|
| Status |
Public on Jul 23, 2020 |
| Title |
23_TronC_BBB031_J7: Brain Endothetlail Cells (BECs)_Brainstem_P0D7 _rep5 |
| Sample type |
SRA |
| |
|
| Source name |
BECs_Brainstem
|
| Organism |
Macaca fascicularis |
| Characteristics |
brain structure: Brainstem
fraction: P0D7
|
| Treatment protocol |
P0D0: Brain microvessel isolation obtained through enzymatic digestion and gradient centrifugation yields a vascular fraction (P0D0) that is highly enriched in endothelial cells
P0D7: P0D0 cells were cultivated in endothelial cell medium (EBM-2 supplemented with Kit EGM-2 MV SingleQuots, Lonza) for 7 days (P0D7)
P1D7: Following 7 days of expansion, BECs from cortex, were further singularized and re-plated de novo for further 7-day cell expansion (P1D7)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets were lysed using QIAzol Lysis Reagent (Qiagen, # 79306).
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E 7765S) with the NEBNext rRNA Depletion Kit (New England Biolabs, #E6310L)
Paired-end sequencing (75 cycles x2) on the NovaSeq 6000 instrument (Illumina) using the NovaSeq 6000 SP Reagent Kit (300 cycles; # 20027465).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
23_TronC_BBB031_J7_S23_001.filtered
|
| Data processing |
ArrayStudio (QIAGEN Inc.)
Filtering step to remove reads corresponding to rRNAs as well as reads having low quality score or shorter than 25 nt
Reads were mapped to the macaque genome (Cyno.WashU2013) using OSA4 (Omicsoft Sequence Aligner, version 4) and quantified using Ensembl.R94 model of transcriptome.
Gene expression was measured calculating Fragments per Kilobase, per Million Mapped reads (FPKM) and raw counts.
Genome_build: Cyno.WashU 2013 genome based on the contigs assembled from a WGS project submitted by Washington University (WashU) in 2013
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample
|
| |
|
| Submission date |
Jul 22, 2020 |
| Last update date |
Jul 23, 2020 |
| Contact name |
Dominique Lesuisse |
| E-mail(s) |
dominique.lesuisse@sanofi.com
|
| Phone |
+33160496857
|
| Organization name |
Sanofi
|
| Department |
Rare and neurologic diseases therapeutic area
|
| Lab |
Tissue Barriers group
|
| Street address |
1, avenue Pierre Brossolette
|
| City |
Chilly-Mazarin |
| ZIP/Postal code |
91385 |
| Country |
France |
| |
|
| Platform ID |
GPL28212 |
| Series (1) |
| GSE154901 |
Non-human primate blood-brain barrier and in vitro brain endothelium: from transcriptome to the establishment of a new model |
|
| Relations |
| BioSample |
SAMN15600532 |
| SRA |
SRX8791112 |
