ExperimentSetReplicate

ExperimentSet4DNESH3GQ3QH
released
View JSON

in situ Hi-C on cerebellar granule neurons with control vector isolated using FANS at day 14 after in vivo electroporation from dCas9-KRAB mouse postnatal day 20

   February 27th, 2024 at 5:25pm

Data Usage Guidelines  

Data Use Guidelines: This is a data set generated by the 4DN Network and made freely available to the scientific community. If you are intending to use these data for a publication, we ask that you please contact the data generating lab to discuss possible coordinated publication. In your manuscript, please cite the 4DN White Paper (doi:10.1038/nature23884) and the 4DN Data Portal paper (doi:10.1038/s41467-022-29697-4), and please acknowledge the 4DN lab which generated the data. Please direct any questions to the Data Coordination and Integration Center.

Assay Description  

Experiment Set Properties  

Set Type 
Replicate
Organism 
M. musculus
Sample Type 
primary cells
Sample 
cerebellar granule neuron - 14 days old
Experiment Type(s) 
in situ Hi-C
Modification Type 
Crispr
Treatment Type 
None
Assay Details 
Enzyme: MboI

16 Processed Files

Quality Metrics

Experiment
For File
Filtered Reads
Cis reads (>20kb)
Short cis reads
Trans Reads
Details
From Multiple Experiments
4DNESH3GQ3QH
Multiple Experiments
File
Contact List-combined (pairs)
4DNFIH4NBUVP
461.22m
63.124%
14.208%
22.668%
Experiment
4DNEXJFRADI7
Bio Rep 1, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 14 days old with MboI
File
Contact List-replicate (pairs)
4DNFIL2ZB3M7
71.71m
62.82%
15.829%
21.352%
Experiment
4DNEX1U91RK4
Bio Rep 2, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 14 days old with MboI
File
Contact List-replicate (pairs)
4DNFI1KMIZPE
71.1m
61.403%
13.5%
25.097%
Experiment
4DNEX8QM44AC
Bio Rep 3, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 14 days old with MboI
File
Contact List-replicate (pairs)
4DNFIIP5WGI6
114.98m
63.385%
13.369%
23.246%
Experiment
4DNEXP7RRABQ
Bio Rep 4, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 14 days old with MboI
File
Contact List-replicate (pairs)
4DNFIFBKVALG
112.9m
63.784%
15.879%
20.337%
Experiment
4DNEX5ROW4N9
Bio Rep 5, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 14 days old with MboI
File
Contact List-replicate (pairs)
4DNFIWJKYSF5
90.53m
63.562%
12.462%
23.976%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESH3GQ3QH
Multiple Experiments
File
Contact Matrix (mcool)
4DNFI3KH2H23
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEXJFRADI7
Bio Rep 1, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 14 days old with MboI
File
Alignments (bam)
4DNFIGMYXT5X
155m
22.792%
24.527%
6.417%
0.0%
0.046%
Experiment
4DNEX1U91RK4
Bio Rep 2, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 14 days old with MboI
File
Alignments (bam)
4DNFIJ96A78V
149.63m
21.776%
25.074%
5.631%
0.0%
0.05%
Experiment
4DNEX8QM44AC
Bio Rep 3, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 14 days old with MboI
File
Alignments (bam)
4DNFIFG4FL3Q
286.65m
20.754%
25.423%
13.711%
0.0%
0.047%
Experiment
4DNEXP7RRABQ
Bio Rep 4, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 14 days old with MboI
File
Alignments (bam)
4DNFI2V44TIA
273.93m
21.752%
25.836%
11.198%
0.0%
0.04%
Experiment
4DNEX5ROW4N9
Bio Rep 5, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 14 days old with MboI
File
Alignments (bam)
4DNFI2BMQKO9
350.03m
23.587%
24.649%
25.901%
0.0%
0.029%