From ccf16aa5bffaf4c19a4a0ec63b133cbb56f3dc37 Mon Sep 17 00:00:00 2001 From: Kim Rutherford Date: Fri, 3 Jan 2025 17:13:50 +1300 Subject: [PATCH] Fix missing data file for TF binding track Refs pombase/website#2308 --- website/jbrowse_track_metadata.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/website/jbrowse_track_metadata.csv b/website/jbrowse_track_metadata.csv index 4667af4..3f593c9 100644 --- a/website/jbrowse_track_metadata.csv +++ b/website/jbrowse_track_metadata.csv @@ -134,7 +134,7 @@ Transcripts,yes,yes,Transcripts during vegetative growth; repeat 2 - Wilhelm et Transcripts,yes,yes,Transcripts in prp2-1 mutant; repeat 1 - Wilhelm et al. (2012),,,h-,mutant,prp2-1,high temperature,vegetative growth,,RNA-Seq,Wilhelm,2012,18488015,ArrayExpress,E-MTAB-5,ERS078445,High throughput sequenceing of fission yeast to survey the dynamic repertoire of a eukaryotic transcriptome at the single nucleotide resolution,bigWig,https://www.pombase.org/external_datasets/Wilhelm_2012_PMID_18488015/ERS078445.bw Transcripts,yes,yes,Transcripts in prp2-1 mutant; repeat 2 - Wilhelm et al. (2012),,,h-,mutant,prp2-1,high temperature,vegetative growth,,RNA-Seq,Wilhelm,2012,18488015,ArrayExpress,E-MTAB-5,ERS078468,High throughput sequenceing of fission yeast to survey the dynamic repertoire of a eukaryotic transcriptome at the single nucleotide resolution,bigWig,https://www.pombase.org/external_datasets/Wilhelm_2012_PMID_18488015/ERS078468.bw DNA duplex stability,yes,yes,Position specific G(x) scores - Yadav et al. (2012),free energy needed to separate a base pair,,,WT,not applicable,,not applicable,,SIDD,Yadav,2012,23163955,,not available,,,bed,https://www.pombase.org/external_datasets/Yadav_2012_PMID_23163955_SIDD/Yadav_and_Dubey_SIDD_PMID23163955.sorted.bed.gz -Promoters,yes,no,Consensus transcription factor DNA binding motifs,,,,WT,not applicable,,not applicable,,predicted,McDowall,2015,25361970,,https://www.pombase.org/browse-curation/dna-binding-sites,,,bed,https://www.pombase.org/pombase_datasets/genome_sequence_and_features/feature_coordinates/TF_binding_motifs.bed.gz +Promoters,yes,no,Consensus transcription factor DNA binding motifs,,,,WT,not applicable,,not applicable,,predicted,McDowall,2015,25361970,,https://www.pombase.org/browse-curation/dna-binding-sites,,,bed,https://www.pombase.org/internal_datasets/TF_binding_motifs.bed.gz Transcription start sites,yes,yes,Transcription start sites during vegetative growth in minimal medium (forward strand) - Thodberg et al. (2018),,,h-,WT,not applicable,glucose MM,vegetative growth,forward,CAGE,Thodberg,2018,30566651,GEO,GSE110976,"GSM3019616, GSM3019617, GSM3019618",,bigWig,https://www.pombase.org/external_datasets/Thodberg_2018_PMID_30566651/GSE110976_EMM_exp_plus.bw Transcription start sites,yes,yes,Transcription start sites during vegetative growth in minimal medium (reverse strand) - Thodberg et al. (2018),,,h-,WT,not applicable,glucose MM,vegetative growth,reverse,CAGE,Thodberg,2018,30566651,GEO,GSE110976,"GSM3019616, GSM3019617, GSM3019618",,bigWig,https://www.pombase.org/external_datasets/Thodberg_2018_PMID_30566651/GSE110976_EMM_exp_minus.bw Transcription start sites,yes,yes,Transcription start sites during vegetative growth in rich medium (forward strand) - Thodberg et al. (2018),,,h-,WT,not applicable,YES,vegetative growth,forward,CAGE,Thodberg,2018,30566651,GEO,GSE110976,"GSM3019622, GSM3019623, GSM3019624",,bigWig,https://www.pombase.org/external_datasets/Thodberg_2018_PMID_30566651/GSE110976_YES_exp_plus.bw