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Series GSE114121 Query DataSets for GSE114121
Status Public on May 07, 2018
Title 5C-ID: Increased resolution Chromosome-Conformation-CaptureCarbon-Copy with in situ 3C and double alternating primer design
Organism Mus musculus
Experiment type Other
Summary Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C generates high quality, high resolution maps of looping interactions genome-wide, but is intractable for high-throughput screening of loops across conditions due to the requirement of an enormous number of reads (>6 Billion) per library. Here, we describe 5C-ID, an updated version of Chromosome-Conformation-Capture-Carbon-Copy (5C) with restriction digest and ligation performed in the nucleus (in situ ChromosomeConformation-Capture (3C)) and ligation-mediated amplification performed with a new double alternating design. 5C-ID reduces spatial noise and enables higher resolution 3D genome folding maps than canonical 5C, allowing for a marked improvement in sensitivity and specificity of loop detection. 5C-ID enables the creation of high-resolution, high-coverage maps of chromatin loops in up to a 30 Megabase subset of the genome at a fraction of the cost of Hi-C.
Overall design Total of 7 samples of 5C using double alternating primers, including 1 sample from dilution 3C/5C and 6 samples from different genome copies of in situ 3C/5C
Contributor(s) Kim JH, Titus KR, Phillips-Cremins JE
Citation(s) 29772275
Submission date May 07, 2018
Last update date Mar 25, 2019
Contact name Jennifer E Phillips-Cremins
Organization name University of Pennsylvania
Department Bioengineering
Street address 415 Curie Blvd
City Philadelphia
State/province Pennsylvania
ZIP/Postal code 19104
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (7)
GSM3133242 5C-dilution-mEs-2i-GenomeCopies-200k
GSM3133243 5C-insitu-mEs-2i-GenomeCopies-200k
GSM3133244 5C-insitu-mEs-2i-GenomeCopies-100k
BioProject PRJNA464369
SRA SRP144756

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE114121_4000_pixelmap.bed.gz 15.7 Kb (ftp)(http) BED
GSE114121_BED_314-ES-NPC-LOCI_mm9.bed.gz 24.2 Kb (ftp)(http) BED
GSE114121_BED_6697-mm9-pluripotent.bed.gz 68.0 Kb (ftp)(http) BED
GSE114121_Figure2_dbl_alt_pixelmap.bed.gz 8.8 Kb (ftp)(http) BED
GSE114121_Figure2_single_alt_pixelmap.bed.gz 13.7 Kb (ftp)(http) BED
GSE114121_RAW.tar 634.1 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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