|
| Status |
Public on Jun 21, 2023 |
| Title |
Characterisation by Next generation Capture-C of Pax6 locus in a mouse cell line with bleomycin treatment to relieve topological stress |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
NG-Capture-C profiling of chromatin interactions (using DpnII 3C and Oligo nucleotide sequence capture followed by Next generation sequencing) of enhancers, promoters and CTCF/Rad21 binding sites throughout a ~600kb region of the mouse Pax6 locus in β-TC3 cells treated with alpha amanitin. β-TC3 cell are a mouse pancreatic β cell derived from mouse insulinoma.
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| Overall design |
β-TC3 mouse cells were analysed after being treated either with bleomycin or with mock treatment (PBS alone). Two separate panels of capture oligos were used (denoted the CTCF pool and the PROM pool), with two biological replicates generated in each case.
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| |
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| Contributor(s) |
Forte G, Buckle A, Boyle S, Marenduzzo D, Gilbert N, Brackley CA |
| Citation(s) |
37537334 |
| |
| Submission date |
Jun 20, 2023 |
| Last update date |
Sep 20, 2023 |
| Contact name |
Giada Forte |
| E-mail(s) |
gforte@ed.ac.uk
|
| Organization name |
The University of Edinburgh
|
| Street address |
Peter Guthrie Tait Road
|
| City |
Edinburgh |
| ZIP/Postal code |
EH93FD |
| Country |
United Kingdom |
| |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE235416 |
Transcription modulates chromatin dynamics and locus configuration sampling |
|
| Relations |
| BioProject |
PRJNA985712 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE235335_capture_oligo_panel.xlsx |
8.7 Kb |
(ftp)(http) |
XLSX |
| GSE235335_captured_bin_3000_6000_RPM_7CE12_CTCF_BL.bedgraph.gz |
246.4 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_7CE12_CTCF_WT.bedgraph.gz |
251.7 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_CTCF10B_BL.bedgraph.gz |
234.8 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_CTCF10B_WT.bedgraph.gz |
254.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_CTCF4_BL.bedgraph.gz |
217.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_CTCF4_WT.bedgraph.gz |
227.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_CTCF5_BL.bedgraph.gz |
263.8 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_CTCF5_WT.bedgraph.gz |
274.9 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_CTCF6_BL.bedgraph.gz |
244.2 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_CTCF6_WT.bedgraph.gz |
263.4 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_CTCF7_BL.bedgraph.gz |
258.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_CTCF7_WT.bedgraph.gz |
275.8 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_CTCFp11_BL.bedgraph.gz |
233.7 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_CTCFp11_WT.bedgraph.gz |
244.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_Elp4_BL.bedgraph.gz |
221.4 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_Elp4_WT.bedgraph.gz |
231.9 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_Pax6_P0_BL.bedgraph.gz |
225.6 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_Pax6_P0_WT.bedgraph.gz |
232.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_Pax6_P1_BL.bedgraph.gz |
231.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_Pax6_P1_WT.bedgraph.gz |
236.5 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_Pax6_Palpha_BL.bedgraph.gz |
240.5 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_Pax6_Palpha_WT.bedgraph.gz |
249.5 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_Rcn1_prom_BL.bedgraph.gz |
262.9 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_Rcn1_prom_WT.bedgraph.gz |
273.1 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_e200_BL.bedgraph.gz |
257.2 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_bin_3000_6000_RPM_e200_WT.bedgraph.gz |
270.5 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_7CE12_CTCF_BL.bedgraph.gz |
282.4 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_7CE12_CTCF_WT.bedgraph.gz |
296.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_CTCF10B_BL.bedgraph.gz |
264.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_CTCF10B_WT.bedgraph.gz |
305.6 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_CTCF4_BL.bedgraph.gz |
226.7 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_CTCF4_WT.bedgraph.gz |
242.6 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_CTCF5_BL.bedgraph.gz |
330.1 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_CTCF5_WT.bedgraph.gz |
360.4 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_CTCF6_BL.bedgraph.gz |
288.6 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_CTCF6_WT.bedgraph.gz |
327.8 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_CTCF7_BL.bedgraph.gz |
320.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_CTCF7_WT.bedgraph.gz |
359.4 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_CTCFp11_BL.bedgraph.gz |
262.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_CTCFp11_WT.bedgraph.gz |
284.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_Elp4_BL.bedgraph.gz |
235.9 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_Elp4_WT.bedgraph.gz |
253.5 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_Pax6_P0_BL.bedgraph.gz |
242.4 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_Pax6_P0_WT.bedgraph.gz |
250.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_Pax6_P1_BL.bedgraph.gz |
254.7 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_Pax6_P1_WT.bedgraph.gz |
263.2 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_Pax6_Palpha_BL.bedgraph.gz |
276.8 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_Pax6_Palpha_WT.bedgraph.gz |
295.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_Rcn1_prom_BL.bedgraph.gz |
342.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_Rcn1_prom_WT.bedgraph.gz |
369.2 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_e200_BL.bedgraph.gz |
336.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_captured_rawpileup_e200_WT.bedgraph.gz |
373.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSE235335_targetPositions_mm9_DpnIIfrag_poolCTCF.bed.gz |
187 b |
(ftp)(http) |
BED |
| GSE235335_targetPositions_mm9_DpnIIfrag_poolPROM.bed.gz |
186 b |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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