 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5482184_PFC_WT_RNAseq_Rep1.bw |
28.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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