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Sample GSM7306201 Query DataSets for GSM7306201
Status Public on May 15, 2024
Title 4 hours, IL-12 at 200 pg/mL, IFNg block, mouse 3
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
treatment: 4 hours, IL-12 at 200 pg/mL, IFNg block
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 4 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 SAMN34999056
SRA SRX20253254

Supplementary file Size Download File type/resource
GSM7306201_IL12_at_200pgmL_IFNg_block_4h_mouse3.txt.gz 73.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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