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Sample GSM7306214 Query DataSets for GSM7306214
Status Public on May 15, 2024
Title 24 hours, IL-12 block, IFNg at 0.5 ng/mL, mouse 1
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Spleen
treatment: 24 hours, IL-12 block, 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 SAMN34999043
SRA SRX20253267

Supplementary file Size Download File type/resource
GSM7306214_IL12_block_IFNg_at_0.5ngmL_24h_mouse1.txt.gz 72.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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