|
| Status |
Public on Feb 19, 2019 |
| Title |
aCSF-treated |
| Sample type |
SRA |
| |
|
| Source name |
Hypothalamus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 8 weeks old
genotype: wild type
tissue: Hypothalamus
|
| Treatment protocol |
scRNA-Seq - brains were treated with aCSF or leptin 1 hour before collection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bulk-RNA-Seq - polyadenylated RNA was purified from the total RNA samples using Oligo dT conjugated magnetic bead
scRNA-Seq -following the manufacturer's (10x Genomics)
Bulk-RNA-Seq (TruSeq SBS kit on NextSeq 500 system)
scRNA-Seq (Illumina NextSeq)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
scRNA-Seq
|
| Data processing |
Bulk-RNA-Seq: Filtered sequencing reads were mapped to the mouse reference genome (mm10) using TopHat. FPKM value for each gene was estimated using Cufflink.
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Both treatment groups (saline and leptin) were aggregated together for downstream analysis. Seurat was used to perform downstream analysis following the standard pipeline using cells with more than 500 genes and 1000 UMI counts. Clusters were annotated based on previous literature, and differential gene expression test was performed in each cluster, between treatment groups.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-Seq: matrix file; Bulk-RNA-Seq Cuffdiff output
|
| |
|
| Submission date |
Feb 18, 2019 |
| Last update date |
Feb 19, 2019 |
| Contact name |
Dong Won Thomas Kim |
| E-mail(s) |
kimtho87@gmail.com
|
| Organization name |
Johns Hopkins University
|
| Department |
Neuroscience
|
| Lab |
Blackshaw lab
|
| Street address |
733 N.Broadway, MRB building (Rm 332)
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE126707 |
Tanycyte-independent control of hypothalamic leptin signaling |
|
| Relations |
| BioSample |
SAMN10962610 |
| SRA |
SRX5388305 |
