|
| Status |
Public on Dec 15, 2017 |
| Title |
M1_nB_neg |
| Sample type |
SRA |
| |
|
| Source name |
naïve B cells
|
| Organism |
Mus musculus |
| Characteristics |
Sex: female
sorting markers: Thy1.1- F4/80- CD11c- B220+ GL7- CD138- CD45.1+ CD45.2+
organ: spleen
stimulation: LPS
ezh2 status: wild-type
|
| Treatment protocol |
Chimeric mice were generated by transferring CD45.1/2 CRE negative and CD45.2 CRE positive Ezh2-floxed bone marrow into lethally irradiated CD45.1 wild-type mice. After allowing the immune system to reconstitute the animals were treated with tamoxifen to induce deletion of Ezh2 and subsequently inoculated with LPS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Three days post-LPS naïve B cell (nB, B220+GL7-CD138-) and plasmablast (Pb, CD138+) populations were isolated by FACS from the spleens of chimeric mice.
2000-4000 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 mm9 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: mm9
Supplementary_files_format_and_content: bigwig files are normalized to reads per peak million (rpm) using R/Bioconductor
|
| |
|
| Submission date |
Aug 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chris Scharer |
| E-mail(s) |
[email protected]
|
| Organization name |
Emory University
|
| Department |
Microbiology and Immunology
|
| Lab |
Chris Scharer
|
| Street address |
1510 Clifton Rd, Suite 3086A
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE103142 |
EZH2-dependent chromatin accessibility changes during B cell differentiation |
| GSE103195 |
Defects in T cell independent B cell differentiation in the absence of EZH2 |
|
| Relations |
| BioSample |
SAMN07562247 |
| SRA |
SRX3135961 |
