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Sample GSM5510223 Query DataSets for GSM5510223
Status Public on Dec 19, 2022
Title DZ_Double_1
Sample type SRA
 
Source name Spleen
Organism Mus musculus
Characteristics strain: NZBWF1/J
treatment: 6 Doses of CTLA4-IG and 6 doses of Anti-CD40L
tissue: Spleen
Treatment protocol treated mice were given 6 doses each of 200ug and 250ug of CTLA4-IG and Anti-CD40L, respectively, over a 2 week period starting at 18 weeks of age.
Extracted molecule total RNA
Extraction protocol Spleens removed and prepared into single cell suspension using frosted slides. Lysed Spenocytes were stained negatively selected for B cells and stained with antibody for FACS Sorting of Germinal Center Dark zone and Germinal center Light zone. 1000 Cells were acquired for each sample and subjected to cDNA synthesis and amplification using SMART-Seq Ultra v4 Ultra kit.
 Sequencing libraries of the amplicons passing QC were constructed using the Nextera XT DNA Library Preparation Kit (Illumina, Inc.). 
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description Germinal center B cells Isolated from Spleen Using Facs sorting
Data processing The reads with good quality were firstly aligned to several mouse reference databases including mm10 mouse genome, exon, splicing junction segment and contamination database including ribosome and mitochondria sequences using BWA alignment algorithm. After filtering reads mapped to contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 mis-matches for each transcript were then counted as expression level for corresponding transcript. After filtering out of the transcripts with low read (<100) across all samples, the read counts were log2 transformed and quantile-normalized at an equal global median value in order to compare transcription level across samples.
Genome_build: mm10
Supplementary_files_format_and_content: text file of raw counts
 
Submission date Aug 09, 2021
Last update date Dec 19, 2022
Contact name Weijia Zhang
E-mail(s) [email protected]
Organization name Icahn School of Medicine at Mount Sinai
Department Renal
Lab Bioinfomatics
Street address 1 Gustave L. Levy Pl
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platform ID GPL21103
Series (1)
GSE181742 Combination CTLA4Ig and anti-CD40L treatment modifies T and B cell metabolic profiles and promotes BCR and membrane protein remodeling in a mouse model of SLE
Relations
BioSample SAMN20691317
SRA SRX11686865

Supplementary file Size Download File type/resource
GSM5510223_S38.txt.gz 59.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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