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Sample GSM1673659 Query DataSets for GSM1673659
Status Public on Apr 30, 2019
Title MEL_4H8_ChIAPET_D0R2
Sample type SRA
Source name MEL
Organism Mus musculus
Characteristics cell type: MEL
time: D0
Treatment protocol MELs grown to a density of 1 million/ml were differentiated using 2% DMSO (VWR) added to the medium and the cells were grown for another 5 days to induce the expression of hemoglobin genes. At least 80-90% of cells expressed hemoglobin based on their color and benzidine/hydrogen peroxide staining result.
Growth protocol Mouse erythroleukemia cells (MEL, ATCC, Manassas, VA) were grown in RPMI-1640 medium (Life Technologies, Carlsbad, CA) supplemented with penicillin/streptomycin (Life Technologies) and 10% FBS (VWR, Radnor, PA). Trypan Blue (VWR) staining was performed before harvesting the cells for each assay in order to make sure that at least 90% of the cells were viable. All experiments were done with 2 biological replicates.
Extracted molecule genomic DNA
Extraction protocol Biological replicates of RNA Polymerase II ChIA-PET libraries for uninduced (MEL) and induced (MEL+DMSO) MEL were essentially constructed as previously described (Li et al. 2012) with additional changes to volume used in circularization (Heidari et al. 2014). The starting material was from 100-200 million cells and the ChIPs were performed using mouse anti-RNA polymerase II 4H8 antibody (catalog number sc-47701X, Santa Cruz Biotechnology, CA) and Dynabeads M-280 sheep anti-mouse beads (Life Technologies).
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Description ChIA-PET
processed_data_file: MEL_D0_3kb_edge_list.txt, MEL_D0_1kb_edge_list.txt, MEL_D0_3kb_vertices_with_connection_edge.bed, MEL_D0_1kb_vertices_with_connection_edge.bed
Data processing Half linker sequences were removed from reads and only the 20bp tags from each end were used for mapping. Tags were separated into two groups based on the half linker barcode information of the pair-end reads: the AA/BB group that should hold true interactions as well as some non-specific random ligations and the AB chimeric ligation group to estimate the extent of non-specific random ligations.
The tags were mapped to mm9 reference genomes with Bowtie, respectively using the parameters -S -q -v 2 -k 1 -m 1 --best –strata.
petNet pipeline was used to build Chromatin Interaction Graphs (Jansen el al, in preparation)
genome build: mm9
processed data files format and content: 3kb and 1kb vertices are generated from DNase-seq consolidated hotspots, together with the connection edges list and vertice list with edges based on both 3kb and 1kb vertices from day0 and day5 MEL ChIA-PET data
Submission date May 03, 2015
Last update date May 15, 2019
Contact name Marissa Macchietto
Organization name University of Minnesota, Minneapolis
Department Minnesota Supercomputing Institute
Street address 117 Pleasant Street SE
City Minneapolis
ZIP/Postal code 55455
Country USA
Platform ID GPL19057
Series (1)
GSE67955 The landscape of global-long range interactions in mouse and human blood cell lines mediated by Yy1, GATA1, and CTCF during differentiation
BioSample SAMN03580699
SRA SRX1016132

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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