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Description: refTSS coordinates on human hg38 genome.
More details: https://reftss.riken.jp
Author: MasakiM
Session Name: refTSS4 on hg38
Genome Assembly: hg38
Creation Date: 2023-07-03
Views: 29
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Description: The genes HBB and HBD are both expressed in red blood cells , but HBB is also expressed in many other tissues , whereas HBD is expressed in red cells almost exclusively.
Author: yrajat7900
Session Name: hg19_hemoglobin
Genome Assembly: hg19
Creation Date: 2022-02-06
Views: 116
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116 |
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Description:
Author: bzswmu
Session Name: pf47_part2_new
Genome Assembly: hub_132305_pf47
Creation Date: 2022-01-28
Views: 239
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239 |
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Description:
Author: bzswmu
Session Name: pf47_part1
Genome Assembly: hub_132305_pf47
Creation Date: 2021-12-16
Views: 530
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530 |
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Description:
Author: zahra jafari
Session Name: homwork
Genome Assembly: hg19
Creation Date: 2021-12-03
Views: 124
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124 |
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Description:
Author: BowenYang
Session Name: part 4
Genome Assembly: hg19
Creation Date: 2021-08-31
Views: 258
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258 |
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Description:
Author: zzhmark
Session Name: germlayer_enh
Genome Assembly: mm10
Creation Date: 2021-03-14
Views: 324
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324 |
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Description:
Author: chenchuanhuizi
Session Name: TP53
Genome Assembly: hg38
Creation Date: 2021-03-05
Views: 337
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337 |
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Description:
Author: Aragon
Session Name: hg19
Genome Assembly: hg19
Creation Date: 2021-02-12
Views: 313
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313 |
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Description:
Author: Aragon
Session Name: hg19_joydip
Genome Assembly: hg19
Creation Date: 2021-02-12
Views: 342
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342 |
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Description:
Author: SAYANTANI SANTRA
Session Name: hg19 8-2-21
Genome Assembly: hg19
Creation Date: 2021-02-08
Views: 304
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304 |
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Description:
Author: akhileshwar_namani@yahoo.co.in
Session Name: TXA549CHIPSEQ
Genome Assembly: hg19
Creation Date: 2021-01-17
Views: 307
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307 |
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Description:
Author: Shadab79
Session Name: shadab
Genome Assembly: hg19
Creation Date: 2020-07-20
Views: 400
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400 |
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Description:
Author: lkh
Session Name: pol2_subunits
Genome Assembly: mm10
Creation Date: 2019-11-21
Views: 1069
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1069 |
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Description:
Author: jieMM
Session Name: hg38_FINAL
Genome Assembly: hg38
Creation Date: 2019-11-05
Views: 815
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815 |
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Description: The latest version of imomdb data, uploaded on April 2020
Author: imomdb
Session Name: imomdb_v0
Genome Assembly: hg19
Creation Date: 2020-04-15
Views: 394
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394 |
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Description:
Author: QAtester2
Session Name: hg18_SNP
Genome Assembly: hg18
Creation Date: 2019-08-01
Views: 474
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474 |
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Description:
Author: brianlee
Session Name: hg38_test
Genome Assembly: hg38
Creation Date: 2019-06-11
Views: 466
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466 |
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Description:
Author: geneHunter23
Session Name: hg19Default
Genome Assembly: hg19
Creation Date: 2019-06-11
Views: 484
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484 |
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Description:
Author: Lou
Session Name: bosTau9_Interesting
Genome Assembly: bosTau9
Creation Date: 2019-06-08
Views: 556
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556 |
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Description: This is an interact track type using GeneHancer data.
Author: brianlee
Session Name: InteractSession
Genome Assembly: hg38
Creation Date: 2019-06-07
Views: 490
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490 |
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Description:
Author: XinDong
Session Name: TAD_with_Hsitone_and_RNAseq
Genome Assembly: hg38
Creation Date: 2019-03-25
Views: 472
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472 |
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Description:
Author: pdl.tyh
Session Name: hg19_PDL CNV analysis
Genome Assembly: hg19
Creation Date: 2018-12-29
Views: 1022
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1022 |
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Description:
Author: QAtester3
Session Name: genomeAsia
Genome Assembly: hub_80308_linHum0
Creation Date: 2018-12-22
Views: 442
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442 |
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Description:
Author: malaysia2018
Session Name: hg19_UPD2
Genome Assembly: hg19
Creation Date: 2018-08-29
Views: 479
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479 |
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Description:
Author: malaysia2018
Session Name: hg19_UPD
Genome Assembly: hg19
Creation Date: 2018-08-29
Views: 1213
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1213 |
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Description:
Author: maskyjg
Session Name: hg19_TRPS1_ChIPSeq
Genome Assembly: hg38
Creation Date: 2018-08-08
Views: 418
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418 |
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Description:
Author: lipan
Session Name: hg38_dynamics
Genome Assembly: hg38
Creation Date: 2018-07-13
Views: 1815
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Description:
Author: lipan
Session Name: mm10_dynamics
Genome Assembly: mm10
Creation Date: 2018-07-13
Views: 1010
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1010 |
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Description:
Author: Lin Xia
Session Name: hg19 HEK293T
Genome Assembly: hg19
Creation Date: 2018-05-10
Views: 610
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610 |
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Description:
Author: cehnouz
Session Name: hg19
Genome Assembly: hg19
Creation Date: 2017-08-25
Views: 472
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Description: We have recently released a file type called "longTabix" which supports inter & intra-chromosomal interactions by drawing an "arc" among paired regions in the UCSC Genome Browser. Note the first track at the top of the display, you can click on any of the "arcs" or interaction connections to see details such as ID and score.
Credit goes to Cath Tyner for the creation of this session.
Link to the original question:
https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/kE2pIZUvfnA/jfopk7pFAQAJ
Author: PublicSessions
Session Name: Viewing inter- & intra-chromosomal interactions
Genome Assembly: hg19
Creation Date: 2017-03-22
Views: 439
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439 |
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Description:
Author: vivekgopalanmedgenome
Session Name: MSH3_DHFR_region2
Genome Assembly: hg19
Creation Date: 2016-09-21
Views: 487
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487 |
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Description:
Author: vivekgopalanmedgenome
Session Name: MSH3_DHFR_region1
Genome Assembly: hg19
Creation Date: 2016-09-21
Views: 502
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Description:
Author: vivekgopalanmedgenome
Session Name: MSH3_DHFR_region
Genome Assembly: hg19
Creation Date: 2016-09-21
Views: 454
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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: 471
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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: 2016-05-24
Views: 455
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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: 2016-05-24
Views: 480
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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: 2016-05-24
Views: 507
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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: 2016-05-24
Views: 574
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574 |
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Description:
Author: lijin
Session Name: session6 lung specific enhancer example
Genome Assembly: hg19
Creation Date: 2016-04-29
Views: 425
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425 |
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Description:
Author: lijin
Session Name: session2 four types
Genome Assembly: hg19
Creation Date: 2016-04-17
Views: 433
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433 |
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Description:
Author: lijin
Session Name: test
Genome Assembly: hg19
Creation Date: 2016-04-16
Views: 450
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450 |
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Description:
Author: lijin
Session Name: session5 whole genome methy
Genome Assembly: hg19
Creation Date: 2016-04-29
Views: 441
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Description:
Author: mspeir
Session Name: hg19_CAGrepeat
Genome Assembly: hg19
Creation Date: 2016-06-21
Views: 440
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440 |
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Description:
Author: mspeir
Session Name: hg19_wobble
Genome Assembly: hg19
Creation Date: 2016-06-21
Views: 475
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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: 2016-06-21
Views: 426
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426 |
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Description:
Author: lijin
Session Name: session1 Liver 97L exp meth
Genome Assembly: hg19
Creation Date: 2016-04-17
Views: 428
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428 |
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Description:
Author: lijin
Session Name: session4 plus h3k27ac density andpeaks
Genome Assembly: hg19
Creation Date: 2016-04-28
Views: 422
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422 |
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Description:
Author: lijin
Session Name: session3 plus h3k27ac
Genome Assembly: hg19
Creation Date: 2016-04-28
Views: 415
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415 |
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Description:
Author: ARKLAB_iwoo
Session Name: arklab_hg19_hemo_demonstration
Genome Assembly: hg19
Creation Date: 2017-03-31
Views: 535
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Description: This session shows a search of primers. A researcher had an issue building PCR primers and Browser staff discovered that a desired reverse primer falls into an area of repeats. The original primer at 20 bases was near the limit of BLAT's sensitivity. With such short sequences, if BLAT has an over-used tile, a section of the query used to match and trigger an alignment, the algorithm will not be able to seed and extend an original BLAT hit in an area of repeats, which was what was likely happening to the reverse primer sequence in this session. In the session a larger BLAT query will result in a hit. Since primers are typically chosen from unique locations, Browser staff suggested it might be best to avoid a repeat-region, and noted that the nearby chr13:50,593,214-50,593,267 section appears to not have any repeats.
Author: brianlee
Session Name: Primers Blat Search
Genome Assembly: hg19
Creation Date: 2013-07-23
Views: 70
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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: 2015-08-11
Views: 466
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