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| Status |
Public on Apr 24, 2024 |
| Title |
Sample A1-Ei1 technical replicate c |
| Sample type |
SRA |
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| Source name |
Cerebral cortex
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Cerebral cortex
cell type: Endothelial cell
treatment: ad libitum
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total mRNAs were extracted from purified using the RNeasy Micro kit (Qiagen)
Messenger (polyA+) RNAs were purified from 150 ng of total RNA using oligo(dT). Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Endothelial cells from pooled cerebral cortexes from no fast rats, sample A1-Ei1, technical replicate c
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| Data processing |
Illumina bcl2fastq 2.18.0.12 software used for basecalling.
The analyses were performed using the Eoulsan pipeline version 2.3. Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Rattus norvegicus genome (Rnor_6.0 from Ensembl version 91) using the STAR mapper (version 2.6.1b, with –outSAMunmapped Within parameter). Alignments from reads matching more than once on the reference genome were removed. To compute gene expression, Rattus norvegicus GTF genome annotation version 91 from Ensembl database was used (GTF annotation from Ensembl 106 for the Pecam1 gene, transcripts and exons was merged in GTF annotation from Ensembl 91). All overlapping regions between alignments and referenced exons were counted and aggregated by genes using HTSeq-count 0.5.3.
Assembly: Rnor_6.0 from Ensembl 91
Supplementary files format and content: tab-delimited text files include transcripts counting for each Sample
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| Submission date |
Aug 29, 2023 |
| Last update date |
Apr 24, 2024 |
| Contact name |
Stephane Le Crom |
| Organization name |
IBENS
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| Department |
Genomic Core Facility
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| Street address |
46 rue Ulm
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| City |
PARIS |
| ZIP/Postal code |
75230 |
| Country |
France |
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| Platform ID |
GPL20084 |
| Series (1) |
| GSE241803 |
Fasting upregulates the monocarboxylate transporter Mct1 at the rat blood-brain barrier through Ppar δ activation |
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| Relations |
| BioSample |
SAMN37179348 |
| SRA |
SRX21497743 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7743961_expression_output_expression_2019176c.tsv.gz |
115.5 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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