Assay type
Assay title
- TF ChIP-seq3944
- Histone ChIP-seq3340
- Control ChIP-seq2399
- scRNA-seq1185
- DNase-seq927
- polyA plus RNA-seq831
- total RNA-seq709
- shRNA RNA-seq650
- RNA microarray291
- WGBS268
- DNAme array257
- Control eCLIP238
- eCLIP231
- microRNA-seq225
- RRBS218
- small RNA-seq216
- ATAC-seq180
- RAMPAGE168
- RNA Bind-n-Seq161
- genotyping array142
- CAGE121
- Repli-seq119
- microRNA counts115
- siRNA RNA-seq113
- CRISPRi RNA-seq77
- RIP-seq73
- MRE-seq68
- Hi-C67
- Repli-chip63
- ChIA-PET62
- MeDIP-seq55
- CRISPR RNA-seq50
- PAS-seq47
- GM DNase-seq46
- FAIRE-seq37
- RIP-chip32
- polyA minus RNA-seq32
- RNA-PET31
- WGS28
- genotyping HTS22
- long read RNA-seq18
- MS-MS14
- 5C13
- TAB-seq8
- snATAC-seq8
- iCLIP7
- DNA-PET6
- icSHAPE6
- 5' RLM RACE2
- MNase-seq2
RFA
Genome assembly
Target category
Target of assay
- H3K4me3550
- H3K4me1457
- H3K36me3443
- H3K27me3440
- H3K27ac428
- H3K9me3415
- CTCF369
- H3K9ac191
- POLR2A152
- H3K4me2134
- EP30096
- RAD2175
- H3K79me255
- Methylcytidine55
- H2AFZ51
- POLR2AphosphoS549
- H4K20me142
- JUN31
- NR3C131
- CEBPB30
- REST30
- EZH229
- MAX26
- MYC25
- SMC322
- JUND20
- H3K9me219
- ama-119
- YY118
- EZH2phosphoT48717
- FOSL217
- GABPA17
- GATA117
- H3F3A16
- JUNB16
- SIN3A16
- USF116
- BCL315
- CHD115
- MAFK15
- TAF115
- bromodeoxyuridine15
- ELF114
- NRF114
- TARDBP14
- TCF1214
- USF214
- ZBTB3314
- ATF313
- CREB113
Organism
Biosample classification
Biosample term name
- whole organism2652
- K5621629
- forelimb1072
- HepG21004
- A549479
- GM12878382
- HEK293279
- MCF-7258
- liver249
- H1216
- stomach201
- heart190
- cell-free sample161
- HeLa-S3158
- lung146
- forebrain127
- spleen127
- kidney124
- SK-N-SH123
- adrenal gland119
- midbrain118
- hindbrain116
- sigmoid colon108
- transverse colon105
- IMR-90102
- foreskin keratinocyte99
- limb96
- MEL94
- bone marrow-derived macrophage92
- S286
- embryonic facial prominence86
- upper lobe of left lung81
- common myeloid progenitor, CD34-positive78
- mesenchymal stem cell78
- neural tube75
- small intestine73
- thyroid gland73
- gastrocnemius medialis72
- brain70
- esophagus muscularis mucosa70
- endothelial cell of umbilical vein68
- CH12.LX66
- body of pancreas66
- dendritic cell66
- gastroesophageal sphincter66
- tibial nerve65
- esophagus squamous epithelium63
- neurosphere63
- Purkinje cell62
- mammary epithelial cell62
Organ
- blood2894
- bodily fluid2894
- epithelium2881
- exocrine gland1791
- endocrine gland1571
- limb1488
- liver1322
- embryo1148
- brain1103
- lung983
- connective tissue771
- skin of body635
- intestine633
- musculature of body632
- kidney590
- mammary gland451
- large intestine408
- heart377
- colon338
- bone element332
- bone marrow297
- stomach293
- immune organ292
- vasculature265
- penis249
- uterus245
- blood vessel243
- spleen227
- extraembryonic component221
- pancreas162
- esophagus161
- gonad148
- arterial blood vessel144
- lymph node134
- prostate gland129
- adipose tissue127
- adrenal gland119
- small intestine107
- spinal cord88
- placenta82
- testis82
- breast80
- thyroid gland74
- vein71
- eye70
- ovary67
- lymphoid tissue66
- nerve65
- thymus53
- vagina37
Cell
- cancer cell4531
- hematopoietic cell3242
- leukocyte3053
- epithelial cell2620
- stem cell888
- B cell816
- connective tissue cell577
- embryonic cell559
- fibroblast495
- T cell300
- neural cell272
- myeloid cell225
- keratinocyte160
- progenitor cell152
- neuroblastoma cell146
- induced pluripotent stem cell143
- endothelial cell118
- myoblast68
- cardiocyte48
- melanocyte48
- monocyte46
- smooth muscle cell46
- pericyte8
- lymphoblast6
Life stage
- adult7224
- embryonic5403
- unknown1711
- child1446
- newborn336
- postnatal251
- L1 larva199
- young adult179
- L4 larva159
- late embryonic142
- prepupa139
- wandering third instar larva124
- L3 larva119
- L2 larva106
- mixed stage (embryonic)78
- third instar larva78
- pupa40
- early embryonic24
- L4/young adult6
- first instar larva5
- larva5
- midembryonic4
- second instar larva4
- dauer2
Biosample treatment
- dexamethasone293
- lipopolysaccharide69
- ethanol57
- calcium52
- dimethyl sulfoxide42
- 17β-estradiol38
- doxycycline hyclate33
- copper(II) sulfate32
- all-trans-retinoic acid29
- Activin A24
- Bone morphogenetic protein 424
- Fibroblast growth factor 224
- 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
- G-CSF6
- darkness6
- 17β-hydroxy-17-methylestra-4,9,11-trien-3-one5
- 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
- serum free2
- tamoxifen2
- 2-Deoxy-D-glucose1
- Sendai virus1
- Transforming growth factor beta-11
- cisplatin1
- differentiation1
- doxycycline1
- flavopiridol1
- heat shock treatment1
- hydroxyurea1
- oligomycin1
- resveratrol1
- trichostatin A1
- vorinostat1
Available file types
- fastq16240
- bam14856
- bigWig13605
- bed narrowPeak7961
- bigBed narrowPeak7952
- tsv3568
- bed broadPeak2513
- bigBed broadPeak2054
- tagAlign1368
- bed bed3+965
- sra672
- tar582
- bed bedRnaElements288
- bigBed bedRnaElements288
- bed bedMethyl284
- bigBed bedMethyl284
- gtf284
- idat275
- bed tss_peak235
- bigBed tss_peak235
- gff gff3235
- bed idr_peak134
- bigBed idr_peak134
- bed bed6+115
- bigBed bed6+115
- rcc115
- bed idr_ranked_peak74
- bed bedLogR64
- bigBed bedLogR63
- sam59
- wig59
- bed bed1243
- bigBed bed1243
- bed bedGraph30
- bed bedExonScore27
- bigBed bedExonScore27
- csfasta25
- hic25
- vcf21
- hdf520
- bed bed918
- bigBed bed918
- bigBed bed3+13
- csqual13
- bedpe9
- bed peptideMapping8
- bigBed peptideMapping8
- bed bed37
- bigBed bed37
- bed modPepMap6
- bed pepMap6
- bigBed modPepMap6
- bigBed pepMap6
- CEL4
- fasta3
Platform
- Illumina HiSeq 20006374
- Illumina HiSeq 25003938
- Illumina Genome Analyzer IIx2418
- Illumina HiSeq 40002109
- Illumina Genome Analyzer976
- Illumina NextSeq 500778
- Illumina Genome Analyzer II765
- Illumina Infinium Methylation EPIC BeadChip154
- Illumina Genome Analyzer I135
- Illumina Genome Analyzer IIe97
- Illumina NovaSeq 600065
- Illumina HiSeq X Ten64
- Illumina - Methylation 450K BeadChip62
- Illumina Infinium Omni5Exome-4 Kit59
- nCounter Mouse V1.3 miRNA Expression array58
- Applied Biosystems SOLiD System 3 Plus50
- nCounter Human V2 miRNA Expression array38
- Nimbelgen - Human 3x720K Whole Genome CGH Tiling Array34
- Mouse 385K Whole Genome CGH Tiling Array16
- Pacific Biosciences Sequel16
- 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
- Pacific Biosciences Sequel II3
- Mouse 3x720K Whole Genome CGH Tiling Array2
- Roche 454 Genome Sequencer FLX2
- Pacific Biosciences RS II1
Read length (nt)
- 185
- 20153
- 2584
- 2790
- 2859
- 299
- 30119
- 3173
- 32526
- 3344
- 3478
- 3542
- 364585
- 3779
- 387
- 3938
- 40202
- 4123
- 4215
- 43109
- 44115
- 45337
- 4660
- 472
- 4835
- 4915
- 504095
- 51394
- 522
- 531
- 55170
- 5610
- 581
- 591
- 611
- 621
- 702
- 712
- 7210
- 7330
- 7426
- 75609
- 761839
- 7842
- 8027
- 822
- 8310
- 841
- 856
- 867
- 875
- 881
- 901
- 941
- 951
- 968
- 981
- 999
- 1002196
- 1011244
- 10811
- 1131
- 1172
- 12511
- 13040
- 1311
- 1323
- 1333
- 1362
- 1393
- 1491
- 15016
- 15180
- 1526
- 1761
- 1911
- 20217
- 2501
- 3002
- 4581
Mapped read length (nt)
Library fragment size (nt)
- >2002666
- 300-5001712
- 450-6501100
- 200-8001082
- 200-6001080
- 150-350537
- 175-300469
- 350-600335
- <30271
- <200216
- 200-500183
- 20-20132
- 120-200128
- 200-40097
- 250-40092
- 300-60091
- 180-50084
- 200-75082
- 19-2566
- 200-25048
- 150-25047
- 250-45045
- 300-100043
- 150-15035
- 175-50035
- 299-30028
- 40-4027
- 350-45026
- 100-30024
- 300-80019
- 100-35017
- 100-50017
- >17517
- 150-40015
- 150-100013
- 240-42013
- 50-30011
- 200-10009
- 200-15006
- 200-2006
- 200-3005
- 150-3004
- 250-4304
- 300-3504
- 100-1003
- 175-2503
- 175-2753
- 200-2753
- 400-4003
- 10-502
- 200-6502
- 250-4702
- 267-4002
- >10002
- 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
- 168-3671
- 169-2251
- 170-2021
- 171-2011
- 172-14521
- 172-2001
- 175-1961
- 175-2251
- 177-2071
- 184-2241
- 185-2341
- 186-7471
- 187-16061
- 200-3251
- 200-4911
- 200-5941
- 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
- 270-5001
- 275-4701
- 280-5091
- 285-4771
- 287-3471
- 287-4781
- 289-4811
- 2963-29631
- 300-4001
- 300-7001
- 3062-30621
- 309-3651
- 312-5061
- 312-5311
- 325-4251
- 325-4501
- 354-5981
- 354-6531
- 373-3731
- 387-4661
- 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
Perturbation
Lab
- Michael Snyder, Stanford2463
- Bradley Bernstein, Broad2303
- John Stamatoyannopoulos, UW1654
- Richard Myers, HAIB1509
- Bing Ren, UCSD1387
- Barbara Wold, Caltech1352
- Kevin White, UChicago1350
- Brenton Graveley, UConn789
- Thomas Gingeras, CSHL739
- Joseph Costello, UCSF595
- Gene Yeo, UCSD476
- Valerie Reinke, Yale363
- Susan Celniker, LBNL356
- Tim Reddy, Duke298
- Ali Mortazavi, UCI289
- Robert Waterston, UW218
- Joe Ecker, Salk193
- Gregory Crawford, Duke162
- Chris Burge, MIT161
- Ross Hardison, PennState128
- Peggy Farnham, USC125
- Xiang-Dong Fu, UCSD97
- Alexander Hoffmann, UCLA92
- Vishwanath Iyer, UTA85
- Piero Carninci, RIKEN78
- David Gilbert, FSU77
- Manuel Garber, UMass68
- Sherman Weissman, Yale65
- Yijun Ruan, JAX48
- Kevin Struhl, HMS43
- Scott Tenenbaum, SUNY-Albany42
- David MacAlpine, Duke39
- Jason Lieb, UNC37
- John Rinn, Broad35
- Christina Leslie, MSKCC32
- Eric Lécuyer, IRCM30
- Erez Aiden, Baylor29
- Brian Oliver, NIH27
- Job Dekker, UMass26
- Morgan Giddings, UNC14
- Paul Khavari, Stanford13
- Will Greenleaf, Stanford13
- Feng Yue, PSU7
- Alexander Urban, Stanford6
- Rob Spitale, UCI6
- Andrew Z. Fire, Stanford4
- Terry Orr-Weaver, MIT2
Replication type
Audit category:
- extremely low read depth225
- inconsistent ontology term140
- missing control alignments109
- missing antibody75
- extremely low spot score48
- control extremely low read depth25
- missing queried_RNP_size_range19
- inconsistent library biosample12
- extremely low read length10
- file validation error8
- extremely low coverage7
- missing raw data in replicate7
- inconsistent control3
- inconsistent read count3
- missing analysis_step_run3
- missing possible_controls2
- missing donor1
- mixed biosample perturbations1
Audit category:
- insufficient read depth1802
- control insufficient read depth971
- insufficient read length580
- severe bottlenecking295
- poor library complexity292
- unreplicated experiment225
- missing spikeins173
- partially characterized antibody140
- missing documents130
- insufficient replicate concordance49
- antibody not characterized to standard26
- missing possible_controls26
- uncharacterized antibody11
- insufficient coverage4
- insufficient number of aligned reads2
- missing RNA fragment size2
- missing input control2
Audit category:
- low read length3292
- mild to moderate bottlenecking3139
- missing biosample characterization3135
- low read depth2612
- missing genetic modification characterization2508
- lacking processed data1560
- moderate library complexity1453
- inconsistent platforms1205
- missing controlled_by974
- mixed read lengths942
- inconsistent control read length908
- antibody characterized with exemption726
- control low read depth677
- missing genetic modification reagents511
- borderline replicate concordance486
- low spot score349
- missing external identifiers266
- missing analysis_step_run236
- improper control_type of control experiment207
- inconsistent control run_type158
- missing genotype116
- mixed run types101
- inconsistent assembly95
- low replicate concordance91
- matching md5 sums37
- borderline number of aligned reads32
- missing spikeins28
- missing fragmentation method22
- missing control_type of control experiment11
- unexpected target of control experiment11
- missing paired_with5
- low coverage4
- high lambda C methylation ratio3
- borderline sequencing depth1
- inconsistent paired_with1
Showing 25 of 17925 results
- microRNA-seq of osteocyteHomo sapiens osteocyte originated from osteocyteLab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of neural crest cellHomo sapiens neural crest cell originated from neural crest cellLab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of progenitor cell of endocrine pancreasHomo sapiens progenitor cell of endocrine pancreas originated from progenitor cell of endocrine pancreasLab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of endodermal cellHomo sapiens endodermal cell originated from endodermal cellLab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of left colonHomo sapiens left colon female adult (59 years)Lab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of pancreasHomo sapiens pancreas female adult (41 years)Lab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of spleenHomo sapiens spleen female adult (59 years)Lab: Ali Mortazavi, UCIProject: ENCODE
- microRNA-seq of spleenHomo sapiens spleen female adult (41 years)Lab: Ali Mortazavi, UCIProject: ENCODE