|
| Status |
Public on Apr 30, 2019 |
| Title |
MEL_4H8_ChIAPET_D5R1 |
| Sample type |
SRA |
| |
|
| Source name |
MEL
|
| Organism |
Mus musculus |
| Characteristics |
cell type: MEL
time: D5
|
| 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_D5_3kb_edge_list.txt, MEL_D5_1kb_edge_list.txt, MEL_D5_3kb_vertices_with_connection_edge.bed, MEL_D5_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 |
| E-mail(s) |
[email protected]
|
| 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 |
|
| Relations |
| BioSample |
SAMN03580700 |
| SRA |
SRX1016133 |
