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Status |
Public on Jan 04, 2021 |
Title |
DMSO SON TSA-seq Input Replicate2 |
Sample type |
SRA |
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Source name |
IMR90
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Organism |
Homo sapiens |
Characteristics |
treatment: DMSO
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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.
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Growth protocol |
Proliferative IMR90 cells were grown in 3% oxygen at 37C in DMEM media with 10% FBS
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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
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
NextSeq 550 |
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Description |
DMSO_rep2.bw
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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
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Submission date |
Jul 09, 2020 |
Last update date |
Jan 04, 2021 |
Contact name |
Katherine A Alexander |
E-mail(s) |
kaalexa@pennmedicine.upenn.edu
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Organization name |
University of Pennsylvania
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Street address |
Smilow Center for Translational Research
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City |
Philadelphia |
State/province |
Pennsylvania |
ZIP/Postal code |
19104 |
Country |
USA |
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Platform ID |
GPL21697 |
Series (1) |
GSE154095 |
p53 transcription factor mediates nuclear speckle association of target genes |
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Relations |
BioSample |
SAMN15493143 |
SRA |
SRX8699729 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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