ENCODE
Home
Data
Functional Genomics data
Experiment search
Experiment matrix
ChIP-seq matrix
Human and mouse body maps
Functional genomics series
Single-cell experiments
Functional Characterization data
Experiment search
Experiment matrix
Cloud Resources
AWS Open Data
Azure Open Datasets
Collections
RNA-protein interactions (ENCORE)
Epigenomes from four individuals (ENTEx)
Rush Alzheimer’s disease study
Stem cell differentiation
Deeply profiled cell lines
Human donor matrix
Immune cells
Human reference epigenomes
Mouse reference epigenomes
Mouse development matrix
Protein knockdown (Degron)
Search by region
Publications
RNA-Get (gene expression)
Encyclopedia
About
Visualize (SCREEN)
Encyclopedia browser
Search
Methods
Materials & Methods
Antibodies
Genome references
Assays and standards
Glossary
File formats
Software tools
Pipelines
Data organization
Release policy
Schemas
Help
Using the portal
Cart
REST API
Citing ENCODE
FAQ
Project Overview
Collaborations
ENCODE workshops
About the DCC
Sign in / Create account
Listed carts
Search
Deeply Profiled Cell Lines
Cell line samples that were deeply profiled using a set of diverse biochemical approaches.
All
Uniform batch growth
Showing 2628 results
List
Report
Download
Visualize
{ ; }
Loading
Assay type
Assay title
Status
released
Perturbation
Target category
Target of assay
Organism
Biosample classification
Biosample
Organ
Cell
Systems
Life stage
Sex
Hide control experiments
Biosample treatment
Project
RFA
Genome assembly
Available file types
Platform
Run type
Read length (nt)
Mapped read length (nt)
Library fragment size (nt)
Library material
Library depleted in
Lab
Replication type
Cellular component
Library construction platform
Library construction method
Audit category:
Audit category:
Audit category:
replicates.library.biosample.biosample_ontology.term_id
CL:0002327
EFO:0001099
EFO:0001187
EFO:0001200
EFO:0001203
EFO:0002106
EFO:0002713
EFO:0002784
EFO:0002819
EFO:0002824
EFO:0002847
EFO:0006711
EFO:0009318
All
Assay
Cell Line (batch identifier)
intact Hi-C
PRO-cap
in situ Hi-C
dilution Hi-C
GRO-cap
Histone ChIP-seq
Mint-ChIP-seq
TF ChIP-seq
RIP-chip
RIP-seq
eCLIP
ATAC-seq
DNase-seq
FAIRE-seq
MNase-seq
5C
ChIA-PET
Bru-seq
BruChase-seq
BruUV-seq
CAGE
CRISPR RNA-seq
PAS-seq
PRO-seq
RAMPAGE
RNA microarray
RNA-PET
long read RNA-seq
microRNA counts
microRNA-seq
polyA minus RNA-seq
polyA plus RNA-seq
shRNA RNA-seq
siRNA RNA-seq
small RNA-seq
total RNA-seq
DNAme array
MRE-seq
MeDIP-seq
RRBS
WGBS
Repli-seq
DNA-PET
genotyping array
scRNA-seq
snATAC-seq
WGS
icSHAPE
MS-MS
A673
1
1
6
2
2
2
2
2
1
1
1
1
1
ENCBS564CLS
1
1
2
2
2
1
1
1
1
ENCBS826LEP
1
1
1
2
2
1
1
1
1
1
ENCBS385OLC
6
2
Caco-2
1
1
5
6
2
3
1
2
2
2
1
1
1
1
1
1
1
1
1
ENCBS095ZZD
1
1
1
2
2
2
1
1
1
1
ENCBS072CVQ
1
1
2
2
1
1
1
1
1
ENCBS257JWV
6
Calu3
1
1
6
1
1
1
2
2
1
1
1
1
1
ENCBS992CLK
1
1
1
1
2
2
1
1
1
1
ENCBS961PLX
1
1
2
2
1
1
1
1
1
ENCBS827USO
6
GM12878
1
5
2
2
15
189
7
4
2
1
1
1
2
6
2
2
1
6
1
1
7
2
4
1
2
3
13
6
5
3
1
1
2
1
6
3
2
2
3
1
5
ENCBS110ENC
48
1
3
1
ENCBS630AAA
41
1
1
3
ENCBS339VHO
21
HCT116
17
14
8
17
92
43
17
16
33
18
2
1
16
1
1
1
2
1
17
2
1
7
ENCBS389ENC
19
1
ENCBS177ZJV
1
1
6
1
1
1
2
1
1
1
ENCBS228RKP
1
1
6
1
1
1
2
1
1
1
HFFc6
6
1
1
1
1
6
ENCBS252IDB
1
1
6
ENCBS508JLR
1
1
6
ENCBS249LEB
1
1
5
HepG2
1
1
15
825
2
105
2
2
1
1
4
2
2
1
6
187
6
2
3
1
2
3
11
232
3
6
3
2
2
6
2
3
3
1
ENCBS114ENC
40
2
1
1
ENCBS638AAA
1
26
1
1
ENCBS308ZPA
25
MCF 10A
1
1
6
13
3
2
2
2
1
1
1
1
3
2
3
1
ENCBS401NZE
1
1
2
2
1
1
1
1
ENCBS967KPZ
1
2
2
1
1
1
1
1
ENCBS067ENC
4
1
1
1
MCF-7
1
18
152
1
7
3
1
4
2
2
1
3
4
3
1
1
2
1
4
1
7
1
2
5
6
2
3
ENCBS056AAA
19
ENCBS789UPK
13
1
ENCBS967MVZ
13
1
OCI-LY7
1
10
2
1
2
2
2
1
1
1
1
1
2
1
1
1
1
ENCBS149SHY
1
1
2
2
1
1
1
1
1
ENCBS928AXI
1
2
2
1
1
1
1
ENCBS699NWP
5
2
PC-9
1
13
3
2
2
2
2
1
1
1
1
1
ENCBS177ANS
13
3
ENCBS987JQH
13
3
ENCBS739NKR
1
1
2
2
2
1
1
1
1
Panc1
1
1
7
7
1
1
2
2
2
1
1
1
1
1
1
3
2
3
1
1
ENCBS378LMT
1
1
2
2
2
1
1
1
1
1
ENCBS425ENC
5
1
1
1
2
ENCBS254ODH
1
2
2
2
1
mammary epithelial cell
1
2
1
19
3
3
1
2
2
1
1
1
1
3
1
2
1
2
3
1
1
2
ENCBS091ENC
12
2
1
1
ENCBS045GHW
11
2
ENCBS956YQM
1
1
2
2
1
1
1
1