|
Status |
Public on Aug 20, 2022 |
Title |
IgG_etoposide_rep3_etoposide, 100 micromolar, 6hrs |
Sample type |
SRA |
|
|
Source name |
colon
|
Organism |
Homo sapiens |
Characteristics |
tissue: colon cell line: HCT116 cell type: colon carcinoma genotype: TP53+/+ treatment: etoposide, 100 micromolar, 6hrs
|
Treatment protocol |
Fresh media (McCoy's 5A with 10% fetal bovine serum) was added to cells which were then treated with either DMSO, etoposide, histidinol, or tunicamycin at the specified concentrations for 6 hrs before RNA was harvested
|
Growth protocol |
Cells were grown in McCoy's 5A media supplemented with 10% fetal bovine serum at 37˚C and 5% carbon dioxide in a humidified, water-jacketed incubator.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA fragments released by ATF4-targeted Mnase were isolated via Cut&Run using standard methods. Cut&Run-released DNA fragments were used as the template for Illumina-compatible DNA library prep (adapter ligation and multiplexing via NEBNext Ultra 2 DNA Library Prep)
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|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
NextSeq 2000 |
|
|
Data processing |
Paired end Cut&Run reads were aligned to the hg38 human reference genome using HISAT2 (v.2.2.1) and saved as sorted BAM files HISAT2 options (-X 700 -I 10 --phred33 --no-spliced-alignment --no-discordant --no-mixed --no-unal) Aligned reads were processed for visualization and other analyses using the deepTools (v.3.4.1) bamCoverage module deepTools options (--effectiveGenomeSize 2913022398 --binSize 5 --ignoreDuplicates --normalizeUsing RPKM) Assembly: hg38 Supplementary files format and content: bigWig files, bin size of 5, unique alignments only, RPKM normalized Library strategy: CUT&Run
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|
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Submission date |
Aug 15, 2022 |
Last update date |
Aug 20, 2022 |
Contact name |
Morgan A Sammons |
E-mail(s) |
masammons@albany.edu
|
Organization name |
University at Albany - SUNY
|
Department |
Biological Sciences
|
Lab |
Sammons
|
Street address |
1400 Washington Ave, Life Sciences 2075
|
City |
Albany |
State/province |
NY |
ZIP/Postal code |
12222 |
Country |
USA |
|
|
Platform ID |
GPL30173 |
Series (1) |
GSE211264 |
Cut&Run Analysis of ATF4 genomic occupancy in HCT116 colon carcinoma cell lines after treatment with DMSO, etoposide, tunicamycin, or histidinol |
|
Relations |
BioSample |
SAMN30321074 |
SRA |
SRX17075554 |