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Sample GSM4663845 Query DataSets for GSM4663845
Status Public on Jan 04, 2021
Title DMSO SON TSA-seq Input Replicate2
Sample type SRA
 
Source name IMR90
Organism Homo sapiens
Characteristics treatment: DMSO
Treatment protocol Cells were treated at 1:1000 with DMEM or Nutlin-3a for 6 hours for a final concentration of 5uM Nutlin from a 5mM DMSO-dissolved stock solution.
Growth protocol Proliferative IMR90 cells were grown in 3% oxygen at 37C in DMEM media with 10% FBS
Extracted molecule genomic DNA
Extraction protocol Pulldown and input DNA was prepared using the SON TSA-seq protocol according to Condition E from https://www.biorxiv.org/content/10.1101/824433v2.full, with DNA sheared to an average 250bp size using a Covaris S220 as in ChIP-seq protocols.
Libraries were prepared from sheared DNA using the NEBnext Ultra II DNA Library Prep Kit for Illumina
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model NextSeq 550
 
Description DMSO_rep2.bw
Data processing Library strategy: SON TSA-seq
Demultiplexed paired-end fastq files were aligned to the hg19 genome using Bowtie2 with a maximum fragment length of 1000 base pairs (-X 1000) and otherwise default conditions.
SAM files were converted to BAM files using samtools-1.1 function samtools view, BAM files were sorted using samtools sort (samtools sort -n -@ 4 -m 1G -O bam -o sorted.bam -T prefix bamFile), and duplicate reads were removed using Picard MarkDuplicates (with REMOVE_DUPLICATES=True and ASSUME_SORT_ORDER=queryname)
Input-subtracted SON TSA-seq signal was quantified and significance was determined across sliding windows of different sizes (25kb, 50kb, 100kb, and 500kb) using DiffBind (https://github.com/katealexander/TSAseq-Alexander2020/tree/master/genomicBins_DiffBind)
Significant domains with various adjusted p-values were extracted from DiffBind results, and domains were merged using bedtools sort and bedtools merge (https://github.com/katealexander/TSAseq-Alexander2020/tree/master/genomicBins_DiffBind). The text file, genes_sigUp_25to100_padj0.01.txt contains a list of genes that were within significantly increasing SON bins between Nutlin and DMSO with an adjusted p-value of less than 0.01 from sliding windows of 25kb, 50kb, and 100kb
A list of genes with transcription start sites within significantly changing domains was extracted using python (https://github.com/katealexander/TSAseq-Alexander2020/tree/master/genomicBins_DiffBind).
Genome_build: hg19
Supplementary_files_format_and_content: DiffBind results text files (starting with "DiffBindResults_") of 9 sliding 25kb, 50kb, 100kb, and 500kb windows
Supplementary_files_format_and_content: Gene list text files (starting with "genes_") containing the genes that increase SON signal from 25kb, 50kb, and 100kb merged DiffBind binds at different adjusted p-value cutoffs designated at the end of the file name, before ".txt"
Supplementary_files_format_and_content: Text file list of IMR90 p53 targets (defined using https://github.com/katealexander/TSAseq-Alexander2020/tree/master/IMR90_p53targets)
Supplementary_files_format_and_content: Text file lists of IMR90 p53 targets that do ("IMR90_p53targs_upSONpadj0.01.txt") or do not ("IMR90_p53targs_nsSONpadjOver0.1.txt") increase SON signal upon Nutlin treatment.
Supplementary_files_format_and_content: bigWig files (ending in ".bw") for USCS genome browser veiwing of input-subtracted SON TSA-seq and no primary experiments.
Supplementary_files_format_and_content: BED files (ending in ".bed") of merged domains that increase SON signal upon Nutlin treatment called at 25kb, 50kb, and 100kb window sizes with different DiffBind adjusted p-value cutoffs
 
Submission date Jul 09, 2020
Last update date Jan 04, 2021
Contact name Katherine A Alexander
E-mail(s) kaalexa@pennmedicine.upenn.edu
Organization name University of Pennsylvania
Street address Smilow Center for Translational Research
City Philadelphia
State/province Pennsylvania
ZIP/Postal code 19104
Country USA
 
Platform ID GPL21697
Series (1)
GSE154095 p53 transcription factor mediates nuclear speckle association of target genes
Relations
BioSample SAMN15493143
SRA SRX8699729

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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