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GEO accession:
Sample GSM7789305
Query DataSets for GSM7789305
Status
Public on Sep 19, 2023
Title
in situ Hi-C on immediate neuronal precursor cell with DpnII - 4DNEXTDMNUOO
Sample type
SRA
Source name
biosource_summary: immediate neuronal precursor cell
Organism
Mus musculus
Characteristics
cell_line: immediate neuronal precursor cell
mouse_strain: FVB/NTac
tissue: olfactory epithelium
modifications_summary: None
description: FACS-sorted immediate neural precursor cells - biological replicate 2
Sex: mixed
treatments_summary: None
mouse_life_stage: pup
biosample_type: primary cells
url:
https://data.4dnucleome.org/biosamples/4DNBSQ8JZXSP/
Treatment protocol
description: FACS plots for immature olfactory sensory neurons from Ngn1-GFP mice. HiC from P4 in FACS plot
download:
https://data.4dnucleome.org/protocols/0974d1b7-23f7-45ab-b22a-bf394a995cf4/@@download/attachment/FACS.NgnBright.170717.P0.pdf
Extracted molecule
genomic DNA
Extraction protocol
description: The Official 4DN Standard in situ Hi-C protocol adapted from Rao et al. 2014 PMID: 25497547 - with accepted deviations approved by SC 02/21/2017
download:
https://data.4dnucleome.org/protocols/fdc20e37-f22e-42dc-8026-0a132739bad1/@@download/attachment/4DN_in_situ_Hi-C_protocol_20170729.pdf
Library strategy
Hi-C
Library source
genomic
Library selection
other
Instrument model
Illumina NextSeq 500
Description
lab: Stavros Lomvardas, COLUMBIA
award: 1U01DA040582-01
4DN accession: 4DNEXTDMNUOO
description: HiC from immediate neural precursors - bioreplicate 2
submitted_by: Adan Horta
ligation_time: 240
digestion_time: 960
tagging_method: Biotin-11-GTP
experiment_type: in situ Hi-C
ligation_volume: 1.2
digestion_enzyme: DpnII
crosslinking_time: 10
biosample_quantity: 2100000 cells
crosslinking_method: 1% Formaldehyde
fragmentation_method: sonication
ligation_temperature: 25
digestion_temperature: 37
crosslinking_temperature: 25
fragment_size_selection_method: SPRI beads
url:
https://data.4dnucleome.org/experiments-hi-c/4DNEXTDMNUOO/
Data processing
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline
***************
workflow_run:
https://data.4dnucleome.org/workflow-runs-awsem/5bd9ec3e-9907-4d07-9231-fbcb1cfbae3b/
genome_assembly: GRCm38
derived_from: 4DNFIKHEJR3T.bam, 4DNFI3UBJ3HZ.chrom.sizes
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
file name: 4DNFIBO9M2WY.pairs.gz
Submission date
Sep 18, 2023
Last update date
Sep 19, 2023
Contact name
4DN DCIC
E-mail(s)
support@4dnucleome.org
Organization name
4D Nucleome - Data Coordination and Integration Center
Street address
10 Shattuck St
City
Boston
State/province
MA
ZIP/Postal code
02115
Country
USA
Platform ID
GPL19057
Series (1)
GSE243477
4DNES425UDGS - Replicate experiments of in situ Hi-C on immediate neuronal precursor cell with DpnII
Relations
BioSample
SAMN37442959
SRA
SRX21810616
Supplementary file
Size
Download
File type/resource
GSM7789305_4DNFIBO9M2WY.pairs.gz
7.2 Gb
(ftp)
(http)
PAIRS
SRA Run Selector
Raw data are available in SRA
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