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Sample GSM2878059 Query DataSets for GSM2878059
Status Public on Nov 01, 2021
Title Mouse erythroid cells biological replicate 2; Capture-C, interacting promoters viewpoints
Sample type SRA
Source name Primary erythroid cells
Organism Mus musculus
Characteristics strain: C57Bl6
cell type: Ter-119+ cells isolated from phenylhydrazine treated spleen
viewpoint analyzed: Prom_interacting_chac2, Prom_interacting_cpeb4, Prom_interacting_fbxw11
Treatment protocol Ter-119+ erythroid cells were obtained from the spleens of female C57BL/6 mice treated with phenylhydrazine (three doses of 40 mg/g body weight given 12 hours apart; mice were sacrificed after five days).
Extracted molecule genomic DNA
Extraction protocol Spleens were gently dissociated into a single cell suspension and cells were passed through a 70 μm strainer to remove clumps. For ter-119+ cell selection, cells were stained with phycoerythrin conjugated anti-ter-119 antibodies and positively selected using anti-phycoerythrin MACS beads before fixation with formaldehyde.
Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments, as described in Davies et al, Nature Methods, 2016.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina MiSeq
Description Next generation Capture-C product (DNA)
3C library preparation followed by double oligonucleotide capture
Processed data file: See All_gfc_files.tar.gz and README_Samples_and_processedfiles.txt.
Data processing Library strategy: Capture-C
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2 -v 3) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)
Submission date Dec 06, 2017
Last update date Nov 01, 2021
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
Platform ID GPL16417
Series (1)
GSE114046 Tiled Capture-C
BioSample SAMN08136912

Supplementary data files not provided
Raw data provided as supplementary file
Processed data are available on Series record

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