|
| Status |
Public on May 15, 2024 |
| Title |
24 hours, IL-12 at 20 pg/mL, IFNg at 0.5 ng/mL, mouse 3 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen
treatment: 24 hours, IL-12 at 20 pg/mL, IFNg at 0.5 ng/mL
|
| Treatment protocol |
Cells were stimulated for 4 or 24 hours with LPS and the indicated cytokines or blocking antibodies.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed in PBS, resuspended in 350 ul RLT Plus Buffer (Qiagen) with 1% 2-Me, and frozen at -80 ⁰C. RNA purification was performed using the Qiagen RNeasy Micro Plus Kit.
cDNA was generated using the Takara Smart-Seq v4 Ultra Low Input RNA kit. Libraries were prepared using Illumina Nextera FLEX Kit with UDI set B indexes. Samples were sequenced using NextSeq 2000 P3 reagents (200 cycles) to obtain 20M 2x101 bp reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
C57BL/6 purified B cells cultured 24 hours
|
| Data processing |
Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.5).
Filtered adaptor and poor quality sequences respectively, using cutadapt (v. 1.8.3) (minimum phred quality score = 20).
The reference genome (mm10) based alignment of clean reads were performed using STAR (v. 2.6.0c) (Dobin et al., 2013).
Gene-level counts were determined using featureCounts packgae by subread/1.6.2 (Liao et al. 2014).
Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
Assembly: Mus musculus reference genome (mm10).
Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.
|
| |
|
| Submission date |
May 08, 2023 |
| Last update date |
May 15, 2024 |
| Contact name |
Mark Shlomchik |
| E-mail(s) |
shlomchiklab@gmail.com
|
| Organization name |
University of Pittsburgh
|
| Department |
Department of Immunology
|
| Street address |
The Assembly, 5051 Centre Avenue
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE231931 |
RNA-seq analysis of B cells cultured with LPS and IL-12 and/or IFN gamma |
|
| Relations |
| BioSample |
SAMN34999047 |
| SRA |
SRX20253263 |
