Assay type
Assay title
- TF ChIP-seq3608
- Histone ChIP-seq3179
- Control ChIP-seq2229
- DNase-seq836
- polyA plus RNA-seq770
- total RNA-seq704
- shRNA RNA-seq640
- DNAme array257
- Control eCLIP234
- eCLIP225
- small RNA-seq214
- WGBS201
- microRNA-seq198
- ATAC-seq180
- RNA microarray170
- RAMPAGE168
- RNA Bind-n-Seq158
- genotyping array123
- CAGE120
- microRNA counts115
- siRNA RNA-seq113
- Repli-seq104
- RRBS103
- CRISPRi RNA-seq77
- Repli-chip63
- Hi-C60
- ChIA-PET57
- CRISPR RNA-seq50
- PAS-seq47
- GM DNase-seq46
- RIP-seq45
- scRNA-seq41
- FAIRE-seq37
- RIP-chip32
- polyA minus RNA-seq32
- RNA-PET31
- genotyping HTS16
- long read RNA-seq15
- MS-MS14
- 5C13
- WGS10
- snATAC-seq8
- DNA-PET6
- icSHAPE6
- MRE-seq4
- MeDIP-seq4
- iCLIP3
- 5' RLM RACE2
- MNase-seq2
- Switchgear2
RFA
Target category
Target of assay
- H3K4me3522
- H3K4me1438
- H3K36me3424
- H3K27ac407
- H3K27me3407
- H3K9me3394
- CTCF356
- H3K9ac176
- POLR2A144
- H3K4me2134
- RAD2170
- EP30064
- H3K79me255
- H2AFZ51
- POLR2AphosphoS548
- H4K20me142
- JUN31
- CEBPB30
- NR3C129
- REST29
- EZH227
- MAX25
- MYC24
- SMC322
- JUND20
- YY118
- FOSL217
- GATA117
- H3K9me217
- GABPA16
- H3F3A16
- JUNB16
- SIN3A16
- USF116
- EZH2phosphoT48715
- TAF115
- BCL314
- ELF114
- MAFK14
- NRF114
- TARDBP14
- TCF1214
- ATF313
- SP113
- USF213
- ZBTB3313
- CREB112
- FOXA112
- GTF2F112
- HES212
Organism
Biosample classification
Biosample term name
- whole organism2464
- K5621529
- HepG2909
- A549454
- GM12878331
- HEK293264
- MCF-7245
- liver234
- stomach193
- H1189
- heart176
- cell-free sample158
- HeLa-S3152
- lung131
- forebrain125
- kidney118
- spleen118
- midbrain117
- hindbrain115
- SK-N-SH112
- adrenal gland111
- sigmoid colon103
- IMR-9094
- bone marrow-derived macrophage92
- transverse colon92
- limb90
- foreskin keratinocyte89
- MEL cell line86
- embryonic facial prominence85
- upper lobe of left lung79
- S278
- neural tube75
- gastrocnemius medialis71
- thyroid gland69
- dendritic cell66
- endothelial cell of umbilical vein66
- esophagus muscularis mucosa66
- CH12.LX65
- small intestine64
- gastroesophageal sphincter63
- tibial nerve63
- body of pancreas62
- esophagus squamous epithelium61
- heart left ventricle60
- HCT11659
- intestine58
- testis58
- Peyer's patch57
- ovary57
- common myeloid progenitor, CD34-positive56
Organ
- epithelium2651
- blood2581
- bodily fluid2581
- exocrine gland1600
- endocrine gland1438
- liver1208
- lung921
- embryo884
- brain835
- connective tissue607
- musculature of body586
- intestine576
- kidney551
- skin of body501
- limb421
- mammary gland376
- large intestine366
- heart358
- colon309
- stomach277
- immune organ269
- vasculature252
- uterus236
- blood vessel229
- penis212
- spleen205
- extraembryonic component184
- esophagus155
- pancreas150
- gonad142
- arterial blood vessel137
- lymph node125
- adipose tissue123
- prostate gland121
- bone element113
- adrenal gland111
- small intestine95
- bone marrow90
- testis76
- thyroid gland69
- vein69
- lymphoid tissue63
- nerve63
- ovary63
- placenta62
- breast56
- thymus49
- eye37
- vagina35
- spinal cord28
Cell
- cancer cell3991
- hematopoietic cell2945
- leukocyte2784
- epithelial cell2410
- B cell740
- stem cell642
- fibroblast379
- T cell224
- myeloid cell214
- neural cell179
- keratinocyte147
- neuroblastoma cell135
- endothelial cell115
- induced pluripotent stem cell97
- myoblast65
- cardiocyte48
- smooth muscle cell42
- monocyte40
- melanocyte39
- pericyte8
- lymphoblast6
Life stage
- adult6500
- embryonic3960
- unknown1595
- child1322
- newborn297
- postnatal244
- L1 larva191
- young adult173
- L4 larva148
- prepupa139
- late embryonic134
- wandering third instar larva118
- L3 larva102
- L2 larva100
- mixed stage (embryonic)72
- third instar larva66
- pupa38
- early embryonic24
- L4/young adult6
- larva5
- midembryonic4
- second instar larva4
- first instar larva3
- dauer2
Biosample treatment
- dexamethasone291
- lipopolysaccharide69
- ethanol55
- calcium52
- dimethyl sulfoxide40
- 17β-estradiol38
- copper(II) sulfate32
- doxycycline hyclate32
- Activin A24
- Bone morphogenetic protein 424
- Fibroblast growth factor 224
- all-trans-retinoic acid21
- tumor necrosis factor20
- interferon alpha19
- Interferon gamma18
- 20-hydroxyecdysone16
- afimoxifene16
- phorbol 13-acetate 12-myristate15
- ionomycin14
- lipoprotein A13
- erythropoietin9
- hydrocortisone succinate9
- interleukin-39
- kit ligand9
- estradiol8
- forskolin8
- pyruvate8
- darkness6
- 17β-hydroxy-17-methylestra-4,9,11-trien-3-one5
- G-CSF5
- MEDII4
- Sindbis virus4
- bisphenol A4
- cadmium dichloride4
- genistein4
- pravastatin4
- 17β-hydroxy-5α-androstan-3-one3
- Interleukin-43
- NAI-N33
- UT1893
- anti-CD1803
- caffeine3
- lactate3
- rotenone3
- sodium butyrate3
- zinc dichloride3
- 22-hydroxycholesterol2
- cold shock treatment2
- insulin2
- paraquat2
- retinoic acid2
- tamoxifen2
- 2-Deoxy-D-glucose1
- Sendai virus1
- cisplatin1
- doxycycline1
- flavopiridol1
- heat shock treatment1
- hydroxyurea1
- oligomycin1
- resveratrol1
- trichostatin A1
- vorinostat1
Available file types
- fastq14563
- bam13382
- bigWig12229
- bed narrowPeak7742
- bigBed narrowPeak7735
- bed broadPeak2435
- tsv2375
- bigBed broadPeak1981
- tagAlign1270
- bed bed3+904
- tar579
- sra496
- bed bedRnaElements288
- bigBed bedRnaElements288
- gtf284
- bed bedMethyl283
- bigBed bedMethyl283
- idat275
- bed tss_peak235
- bigBed tss_peak235
- gff gff3235
- bed idr_peak134
- bigBed idr_peak134
- bed bed6+115
- bigBed bed6+115
- rcc115
- bed bedLogR64
- bigBed bedLogR63
- sam59
- wig59
- bed bed1243
- bigBed bed1243
- bed bedGraph30
- bed bedExonScore27
- bigBed bedExonScore27
- csfasta24
- hdf520
- hic20
- bed bed918
- bigBed bed918
- vcf15
- bigBed bed3+13
- csqual12
- bed peptideMapping8
- bedpe8
- bigBed peptideMapping8
- bed bed37
- bigBed bed37
- bed modPepMap6
- bed pepMap6
- bigBed modPepMap6
- bigBed pepMap6
- CEL4
- fasta3
Platform
- Illumina HiSeq 20006142
- Illumina HiSeq 25002809
- Illumina Genome Analyzer IIx2227
- Illumina HiSeq 40002025
- Illumina Genome Analyzer965
- Illumina Genome Analyzer II733
- Illumina NextSeq 500714
- Illumina Infinium Methylation EPIC BeadChip154
- Illumina Genome Analyzer I135
- Illumina Genome Analyzer IIe96
- Illumina - Methylation 450K BeadChip62
- Illumina HiSeq X Ten62
- Illumina Infinium Omni5Exome-4 Kit59
- nCounter Mouse V1.3 miRNA Expression array58
- Applied Biosystems SOLiD System 3 Plus49
- nCounter Human V2 miRNA Expression array38
- Nimbelgen - Human 3x720K Whole Genome CGH Tiling Array34
- Mouse 385K Whole Genome CGH Tiling Array16
- Pacific Biosciences Sequel15
- nCounter Mouse V1.5 miRNA Expression array14
- Nimblegen - Human 6x630K CGH Whole Genome tiling array12
- Illumina HiSeq 10008
- Nimblegen - Human 2.1M Whole-Genome CGH Tiling Array v2.08
- Illumina MiSeq5
- nCounter Mouse V1.2 miRNA Expression array5
- Affymetrix - Human Exon 1.0 ST V2 tilling array4
- Mouse 3x720K Whole Genome CGH Tiling Array2
- Roche 454 Genome Sequencer FLX2
Run type
Read length (nt)
- 185
- 20153
- 2581
- 2783
- 2858
- 291
- 30105
- 3149
- 32498
- 3344
- 3473
- 3542
- 364430
- 3777
- 387
- 3938
- 40201
- 4123
- 4215
- 4390
- 44102
- 45335
- 4660
- 472
- 4835
- 4915
- 503047
- 51387
- 522
- 531
- 55170
- 5610
- 581
- 591
- 611
- 621
- 702
- 712
- 726
- 7422
- 75587
- 761731
- 7842
- 8027
- 822
- 8310
- 841
- 856
- 862
- 875
- 881
- 901
- 941
- 951
- 965
- 981
- 999
- 1001909
- 1011239
- 10811
- 1131
- 1172
- 12511
- 13040
- 1311
- 1323
- 1333
- 1362
- 1393
- 1491
- 15011
- 15179
- 1761
- 1911
- 2501
- 3002
- 4581
Mapped read length (nt)
Library fragment size (nt)
- >2002427
- 200-8001081
- 450-6501064
- 200-6001028
- 300-500660
- 175-300459
- 150-350449
- 350-600335
- <30245
- <200214
- 200-500168
- 20-20132
- 120-200128
- 200-40094
- 250-40092
- 300-60090
- 180-50084
- 200-75082
- 19-2566
- 150-25047
- 200-25046
- 300-100036
- 175-50035
- 350-45026
- 40-4026
- 100-30024
- 100-35017
- 100-50017
- >17517
- 300-80016
- 150-40015
- 150-100013
- 240-42013
- 299-30011
- 50-30010
- 200-10009
- 150-1507
- 200-3005
- 150-3004
- 250-4304
- 300-3504
- 100-1003
- 175-2503
- 175-2753
- 200-2753
- 10-502
- 250-4702
- 120-2801
- 125-2781
- 138-10001
- 149-5121
- 151-3471
- 151-3791
- 151-4991
- 153-3091
- 153-4991
- 156-3121
- 157-4971
- 159-1961
- 165-2031
- 169-2251
- 170-2021
- 172-14521
- 175-2251
- 186-7471
- 187-16061
- 200-15001
- 200-3251
- 200-4911
- 200-5941
- 200-6501
- 200-7121
- 200-7641
- 200-9001
- 208-4421
- 209-8911
- 210-4801
- 213-4511
- 215-10001
- 217-4751
- 221-10001
- 222-3181
- 225-3001
- 225-3501
- 232-10001
- 244-3011
- 266-4701
- 268-4781
- 275-4701
- 280-5091
- 285-4771
- 287-3471
- 287-4781
- 289-4811
- 2963-29631
- 300-7001
- 3062-30621
- 309-3651
- 312-5061
- 312-5311
- 325-4251
- 325-4501
- 354-5981
- 354-6531
- 373-3731
- 387-4661
- 400-4001
- 425-5191
- 442-4421
- 452-5161
- 471-5271
- 472-5541
- 472-5581
- 482-5601
- 487-5711
- 493-6621
- 555-6171
- 555-6781
Library material
Library depleted in
Lab
- Michael Snyder, Stanford2281
- Bradley Bernstein, Broad2011
- John Stamatoyannopoulos, UW1463
- Richard Myers, HAIB1358
- Bing Ren, UCSD1327
- Kevin White, UChicago1250
- Brenton Graveley, UConn776
- Thomas Gingeras, CSHL726
- Gene Yeo, UCSD462
- Joseph Costello, UCSF404
- Valerie Reinke, Yale361
- Susan Celniker, LBNL356
- Tim Reddy, Duke298
- Ali Mortazavi, UCI260
- Robert Waterston, UW218
- Barbara Wold, Caltech207
- Joe Ecker, Salk183
- Chris Burge, MIT158
- Gregory Crawford, Duke139
- Ross Hardison, PennState128
- Peggy Farnham, USC118
- Xiang-Dong Fu, UCSD94
- Alexander Hoffmann, UCLA92
- David Gilbert, FSU77
- Piero Carninci, RIKEN77
- Vishwanath Iyer, UTA74
- Manuel Garber, UMass68
- Sherman Weissman, Yale57
- Yijun Ruan, JAX48
- Scott Tenenbaum, SUNY-Albany42
- Kevin Struhl, HMS41
- Jason Lieb, UNC37
- Christina Leslie, MSKCC32
- Eric Lécuyer, IRCM30
- Job Dekker, UMass26
- Erez Aiden, Baylor22
- Morgan Giddings, UNC14
- Paul Khavari, Stanford13
- Will Greenleaf, Stanford13
- Feng Yue, PSU7
- John Rinn, Broad7
- Alexander Urban, Stanford6
- Rob Spitale, UCI6
- Andrew Z. Fire, Stanford4
- Brian Oliver, NIH2
Replication type
Audit category:
- extremely low read depth206
- missing antibody72
- extremely low spot score42
- missing control alignments40
- control extremely low read depth20
- extremely low coverage7
- extremely low read length7
- file in uploading state4
- inconsistent library biosample4
- inconsistent read count3
- file validation error2
- inconsistent control2
- missing analysis_step_run1
Audit category:
- insufficient read depth1762
- control insufficient read depth933
- insufficient read length583
- unreplicated experiment374
- severe bottlenecking280
- poor library complexity276
- missing spikeins173
- missing documents124
- partially characterized antibody91
- insufficient replicate concordance47
- missing possible_controls20
- insufficient coverage4
- insufficient number of aligned reads2
- missing input control2
Audit category:
- low read length3230
- missing biosample characterization3006
- mild to moderate bottlenecking3004
- low read depth2564
- missing genetic modification characterization2386
- moderate library complexity1397
- inconsistent platforms1156
- missing controlled_by927
- inconsistent control read length866
- antibody characterized with exemption673
- control low read depth654
- mixed read lengths467
- borderline replicate concordance466
- missing genetic modification reagents397
- low spot score317
- missing external identifiers248
- improper control_type of control experiment207
- inconsistent control run_type147
- missing analysis_step_run112
- missing genotype112
- mixed run types98
- inconsistent assembly95
- low replicate concordance91
- matching md5 sums37
- borderline number of aligned reads29
- missing spikeins28
- missing fragmentation method22
- missing control_type of control experiment11
- unexpected target of control experiment11
- inconsistent paired_with9
- low coverage4
- high lambda C methylation ratio3
- borderline sequencing depth1
Showing 25 of 15373 results
- long read RNA-seq of left lungHomo sapiens left lung male adult (40 years)Lab: Ali Mortazavi, UCIProject: ENCODE
- long read RNA-seq of left lungHomo sapiens left lung female child (16 years)Lab: Ali Mortazavi, UCIProject: ENCODE
- long read RNA-seq of ovaryHomo sapiens ovary female adult (41 year)Lab: Ali Mortazavi, UCIProject: ENCODE
- long read RNA-seq of mucosa of descending colonHomo sapiens mucosa of descending colon female adult (61 year)Lab: Ali Mortazavi, UCIProject: ENCODE
- long read RNA-seq of forelimbMus musculus C57BL/6 forelimb embryo (13 days)Lab: Ali Mortazavi, UCIProject: ENCODE
- long read RNA-seq of forelimbMus musculus C57BL/6 forelimb embryo (11 days)Lab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of ovaryHomo sapiens ovary female adult (41 year)Lab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of pancreasHomo sapiens pancreas female adult (61 year)Lab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of colonic mucosaHomo sapiens colonic mucosa female adult (41 year)Lab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of mucosa of descending colonHomo sapiens mucosa of descending colon female adult (61 year)Lab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of spleenHomo sapiens spleen female adult (61 year)Lab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of left lungHomo sapiens left lung male adult (40 years)Lab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of left lungHomo sapiens left lung female child (16 years)Lab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of right lobe of liverHomo sapiens right lobe of liver female adult (47 years)Lab: Ali Mortazavi, UCIProject: ENCODE
- DNase-seq of tibial nerveHomo sapiens tibial nerve male adult (54 years)Lab: John Stamatoyannopoulos, UWProject: ENCODE
- DNase-seq of gastrocnemius medialisHomo sapiens gastrocnemius medialis male adult (37 years)Lab: John Stamatoyannopoulos, UWProject: ENCODE
- DNase-seq of breast epitheliumHomo sapiens breast epithelium male adult (54 years)Lab: John Stamatoyannopoulos, UWProject: ENCODE
- microRNA-seq of adrenal glandHomo sapiens adrenal gland male adult (37 years)Lab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of heart left ventricleHomo sapiens heart left ventricle female adult (53 years)Lab: Ali Mortazavi, UCIProject: ENCODE
- long read RNA-seq of heart left ventricleHomo sapiens heart left ventricle female adult (53 years)Lab: Ali Mortazavi, UCIProject: ENCODE
- Histone ChIP-seq of vaginaHomo sapiens vagina female adult (51 year)Target: H3K27me3Lab: Bradley Bernstein, BroadProject: ENCODE
- Histone ChIP-seq of vaginaHomo sapiens vagina female adult (51 year)Target: H3K4me1Lab: Bradley Bernstein, BroadProject: ENCODE
- Histone ChIP-seq of vaginaHomo sapiens vagina female adult (51 year)Target: H3K9me3Lab: Bradley Bernstein, BroadProject: ENCODE
- DNase-seq of tibial nerveHomo sapiens tibial nerve male adult (37 years)Lab: John Stamatoyannopoulos, UWProject: ENCODE
- DNase-seq of gastrocnemius medialisHomo sapiens gastrocnemius medialis female adult (51 year)Lab: John Stamatoyannopoulos, UWProject: ENCODE