Add collection-type sequence_feature and two collections of transcrip…

…tion-start-sites (will remove collection transcription)

Glycine/max/sequence_feature/Wm82.gnm2.trnsc.Wang_Duan_2024/CHECKSUM.Wm82.gnm2.trnsc.Wang_Duan_2024.md5

@@ -0,0 +1,7 @@
+b08d58999360fecce3c86a487c7e1d5d  ./CHANGES.Wm82.gnm2.trnsc.Wang_Duan_2024.txt
+618232eac72c139ac00f9ea5de470410  ./glyma.Wm82.gnm2.trnsc.Wang_Duan_2024.tsr.gff3.gz
+52d844f022b801862582643a784371b8  ./glyma.Wm82.gnm2.trnsc.Wang_Duan_2024.tsr.gff3.gz.tbi
+fd900fe81ce6aa8e9748c35b30527112  ./MANIFEST.Wm82.gnm2.trnsc.Wang_Duan_2024.yml
+55b44cbe2a97dd72914fbdd240a7f06a  ./glyma.Wm82.gnm2.trnsc.Wang_Duan_2024.tss.gff3.gz
+ef7515da1ec71f3ffadc5e8220b1c1dc  ./glyma.Wm82.gnm2.trnsc.Wang_Duan_2024.tss.gff3.gz.tbi
+102fba40145275c94a3cadd953938698  ./README.Wm82.gnm2.trnsc.Wang_Duan_2024.yml

Glycine/max/sequence_feature/Wm82.gnm2.trnsc.Wang_Duan_2024/MANIFEST.Wm82.gnm2.trnsc.Wang_Duan_2024.yml

@@ -0,0 +1,13 @@
+---
+- name: glyma.Wm82.gnm2.trnsc.Wang_Duan_2024.tsr.gff3.gz
+  description: TSS clusters/regions (TSRs) identified in Wm82 genome assembly 2
+  applications:
+    - jbrowse
+  prior_names:
+    - TSR_annotated.V2.gff3.gz
+- name: glyma.Wm82.gnm2.trnsc.Wang_Duan_2024.tss.gff3.gz
+  description: Transcription start sites (TSS) identified in Wm82 genome assembly 2
+  applications:
+    - jbrowse
+  prior_names:
+    - tss_annotated.V2.gff3.gz

Glycine/max/sequence_feature/Wm82.gnm2.trnsc.Wang_Duan_2024/README.Wm82.gnm2.trnsc.Wang_Duan_2024.yml

@@ -0,0 +1,41 @@
+---
+identifier: Wm82.gnm4.trnsc.Wang_Duan_2024
+
+provenance: "The files in this directory originated from the lab of Dr. Jianxin Ma, Purdue Univeristy. Files in this present directory are derived, and may have changes, as noted below. The files here are held as part of the SoyBase and LegumeInfo projects, and are made available here for the purpose of reproducibility of analyses at these sites (e.g. gene family alignments and phylogenies, genome browsers, etc.) and for further use by researchers, as that research extends other analyses at the SoyBase and LegumeInfo projects. If you are conducting research on large-scale data sets for this species, please consider retrieving the data from the primary repositories. If you use the data in the present directory, please 1) please cite the data appropriately - generally referring to the original publications for this data; and if you make use of any significant modifications in the files (noted below under Transformations where applicable), then please also cite the respective database project(s) related to this directory."
+
+source: "http://soybase.org"
+
+synopsis: Transcription initiation-site information for Glycine max accession Williams 82 genome assembly 2
+
+scientific_name: Glycine max
+
+taxid: 3847
+
+bioproject:
+
+scientific_name_abbrev: glyma
+
+genotype:
+  - Williams 82
+
+description: "Transcription initiation-site information (transcription start sites and transcription start regions) for Glycine max accession Williams 82 genome assembly 2"
+
+original_file_creation_date: "2024-05-01"
+
+local_file_creation_date: "2024-07-05"
+
+publication_doi: 10.1101/2024.03.27.587116
+
+publication_title: "Widespread transcription initiation within coding sequences marks tissue identity and accessible chromatin"
+
+contributors: "Xutong Wang, Jingbo Duan, Chancelor B. Clark, Wanjie Feng, Jianxin Ma bioRxiv 2024.03.27.587116; doi: https://doi.org/10.1101/2024.03.27.587116"
+
+data_curators: Steven Cannon
+
+public_access_level: public
+
+license: Open
+
+keywords: soybean, transcription start sites, transcription start site clusters, TSS, TSR
+
+citation: "Widespread transcription initiation within coding sequences marks tissue identity and accessible chromatin. Xutong Wang, Jingbo Duan, Chancelor B. Clark, Wanjie Feng, Jianxin Ma. bioRxiv 2024.03.27.587116; doi: https://doi.org/10.1101/2024.03.27.587116"

Glycine/max/sequence_feature/Wm82.gnm4.trnsc.Wang_Duan_2024/CHECKSUM.Wm82.gnm4.trnsc.Wang_Duan_2024.md5

@@ -0,0 +1,7 @@
+764e0d71101b57149eee1533530bab81  ./MANIFEST.Wm82.gnm4.trnsc.Wang_Duan_2024.yml
+386e1f63fa7c9c5a0d8586f2dde8bebb  ./CHANGES.Wm82.gnm4.trnsc.Wang_Duan_2024.txt
+102fba40145275c94a3cadd953938698  ./README.Wm82.gnm4.trnsc.Wang_Duan_2024.yml
+e90c9df893ffee01cdd8e1e4ee2282d9  ./glyma.Wm82.gnm4.trnsc.Wang_Duan_2024.tsr.gff3.gz
+f744351dbaf6cec50ef70ae94aa6a94e  ./glyma.Wm82.gnm4.trnsc.Wang_Duan_2024.tsr.gff3.gz.tbi
+347fceea0aa2eb13374bc24c01c54aec  ./glyma.Wm82.gnm4.trnsc.Wang_Duan_2024.tss.gff3.gz
+fcccc788651638a6f1d791ac40433a88  ./glyma.Wm82.gnm4.trnsc.Wang_Duan_2024.tss.gff3.gz.tbi

Glycine/max/sequence_feature/Wm82.gnm4.trnsc.Wang_Duan_2024/MANIFEST.Wm82.gnm4.trnsc.Wang_Duan_2024.yml

@@ -0,0 +1,13 @@
+---
+- name: glyma.Wm82.gnm4.trnsc.Wang_Duan_2024.tsr.gff3.gz
+  description: TSS clusters/regions (TSRs) identified in Wm82 genome assembly 4
+  applications:
+    - jbrowse
+  prior_names:
+    - TSR_annotated.V4.gff3.gz
+- name: glyma.Wm82.gnm4.trnsc.Wang_Duan_2024.tss.gff3.gz
+  description: Transcription start sites (TSS) identified in Wm82 genome assembly 4
+  applications:
+    - jbrowse
+  prior_names:
+    - tss_annotated.V4.gff3.gz

Glycine/max/sequence_feature/Wm82.gnm4.trnsc.Wang_Duan_2024/README.Wm82.gnm4.trnsc.Wang_Duan_2024.yml

@@ -0,0 +1,41 @@
+---
+identifier: Wm82.gnm4.trnsc.Wang_Duan_2024
+
+provenance: "The files in this directory originated from the lab of Dr. Jianxin Ma, Purdue Univeristy. Files in this present directory are derived, and may have changes, as noted below. The files here are held as part of the SoyBase and LegumeInfo projects, and are made available here for the purpose of reproducibility of analyses at these sites (e.g. gene family alignments and phylogenies, genome browsers, etc.) and for further use by researchers, as that research extends other analyses at the SoyBase and LegumeInfo projects. If you are conducting research on large-scale data sets for this species, please consider retrieving the data from the primary repositories. If you use the data in the present directory, please 1) please cite the data appropriately - generally referring to the original publications for this data; and if you make use of any significant modifications in the files (noted below under Transformations where applicable), then please also cite the respective database project(s) related to this directory."
+
+source: "http://soybase.org"
+
+synopsis: Transcription initiation-site information for Glycine max accession Williams 82 genome assembly 2
+
+scientific_name: Glycine max
+
+taxid: 3847
+
+bioproject:
+
+scientific_name_abbrev: glyma
+
+genotype:
+  - Williams 82
+
+description: "Transcription initiation-site information (transcription start sites and transcription start regions) for Glycine max accession Williams 82 genome assembly 2"
+
+original_file_creation_date: "2024-05-01"
+
+local_file_creation_date: "2024-07-05"
+
+publication_doi: 10.1101/2024.03.27.587116
+
+publication_title: "Widespread transcription initiation within coding sequences marks tissue identity and accessible chromatin"
+
+contributors: "Xutong Wang, Jingbo Duan, Chancelor B. Clark, Wanjie Feng, Jianxin Ma bioRxiv 2024.03.27.587116; doi: https://doi.org/10.1101/2024.03.27.587116"
+
+data_curators: Steven Cannon
+
+public_access_level: public
+
+license: Open
+
+keywords: soybean, transcription start sites, transcription start site clusters, TSS, TSR
+
+citation: "Widespread transcription initiation within coding sequences marks tissue identity and accessible chromatin. Xutong Wang, Jingbo Duan, Chancelor B. Clark, Wanjie Feng, Jianxin Ma. bioRxiv 2024.03.27.587116; doi: https://doi.org/10.1101/2024.03.27.587116"