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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
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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.
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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
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Contributor(s) |
Sos BC, Zhang K |
Citation(s) |
26846207 |
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Submission date |
Aug 14, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Kun Zhang |
E-mail(s) |
kzhang@eng.ucsd.edu
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Phone |
8585341348
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Organization name |
University of California San Diego
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Department |
Bioengineering
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Street address |
9500 Gilman Drive, MC0412, PFBH402
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City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92093 |
Country |
USA |
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Platforms (2) |
GPL15520 |
Illumina MiSeq (Homo sapiens) |
GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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Samples (11)
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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 |
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 Selector |
Processed data provided as supplementary file |
Processed data are available on Series record |
Raw data are available in SRA |
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