Included Properties
Data Type
Lab
Experiment Type
Dataset
Sample Category
Sample
Publication
Assay Details
Center
Set Type
Status
Commendations
Warnings
9 Common Properties
Project
4DN
Experiment Category
Sequencing
Organism
Human
Sample Type
immortalized cells
Sample Tier
Tier 1
Organ/System
immune system
Tissue Source
B-lymphocyte
Modifications
No value
Treatments
No value
Title
Experiment Type
Biosample
Dataset
Condition
Assay Details
Lab
TCC
GM12878 (Tier 1)
cryomilling TCC protocol variations
in vitro crosslinking, with SDS, NcoI digestion
Enzyme
NcoI
TCC
GM12878 (Tier 1)
cryomilling TCC protocol variations
in vitro crosslinking, with SDS, MboI digestion
Enzyme
MboI
TCC
GM12878 (Tier 1)
cryomilling TCC protocol variations
in situ crosslinking, without SDS treatment, without restriction digestion
-
TCC
GM12878 (Tier 1)
cryomilling TCC protocol variations
in situ crosslinking, with SDS treatment, without restriction digestion
-
TCC
GM12878 (Tier 1)
cryomilling TCC protocol variations
in vitro crosslinking, with SDS, with RNase A digestion, without HindIII digestion
-
TCC
GM12878 (Tier 1)
cryomilling TCC protocol variations
in vitro crosslinking, with SDS, without restriction digestion
-
TCC
GM12878 (Tier 1)
cryomilling TCC protocol variations
in vitro crosslinking, with SDS, HindIII digestion
Enzyme
HindIII
ChIP-seq
GM12878 (Tier 1)
H3K27ac ChIP-seq
Diagenode, C15200184-50
Target
H3K27ac
ChIP-seq
GM12878 (Tier 1)
CTCF ChIP-seq
Santa Cruz, sc-271514
Target
CTCF protein
ChIP-seq
GM12878 (Tier 1)
CTCF ChIP-seq
Santa Cruz, sc-271474
Target
CTCF protein
ChIP-seq
GM12878 (Tier 1)
CTCF ChIP-seq
Cell Signaling, 3418T
Target
CTCF protein
PLAC-seq
GM12878 (Tier 1)
low coverage parameterization
0.3% SDS in 1xNEB2, 42ºC, 10'+ short nuclei prep
Target
H3K27ac
PLAC-seq
GM12878 (Tier 1)
low coverage parameterization
0.3% SDS in 1xNEB2, 42ºC, 10'+ long nuclei prep
Target
H3K27ac
PLAC-seq
GM12878 (Tier 1)
low coverage parameterization
0.5% SDS in H2O, 62ºC, 10' + long nuclei prep
Target
H3K27ac
PLAC-seq
GM12878 (Tier 1)
low coverage parameterization
0.3% SDS in 1xNEB2, 42ºC, 10'+ short nuclei prep
Target
H3K4me3
PLAC-seq
GM12878 (Tier 1)
low coverage parameterization
0.3% SDS in 1xNEB2, 42ºC, 10'+ long nuclei prep
Target
H3K4me3
PLAC-seq
GM12878 (Tier 1)
low coverage parameterization
0.5% SDS in H2O, 62ºC, 10' + long nuclei prep
Target
H3K4me3
CUT&RUN
GM12878 (Tier 1)
H2A.Z - GM12878
Active Motif 39113
Target
H2A.Z protein
CUT&RUN
GM12878 (Tier 1)
Suz12 - GM12878
ab12073
Target
SUZ12 protein
CUT&RUN
GM12878 (Tier 1)
Ring1B - GM12878
ab101273
Target
Ring2_1b protein
CUT&RUN
GM12878 (Tier 1)
NPAT - GM12878
PA5-66839
Target
NPAT protein
CUT&RUN
GM12878 (Tier 1)
H3K4me3 - GM12878
Active Motif 39159
Target
H3K4me3