|
| Status |
Public on Dec 19, 2022 |
| Title |
DZ_Control_3 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: NZBWF1/J
treatment: untreated
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.).Â
|
| |
|
| 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 |
SAMN20691316 |
| SRA |
SRX11686864 |
