|
| Status |
Public on Oct 11, 2021 |
| Title |
GC_B_Doc_1_ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
Germinal Center B cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Germinal Center B cells
treatment: LCMV Docile
assay: ATAC-Seq
|
| Treatment protocol |
C57BL/6 mice were either treated with LCMV WE or Docile for 14 days. Germinal Center B cells were sort-purified from total splenocytes.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fresh cell pellets were lysed and genomic DNA tagmented.
Tagmented DNA library was built using the Illumina Library Quantification Kit for BioRad iCycler (KAPA Biosystems)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie2 with the default settings.
For each sample peaks of accessibility were identified and annotated using MACS2 with the default settings
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files are normalized to reads per million (rpm) using R/Bioconductor and tab delimited text file containing rpm normalized data for all peaks and all samples as well as peak annotations and locations.
|
| |
|
| Submission date |
Dec 16, 2020 |
| Last update date |
Oct 11, 2021 |
| Contact name |
Andrea Di Pietro |
| E-mail(s) |
dipi.andrea@gmail.com
|
| Phone |
+610450240751
|
| Organization name |
Monash University
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
B cells, Antibody, Memory Laboratory
|
| Street address |
15 Innovation Walk, Monash University
|
| City |
Clayton |
| State/province |
VIC |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL21626 |
| Series (2) |
| GSE163363 |
Chromatin accessibility regions in GC B cells during acute and chronic viral infection |
| GSE163365 |
Targeting BMI-1 in B cells restores effective humoral immune responses and controls chronic viral infection |
|
| Relations |
| BioSample |
SAMN17097264 |
| SRA |
SRX9691945 |
