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Sample GSM7100691 Query DataSets for GSM7100691
Status Public on Sep 27, 2023
Title Hi-C_TauWT_11months
Sample type SRA
 
Source name Forebrain
Organism Mus musculus
Characteristics tissue: Forebrain
cell type: Neuron
genotype: Tau P301S
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
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
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/)
 
Submission date Mar 15, 2023
Last update date Sep 27, 2023
Contact name Vishnu Dileep
E-mail(s) vdileep@mit.edu
Organization name Massachusetts Institute of Technology
Department Brain and Cognitive Sciences
Lab Tsai
Street address 43 Vassar St
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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