|
| Status |
Public on Jun 12, 2019 |
| Title |
MM6 KO6 |
| Sample type |
SRA |
| |
|
| Source name |
Germinal Center B cells HVEM KO
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Germinal Center B cells
genotype: HVEM KO
strain: HVEM KO C57BL/6 CD45.2
background strain: C57BL/6
|
| Treatment protocol |
Bone marrow chimeras were generated, reconstituted for 8 weeks, immunized with NP-CGG alum, and analyzed at day 11.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were euthanized and 5x10^4 GC B cells were FACS sorted for purity (B220+IgDloCD38loGL7+Fas+), flash frozen and RNA from extracted using Qiagen RNeasy Micro Kit
Ovation RNA-seq System V2 from Nugen for amplification, KAPA Hyper prep labeling kit and NEXTFlex DNA barcodes adapter from Bioo Scientific to label the adaptors.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Base calling performed using RTA (Real-time Analysis), demultiplexed FASTQ files generated using CASAVA
RNA-seq paired end reads were aligned using Tophat (ver. 2.0.8b, Linux) to output read alignments that map once to the genome; other parameters were set as default
Aligned reads were then analyzed for differential expression using cufflinks (ver. 2.1.1).
Cufflinks output was transferred to excel file and then formatted.
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet containing gene expression matrix reported as FPKM values
|
| |
|
| Submission date |
Apr 19, 2019 |
| Last update date |
Jun 12, 2019 |
| Contact name |
Michelle Amy Mintz |
| E-mail(s) |
michelle.mintz@ucsf.edu
|
| Phone |
5145026638
|
| Organization name |
University of California San Francisco
|
| Department |
Microbiology and Immunology
|
| Lab |
Jason Cyster
|
| Street address |
513 Parnassus Ave
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE130095 |
B cell HVEM interaction with T cell BTLA restrains the help delivered to germinal center B cells |
|
| Relations |
| BioSample |
SAMN11467961 |
| SRA |
SRX5713571 |
