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Series GSE121840 Query DataSets for GSE121840
Status Public on Oct 27, 2018
Title CTCF sites display cell cycle dependent dynamics in factor binding and nucleosome positioning
Organism Homo sapiens
Experiment type Other
Genome binding/occupancy profiling by high throughput sequencing
Summary Using 5C, ATAC-seq and CUT&RUN we find loss of CTCF binding, CTCF loops and TADs in mitosis
 
Overall design 5C, ATAC-seq and CUT&RUN
 
Contributor(s) Oomen ME, Hansen AS, Liu Y, Darzacq X, Dekker J
Citation(s) 30655336
Submission date Oct 26, 2018
Last update date Mar 27, 2019
Contact name Marlies E Oomen
E-mail(s) marlies.oomen@helmholtz-munich.de
Organization name Helmholtz Zentrum München
Department Institute of Epigenetics and Stem Cells
Lab Torres-Padilla Lab
Street address Feodor-Lynen-Strasse 21
City München
ZIP/Postal code 81377
Country Germany
 
Platforms (3)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (160)
GSM3447650 HeLa Mitotic Chromatin 5C R2T1
GSM3447651 HeLa Mitotic Cell 5C R2T1
GSM3447652 HeLa Non sync Cell 5C R2T1
Relations
BioProject PRJNA498618
SRA SRP166944

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
GSE121840_CUT_and_RUN_BED_files.tar.gz 622.6 Mb (ftp)(http) TAR
GSE121840_MC_peaks.txt.HOMER_score.bed.no_blacklisted.bed.gz 279.4 Kb (ftp)(http) BED
GSE121840_MCl-peaks.txt.HOMER_score.bed.no_blacklisted.bed.gz 400.7 Kb (ftp)(http) BED
GSE121840_MO5CM-Hela-M-C-combined_5158-TalLmoHindIIIDA.score.sorted.subset.singletonFiltered.anchorFiltered.symmetrical.selfMerged.scaled-200000000.balanced_15000_6.balanced.matrix.txt.gz 3.1 Mb (ftp)(http) TXT
GSE121840_MO5CM-Hela-M-Cl-combined_5158-TalLmoHindIIIDA.score.sorted.subset.singletonFiltered.anchorFiltered.symmetrical.selfMerged.scaled-200000000.balanced_15000_6.balanced.matrix.txt.gz 3.2 Mb (ftp)(http) TXT
GSE121840_MO5CM-Hela-NS-C-combined_5158-TalLmoHindIIIDA.score.sorted.subset.singletonFiltered.anchorFiltered.symmetrical.selfMerged.scaled-200000000.balanced_15000_6.balanced.matrix.txt.gz 3.1 Mb (ftp)(http) TXT
GSE121840_MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz 1.1 Gb (ftp)(http) BED
GSE121840_MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw 624.1 Mb (ftp)(http) BW
GSE121840_MOAM-HFF-M-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed.gz 718.3 Kb (ftp)(http) BED
GSE121840_MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz 2.5 Gb (ftp)(http) BED
GSE121840_MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw 689.5 Mb (ftp)(http) BW
GSE121840_MOAM-HFF-M-FCl-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed.gz 1.1 Mb (ftp)(http) BED
GSE121840_MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.full_fragment.bed.gz 839.9 Mb (ftp)(http) BED
GSE121840_MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw 573.6 Mb (ftp)(http) BW
GSE121840_MOAM-HFF-NS-C-R1-R2_libraries_combined.bam.no_blacklist.bam.tagDir.peaks.bed.gz 1.8 Mb (ftp)(http) BED
GSE121840_MOAM-HeLa-M-C_ALL.bam.no_blacklist_regions.bam.full_fragment.bed.gz 1.2 Gb (ftp)(http) BED
GSE121840_MOAM-HeLa-M-C_ALL.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw 643.1 Mb (ftp)(http) BW
GSE121840_MOAM-HeLa-M-Cl-FCl_ALL.bam.no_blacklist_regions.bam.full_fragment.bed.gz 1.0 Gb (ftp)(http) BED
GSE121840_MOAM-HeLa-M-Cl-FCl_ALL.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw 623.5 Mb (ftp)(http) BW
GSE121840_MOAM-HeLa-NS-C_ALL.bam.no_blacklist_regions.bam.full_fragment.bed.gz 1.0 Gb (ftp)(http) BED
GSE121840_MOAM-HeLa-NS-C_ALL.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw 623.0 Mb (ftp)(http) BW
GSE121840_MOAM-U20S-MC_ALL.bam.no_blacklist.bam.full_fragment.bed.gz 1.3 Gb (ftp)(http) BED
GSE121840_MOAM-U20S-MC_ALL.bam.no_blacklist.bam.single_end.bed.gz.tagDir.peaks.bed.gz 367.4 Kb (ftp)(http) BED
GSE121840_MOAM-U20S-MC_ALL.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw 648.8 Mb (ftp)(http) BW
GSE121840_MOAM-U20S-NS_ALL.bam.no_blacklist.bam.full_fragment.bed.gz 1.3 Gb (ftp)(http) BED
GSE121840_MOAM-U20S-NS_ALL.bam.no_blacklist.bam.single_end.bed.gz.tagDir.peaks.bed.gz 954.3 Kb (ftp)(http) BED
GSE121840_MOAM-U20S-NS_ALL.bam.no_blacklist.bam.single_end.sort.bedGraph.bin.20bp.bed.gz.norm.bw 648.8 Mb (ftp)(http) BW
GSE121840_NS_peaks.txt.HOMER_score.bed.no_blacklisted.bed.gz 1.2 Mb (ftp)(http) BED
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Raw data are available in SRA
Processed data are available on Series record

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