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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 30, 2015 |
| Title |
Hi-C NPC-NcoI |
| Sample type |
SRA |
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| Source name |
Mouse NPC cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: neural progenitor cells
restriction enzyme: NcoI
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C libraries were generated as previously published (Lieberman-Aiden et al, 2009), with modifications to increase DNA yield. See associated publication for details.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Library strategy: Hi-C
The paired end Hi-C reads were mapped and filtered with the hiclib pipeline (Imakaev et al., 2012, Downloaded November 2013) using default parameters. Data was binned at 50kb or 100kb, depending on the application.
Hi-C matrices were corrected using Iterative Correction (Imakaev et al., 2012) and further processed with custom code to generate normalized heatmaps (See associated publication for details).
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files are tab-delimited text files that contain raw or normalized interaction scores between genomic loci for a given chromosome. The coordinates of each loci are marked in the first row and first column of the table.
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| Submission date |
Jul 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Josee Dostie |
| E-mail(s) |
[email protected]
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| Organization name |
McGill University
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| Department |
Biochemistry
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| Street address |
3655 Prom. Sir-William-Osler
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| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3G 1Y6 |
| Country |
Canada |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE59027 |
Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation |
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| Relations |
| Reanalyzed by |
GSE87112 |
| BioSample |
SAMN02900463 |
| SRA |
SRX644423 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1424559_Normalized_Heatmaps.50kb.NPC.NcoI.tar.gz |
123.9 Mb |
(ftp)(http) |
TAR |
| GSM1424559_Raw_Heatmaps.50kb.NPC.NcoI.tar.gz |
39.2 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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