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Sample GSM6460098 Query DataSets for GSM6460098
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)
 
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
 
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

Supplementary file Size Download File type/resource
GSM6460098_HCT116.IgG.CNR.Etop.Rep3.Mar2022.bam.bin5.dedup.RPKM.bw 146.3 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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