|
| Status |
Public on Apr 19, 2019 |
| Title |
JH044_whole_brain_48h_hypoxia_R2 |
| Sample type |
SRA |
| |
|
| Source name |
adult whole brain, 48-hour hypoxia
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WT
strain: C57BL/6J
age: 2 month
Sex: Male
tissue: brain
treatment: Mouse was exposed to 48 hours of 7.5% oxygen in a normobaric chamber
|
| 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
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from homogenized whole brain using the TRIzol reagent (ThermoFisher) as per the manufacturer's protocol. Extracted RNA was further purified using the RNeasy Mini kit (74104, QIAGEN, Venlo, Netherlands) as per the manufacturer's protocol/
Libraries were constructed using the NuGEN single cell RNA-seq library preparation kit as per the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Whole brain
|
| Data processing |
scRNA-seq data were pre-processed using the Cell Ranger pipeline (v2.1.0; 10x Genomics) with default settings. The normalized gene x cell matrix was used as input for the MonocleR/Bioconductor package (Trapnell et al., 2014). Log-normalized expression estimates (with a pseudocount of 1) were used as input for a modified dpFeature analysis. For preliminary cell clustering, PCA was performed on the high variance genes, and appropriate components were visualized in two dimensions using UMAP. Initial clusters were identified from the 2-D embedding using k-means clustering. Cell type identity was determined by cross-referencing clusters with expression of multiple known cell type markers.
RiboTag, whole retina, and whole brain RNA-seq data were pseudoaligned to the mouse genome (mm10) using the Kallisto software (Bray et al., 2016). Aligned counts were obtained for differential gene expression analysis using EBseq (Leng et al., 2013) and posterior probability ³0.95 that a gene/transcript is differentially expressed was considered statistically significant.
Genome_build: mm10
|
| |
|
| Submission date |
Jan 27, 2019 |
| Last update date |
Apr 19, 2019 |
| Contact name |
Jacob S Heng |
| E-mail(s) |
jacob.heng@outlook.com
|
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
Molecular Biology and Genetics
|
| Lab |
Nathans Lab
|
| Street address |
725 North Wolfe Street
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21210 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE125708 |
Hypoxia tolerance in the Norrin-deficient retina and the chronically hypoxic brain stuied at single-cell resolution |
|
| Relations |
| BioSample |
SAMN10826882 |
| SRA |
SRX5296670 |
