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Description: NA
Author: jillianwu
Session Name: Quiz2 Q8
Genome Assembly: hg38
Creation Date: 2024-03-19
Views: 17
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Description: This session allows for the browsing of the Cut&Run (ph, H3K27me3, H2AK118Ub, and H3K27ac), ATAC-seq, and RNA-seq datasets from the paper entitled "Transient loss of Polycomb components induces an epigenetic cancer fate”; DOI:10.1038/s41586-024-07328-w. It shows data for three conditions: "no ph-KD" - this corresponds to the Control condition; "Constant ph-KD”, which correspond to tumors obtained upon depleting the Polycomb PRC1 subunit Polyhomeotic throughout development of the eye-precursor tissue, and "Transient ph-KD D11”, which corresponds to tumors that arise upon a transient depletion of the same protein for 24 hours at the beginning of larval development, followed by recovery of the protein and 8 days of growth. See the paper for details. Note that an earlier version of the work has been published in bioRxiv and can be accessed at the link: https://www.biorxiv.org/content/10.1101/2023.01.04.522799v1.
Author: cavalli
Session Name: EpiCancer
Genome Assembly: dm6
Creation Date: 2023-02-20
Views: 111
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Description: Sessions shows part of spike protein on SARS-CoV-2 genome. One track shows the reference amino acids for the spike protein. A custom track at the top shows the location of two amino acids that are substituted by prolines to hold the protein in the pre-fusion conformation. A track near the bottom shows the Moderna and Pfizer/BioNtech vaccines with the two prolines substituted for lysine and valine of the reference. The last rack shows current variants of concern (VoC). Reconfigure the vaccine track to see the "different RNA bases" by clicking the gray button to the left of track.
Author: Example
Session Name: wuhCor1_ProPro2
Genome Assembly: wuhCor1
Creation Date: 2022-06-16
Views: 127
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127 |
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Description: rhi_Chip dataset
Author: kotov_alexei
Session Name: rhi_Chip_Chen
Genome Assembly: dm6
Creation Date: 2022-05-13
Views: 161
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Description:
Author: GeMi
Session Name: genetic analysis 2022
Genome Assembly: hg19
Creation Date: 2022-03-24
Views: 139
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139 |
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Description:
Author: kirkorneev
Session Name: TNF locus epigenetics EIMB
Genome Assembly: hg19
Creation Date: 2022-03-16
Views: 110
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Description: Chip data by Buecker et al.
Author: abarral
Session Name: mm9_Buecker_v2
Genome Assembly: mm9
Creation Date: 2022-03-02
Views: 60
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60 |
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Description:
Author: Lluc
Session Name: DNAse_50bp
Genome Assembly: hg38
Creation Date: 2022-03-01
Views: 147
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147 |
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Description:
Author: Augusto
Session Name: zona de trabajo
Genome Assembly: hg19
Creation Date: 2022-02-18
Views: 158
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158 |
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Description:
Author: agonzalezde.1
Session Name: Sesin 5
Genome Assembly: hg38
Creation Date: 2022-02-18
Views: 94
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94 |
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Description:
Author: agonzalezde.1
Session Name: Trabajo final
Genome Assembly: hg19
Creation Date: 2022-02-20
Views: 144
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Description:
Author: asyanda
Session Name: MIR_07FEB
Genome Assembly: hg38
Creation Date: 2022-02-07
Views: 101
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101 |
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Description:
Author: tandrew3
Session Name: hg19_islet_tracks
Genome Assembly: hg19
Creation Date: 2021-11-01
Views: 333
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333 |
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Description:
Author: Augusto
Session Name: Grupo 5 dia 2
Genome Assembly: hg19
Creation Date: 2022-02-15
Views: 127
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127 |
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Description:
Author: sr467
Session Name: hg19-astad
Genome Assembly: hg19
Creation Date: 2021-08-19
Views: 289
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289 |
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Description:
Author: Benoit Ballester
Session Name: EU_hg38_ReMap2022
Genome Assembly: hg38
Creation Date: 2021-08-11
Views: 1977
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1977 |
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Description:
Author: Benoit Ballester
Session Name: EU_mm10_ReMap2022
Genome Assembly: mm10
Creation Date: 2021-08-11
Views: 1065
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1065 |
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Description:
Author: Benoit Ballester
Session Name: EU_dm6_ReMap2022
Genome Assembly: dm6
Creation Date: 2021-08-11
Views: 447
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447 |
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Description:
Author: Benoit Ballester
Session Name: EU_araTha1_ReMap2022
Genome Assembly: hub_99317_araTha1
Creation Date: 2021-08-11
Views: 888
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888 |
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Description:
Author: trandoanduyhai
Session Name: Tran et al.
Genome Assembly: hg38
Creation Date: 2021-06-25
Views: 282
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282 |
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Description:
Author: Kjmorris
Session Name: Winick_Ng_2021_GAMbrainpublicsession
Genome Assembly: mm10
Creation Date: 2021-05-07
Views: 603
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603 |
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Description:
Author: giancarlo.castellano
Session Name: Projecte_21_multiQC_AE_2_hg38
Genome Assembly: hg38
Creation Date: 2021-05-04
Views: 294
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294 |
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Description:
Author: HRC
Session Name: AngiogenesisProtocol_2021_DeVal
Genome Assembly: hg19
Creation Date: 2021-04-09
Views: 330
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330 |
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Description:
Author: chantal_bachmann
Session Name: mm39_Lib1_Flies_Ig-SF (PINCER 6sgRNA library)
Genome Assembly: mm39
Creation Date: 2021-04-28
Views: 291
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Description:
Author: DaniApel
Session Name: hg19_hemoglobin
Genome Assembly: hg19
Creation Date: 2021-04-19
Views: 323
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323 |
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Description:
Author: Tomkap
Session Name: hg19_tmp_lung
Genome Assembly: hg19
Creation Date: 2021-04-12
Views: 267
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267 |
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Description:
Author: Jairo
Session Name: hg38
Genome Assembly: hg38
Creation Date: 2021-04-01
Views: 305
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305 |
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Description:
Author: Mridley
Session Name: hg38- B cells
Genome Assembly: hg38
Creation Date: 2021-03-31
Views: 341
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341 |
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Description:
Author: ElisaMarin_10
Session Name: Group 6 project (hg19)
Genome Assembly: hg19
Creation Date: 2021-03-05
Views: 312
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312 |
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Description:
Author: Tomkap
Session Name: hg19_grail_nov20
Genome Assembly: hg19
Creation Date: 2020-11-04
Views: 678
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678 |
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Description:
Author: shmoha
Session Name: hg38_THBS1
Genome Assembly: hg38
Creation Date: 2021-05-01
Views: 317
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317 |
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Description:
Author: EsterCastillo
Session Name: HNPCC_v2
Genome Assembly: hg19
Creation Date: 2020-12-11
Views: 456
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456 |
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Description:
Author: EsterCastillo
Session Name: Breast+
Genome Assembly: hg19
Creation Date: 2020-11-27
Views: 395
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395 |
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Description:
Author: EsterCastillo
Session Name: HNPCC
Genome Assembly: hg19
Creation Date: 2020-11-27
Views: 421
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421 |
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Description:
Author: EsterCastillo
Session Name: BOCP
Genome Assembly: hg19
Creation Date: 2020-11-27
Views: 429
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429 |
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Description:
Author: EsterCastillo
Session Name: JAPuig
Genome Assembly: hg19
Creation Date: 2020-10-07
Views: 628
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628 |
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Description:
Author: dolphinboy666
Session Name: hg38_AR_H3K27Ac_Med1_VCAP
Genome Assembly: hg38
Creation Date: 2020-09-03
Views: 1160
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1160 |
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Description:
Author: dolphinboy666
Session Name: hg38_AR
Genome Assembly: hg38
Creation Date: 2020-09-03
Views: 465
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465 |
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Description:
Author: Tore
Session Name: PRDM14/NANOG overexpression
Genome Assembly: mm10
Creation Date: 2020-07-07
Views: 672
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672 |
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Description:
Author: Tore
Session Name: Comparison of the pluripotent stages
Genome Assembly: mm10
Creation Date: 2020-07-07
Views: 681
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681 |
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Description:
Author: otnyukov
Session Name: mm10
Genome Assembly: mm10
Creation Date: 2020-05-18
Views: 471
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471 |
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Description:
Author: dilipdurai
Session Name: hg38AZ
Genome Assembly: hg38
Creation Date: 2020-04-26
Views: 493
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493 |
Screenshot not available
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Description:
Author: ltoker
Session Name: H3K27ChIP_PD
Genome Assembly: hg19
Creation Date: 2020-04-12
Views: 609
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609 |
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Description: Capture kit and bait sets from Clinical Genomics Stockholm https://github.com/Clinical-Genomics/target_capture_bed
Author: hassanfa
Session Name: Clinical Genomics Gene Panels
Genome Assembly: hg19
Creation Date: 2019-09-16
Views: 592
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592 |
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Description:
Author: giancarlo.castellano
Session Name: Drip-seq-27032020
Genome Assembly: hg19
Creation Date: 2020-03-27
Views: 634
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634 |
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Description:
Author: vdr
Session Name: danRer7_4Cseq_nog2
Genome Assembly: danRer7
Creation Date: 2020-02-29
Views: 596
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596 |
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Description:
Author: Khadija Sana
Session Name: Anril
Genome Assembly: hg19
Creation Date: 2020-02-25
Views: 518
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518 |
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Description:
Author: ilasa.5
Session Name: Genomics day 2
Genome Assembly: hg38
Creation Date: 2020-02-11
Views: 1329
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1329 |
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Description:
Author: Mirian
Session Name: genomics day 2
Genome Assembly: hg38
Creation Date: 2020-02-11
Views: 489
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489 |
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Description:
Author: mariolamunarriz
Session Name: genomics day 2
Genome Assembly: hg38
Creation Date: 2020-02-11
Views: 501
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Description:
Author: vdr
Session Name: hg38_PC_JT_2
Genome Assembly: hg38
Creation Date: 2019-11-12
Views: 521
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Description: ReMap 2020: An atlas of regulatory regions from an integrative analysis of Human and Arabidopsis thaliana DNA-binding sequencing experiments. Go to <a href="http://remap.univ-amu.fr">ReMap</a> for more info.
Author: Benoit Ballester
Session Name: EU_hg38_ReMap2020
Genome Assembly: hg38
Creation Date: 2019-09-04
Views: 1454
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1454 |
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Description:
Author: colm.nestor@liu.se
Session Name: MGGT - MeDIP Lab 2019
Genome Assembly: mm9
Creation Date: 2019-11-26
Views: 575
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575 |
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Description: AMPH/WT Pancreas differential methylation (RRBS)
Author: EugOT
Session Name: AMPHpanDifMeth
Genome Assembly: mm10
Creation Date: 2019-10-22
Views: 591
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591 |
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Description:
Author: afanas
Session Name: TIM3 guides vs repeats
Genome Assembly: mm10
Creation Date: 2019-10-01
Views: 634
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634 |
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Description:
Author: Ccohen
Session Name: NOS2
Genome Assembly: hg19
Creation Date: 2019-09-25
Views: 520
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520 |
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Description: ReMap 2020: An atlas of regulatory regions from an integrative analysis of Arabidopsis thaliana DNA-binding sequencing experiments. Go to <a href="http://remap.univ-amu.fr">ReMap</a> for more info.
Author: Benoit Ballester
Session Name: EU_araTha1_ReMap2020
Genome Assembly: hub_30910_araTha1
Creation Date: 2019-10-16
Views: 681
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681 |
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Description:
Author: jdrf28
Session Name: hg19
Genome Assembly: hg19
Creation Date: 2021-09-17
Views: 278
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278 |
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Description:
Author: QAtester2
Session Name: mm9.something
Genome Assembly: mm9
Creation Date: 2019-07-31
Views: 503
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503 |
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Description:
Author: Tore
Session Name: H3K4me1/2 deficiency and Otx2-/-
Genome Assembly: mm10
Creation Date: 2020-07-07
Views: 547
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547 |
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Description:
Author: rvelde
Session Name: testChipSeq
Genome Assembly: hg38
Creation Date: 2019-03-20
Views: 528
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528 |
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Description:
Author: Example
Session Name: hg19_wobble
Genome Assembly: hg19
Creation Date: 2019-03-04
Views: 512
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512 |
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Description:
Author: nikomari
Session Name: chr6_NM
Genome Assembly: hg19
Creation Date: 2019-03-03
Views: 514
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514 |
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Description:
Author: nikomari
Session Name: hg19_NM_FGFR1
Genome Assembly: hg19
Creation Date: 2019-03-03
Views: 520
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520 |
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Description:
Author: mridley
Session Name: hg38-monocyte macrophage
Genome Assembly: hg38
Creation Date: 2016-10-01
Views: 557
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557 |
Screenshot not available
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Description:
Author: QAtester3
Session Name: genome-euro
Genome Assembly: hub_24394_linHum0
Creation Date: 2018-12-21
Views: 568
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Description:
Author: mcatoni
Session Name: Pack-CACTA
Genome Assembly: hub_21716_araTha1
Creation Date: 2018-10-02
Views: 539
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539 |
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Description:
Author: mahogny
Session Name: th2crispr_human
Genome Assembly: hg38
Creation Date: 2018-09-19
Views: 836
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836 |
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Description:
Author: mahogny
Session Name: th2crispr_OE
Genome Assembly: mm10
Creation Date: 2018-09-19
Views: 683
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683 |
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Description:
Author: kpaschos
Session Name: BMI1-SUZ12
Genome Assembly: hg19
Creation Date: 2018-09-15
Views: 612
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612 |
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Description:
Author: Dos Santos Matthieu
Session Name: ChipseqMuscle lent vs rapide
Genome Assembly: mm10
Creation Date: 2018-09-24
Views: 497
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497 |
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Description:
Author: ilasa.5
Session Name: Day 3 2nd exercise group 5
Genome Assembly: hg19
Creation Date: 2020-02-12
Views: 462
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Description:
Author: petersvensson
Session Name: hub_12832_spo2
Genome Assembly: hub_12832_spo2
Creation Date: 2018-07-17
Views: 494
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494 |
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Description:
Author: amanchenoferris
Session Name: bohere_etal
Genome Assembly: dm6
Creation Date: 2018-10-18
Views: 570
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570 |
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Description:
Author: Mridley
Session Name: hg38-blueprint tcell2
Genome Assembly: hg38
Creation Date: 2018-05-14
Views: 941
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941 |
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Description:
Author: Tung
Session Name: b1_promoters
Genome Assembly: hg38
Creation Date: 2018-04-25
Views: 542
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542 |
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Description:
Author: s.knop
Session Name: SESSION 1
Genome Assembly: hg19
Creation Date: 2018-03-01
Views: 507
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507 |
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Description:
Author: hilasha
Session Name: CATCH BRCA1
Genome Assembly: hg38
Creation Date: 2018-02-26
Views: 702
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702 |
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Description:
Author: vahidelyasi
Session Name: control732_nayd684_et2dnbmi52_atypicald50_1518EU
Genome Assembly: hg19
Creation Date: 2021-01-17
Views: 355
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Description: ReMap 2018: An atlas of regulatory regions from an integrative analysis of Human DNA-binding sequencing experiments. Go to <a href="http://remap.univ-amu.fr">ReMap</a> for more info. <a href="https://academic.oup.com/nar/article/46/D1/D267/4602873">ReMap 2018 paper</a>.
Author: Benoit Ballester
Session Name: hg38_ReMap2018
Genome Assembly: hg38
Creation Date: 2017-08-10
Views: 1793
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Description: Educational: evolution. Dog chr6 showing cat synteny -- no major rearrangements between the two closely related animals. Rat and mouse, however, both show many rearrangements (different colors) relative to dog and cat, but the breakpoints are the same -- showing that mouse and rat are closely related to each other.
Author: Example
Session Name: canFam3_catRatMouse
Genome Assembly: canFam3
Creation Date: 2017-11-01
Views: 512
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Description:
Author: Grunewald
Session Name: hg19_chr7_NAMPT_locus
Genome Assembly: hg19
Creation Date: 2017-09-19
Views: 520
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Description:
Author: chardman
Session Name: Dengue seq
Genome Assembly: hg38
Creation Date: 2017-07-28
Views: 551
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551 |
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Description:
Author: hilasha
Session Name: methylation OM
Genome Assembly: hg19
Creation Date: 2018-05-07
Views: 564
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564 |
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Description:
Author: krebsarnaud
Session Name: Hartl_et_al_retina_2017
Genome Assembly: mm9
Creation Date: 2017-07-26
Views: 664
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664 |
Screenshot not available
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Description: MLL-AF4 ChIP-seq in SEM and Cord Blood cells
Author: Thomas MIlne
Session Name: f-MLL-Af4 vs SEM MLL-AF4
Genome Assembly: hg38
Creation Date: 2017-01-13
Views: 134
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Description:
Author: vsabine
Session Name: allibs_928_925
Genome Assembly: sacCer3
Creation Date: 2018-11-12
Views: 536
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536 |
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Description:
Author: Mridley
Session Name: hg19-corces
Genome Assembly: hg19
Creation Date: 2017-07-13
Views: 747
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747 |
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Description:
Author: anah
Session Name: forpicsTADsjan
Genome Assembly: hg19
Creation Date: 2017-01-24
Views: 568
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Description: MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses
Author: schoteau
Session Name: MetamORF mm10
Genome Assembly: mm10
Creation Date: 2022-06-02
Views: 107
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Description: MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses
Author: schoteau
Session Name: MetamORF hg38
Genome Assembly: hg38
Creation Date: 2022-06-02
Views: 127
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Screenshot not available
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Description:
Author: musomilan
Session Name: ARL15 locus and SNPs
Genome Assembly: hg19
Creation Date: 2016-11-17
Views: 556
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Description:
Author: Mridley
Session Name: T cell-2
Genome Assembly: hg38
Creation Date: 2016-10-01
Views: 536
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536 |
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Description:
Author: hs451
Session Name: Codex hg19
Genome Assembly: hg19
Creation Date: 2016-09-01
Views: 521
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521 |
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Description:
Author: mspeir
Session Name: hg19_CAGrepeat
Genome Assembly: hg19
Creation Date: 2016-06-20
Views: 546
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Description:
Author: mspeir
Session Name: hg19_wobble
Genome Assembly: hg19
Creation Date: 2016-06-20
Views: 563
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Description: Session displays the promoter region of DARC on human assembly hg19 including UCSC Genes, dbSNP 146 (Common subset) and the Publications track showing sequences and SNPs text-mined from PubMed Central and Elsevier. Adapted from Figure 1 in Meyer, et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 2013 Jan;41(Database issue):D64-9: http://nar.oxfordjournals.org/content/41/D1/D64.long.
Author: mspeir
Session Name: hg19_NAR_2013_Fig1
Genome Assembly: hg19
Creation Date: 2016-06-20
Views: 520
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Description: Session displays the promoter region and transcription start of IRF1 on human assembly hg19 showing UCSC Genes, 1000 Genomes Phase 3 Integrated Variant Calls in the haplotype sorting VCF display mode, histone mark H3K27Ac binding in overlays of 7 ENCODE cell lines and PhyloP conservation scores from alignments of 100 vertebrates. Adapted from Figure 2 in Meyer, et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 2013 Jan;41(Database issue):D64-9: http://nar.oxfordjournals.org/content/41/D1/D64.long.
Author: mspeir
Session Name: hg19_NAR_2013_Fig2
Genome Assembly: hg19
Creation Date: 2016-06-20
Views: 533
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Description: Session displays the dyskeratosis congenita 1 (DKC1) gene using the exon-only multi-region mode in the human assembly hg38. Alongside the gene structure, tracks displaying dbSNP "flagged" variants, OMIM clinical variants, ENCODE transcription levels from 9 cell lines, a 100-way vertebrate alignment (only a subset of species displayed), and conservation scores calculated using phyloP across this 100-way alignment.
Author: mspeir
Session Name: hg38_DKC1_SNPs_Cons_Transcription
Genome Assembly: hg38
Creation Date: 2016-06-20
Views: 573
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Description: This session is demonstrating the exon-only mode of the multi-region feature. The exon-only mode uses the GENCODE v22 track to slice up the normal display and remove both intronic and intergenic regions from the display. Only those regions covered by exons, both coding and noncoding, are left in the display. For more on the multi-region display see the user guide: http://genome.ucsc.edu/goldenPath/help/multiRegionHelp.html.
Author: mspeir
Session Name: hg38_exonOnlyExample
Genome Assembly: hg38
Creation Date: 2016-06-20
Views: 540
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Description: This session displays a region of the LHX6 gene that highlights a selection of the new tracks added in the previous year for the hg38/GRCh38 human assembly. The tracks shown in this display (from top to bottom) include GENCODE Genes V22, transcription levels assayed across 9 ENCODE cell lines, DNase hypersensitive regions based on data from 95 ENCODE cell lines, genome-wide conservation scores calculated using phastCons, a multiple genome alignment created using Lastz and Multiz, and pathogenic CNVs from the ClinGen database. Adapted from Figure 1 in Speir, et al. The UCSC Genome Browser database: 2016 update. Nucleic Acids Res. 2016 Jan 4;44(D1):D717-25: http://nar.oxfordjournals.org/content/44/D1/D717.full
Author: mspeir
Session Name: hg38_NAR_2016_Fig1
Genome Assembly: hg38
Creation Date: 2016-06-20
Views: 538
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Description: Session highlights a mouse-specific repeat on chromosome 12. You can see the gap in the 60-way vertebrate alignment surrounding the repeat, which is highlighted in light blue. The repeat is classified as a LINE and is part of the L1 family of repeats. Additionally, on the far right-hand side of the display, you can see the retrotransposed Bf3 gene.
Author: mspeir
Session Name: mm10_MouseSpecificRepeat_plus_RetroposedGene
Genome Assembly: mm10
Creation Date: 2016-06-20
Views: 529
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529 |
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Description: This session demonstrates the GTEx track on the human assembly hg19. The GTEx track shows data from the NIH Genotype-Tissue Expression project and displays expression data for each gene, based on GENCODE gene models, from 51 tissues collected from 570 individual. This session also demonstrates the gene-only mode of the multi-region feature, which removes intergenic regions from the display.
Author: mspeir
Session Name: hg19_gtexAnnouncement
Genome Assembly: hg19
Creation Date: 2016-06-24
Views: 586
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586 |
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Description:
Author: GeMi
Session Name: ALPL analysis
Genome Assembly: hg19
Creation Date: 2017-07-19
Views: 537
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537 |
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Description:
Author: FAlzaid
Session Name: hg38-GHITM-IRF5
Genome Assembly: hg38
Creation Date: 2021-03-24
Views: 366
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1616540400 |
366 |
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Description: This session was the result of looking at three tables, xenoRefGene, gbCdnaInfo, and organism, and how information can be displayed with with options to filter on each field. One can scroll down to the "rn4.organism based filters" section to change "name" field from the default selection of everything. The session shows some information on rat to illustrate a region.
Author: brianlee
Session Name: rn4.customtracks
Genome Assembly: rn4
Creation Date: 2013-03-05
Views: 50
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1362438000 |
50 |
Screenshot not available
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Description:
Author: maxvcg
Session Name: Es serum vs 2i (mm9)
Genome Assembly: mm9
Creation Date: 2013-03-25
Views: 620
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1364166000 |
620 |
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