|
| Status |
Public on Jun 01, 2021 |
| Title |
CBP-KO_53 |
| Sample type |
SRA |
| |
|
| Source name |
Sorted germinal center B cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
cell type: germinal center (GC) B cells
genotype: CBP-KO
|
| Treatment protocol |
Germinal center B cells (B220+/PNA+/CD95+) were isolated by cytofluorimetric sorting.
|
| Growth protocol |
Mice were immunized by intraperitoneal injection of sheep red blood cells. Analysis was performed 12 days after immunization.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the NucleoSpin RNA XS kit (Machery Nagel), according to the manufacturer's instructions.
Libraries were prepared using the TruSeq RNA Sample Preparation v2 kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Mouse genotype is Crebbpfl/fl;Ep300+/+;Cg1cre/+ (Crebbp-KO)
counts_deseq2_normalized.txt.gz
|
| Data processing |
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the mouse genome (UCSC mm10) using hisat2 with the following options: --threads 4 --add-chrname --ignore-quals -q -x mm10 -k 5.
Reads were mapped to exons using featureCounts to produce abundance tables.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file of DESeq2 normalized counts
|
| |
|
| Submission date |
Dec 20, 2018 |
| Last update date |
Jun 01, 2021 |
| Contact name |
Laura Pasqualucci |
| E-mail(s) |
lp171@cumc.columbia.edu
|
| Organization name |
Columbia University
|
| Department |
Institute for Cancer Genetics
|
| Street address |
1130 St Nicholas Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE124192 |
Transcriptional profiling of murine germinal center (GC) B cells from GC-specific conditional Crebbp and Ep300 knock-out mice |
|
| Relations |
| BioSample |
SAMN10620589 |
| SRA |
SRX5170179 |
