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| Status |
Public on May 19, 2023 |
| Title |
Alk1_iBECs_MUT-3 |
| Sample type |
SRA |
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| Source name |
Endothelial cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Brain
cell type: Endothelial
age: Postnatal day 6
genotype: Alk1f/f; Cdh5-CreERT2
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| Treatment protocol |
Tamoxifen (300µg) was adminstered to new born pups at postnatal days 1,2 and 3 for Smad4 and Eng models; Tamoxifen (100µg) was adminstered to Alk1 pups at postnatal days 4. IgG or LC10 (Ang2 inhibitor) (30ug) were administered at P2 and P4 in Smad4-HHT mouse model.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Whole brain tissue was digested using a Neural Tissue Dissociation Kit (P) (Milteni, 130-092-628) following the manufacture instructions. Brain endothelial cells were purified using dynabeads (Invitrogen 11035) coated with platelet endothelial cell adhesion molecule (PECAM) antibody (BD, 553370), followed by immediate RNA or protein extraction. RNA was extracted using Thermo Fisher GeneJET RNA Purification Kit (Thermo, K0732).
RNA library construction was performed with the TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001) according to the manufacturer instructions. For library preparation, 1 µg of RNA was used for each sample. The resulting mRNA library was quantified using Qubit dsDNA High Sensitivity Assay Kit (Thermofisher, Q32851) and verified using the Bioanalyzer DNA1000 assay kit (Agilent, 5067-1505).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Description |
Raw counts
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| Data processing |
Sequenced reads were aligned to the mouse (mm10) reference genome with RNA-seq alignment tool (version 2.0.1) using the BaseSpace sequence hub.
The aligned reads were used to quantify mRNA expression and determine differentially expressed genes using the RNA-seq Differential Expression tool (version 1.0.1) using the BaseSpace sequence hub.
Genome_build: mm10
Supplementary_files_format_and_content: Comma separated spreadsheet file with raw counts for every gene for every sample.
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| Submission date |
Feb 21, 2022 |
| Last update date |
May 19, 2023 |
| Contact name |
Xingyan Zhou |
| Organization name |
Tulane University
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| Street address |
6823 St Charles Ave
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| City |
New Orleans |
| ZIP/Postal code |
70118 |
| Country |
USA |
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| Platform ID |
GPL21626 |
| Series (1) |
| GSE197105 |
RNA sequencing of isolated brain endothelial cells from Smad4, Alk1, or Eng endothelial cell-specific knock-out mutants, respective wildtypes (WTs), and Angiopoietin-2 inhibition transcriptional changes. |
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| Relations |
| BioSample |
SAMN26135969 |
| SRA |
SRX14240583 |
| 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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