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Series GSE99257 Query DataSets for GSE99257
Status Public on Nov 20, 2017
Title Robust detection of chromosomal contacts from small cell numbers using low-input Capture-C
Organism Mus musculus
Experiment type Other
Summary Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This hampers the investigation of chromatin structure in rare cell populations. We present two new low-input Capture-C protocols that generate high-quality, reproducible interaction profiles from fewer than 20,000 cells, and show that these are not biased by PCR amplification or the degree of formaldehyde fixation.
Overall design The Capture-C technologies combine 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. In this case, the promoters of alpha-globin, beta-globin and Slc25a37 were used as viewpoints. To optimise Capture-C technology for small cell numbers, we developed Low-Input (LI) Capture-C and Tag-Capture-C, and performed experiments with both protocols using 200 ng, 100 ng and 50 ng mouse erythroid 3C libraries, all in triplicates. In the reduced cross-linking experiments, we compared NG Capture-C interactions profiles generated from primary mouse erythroid cells fixed with 5%, 4%, 3%, 2%, 1%, 0.5% or 0% formaldehyde. Experiments were performed in technical duplicates.
Contributor(s) Oudelaar AM, Davies JO, Downes DJ, Higgs DR, Hughes JR
Citation(s) 29186505
Submission date May 24, 2017
Last update date May 15, 2019
Contact name A Marieke Oudelaar
Organization name University of Oxford
Department MRC Weatherall Institute of Molecular Medicine
Street address John Radcliffe Hospital
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
Platforms (2)
GPL16417 Illumina MiSeq (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (44)
GSM2639611 Erythroid cells fixed with 0% formaldehyde replicate 1
GSM2639612 Erythroid cells fixed with 0% formaldehyde replicate 2
GSM2639613 Erythroid cells fixed with 0.5% formaldehyde replicate 1
BioProject PRJNA387734
SRA SRP107948

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE99257_fix_all_HbaCombined.gfc.txt.gz 5.8 Mb (ftp)(http) TXT
GSE99257_fix_all_HbbCombined.gfc.txt.gz 5.6 Mb (ftp)(http) TXT
GSE99257_fix_all_Slc25A37.gfc.txt.gz 3.0 Mb (ftp)(http) TXT
GSE99257_small_cell_nr_alpha_gfc.txt.gz 1.9 Mb (ftp)(http) TXT
GSE99257_small_cell_nr_beta_gfc.txt.gz 1.7 Mb (ftp)(http) TXT
GSE99257_small_cell_nr_full_prot_alpha_gfc.txt.gz 452.8 Kb (ftp)(http) TXT
GSE99257_small_cell_nr_slc25a37_gfc.txt.gz 888.5 Kb (ftp)(http) TXT
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