|
| Status |
Public on Jun 10, 2024 |
| Title |
A3 |
| Sample type |
SRA |
| |
|
| Source name |
monocyte-derived microglia
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: monocyte-derived microglia
treatment: PBS
|
| Treatment protocol |
For sample 1-6, they were treated with SM03 (anti-human CD22 antibody) or IgG1 isotype 21 days before sacrifce. Antibodies were intravenously adminstrated once a week. For sample 7-12, mice were intracerebroventricularly injected with PBS or 9 μg mouse soluble CD22. Mouse cortice were collected 3 days after administration. For sample 13-20, cells were treated with 10 μg/mL sCD22 for 24 hours. Cells were then collected for RNA.
|
| Growth protocol |
For sample 1-12, mice were breed in cages before collection of tissue. For Sample 13 - 14, the monocyte-derived microglia were maintain in RPMI1640 medium, supplemented with 1 % P/S, 0.1 μg/ml IL-34 and 0.01 μg/ml GM-CSF
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from cultured MDMi and mouse cortex samples was extracted using TRIzol Reagent (Invitrogen, 15596026) according to the instruction.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X Plus |
| |
|
| Description |
Raw_3.csv
Normalized_3.csv
|
| Data processing |
Low-quality reads were removed by fastp with default parameters
Remaining clean reads were align to the Homo sapiens (human) genome assembly GRCh38 (hg38)/Mus musculus (house mouse) genome assembly GRCm39 (mm39) according to the corresponding species by Hisat2 with default parameters
Raw gene counts were generated by featurecount and then normalized by DEseq2
Assembly: hg38 or mm39
Supplementary files format and content: Matrix table with raw gene counts
Supplementary files format and content: Matrix table with normalized gene counts
|
| |
|
| Submission date |
Jun 05, 2024 |
| Last update date |
Jun 10, 2024 |
| Contact name |
Jianlin Li |
| Organization name |
The university of Hong Kong
|
| Street address |
L 7-08, Department of Obstetrics and Gynecology Laboratory block, 21th Sassoon Road, Hong Kong
|
| City |
Hong Kong |
| ZIP/Postal code |
999077 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL34284 |
| Series (1) |
| GSE269121 |
CD22 modulation regulates neuroinflammation in microglia |
|
| Relations |
| BioSample |
SAMN41688851 |
| SRA |
SRX24810285 |
