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SRX902502: GSM1625814: Ch17.B76-PM-30mins-bio-replicate1; Mus musculus; OTHER
1 ILLUMINA (Illumina HiSeq 2500) run: 630,829 spots, 32.2M bases, 23.5Mb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Topologically-associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication timing program
show Abstracthide Abstract
This study uncovers a temporal hierarchy of chromatin re-organization during G1 that is linked to the developmental and temporal control of replication timing, revealing a novel link between development and genome organization. Overall design: Analysis of time-course 4C-seq for several baits to study dynamic changes in chromatin organization during early G1
Sample: Ch17.B76-PM-30mins-bio-replicate1
SAMN03389535 • SRS865075 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina HiSeq 2500
Strategy: OTHER
Source: GENOMIC
Selection: other
Layout: SINGLE
Construction protocol: Cell cycle synchronized cultures were crosslinked for 10 minutes at RT in 1% formaldehyde. The reaction was quenched for 5 min at RT. We then applied 4C-seq method. Briefly, nuceli were isolated from the cross-linked cells and digested using the restriction enzyme HindIII. Fragments were ligated under dilute conditions and reversed cross-linked. The samples were then digested with DpnII and circularized. Subsequently bait specific primers were used to amplify the interaction partners and sequenced using the Illumina HiSeq 2500 platform, generating 50 bp reads. Libraries were generated by amplifying the 4C template using bait specific primers with added illumina adaptors. Bait is the genomic loci of interest whose genome-wide interactions are being measured by 4C-seq. We denote each bait by its chromosome followed by letter B and the approximate megabase-scale coordinate of the bait (e.g. Ch8.B26 means bait with a coordinate on 26th megabase of chromosome 8). Twelve baits were chosen based on their replication timing regulation and were named Ch8.B7,Ch8.B26,Ch8.B44,Ch8.B53,Ch8.B87,Ch8.B118,Ch16.B30,Ch16.B41,Ch16.B46,Ch16.B48,Ch17.B50,Ch17.B50 Coordinates are in mm9.
Experiment attributes:
GEO Accession: GSM1625814
Links:
External link:
Runs: 1 run, 630,829 spots, 32.2M bases, 23.5Mb
Run# of Spots# of BasesSizePublished
SRR1840389630,82932.2M23.5Mb2015-04-23

ID:
1296700

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