|
| Status |
Public on Aug 15, 2022 |
| Title |
A673-EWS/FLI-Rescue-HiC 1 |
| Sample type |
SRA |
| |
|
| Source name |
A673 Ewing sarcoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
replicate: 1
transduced shrna: iEF + 3XFLAG-EWS/FLI
condition: EF-Rescue
|
| Treatment protocol |
EWS/FLI knock-down with RNAi followed by rescue of EWS/FLI expression with a 3XFLAG tagged EWS/FLI cDNA construct
|
| Growth protocol |
A673 cells were cultured in DMEM with L-Glutamine, supplemented with 10% FBS, 1% PSQ, 1% sodium pyruvate for 2-3 days, followed by selection in the same media supplemented with 2μg/mL puromycin, and 150μg/mL hygromycin B at 37ºC and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
AMPure XP bead extraction
in situ Hi-C (high throughput chromatin conformation capture)
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
in situ Hi-C
|
| Data processing |
Juicer software used to generate .hic files from concatenated fastq.gz files
Read alignment using BWA-MEM
Filter out chimeric reads, filter by map quality, filter out PCR duplicates using Picard Tools
Paired end reads in BAM files were converted to BEDPE format using SAMTools.
BEDPE files were then used to generate Hi-C Summary files (.hicsum) using the iHiC_BEDPE2HiCSummary function
Homer Hi-C analysis pipeline used to generate petag.FreqDistribution_1000.txt files from .hicsum files
DiffHiC R package used to generate differential interactions at 1mb and 20kb resolution (.bedpe files)
Loop lengths were calculated from 1mb lost and gained loops .bedpe files using excel to generate the Interaction_lengths.xlsx file
iHiC and TopDom software were used to call TAD domains and TAD boundaries from aligned and filtered Hi-C data
DiffHiC R package was used to calculate directionality statistic for 20kb regions in the genome from Hi-C data
Homer Hi-C analysis pipeline used to generate compartment eigenvectors (PC1 values) from EF-Endo, EF-KD and EF-Rescue Hi-C data
DeepTools used to convert bedgraph to bigwig and generate comparative bigwigs of ΔPC1 values for EF-Endo vs. EF-KD and EF-Rescue vs. EF-KD
Genome_build: hg19
Supplementary_files_format_and_content: See file type and description below under processed data files
Supplementary_files_format_and_content: A673_iLuc_197_30.hic: HiC contact matrix for EF-Endo
Supplementary_files_format_and_content: A673_iEF_197_30.hic: HiC contact matrix for EF-KD
Supplementary_files_format_and_content: A673_iEF_714_30.hic: HiC contact matrix for EF-Rescue
Supplementary_files_format_and_content: A673_iLuc197_petag.FreqDistribution_1000.txt: Interaction frequency over genomic distance in basepairs for EF-Endo
Supplementary_files_format_and_content: A673_iEF197_petag.FreqDistribution_1000.txt: Interaction frequency over genomic distance in basepairs for EF-KD
Supplementary_files_format_and_content: A673_iEF714_petag.FreqDistribution_1000.txt: Interaction frequency over genomic distance in basepairs for EF-Rescue
Supplementary_files_format_and_content: all_1_tmm.bedpe: all interaction counts for 1mb differential interactions between EF-Endo and EF-KD
Supplementary_files_format_and_content: si_tmm_1_gainedloops_10filt_0.05FDR_FC4_intrachromosomal.bedpe: gained interactions at 1mb resolution between EF-Endo and EF-KD
Supplementary_files_format_and_content: si_tmm_1_lostloops_10filt_0.05FDR_FC4_intrachromosomal.bedpe: lost interactions at 1mb resolution between EF-Endo and EF-KD
Supplementary_files_format_and_content: all_1R_tmm.bedpe: all interaction counts for 1mb differential interactions between EF-Rescue and EF-KD
Supplementary_files_format_and_content: si_tmm_1R_gainedloops_10filt_0.05FDR_FC4_intrachromosomal.bedpe: gained interactions at 1mb resolution between EF-Rescue and EF-KD
Supplementary_files_format_and_content: si_tmm_1R_lostloops_10filt_0.05FDR_FC4_intrachromosomal.bedpe: lost interactions at 1mb resolution between EF-Rescue and EF-KD
Supplementary_files_format_and_content: Interaction_lengths.xlsx: Excel file calculating lengths of gained and lost interactions
Supplementary_files_format_and_content: a673iluctagdir.20x40kb.PC1.bedGraph: PC1 bedgraph track for EF-Endo
Supplementary_files_format_and_content: a673ieftagdir.20x40kb.PC1.bedGraph: PC1 bedgraph track for EF-KD
Supplementary_files_format_and_content: a673714tagdir.20x40kb.PC1.bedGraph: PC1 bedgraph track for EF-Rescue
Supplementary_files_format_and_content: Endo_PC1_20X40.bw: PC1 bigwig track for EF-Endo
Supplementary_files_format_and_content: KD_PC1_20X40.bw: PC1 bigwig track for EF-KD
Supplementary_files_format_and_content: Rescue_PC1_20X40.bw: PC1 bigwig track for EF-Rescue
Supplementary_files_format_and_content: EndovsKD_PC1_subtract.bw: ΔPC1 bigwig track of EF-Endo PC1 minus EF-KD PC1
Supplementary_files_format_and_content: RescuevsKD_PC1_subtract.bw: ΔPC1 bigwig track of EF-Rescue PC1 minus EF-KD PC1
Supplementary_files_format_and_content: a673iluc20x40pc1_endokd_stable.bed: Stable compartments in EF-Endo vs EF-KD
Supplementary_files_format_and_content: a673iluc20x40pc1_endokd_AB.bed: B like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: a673iluc20x40pc1_endokd_BA.bed: A like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: a67371420x40pc1_rskd_stable.bed: Stable compartments in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: a67371420x40pc1_rskd_AB.bed: B like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: a67371420x40pc1_rskd_BA.bed: A like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: Stable_endoKD_DEG.txt: Differential gene expression in EF-Endo vs EF-KD for Stable compartments in EF-Endo vs EF-KD
Supplementary_files_format_and_content: AB_endoKD_DEG.txt: Differential gene expression in EF-Endo vs EF-KD for B like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: BA_endoKD_DEG.txt: Differential gene expression in EF-Endo vs EF-KD for A like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: Stable_RSKD_DEG.txt: Differential gene expression in EF-Rescue vs EF-KD for stable compartments in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: AB_RSKD_DEG.txt: Differential gene expression in EF-Rescue vs EF-KD for B like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: BA_RSKD_DEG.txt: Differential gene expression in EF-Rescue vs EF-KD for A like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: Stable_EndoKD_H3K27ac.txt: Differential H3K27ac enrichment in EF-Endo vs EF-KD for Stable compartments in EF-Endo vs EF-KD
Supplementary_files_format_and_content: AB_EndoKD_H3K27ac.txt: Differential H3K27ac enrichment in EF-Endo vs EF-KD for B like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: BA_EndoKD_H3K27ac.txt: Differential H3K27ac enrichment in EF-Endo vs EF-KD for A like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: Stable_RSKD_H3K27ac.txt: Differential H3K27ac enrichment in EF-Rescue vs EF-KD for stable compartments in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: AB_RSKD_H3K27ac.txt: Differential H3K27ac enrichment in EF-Rescue vs EF-KD for B like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: BA_RSKD_H3K27ac.txt: Differential H3K27ac enrichment in EF-Rescue vs EF-KD for A like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: A673_EEts_uniq_comps.histogram.txt: Histogram analysis of PC1 values at conserved EWS/FLI sites
Supplementary_files_format_and_content: A673_EEts_MS_comps.histogram.txt: Histogram analysis of PC1 values at GGAA-microsatellite bound EWS/FLI sites
Supplementary_files_format_and_content: A673_EEts_nonMS_comps.histogram.txt: Histogram analysis of PC1 values at non-microsatellite bound EWS/FLI sites
Supplementary_files_format_and_content: a673_endo_EEts_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping conserved EWS/FLI sites for EF-Endo
Supplementary_files_format_and_content: a673_kd_EEts_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping conserved EWS/FLI sites for EF-KD
Supplementary_files_format_and_content: a673_rescue_EEts_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping conserved EWS/FLI sites for EF-Rescue
Supplementary_files_format_and_content: a673_endo_EEts_MS_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping GGAA-microsatellite bound EWS/FLI sites for EF-Endo
Supplementary_files_format_and_content: a673_kd_EEts_MS_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping GGAA-microsatellite bound EWS/FLI sites for EF-KD
Supplementary_files_format_and_content: a673_rescue_EEts_MS_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping GGAA-microsatellite bound EWS/FLI sites for EF-Rescue
Supplementary_files_format_and_content: a673_endo_EEts_nonMS_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping non-microsatellite bound EWS/FLI sites for EF-Endo
Supplementary_files_format_and_content: a673_kd_EEts_nonMS_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping non-microsatellite bound EWS/FLI sites for EF-KD
Supplementary_files_format_and_content: a673_rescue_EEts_nonMS_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping non-microsatellite bound EWS/FLI sites for EF-Rescue
Supplementary_files_format_and_content: A673iLuc197.domain: TAD locations in EF-Endo
Supplementary_files_format_and_content: A673iEF197.domain: TAD locations in EF-KD
Supplementary_files_format_and_content: A673iEF714.domain: TAD locations in EF-Rescue
Supplementary_files_format_and_content: A673_iLuc197_p0.05.tadboundary.bedgraph: TAD boundaries in EF-Endo
Supplementary_files_format_and_content: A673_iEF197_p0.05.tadboundary.bedgraph: TAD boundaries in EF-KD
Supplementary_files_format_and_content: A673_iEF714_p0.05.tadboundary.bedgraph: TAD boundaries in EF-Rescue
Supplementary_files_format_and_content: EF-WTBoundaries.bed: TAD boundaries specific to EF-Endo and EF-Rescue only and not EF-KD
Supplementary_files_format_and_content: EF-KDBoundaries.bed: TAD boundaries specific to EF-KD only
Supplementary_files_format_and_content: StableBoundaries.bed: TAD boundaries common to EF-Endo, EF-KD and EF-Rescue
Supplementary_files_format_and_content: Directionality_Statistic_EndovsKD.txt: Directionality statistic calculated for EF-Endo and EF-KD
Supplementary_files_format_and_content: Directionality_Statistic_ResvsKD.txt: Directionality statistic calculated for EF-Rescue and EF-KD
Supplementary_files_format_and_content: EFEndovsEFKD_20kb_diffhicloops_tmmnormalized.bedpe: all interactions at 20kb resolution between EF-Endo and EF-KD
Supplementary_files_format_and_content: EFRescueVSEFKD_20kb_diffhicloops_tmmnormalized.bedpe: all interactions at 20kb resolution between EF-Rescue and EF-KD
Supplementary_files_format_and_content: si_tmm_20kb_EndovsKD_gainedloops_10filt_0.05FDR_FC4.bedpe: gained interactions at 20kb resolution for EF-Endo vs EF-KD
Supplementary_files_format_and_content: si_tmm_20kb_EndovsKD_lostloops_10filt_0.05FDR_FC4.bedpe: lost interactions at 20kb resolution for EF-Endo vs EF-KD
Supplementary_files_format_and_content: si_tmm_20kb_RescuevsKD_gainedloops_10filt_0.05FDR_FC4.bedpe: gained interactions at 20kb resolution for EF-Rescue vs EF-KD
Supplementary_files_format_and_content: si_tmm_20kb_RescuevsKD_lostloops_10filt_0.05FDR_FC4.bedpe: lost interactions at 20kb resolution for EF-Rescue vs EF-KD
Supplementary_files_format_and_content: all20_EndostableEnh_uniq.bedpe: all interactions at 20kb resolution overlapping Stable enhancers for EF-Endo vs EF-KD
Supplementary_files_format_and_content: all20_EndoLostEnh_uniq.bedpe: all interactions at 20kb resolution overlapping lost enhancers for EF-Endo vs EF-KD
Supplementary_files_format_and_content: all20_EndoGainedEnh_uniq.bedpe: all interactions at 20kb resolution overlapping gained enhancers for EF-Endo vs EF-KD
Supplementary_files_format_and_content: all20R_RescuestableEnh_uniq.bedpe: all interactions at 20kb resolution overlapping Stable enhancers for EF-Rescue vs EF-KD
Supplementary_files_format_and_content: all20R_RescueLostEnh_uniq.bedpe: all interactions at 20kb resolution overlapping lost enhancers for EF-Rescue vs EF-KD
Supplementary_files_format_and_content: all20R_RescueGainedEnh_uniq.bedpe: all interactions at 20kb resolution overlapping gained enhancers for EF-Rescue vs EF-KD
Supplementary_files_format_and_content: up20_anchors_DEG.txt: Differential gene expression for genes overlapping gained loop anchors for EF-Endo vs. EF-KD
Supplementary_files_format_and_content: up20R_anchors_DEG.txt: Differential gene expression for genes overlapping gained loop anchors for EF-Rescue vs. EF-KD
Supplementary_files_format_and_content: down20_anchors_DEG.txt: Differential gene expression for genes overlapping lost loop anchors for EF-Endo vs. EF-KD
Supplementary_files_format_and_content: down20R_anchors_DEG.txt: Differential gene expression for genes overlapping lost loop anchors for EF-Rescue vs. EF-KD
Supplementary_files_format_and_content: homerResults_gained20kb_endovskd.html: Homer motif enrichment containing top motifs occupied by gained interactions at 20 kb resolution for EF-Endo vs EF-KD
Supplementary_files_format_and_content: homerResults_gained20kb_rescuevskd.html: Homer motif enrichment containing top motifs occupied by gained interactions at 20 kb resolution for EF-Rescue vs EF-KD
Supplementary_files_format_and_content: all20EF_uniq.bedpe: all 20kb interactions between EF-Endo and EF-KD intersecting with a conserved EWS/FLI peak
Supplementary_files_format_and_content: all20REF_uniq.bedpe: all 20kb interactions between EF-Rescue and EF-KD intersecting with a conserved EWS/FLI peak
Supplementary_files_format_and_content: 1_all20noEF_uniq.bedpe: all 20kb interactions between EF-Endo and EF-KD intersecting with no conserved EWS/FLI peak
Supplementary_files_format_and_content: 1_all20RnoEF_uniq.bedpe: all 20kb interactions between EF-Rescue and EF-KD intersecting with no conserved EWS/FLI peak
Supplementary_files_format_and_content: 2_all20_bothEF_MSNMS_uniq.bedpe: all 20kb interactions between EF-Endo and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at one anchor and to an EWS/FLI peak bound to a non-microsatellite binding site at the second anchor of the loop/interaction
Supplementary_files_format_and_content: 2_all20R_bothEF_MSNMS_uniq.bedpe: all 20kb interactions between EF-Rescue and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at one anchor and to an EWS/FLI peak bound to a non-microsatellite binding site at the second anchor of the loop/interaction
Supplementary_files_format_and_content: 3_all20EF_bothMS_uniq.bedpe: all 20kb interactions between EF-Endo and EF-KD intersecting with a conserved EWS/FLI peak bound to GGAA-microsatellite at both loop anchors
Supplementary_files_format_and_content: 3_all20REF_bothMS_uniq.bedpe: all 20kb interactions between EF-Rescue and EF-KD intersecting with a conserved EWS/FLI peak bound to GGAA-microsatellite at both loop anchors
Supplementary_files_format_and_content: 4_all20_xorEFNMS_uniq.bedpe: all 20kb interactions between EF-Endo and EF-KD with one and only one anchor intersecting with a conserved EWS/FLI peak bound to non-microsatellite sites
Supplementary_files_format_and_content: 4_all20R_xorEFNMS_uniq.bedpe: all 20kb interactions between EF-Rescue and EF-KD with one and only one anchor intersecting with a conserved EWS/FLI peak bound to non-microsatellite sites
Supplementary_files_format_and_content: 5_all20_bothEFNMS_uniq.bedpe: all 20kb interactions between EF-Endo and EF-KD with both anchors intersecting with a conserved EWS/FLI peak bound to non-microsatellite sites
Supplementary_files_format_and_content: 5_all20R_bothEFNMS_uniq.bedpe: all 20kb interactions between EF-Rescue and EF-KD with both anchors intersecting with a conserved EWS/FLI peak bound to non-microsatellite sites
Supplementary_files_format_and_content: 6_all20_EFMSonly_uniq.bedpe: all 20kb interactions between EF-Endo and EF-KD with one and only one anchor intersecting with a conserved EWS/FLI peak bound to GGAA-microsatellite site
Supplementary_files_format_and_content: 6_all20R_EFMSonly_uniq.bedpe: all 20kb interactions between EF-Rescue and EF-KD with one and only one anchor intersecting with a conserved EWS/FLI peak bound to GGAA-microsatellite site
Supplementary_files_format_and_content: 2_all20_bothEF_MSNMS_sig.bedpe: Significant 20kb interactions between EF-Endo and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at one anchor and to an EWS/FLI peak bound to a non-microsatellite binding site at the second anchor of the loop/interaction
Supplementary_files_format_and_content: 2_all20_bothEF_MSNMS_sig_iLucintraTAD.bed: Significant 20kb interaction region between EF-Endo and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at one anchor and to an EWS/FLI peak bound to a non-microsatellite binding site at the second anchor that exist within a TAD region
Supplementary_files_format_and_content: 2_all20R_bothEF_MSNMS_sig.bedpe: Significant 20kb interactions between EF-Rescue and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at one anchor and to an EWS/FLI peak bound to a non-microsatellite binding site at the second anchor of the loop/interaction
Supplementary_files_format_and_content: 2_all20R_bothEF_MSNMS_sig_714intraTAD.bed: Significant 20kb interaction region between EF-Rescue and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at one anchor and to an EWS/FLI peak bound to a non-microsatellite binding site at the second anchor that exist within a TAD region
Supplementary_files_format_and_content: 3_all20EF_bothMS_sig.bedpe: Significant 20kb interactions between EF-Endo and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at both anchors
Supplementary_files_format_and_content: 3_all20EF_bothMS_sig_iLucintraTAD.bed: Significant 20kb interaction regions for EF-Endo vs EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at both anchors that exist within a TAD region
Supplementary_files_format_and_content: 3_all20REF_bothMS_sig.bedpe: Significant 20kb interactions between EF-Rescue and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at both anchors
Supplementary_files_format_and_content: 3_all20REF_bothMS_sig_714intraTAD.bed: Significant 20kb interaction regions between EF-Rescue and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at both anchors that exist within a TAD region
Supplementary_files_format_and_content: ggaa0to10_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 0-10 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa0to10_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 0-10 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa11to20_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 11-20 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa11to20_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 11-20 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa21to30_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 21-30 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa21to30_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 21-30 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa31to40_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 31-40 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa31to40_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 31-40 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa41up_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with > 40 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa41up_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with >40 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa1to5_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 1-5 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa1to5_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 1-5 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa6to10_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 6-10 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa6to10_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 6-10 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa11to15_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 11-15 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa11to15_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 11-15 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa16to20_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 16-20 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa16to20_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 16-20 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa21to25_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 21-25 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa25up_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with >25 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
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| |
|
| Submission date |
Sep 30, 2021 |
| Last update date |
Aug 15, 2022 |
| Contact name |
Iftekhar Ahmed Showpnil |
| E-mail(s) |
[email protected]
|
| Organization name |
Nationwide Children's Hospital
|
| Department |
CCCBD
|
| Lab |
Lessnick
|
| Street address |
700 Childrens Drive
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43205 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE185125 |
EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (Hi-C) |
| GSE185132 |
EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma |
|
| Relations |
| BioSample |
SAMN21924342 |
| SRA |
SRX12420352 |
