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| Status |
Public on Sep 12, 2023 |
| Title |
HiC_Morphine_rep3 |
| Sample type |
SRA |
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| Source name |
Cortical neuron
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| Organism |
Macaca mulatta |
| Characteristics |
cell type: Adult cortical neuron purified from the cortex regio
Sex: male
age: 3-4 years
treatment: treated with Morphine
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| Treatment protocol |
Four male rhesus monkeys (Macaca mulatta; 3-4-year old; weighing from 3.0 to 5.0 kg), were randomly divided into saline group (n=2) and morphine group (n=2). Morphine was subcutaneously (s.c.) injected into the back legs of monkey three times daily (at 9:00, 14:00, and 21:00 o’clock) for 90 days continuously to produce dependence. The doses of morphine were gradually elevated as following paradigm: day 1-7:3 mg/kg, day 8-14:6 mg/kg, day 15-21:9 mg/kg, day 22-28:12 mg/kg, day 29-90:15 mg/kg. Monkeys in saline group was injected subcutaneously three times daily with same volume of 0.9% saline (0.5 mL/kg) as a control.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The cross-linked cells were lysed in lysis buffer,fragmentation of the genome using restriction enzymes
Hi-C libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
The DLO Hi-C tool (Hong et al., 2019) v0.30 was applied to removes redundancy and reducing noise, removes pair end tags (PETs) of self-ligation, re-ligation, and dangling pairs.
The hiclib package was applied to calculate the eigenvector decomposition of the 1 Mb
A publicly available script (matrix2insulation.pl) was used to detect the TAD boundaries with default parameters at resolutions of 40 kb
The juicer_tools_1.13.01’s HiCCUPS was applied for discovery locally enriched peaks with default parameters at resolutions of 5 kb,10 kb
The juicer_tools’s HiCCUPS Diff was applied for discovery differential loops at resolutions of 5 kb,10 kb
Genome_build: hg19
Supplementary_files_format_and_content: bed,bedpe
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| Submission date |
Feb 06, 2022 |
| Last update date |
Sep 12, 2023 |
| Contact name |
Liang Wang |
| E-mail(s) |
whmichelle@yeah.net
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| Organization name |
University of Helsinki
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| Street address |
Viikinkaari 5
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| City |
Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
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| Platform ID |
GPL24522 |
| Series (2) |
| GSE196209 |
Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neuron [HiC] |
| GSE196212 |
Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neuron |
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| Relations |
| BioSample |
SAMN25690314 |
| SRA |
SRX14060214 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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