 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 13, 2024 |
| Title |
microglia,ABX_Sham,Day7_3 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
cell type: microglia
genotype: WT
treatment: antibiotic cocktail,PBS
time: Day7
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sorted microglia from peri-hematoma were collected in 2mL TRIzol reagent and stored at -80℃.
Gene expression at the mRNA level was analyzed using the SMART-Seq 2 protocol. Specifically, the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, Japan) was employed to prepare the low-input library as follows: 1) Total RNA of pg level was used to prepare the cDNA library; 2) cDNA was purified and size-selected within the 150-300 bp range; 3) A sequencing-ready library was prepared by adding i5/i7 adaptors using the PCR method; 4) Library quality was assessed using an Agilent 2100 Bioanalyzer to determine size and concentration; 5) Libraries were sequenced on an Illumina Novaseq™ 6000 platform using a 2 × 150 bp paired-end sequencing protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ABX_Sham3
|
| Data processing |
Adaptor contamination was removed using Cutadapt 1.9 software. HISAT2 2.0.4 software mapped the reads to the genome, and StringTie 1.3.4d assembled the mapped reads of each sample. Expression levels were estimated and calculated as TPM (TPM = (exon reads in gene) / (total exon reads) × 1 million). Differentially expressed mRNAs were identified using edgeR, selecting those with a fold change > 2 or fold change < 0.5 and a p-value < 0.05, and annotated with GO terms and KEGG Pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each counts
|
| |
|
| Submission date |
May 05, 2024 |
| Last update date |
May 13, 2024 |
| Contact name |
Xuchao He |
| E-mail(s) |
xuchaohe@zju.edu.cn
|
| Phone |
19857131935
|
| Organization name |
zhejiang university
|
| Street address |
88 jiefang RD
|
| City |
hangzhou |
| State/province |
zhejiang |
| ZIP/Postal code |
310009 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE266602 |
Regulation of Microglia-Mediated Neuroinflammation Post-Intracerebral Hemorrhage by Gut Microbiota and Short-Chain Fatty Acid Metabolism |
|
| Relations |
| BioSample |
SAMN41217352 |
| SRA |
SRX24456508 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
