ExperimentSetReplicate

ExperimentSet4DNESFUJBYWO
released
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in situ Hi-C on cerebellar granule neurons with control vector isolated using FANS at day 8 after in vivo electroporation from dCas9-KRAB mouse postnatal day 14

   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 - 8 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
4DNESFUJBYWO
Multiple Experiments
File
Contact List-combined (pairs)
4DNFI96XEXG2
361.35m
62.146%
13.856%
23.999%
Experiment
4DNEX6FW4JVW
Bio Rep 1, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 8 days old with MboI
File
Contact List-replicate (pairs)
4DNFIISGBTGS
69.41m
63.02%
16.349%
20.632%
Experiment
4DNEXDB3PGOS
Bio Rep 2, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 8 days old with MboI
File
Contact List-replicate (pairs)
4DNFIEDFPS2Z
74.62m
63.483%
14.135%
22.382%
Experiment
4DNEX8DGJ554
Bio Rep 3, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 8 days old with MboI
File
Contact List-replicate (pairs)
4DNFI1Z4HQJK
66.99m
60.346%
13.725%
25.928%
Experiment
4DNEXXF1YOGK
Bio Rep 4, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 8 days old with MboI
File
Contact List-replicate (pairs)
4DNFI9SPH9JD
79.57m
62.307%
12.961%
24.732%
Experiment
4DNEXTLH11MP
Bio Rep 5, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 8 days old with MboI
File
Contact List-replicate (pairs)
4DNFIU7IQ6MT
70.77m
61.401%
12.244%
26.354%
Experiment
For File
Failed Balancing
Details
From Multiple Experiments
4DNESFUJBYWO
Multiple Experiments
File
Contact Matrix (mcool)
4DNFIV1ALSIE
None
Experiment
For File
Total Reads
Unmapped Reads
Multimapped Reads
Duplicate Reads
Walks
Minor Contigs
Details
Experiment
4DNEX6FW4JVW
Bio Rep 1, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 8 days old with MboI
File
Alignments (bam)
4DNFIL8XDJB3
142.68m
20.798%
25.31%
5.244%
0.0%
0.04%
Experiment
4DNEXDB3PGOS
Bio Rep 2, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 8 days old with MboI
File
Alignments (bam)
4DNFIBRTL1C9
231.54m
22.41%
24.691%
20.673%
0.0%
0.026%
Experiment
4DNEX8DGJ554
Bio Rep 3, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 8 days old with MboI
File
Alignments (bam)
4DNFIT2DE9ZS
132.88m
21.926%
24.319%
3.342%
0.0%
0.048%
Experiment
4DNEXXF1YOGK
Bio Rep 4, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 8 days old with MboI
File
Alignments (bam)
4DNFIQ5QCTHP
196.07m
22.733%
25.222%
11.466%
0.0%
0.039%
Experiment
4DNEXTLH11MP
Bio Rep 5, Tec Rep 1
in situ Hi-C on cerebellar granule neuron - 8 days old with MboI
File
Alignments (bam)
4DNFIDM1Z3VI
165.08m
22.995%
25.019%
9.114%
0.0%
0.046%