|
| Status |
Public on Sep 06, 2018 |
| Title |
1702_nB_neg [ATAC-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organism |
Mus musculus |
| Characteristics |
cell type: naive B cells
gender: female
sorting markers: Thy1.1- F4/80- CD11c- B220+ GL7- CD138-
strain: C57BL/6J
tissue: spleen
stimulation: LPS
lsd1 status: wild-type
|
| Treatment protocol |
Three days following LPS stimulation, cells were FACS-purified from the spleens of wild-type and LSD1-knockout mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total RNA was extracted using the Zymo Quick-RNA MicroPrep Kit
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 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 |
May 22, 2018 |
| Last update date |
Sep 06, 2018 |
| 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) |
| GSE114774 |
LSD1 regulates plasmablast chromatin accessibility |
| GSE114777 |
LSD1 regulates plasmablast chromatin accessibility and transcriptome |
|
| Relations |
| BioSample |
SAMN09237992 |
| SRA |
SRX4112872 |
