|
| Status |
Public on Jun 01, 2023 |
| Title |
N9 Glucose replicate_3 |
| Sample type |
SRA |
| |
|
| Source name |
N9
|
| Organism |
Mus musculus |
| Characteristics |
cell line: N9
cell type: Microglia
treatment: High glucose media + LPS
|
| Treatment protocol |
N9 microglial cells were cultured in control media (glucose-free dmem, dialyzed serum (5%), glucose (3 mM) and fructose (5 mM)), high glucose media (control media with 15 mM glucose), and high fructose media (control media with 15 mM fructose) for 18 hours and stimulated with LPS (1 µg/ml) for an additional 6 hours.
|
| Growth protocol |
N9 microglial cells were routinely cultured in RPMI 1640 media with FBS (5%) and penicillin/streptomycin (1%).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells using Qiagen Rneasy Plus Mini Kit.
RNA libraries were prepared for sequencing using standard protocols by Novogene.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Each processed file has all the groups in one file.
|
| Data processing |
Library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Paired-end clean reads were aligned to the reference genome using HiStat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include gene counts for each sample.
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample.
|
| |
|
| Submission date |
Apr 25, 2023 |
| Last update date |
Jun 05, 2023 |
| Contact name |
Daniel Shippy |
| E-mail(s) |
dshippy@wisc.edu
|
| Organization name |
UW-Madison
|
| Street address |
1111 Highland Avenue
|
| City |
Madison |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE230564 |
Sugar utilization by microglia in Alzheimer's disease |
|
| Relations |
| BioSample |
SAMN34369733 |
| SRA |
SRX20097516 |
