|
| Status |
Public on Aug 06, 2019 |
| Title |
FoB_del_2 ATACseq |
| Sample type |
SRA |
| |
|
| Source name |
follicular B cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: follicular B cells
Sex: female
sorting markers: Thy1.1- F4/80- CD11b- B220+ CD93- GL7- CD23+ CD21mid CD1d-
strain: C57BL/6J
organ: spleen
stimulation: no stimulation
lsd1 status: knockout
|
| Treatment protocol |
No treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
10,000 cells were centrifuged for 10 minutes at 500xg, resuspended in 50 ul of Lysis Buffer (contents), and immediately centrifuged for 30 minutes at 500xg. Tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1x TD Buffer, 2.5 ul Tn5 Transpoase) and incubating for 60 minutes at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie-1.1.1
For each sample, peaks of accessibility were identified and annotated using MACS2 with the default settings
Genome_build: mm10
Supplementary_files_format_and_content: Data were normalized to reads per peak per million as previously described (Scharer et al. Sci. Rep. 2016. PMID 27249108)
|
| |
|
| Submission date |
Jun 04, 2019 |
| Last update date |
Aug 06, 2019 |
| Contact name |
Jeremy Matthew Boss |
| E-mail(s) |
[email protected]
|
| Organization name |
Emory University
|
| Department |
Microbiology and Immunology
|
| Lab |
Dr. Jeremy M. Boss
|
| Street address |
1510 Clifton Rd NE, Room 3120
|
| City |
Atlanta |
| State/province |
Georgia |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE132196 |
LSD1 regulates splenic B cell chromatin accessibility |
| GSE132227 |
LSD1 cooperates with non-canonical NF-êB signaling to regulate marginal zone B cell development |
|
| Relations |
| BioSample |
SAMN11959267 |
| SRA |
SRX5973574 |
