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Series GSE72089 Query DataSets for GSE72089
Status Public on Jan 09, 2016
Title Validation of THS-seq method, and comparison of published ENCODE DNase-seq data, self-generated ATAC-seq data and published ATAC-seq data, and THS-seq data for quantitation of chromatin accessibility.
Organism Homo sapiens
Experiment type Third-party reanalysis
Other
Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin accessibility captures the binding status of protein factors to chromosomes in vivo, and has been considered a highly informative proxy for functional protein-DNA interactions. Existing DNase I and Tn5 transposase based assays generally require tens of thousands to millions of fresh cells. Applying Tn5 tagmentation to single cells yields very sparse maps. Here we present a transposome hypersensitive sites sequencing assay (THS-seq) for highly sensitive characterizations of chromatin accessibility.
 
Overall design Validation of THS-seq method, and comparison of DNase-seq, ATAC-seq and THS-seq methods for quantitation of chromatin accessibility.

GSE47753, GSM1155957 GM12878_ATACseq_50k_Rep1, data downsampled to 8,351,125 reads for analysis: pub_SRR891268_ATAC-seq_50k_cells_Rep1_downsampled_dfilter_peaks.bed.gz
GSE47753, GSM1155958 GM12878_ATACseq_50k_Rep2, data downsampled to 8,351,125 reads for analysis: pub_SRR891269_ATAC-seq_50k_cells_Rep2_downsampled_dfilter_peaks.bed.gz
GSE47753, GSM1155959 GM12878_ATACseq_50k_Rep3, data downsampled to 8,351,125 reads for analysis: pub_SRR891270_ATAC-seq_50k_cells_Rep3_downsampled_dfilter_peaks.bed.gz
GSE47753, GSM1155960 GM12878_ATACseq_50k_Rep4, data downsampled to 8,351,125 reads for analysis: pub_SRR891271_ATAC-seq_50k_cells_Rep4_downsampled_dfilter_peaks.bed.gz
GSE47753, GSM1155961 GM12878_ATACseq_500_Rep1, data downsampled to 8,351,125 reads for analysis: pub_SRR891272_ATAC-seq_500_cells_Rep1_downsampled_dfilter_peaks.bed.gz
GSE47753, GSM1155962 GM12878_ATACseq_500_Rep2, data downsampled to 8,351,125 reads for analysis: pub_SRR891273_ATAC-seq_500_cells_Rep2_downsampled_dfilter_peaks.bed.gz
raw data files were merged, alignment with bowtie 1.3 using parameters, bowtie -n1 -k1 --best --chunkmbs 10240 --strata -l32 -m1 -p4 --nomaqround --sam, followed by clonal read removal for the final data file for further analysis. GSM816665, raw data obtained from UCSC genome browser, https://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeOpenChromDnase: wgEncodeOpenChromDnaseGm12878RawData_merged_unique_dfilter_peaks.bed.gz
raw data files were merged, alignment with bowtie 1.3 using parameters, bowtie -n1 -k1 --best --chunkmbs 10240 --strata -l32 -m1 -p4 --nomaqround --sam, followed by clonal read removal for the final data file for further analysis. GSM864360, raw data obtained from UCSC genome browser, https://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeOpenChromFaire: wgEncodeOpenChromFaireGm12878RawData_merged_unique_dfilter_peaks.bed.gz
raw data files were merged, alignment with bowtie 1.3 using parameters, bowtie -n1 -k1 --best --chunkmbs 10240 --strata -l32 -m1 -p4 --nomaqround --sam, followed by clonal read removal for the final data file for further analysis. GSM736496, GSM736620, raw data obtained from UCSC genome browser, https://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeUwDnase: wgEncodeUwDnaseGm12878RawData_merged_unique_dfilter_peaks.bed.gz
 
Contributor(s) Sos BC, Zhang K
Citation(s) 26846207
Submission date Aug 14, 2015
Last update date May 15, 2019
Contact name Kun Zhang
E-mail(s) kzhang@eng.ucsd.edu
Phone 8585341348
Organization name University of California San Diego
Department Bioengineering
Street address 9500 Gilman Drive, MC0412, PFBH402
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platforms (2)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (11)
GSM1854465 100_cell_THS-seq_with_Tn5059_Rep1
GSM1854466 100_cell_THS-seq_with_Tn5059_Rep2
GSM1854467 500_cell_ATAC-seq_with_EzTn5_Rep1
Relations
Reanalysis of GSM1155957
Reanalysis of GSM1155958
Reanalysis of GSM1155959
Reanalysis of GSM1155960
Reanalysis of GSM1155961
Reanalysis of GSM1155962
Reanalysis of GSM816665
Reanalysis of GSM864360
Reanalysis of GSM736496
Reanalysis of GSM736620
BioProject PRJNA293169
SRA SRP062540

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE72089_RAW.tar 10.1 Mb (http)(custom) TAR (of BED)
GSE72089_pub_SRR891268_ATAC-seq_50k_cells_Rep1_downsampled_dfilter_peaks.bed.gz 373.1 Kb (ftp)(http) BED
GSE72089_pub_SRR891269_ATAC-seq_50k_cells_Rep2_downsampled_dfilter_peaks.bed.gz 491.3 Kb (ftp)(http) BED
GSE72089_pub_SRR891270_ATAC-seq_50k_cells_Rep3_downsampled_dfilter_peaks.bed.gz 542.7 Kb (ftp)(http) BED
GSE72089_pub_SRR891271_ATAC-seq_50k_cells_Rep4_downsampled_dfilter_peaks.bed.gz 570.8 Kb (ftp)(http) BED
GSE72089_pub_SRR891272_ATAC-seq_500_cells_Rep1_downsampled_dfilter_peaks.bed.gz 180.0 Kb (ftp)(http) BED
GSE72089_pub_SRR891273_ATAC-seq_500_cells_Rep2_downsampled_dfilter_peaks.bed.gz 371.0 Kb (ftp)(http) BED
GSE72089_wgEncodeOpenChromDnaseGm12878RawData_merged_unique_dfilter_peaks.bed.gz 457.3 Kb (ftp)(http) BED
GSE72089_wgEncodeOpenChromFaireGm12878RawData_merged_unique_dfilter_peaks.bed.gz 153.2 Kb (ftp)(http) BED
GSE72089_wgEncodeUwDnaseGm12878RawData_merged_unique_dfilter_peaks.bed.gz 553.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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