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| Status |
Public on Sep 12, 2022 |
| Title |
NPCs D868N Hi-C #3 |
| Sample type |
SRA |
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| Source name |
NPCs
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| Organism |
Homo sapiens |
| Characteristics |
cell type: NPCs
genotype: SETBP1 D868N
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For in situ Hi-C libraries preparation 5 milions of either NPCs or neurons were used. An already published experimental protocol was used 4. The procedures consist in different experimental steps: (i) crosslinking cells with formaldehyde at 1% concentration, (ii) digesting the DNA using a 4-cutter restriction enzyme (e.g., DpnI) within intact permeabilized nuclei, (iii) filling in and biotinylating the resulting 5′-overhangs, (iv) ligating the blunt ends, (v) shearing the DNA, (vi) pulling down the biotinylated ligation junctions with streptavidin beads, and (vii) analyzing these fragments using paired end sequencing. A first sequencing run of 5 milion reads perform to verify the experimental quality. After passing the quality check, sample were sequenced paired end on Nova-seq6000 at San Raffaele hospital omics facility.
TruSeq
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
NPC_D868N_3
dual index library
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| Data processing |
To perform raw data QCs and alignment to hg38 reference Juicer pipeline was used, with default settings (Durand et al, 2016). Contact matrices were then generated up to a resolution of 5kb. The juicer-tools were used to perform all the downstream data analysis after obtaining the contact matrices
Genome_build: hg38
Supplementary files format and content: hic contact matrices
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| Submission date |
Aug 29, 2022 |
| Last update date |
Sep 12, 2022 |
| Contact name |
Luca Massimino |
| E-mail(s) |
admin@lucamassimino.com
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| Phone |
+393389039500
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| Organization name |
Ospedale San Raffaele
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| Department |
Gastroenterology
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| Street address |
Via Olgettina, 58
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| City |
Milano |
| State/province |
MI |
| ZIP/Postal code |
20100 |
| Country |
Italy |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE212252 |
Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition |
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| Relations |
| BioSample |
SAMN30566550 |
| SRA |
SRX17313947 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6519815_NPC_D868N_3.hic |
1.3 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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