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Sample GSM2305573 Query DataSets for GSM2305573
Status Public on Apr 13, 2017
Title EV_plusQ_input
Sample type SRA
Source name HCT116
Organism Homo sapiens
Characteristics cell line: HCT116
treatment1(myc-er+oht or empty vector +oht): vector+OHT
treatment2(glutamine(q) concentration): 2mM
antibody: none
Treatment protocol Cells were treated with 100 nM 4-Hydroxytamoxifen for 15 hours, then glutamine starved for 5 hours in presence of 4-Hydroxytamoxifen.
Growth protocol HCT116 cells were maintained in DMEM supplemented with 10% FBS (Biochrom) and 1% penicillin/streptomycin. Experiments were performed using DMEM reconstituted with 2 mM glutamine, 2.5 g/l glucose, 0.015 g/l phenol red, 10% dialyzed FBS and 1% penicillin/streptomycin, without sodium pyruvate . For starvation experiments, cells were washed twice with PBS and cultured in reconstituted DMEM without glutamine.
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked with 1% formaldehyde for 10' at 37°C. After cell lysis, nuclei were resuspended in RIPA buffer and sonicated (Bransson) until average fragment size was below 500 bps. Antibodies were bound to Dyna beads and incubated with the chromatin. After sequential washing and elution with 1% SDS, crosslinking was reverted and DNA was purified using Qiagen PCR purification columns.
Libraries were constructed following manufacturer's instructions (NEBNext ChIP-Seq Sample Prep Kit). Briefly, ChIP DNA was end repaired, A tailed and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of an agarose gel and extracted with a Qiagen PCR purification column. Afterwards, DNA was enriched with 18 PCR cycles, fragment size was controlled with Biorad Experion system and quantified using picogreen assay. 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Data processing Fastq files were generated using Illumina's CASAVA software.
Reads were mapped to the human genome (hg19) using Bowtie v1.1.1 with default parameters and normalized to the sample with the smallest number of mapped reads.
Bedgraph files were generated with the genomeCoverageBed function from BedTools.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph format as described in the UCSC file format guide (
Submission date Sep 07, 2016
Last update date May 15, 2019
Contact name Martin Eilers
Organization name University of Wuerzburg
Department Chair for Biochemistry and Molecular Biology
Lab Martin Eilers
Street address Am Hubland
City Wuerzburg
ZIP/Postal code 97074
Country Germany
Platform ID GPL18573
Series (1)
GSE86556 The 3’-UTR of MYC couples RNA polymerase II function to ribonucleotide levels
BioSample SAMN05751909
SRA SRX2148696

Supplementary file Size Download File type/resource
GSM2305573_EV_plusQ_input.bedGraph.gz 91.6 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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