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| Status |
Public on Sep 07, 2020 |
| Title |
Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain |
| Organism |
Gallus gallus |
| Experiment type |
Other
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| Summary |
Clustering of strong replicators associated with active promoter are sufficient to establish an early-replicating domain
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| Overall design |
Repli-Seq: A Wt DT40 chicken cell line and one clonal homozygous cell line containing one module of cis-regulatory elements inserted into a mid-late replicating region of chromosome one (chr1:71,981,290-73,532,377 bp, galGal5) on the two alleles were analyzed (See Hassan-Zadeh et al. 2012, Fig.9). Immunoprecipitated nascent strands from the four S-phase fractions collected by flow cytometry or from an asynchronous cell population were sequenced to determine the replication timing profiles of the targeted region.
Hi-C: A Wt DT40 chicken cell line and two clonal cell lines containing two modules of cis-regulatory elements inserted into a mid-late replicating region of chromosome 1 at two genomic positions separated by 30kb (chr1:72,565,520 bp and chr1: 72,536,060 bp, galGal5) on one chromosome (named chromosome 1) and one reporter module inserted in the middle (chr1: 72,548,589 bp, galGal5) on the other chromosome (named chromosome 2) were analyzed. After modification, the chromosome 1 is changing its replication timing toward early replication whereas the chromosome 2 keeps its natural temporal program. Hi-C experiments were used to identify compartment status genome wide. The existence of significant and specific preference of interaction of the allele 1 with different loci was tested.
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| Contributor(s) |
Brossas C, Valton A, Venev SV, Chilaka S, Counillon A, Laurent M, Goncalves C, Duriez B, Picard F, Dekker J, Prioleau M |
| Citation(s) |
32935369 |
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| Submission date |
Jun 30, 2020 |
| Last update date |
Nov 09, 2020 |
| Contact name |
Caroline Brossas |
| E-mail(s) |
caroline.brossas@ijm.fr
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| Phone |
+33(1)57278124
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| Organization name |
Institut Jacques Monod, Université de Paris, CNRS UMR 7592
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| Lab |
Domaines chromatiniens et réplication
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| Street address |
15 rue Hélène Brion
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| City |
Paris |
| ZIP/Postal code |
75013 |
| Country |
France |
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| Platforms (2) |
| GPL19787 |
Illumina NextSeq 500 (Gallus gallus) |
| GPL23499 |
Illumina HiSeq 4000 (Gallus gallus) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA643249 |
| SRA |
SRP269402 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE153566_RAW.tar |
4.8 Gb |
(http)(custom) |
TAR (of BED, MCOOL) |
| GSE153566_all-allele-spe-2percent-highcis.galGal5.mapq_30.1000.mcool |
2.8 Gb |
(ftp)(http) |
MCOOL |
| GSE153566_galGal5.fa.gz |
372.8 Mb |
(ftp)(http) |
FA |
| GSE153566_galGal5.reduced.sorted.chrom.sizes.txt.gz |
326 b |
(ftp)(http) |
TXT |
| GSE153566_timing_Wt_weighted_average_gal5_fraction_by_region.bed.gz |
2.6 Mb |
(ftp)(http) |
BED |
| GSE153566_timing_cl6_weighted_average_gal5_fraction_by_region.bed.gz |
2.6 Mb |
(ftp)(http) |
BED |
| GSE153566_wt.galGal5.mapq_30.1000.mcool |
1.3 Gb |
(ftp)(http) |
MCOOL |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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