Amphioxus (Branchiostoma floridae) superTranscriptome
Amphioxus (Branchiostoma floridae) cDNA superTranscriptome assembly BfsuperV5 was downloaded from the IncDNA-BF (Integrative cDNA library for Branchiostoma floridae) database (http://139.129.29.118/IncDNA) made available by Prof. Zhiliang Ji and Dr. Yangmei Qin of the School of Life Sciences, Xiamen...
| Main Authors: | , , |
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| Format: | Dataset |
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University of Oxford
2020
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| _version_ | 1826272334019821568 |
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| author | Holland, P Herrera-Ubeda, C Li, G |
| author2 | Holland, P |
| author_facet | Holland, P Holland, P Herrera-Ubeda, C Li, G |
| author_sort | Holland, P |
| collection | OXFORD |
| description | Amphioxus (Branchiostoma floridae) cDNA superTranscriptome assembly BfsuperV5 was downloaded from the IncDNA-BF (Integrative cDNA library for Branchiostoma floridae) database (http://139.129.29.118/IncDNA) made available by Prof. Zhiliang Ji and Dr. Yangmei Qin of the School of Life Sciences, Xiamen University, Xiamen, China (appo@xmu.edu.cn). Hox genes were then assembled manually to remove and correct an artefactual fusion between 6 distinct Hox genes and a lncRNA (giving 215,495 sequences). The version deposited here includes this adjustment. Use of these data should acknowledge the IncDNA-BF (Integrative cDNA library for Branchiostoma floridae) database (http://139.129.29.118/IncDNA) and the publication cited in this ORA-Data entry.
Files included:
BfsuperV5_fix.fa
= fasta file of all sequences
BfsuperV5-4_FIX.gtf
= tab-delineated text file in gtf format giving feature coordinates and putative identities of transcripts within superTranscripts. Tabs are: (1) seqname [equivalent to contig ID or gene name in Supplementary Data]; (2) source [superTrancript]; (3) feature [transcript, exon or CDS (coding sequence)]; (4) start of feature; (5) end of feature; (6) score [dot]; (7) strand [+]; (8) frame [dot]; (9) attribute [gene_id; transcript_id; gene_Name = example blast hit, uniprot code; Note = putative gene name from uniprot blast hit blast only] |
| first_indexed | 2024-03-06T22:10:54Z |
| format | Dataset |
| id | oxford-uuid:51c9ff65-63c4-4010-a267-4b795cc40abc |
| institution | University of Oxford |
| last_indexed | 2024-03-06T22:10:54Z |
| publishDate | 2020 |
| publisher | University of Oxford |
| record_format | dspace |
| spelling | oxford-uuid:51c9ff65-63c4-4010-a267-4b795cc40abc2022-03-26T16:21:41ZAmphioxus (Branchiostoma floridae) superTranscriptomeDatasethttp://purl.org/coar/resource_type/c_ddb1uuid:51c9ff65-63c4-4010-a267-4b795cc40abcORA DepositUniversity of Oxford2020Holland, PHerrera-Ubeda, CLi, GHolland, PLi, GAmphioxus (Branchiostoma floridae) cDNA superTranscriptome assembly BfsuperV5 was downloaded from the IncDNA-BF (Integrative cDNA library for Branchiostoma floridae) database (http://139.129.29.118/IncDNA) made available by Prof. Zhiliang Ji and Dr. Yangmei Qin of the School of Life Sciences, Xiamen University, Xiamen, China (appo@xmu.edu.cn). Hox genes were then assembled manually to remove and correct an artefactual fusion between 6 distinct Hox genes and a lncRNA (giving 215,495 sequences). The version deposited here includes this adjustment. Use of these data should acknowledge the IncDNA-BF (Integrative cDNA library for Branchiostoma floridae) database (http://139.129.29.118/IncDNA) and the publication cited in this ORA-Data entry. Files included: BfsuperV5_fix.fa = fasta file of all sequences BfsuperV5-4_FIX.gtf = tab-delineated text file in gtf format giving feature coordinates and putative identities of transcripts within superTranscripts. Tabs are: (1) seqname [equivalent to contig ID or gene name in Supplementary Data]; (2) source [superTrancript]; (3) feature [transcript, exon or CDS (coding sequence)]; (4) start of feature; (5) end of feature; (6) score [dot]; (7) strand [+]; (8) frame [dot]; (9) attribute [gene_id; transcript_id; gene_Name = example blast hit, uniprot code; Note = putative gene name from uniprot blast hit blast only] |
| spellingShingle | Holland, P Herrera-Ubeda, C Li, G Amphioxus (Branchiostoma floridae) superTranscriptome |
| title | Amphioxus (Branchiostoma floridae) superTranscriptome |
| title_full | Amphioxus (Branchiostoma floridae) superTranscriptome |
| title_fullStr | Amphioxus (Branchiostoma floridae) superTranscriptome |
| title_full_unstemmed | Amphioxus (Branchiostoma floridae) superTranscriptome |
| title_short | Amphioxus (Branchiostoma floridae) superTranscriptome |
| title_sort | amphioxus branchiostoma floridae supertranscriptome |
| work_keys_str_mv | AT hollandp amphioxusbranchiostomafloridaesupertranscriptome AT herreraubedac amphioxusbranchiostomafloridaesupertranscriptome AT lig amphioxusbranchiostomafloridaesupertranscriptome |