|
| Status |
Public on Mar 08, 2017 |
| Title |
I3_HFF_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
HFF_infected
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hff
infection status: T. gondii infected
|
| Treatment protocol |
Cells were infected with T. gondii and harvested 24 hours after the infection for DNA extraction.
|
| Growth protocol |
HFFs were grown to confluency prior to infection using DMEM supplemented with 10% FBS, 1% penicilin streptomycin and 1% L-glutamine.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Each sample was prepared as previously described in Buenrostro J.D. Nature Methods 2013
Each sample was prepared as previously described in Buenrostro J.D. Nature Methods 2013
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Transposase accessible chromatin
|
| Data processing |
Library strategy: ATAC-seq
The fastq files were aligned using bwa-mem
Genome_build: hg19-TgME49v9.0
Supplementary_files_format_and_content: A bed file of peaks for each sample. See Supplemental materials from publication for more details.
|
| |
|
| Submission date |
Mar 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
John Greally |
| E-mail(s) |
john.greally@einsteinmed.edu
|
| Phone |
7186781234
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Genetics
|
| Street address |
1301 Morris Park Avenue
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE79609 |
Toxoplasma gondii remodels the cis-regulatory landscape of infected human host cells [ATAC-seq] |
| GSE79612 |
Toxoplasma gondii remodels the cis-regulatory landscape of infected human host cells |
|
| Relations |
| BioSample |
SAMN04580028 |
| SRA |
SRX1662133 |
