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Status |
Public on Sep 20, 2019 |
Title |
Pictilisib_IFNg_rep1.rpm |
Sample type |
SRA |
|
|
Source name |
SqCC/Y1 cells
|
Organism |
Homo sapiens |
Characteristics |
agent: 0.5 micromolar Pictilisib and 100 ng/ul IFNg
|
Treatment protocol |
SqCC/Y1 cells were treated with either DMSO, 100 ng/ul IFNg, and/or 0.5 uM Pictilisib (GDC-0941) for 48 hours
|
Growth protocol |
SqCC/Y1 cells were grown in Dulbecco’s Modified Eagle Medium with 4.5 g/L D-glucose and L-Glutamine with 10% fetal bovine serum at 5% CO2
|
Extracted molecule |
genomic DNA |
Extraction protocol |
50,000 cells were centrifuged for 10 minutes at 500xg and resuspended in 25 ul of Tagmentation Reaction mix (1x TD Buffer, 2.5 ul Tn5 Transpoase, 0.2% Digitonin, 0.1% Tween-20) 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).
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|
|
Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 3000 |
|
|
Data processing |
Raw sequencing reads were mapped to the hg19 version of the human genome using Bowtie-1.1.1 with the default settings. For each sample peaks of accessibility were identified and annotated using MACS2 with the default settings Genome_build: hg19 Supplementary_files_format_and_content: bigwig files are normalized to reads per million (rpm) using R/Bioconductor Supplementary_files_format_and_content: tab delimited text file containing rpm normalized data for all peaks and all samples as well as peak annotations and locations.
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|
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Submission date |
Sep 19, 2019 |
Last update date |
Sep 20, 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 |
GPL21290 |
Series (1) |
GSE137719 |
ATAC-seq profiling assessing the impact of IFNg and Pictilisib on human SqCC/Y1 cells |
|
Relations |
BioSample |
SAMN12787847 |
SRA |
SRX6873179 |