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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 03, 2021 |
| Title |
C57BL6J_2m_male_CTX_high |
| Sample type |
SRA |
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| Source name |
sorted brain endothelial cells (CD45-, CD11b-, CD31+)
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| Organism |
Mus musculus |
| Characteristics |
Sex: male
cell type: cortical endothelial cells
strain: C57BL/6J
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| Extracted molecule |
total RNA |
| Extraction protocol |
FACS sorting of endothelial cells using CD45, CD11b negative, CD31 positive endothelial cells (ARIA III, BD) with subsequent RNA isolation (Qiagen AllPrep Kit)
rRNA depletion & SMARTerStranded total RNA Pico Input Kit (Clontech Laboratories).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Raw sequencing read alignment and gene count summarization were performed using the bcbio-nextgen pipeline (v.19.03, https://github.com/bcbio/bcbio-nextgen). Quality encoding of sequencing reads was converted to Sanger format using seqkt (https://github.com/lh3/seqtk).
Sequencing reads were aligned to the Mus musculus genome (mm10) using HISAT2 (v.2.1.0). Sequence alignment map files were converted to binary alignment map files and indexed, and alignment statistics were determined using samtools (v.1.9).
Read count summarization at the gene level was performed using the featureCounts method of the Subread package (v.1.4.4) using the mm10 genome transcriptome annotation (v. 2018-10-10_92)
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: comma-separated value file, combining the output of featureCounts of all samples. The first column contains the Ensembl gene id, the second column contains the gene symbol, and the remaining columns contain the raw counts per sample. The strain, sex, and brain region (HC=hippocampal; CTX=cortex) are contained within column names.
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| Submission date |
May 03, 2021 |
| Last update date |
Aug 03, 2021 |
| Contact name |
Tania Wyss |
| Organization name |
Swiss Institute of Bioinformatics
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| Street address |
Rue du Bugnon 25A
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| City |
Lausanne |
| ZIP/Postal code |
1005 |
| Country |
Switzerland |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE173793 |
Characterization of the blood-brain barrier in genetically diverse laboratory mouse strains |
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| Relations |
| BioSample |
SAMN18992420 |
| SRA |
SRX10761474 |
| 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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