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Status |
Public on Sep 27, 2023 |
Title |
Hi-C_TauWT_11months |
Sample type |
SRA |
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Source name |
Forebrain
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Organism |
Mus musculus |
Characteristics |
tissue: Forebrain cell type: Neuron genotype: Tau P301S
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Extracted molecule |
genomic DNA |
Extraction protocol |
In situ Hi-C was performed as previously described in Rao et al., 2014. Nuclei were permeabilized. DNA was digested with 100 units of MboI, and the ends of restriction fragments were labeled using biotinylated nucleotides and ligated in a small volume. After reversal of crosslinks, ligated DNA was purified and sheared to a length of ∼400 bp, at which point ligation junctions were pulled down with streptavidin beads and prepped for Illumina sequencing. P301S Tau mice and primary neuronal culture Hi-C were performed using FANS isolated nuclei with the Dovetail Hi-C kit (SKU: 21004) Illumina libraries were sequenced in 38 bp paired-end mode. Library construction was performed using the custom protocol as described in Rao et al, 2014 or using the library preparation module in the Dovetail Hi-C kit (SKU: 21004) Illumina libraries were sequenced in 38 bp paired-end mode
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Library strategy |
Hi-C |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
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Data processing |
Hi-C experiments were analyzed using Homer and Juicer pipeline For HOMER pipeline, Reads were trimmed for GATC sites and mapped using bowtie2. Mapped reads were analyzed using the makTagDirectory command in the Homer pipeline. Processed files (.hic) were created using the tagDir2hicFile.pl script in Homer. In addition to homer pipeline, Juicer pipeline was used to create hic files for combined CK-p25 samples Con, Step 1, and Step 2 as described in Rao et al.,2014. In Brief, paired-end read pairs were aligned separately to the mouse genome (mm10) using BWA. Next, duplicates/invalid pairs were removed. Interaction matrices were generated at resolutions of 2.5Mb, 1Mb, 500kb, 250kb, 100kb, 50kb, 25kb, 10kb, and 5kb. Assembly: mm10 Supplementary files format and content: Processed Hi-C data in an indexed binary format (.hic) that can be accessed using the Juicebox tool (https://aidenlab.org/juicebox/)
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Submission date |
Mar 15, 2023 |
Last update date |
Sep 27, 2023 |
Contact name |
Vishnu Dileep |
E-mail(s) |
vdileep@mit.edu
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Organization name |
Massachusetts Institute of Technology
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Department |
Brain and Cognitive Sciences
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Lab |
Tsai
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Street address |
43 Vassar St
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City |
Cambridge |
State/province |
MA |
ZIP/Postal code |
02139 |
Country |
USA |
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Platform ID |
GPL19057 |
Series (2) |
GSE227443 |
Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration [Hi-C] |
GSE227445 |
Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration |
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Relations |
BioSample |
SAMN33773421 |
SRA |
SRX19705062 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7100691_Hi-C_TauWT_11months.hic |
689.5 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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