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| Status |
Public on Jun 23, 2020 |
| Title |
HiC_Early_rep1 |
| Sample type |
SRA |
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| Source name |
Sorted neuronal nuclei
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| Organism |
Mus musculus |
| Characteristics |
tissue: Hippocampus
strain: ArcCreERT2 x R26R-STOP-floxed- yellow fluorescent protein (eYFP)
genotype: +/+
treatment: Foot shock day 0, No recall, tissue collection day 0
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| Treatment protocol |
In order to minimize the nonspecific eYFP label, one day prior to the contextual fear conditioning (CFC), mice were single housed in a 24h dark/dark room. In the next day, mice received one dose of 4-Hydroxytamoxifen, 1h before the CFC test. Following the behavioral task, mice were either euthanized after 1.5-2 h and brain were collected, or placed back into the dark room for the following 48 hr. After mice were taken out of the dark, they were returned to normal 12 hr (06:00–18:00) light-dark cycle, in the same room. 3 days later (total of 5 days after the CFC), half of the mice cohort were euthanized and brain were collected, while the other half returned to the testing room, where they exposed to the fear inducing cue (tone and context).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hippocampal tissue was extracted and flash frozen. After extraction, samples were immediately homogenized in 0.5 mL ice cold PBS with protease inhibitors (Pi) (11836170001, Roche). The suspension was fixed with 1% paraformaldehyde for 10 min, quenched with Glycine 2.5M for 5 min and washed twice with 5 mL of PBS. The suspension was centrifuged at 1200 g, 4°C, for 5 minutes and the pellet was resuspended in 5 mL NF-1 hypotonic buffer (0.5% Triton X-100/0.1M Sucrose/5mM MgCl2/1mM EDTA/10mM Tris-HCl, pH 8.0, Pi). Pelleted nuclei were resuspended in and incubated with NeuN and GFP primary antibodies for overnight in 4°C. Unbound antibodies were washed out twice and nuclei were filtered with 40 µm mesh filter for FACS sorting.
Nuclei from fixed cells were sorted into 1.5 mL eppendorf tubes containing 500 µl fresh ice-cold lysis buffer (10mM Tris pH=8, 10mM NaCl, 0.2% Igepal CA-630, Pi and PCR grade water) and frozen on dry ice and stored at -80c until they were used. Hi-C libraries were prepared from 100,000 cells/per group (collected from two animals) in two biological replicates, using DovetailTM Hi-C kit manual (v.1.03, Dovetail Genomics, Chicago, USA).
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
HOMER Hi-C pipeline was used to filter experimental artefacts such as circularization, self-ligations and PCR duplicates.
Filtered reads were aligned to the reference mouse genome (mm9) and further processed using HOMER HI-C pipeline.
HOMER’s Hi-C tools were used to perform principal component analysis (PCA) on the Hi-C data to identify sub-nuclear compartments (A and B) at 50 Kb resolution.
Genome_build: mm9
Supplementary_files_format_and_content: first principal component (PC1) score
Supplementary_files_format_and_content: bedGraph
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| Submission date |
Jun 22, 2020 |
| Last update date |
Jun 23, 2020 |
| Contact name |
Asaf Marco |
| E-mail(s) |
Asaf.Marco@mail.huji.ac.il
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| Phone |
+972542394501
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| Organization name |
The Hebrew University of Jerusalem
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| Lab |
Asaf Marco
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| Street address |
Herzl 229
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| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE152953 |
Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble |
| GSE152956 |
Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble |
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| Relations |
| BioSample |
SAMN15340129 |
| SRA |
SRX8594704 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4630460_TagDir_early_rep1.50x100kb.PC1.bedGraph.gz |
678.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM4630460_TagDir_early_rep1.50x100kb.PC1.txt.gz |
825.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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