|
| Status |
Public on May 22, 2016 |
| Title |
Frozen.1K |
| Sample type |
SRA |
| |
|
| Source name |
CD19+ B cells
|
| Organism |
Homo sapiens |
| Characteristics |
facs sorting markers: CD19+IgD+CD3-CD27-Mtg-CD24+CD38-
cell type: B cells
tissue: blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The indicated number of naïve B cells (CD19+IgD+CD3-CD27-Mtg-CD24+CD38-) were sorted by FACS
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 using the Illumina Nextera Kit 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 |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Library strategy: ATAC-seq
Raw sequencing reads were mapped to the hg19 version of the human genome using Bowtie version1.1.1 with the default parameters
reads per million normalized bigWig files were generated using the GenomicRanges R/Bioconductor package and UCSC tool bedGraphToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: reads per million normalized bigWig
|
| |
|
| Submission date |
Jul 24, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chris Scharer |
| E-mail(s) |
cdschar@emory.edu
|
| 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 |
GPL11154 |
| Series (1) |
| GSE71338 |
Effects of biobanking on chromatin accessibility |
|
| Relations |
| BioSample |
SAMN03922871 |
| SRA |
SRX1117834 |
