priority browser datasets to host

[ValWood]

Datasets for gene feature boundaries, or ncRNA

Data type/ details	method	PMID	First/last author	data source	status	Comment
intron/spliceosome profiling	RNA-seq	29727662	Chen/Moore	?	BDTH	@Antonialock "need to ask"
transcripts/ curated from multiple merged datasets	curated	20118936	Lantermann/ Korber	GSE16040	BDTH	HIGH PRIORITY dataset for gene structures. https://github.com/pombase/website/issues/62	Data in spreadsheet attached to Jira PB-2623". Kim may have converted it to GFF already? Strain: h90 WT
transcriptome/ strand-specific transcriptome	HybMap	18641648	Dutrow/Cairns	GSE11619	BDTH	used for curated Lantermann
transcripts/ new ncRNA/revised UTR	--	26883383	Eser/Gagneur		BDH ANNOUNCED	https://github.com/pombase/website/issues/50 Issues: 1. No IDs for new ncRNA 2. Redundancy? FUTURE CONSIDER SEPARATING FWD AND REVERSE STRAND
transcripts /RNA-seq	-	32152323	Tsuyuzaki/Sato		BDH announced 2020-09-17	[pombase #8073] mailed Masa 2/9/2020;
TSS	-	25747261	Li/Shao	-	BDH - ANNOUNCED	#736

BDTH = browser datasets to host BDH = Browser dataset hosted

Other datasets

Data type /details	method	PMID/DATA	First/last author	status	Comment
Chromatin modification/ H4 Ac & H3K36 Me	CHIPseq	22121899	Sinah/Ekwall	?
Chromatin modification/histone modifications H3K4me3 +?	CHIPseq	24100010	DeGennaro/Winston	?	possibly RNA seq too? This dataset is used to evaluate Li DeepCAGE
translation/ meiosis and sporulation	ribosome profiling	24929437	Duncan/Mata	?	requested by2 in user survey Q cyclohexamide
translation/ meiosis	proteomics	32594847	Huraiova/Gregan	?
DSBs	?	23395004	Fowler/Smith	?	#1198 Figures 3 and 6 [pombase #6827]; tracks present as of 2021-07-16
DSBs? Rec12 protein binding	?	25024163/GSE49977	Fowler/Smith	?	#1198 rec12 binding is DSB marker? [pombase #6827]
DNA binding motifs	pattern matching	n/a	PomBase	-	#802
Transposon insertion	-	PMID: 32101745	Lee/Levine	ANNOUNCED

[mah11]

@mah11 in progress?

did you look in the browser?

[ValWood]

Add to list

Long read transcriptome (Jeff Boake lab) would complement other transcriptome data (https://pubmed.ncbi.nlm.nih.gov/27856494/)

[ValWood]

Also, https://pubmed.ncbi.nlm.nih.gov/35618415/ suggested by @juanmatacambridge

[ValWood]

intron data (mainly meiosis specific) Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast https://genome.cshlp.org/content/25/6/884.short Table S12

[ValWood]

I'm reviewing the action items from 2022 SAB. This is the only outstanding task. Maybe this can be prioritised (the 3 datasets requested after )CT 2022, not all of them). @kimrutherford could you show @PCarme how to do this at some point?

[kimrutherford]

Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast https://genome.cshlp.org/content/25/6/884.short Table S12

I think it will be straightforward to turn that table into a browser track. It has the critical things: chromosome ID, strand, start and end positions and a feature ID.

[kimrutherford]

I think it will be straightforward to turn that table into a browser track.

The processed data file in BED format is here: https://www.pombase.org/external_datasets/Bitton_2015_PMID_25883323_introns/PMID_25883323_Supplemental_Tables-S12.sorted.bed.gz

[kimrutherford]

I've had a look at the other two datasets.

Long read transcriptome (Jeff Boake lab) would complement other transcriptome data (https://pubmed.ncbi.nlm.nih.gov/27856494/)

For this paper I think it makes sense to show the assembled transcripts as a track, but I can only find the raw reads (in GEO). We can show raw reads but it's probably not what users would want. Also we'd need to align the reads to the genome to make a BAM file.

Also, https://pubmed.ncbi.nlm.nih.gov/35618415/ suggested by @juanmatacambridge

This one looks easier. They have various GTF files on figshare and a BAM file. I approve!

One of the files is "Spom_novel_transcripts.gtf" which sounds immediately useful: https://figshare.com/articles/dataset/Native_RNA_sequencing_in_fission_yeast_reveals_frequent_alternative_splicing_isoforms/19368146?file=34398125

We'd need to read the paper to decide which of the other files would make good browser tracks.

[kimrutherford]

Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast https://genome.cshlp.org/content/25/6/884.short Table S12

That track is now on the site:

• https://www.pombase.org/reference/PMID:25883323
• https://www.pombase.org/jbrowse/?loc=I%3A2819691..2838230&tracks=Forward%20strand%20features%2CReverse%20strand%20features%2CNovel%20introns%20%E2%80%93%20Bitton%20et%20al.%20(2015)&highlight=

We might need to work on how it looks. We can configure colours, labels and sizes of features:

[ValWood]

One small thing. I think we should have a new data type "intron-related". It would group this dataset and the branch point data.

The label "genome sequence and features" was intended to be reserved for the actual genome sequence and annotated features (maybe we could improve that label?