|
| Status |
Public on Feb 14, 2025 |
| Title |
0-1 |
| Sample type |
SRA |
| |
|
| Source name |
T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
age: 3 weeks
agent: vehicle
|
| Treatment protocol |
Mouse naïve CD4+ T cells were activated in vitro for 3 days with CD3/CD28 antibodies under Th1-polarizing conditions in the presence of vehicle control or LPC (20 μM).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells using TRIpure Reagent (Bioteke Cat. RP1001) according to manufacturer’s instructions.
Total RNA was isolated and reverse-transcribed into cDNA to generate an indexed Illumina library, followed by sequencing at the Shenzhen Genomics Institute (Shenzhen, China) using a BGISEQ-500 platform. High-quality reads were aligned to the mouse reference genome (GRCm38) by Bowtie2. The expression of individual genes was normalized to fragments per kilobase of the exon model per million mapped reads from RNA-Seq by Expectation Maximization. Significant differential expression was set if a gene with > 2-fold expression difference versus the control with an adjusted p-value of < 0.05. The differentially expressed genes (DEGs) were analyzed by gene ontology using AMIGO and DAVID software. The enrichment degrees of DEGs were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Total RNA was isolated and reverse-transcribed into cDNA to generate an indexed Illumina library, followed by sequencing at the Shenzhen Genomics Institute (Shenzhen, China) using a BGISEQ-500 platform.
High-quality reads were aligned to the mouse reference genome (GRCm38) by Bowtie2.
The expression of individual genes was normalized to fragments per kilobase of the exon model per million mapped reads from RNA-Seq by Expectation Maximization. Significant differential expression was set if a gene with > 2-fold expression difference versus the control with an adjusted p-value of < 0.05.
The differentially expressed genes (DEGs) were analyzed by gene ontology using AMIGO and DAVID software. The enrichment degrees of DEGs were analyzed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations.
Genome_build: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Feb 16, 2021 |
| Last update date |
Feb 14, 2025 |
| Contact name |
Panpan Liu |
| E-mail(s) |
liupanpan91@hotmail.com
|
| Phone |
+8613007493212
|
| Organization name |
Xiangya hospital
|
| Street address |
Xiangya road
|
| City |
Changsha |
| State/province |
China |
| ZIP/Postal code |
410008 |
| Country |
China |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN17923070 |
| SRA |
SRX10107451 |
