Dataset Open Access

miRNA target finder training datasets

Gallardo-Alba, Cristóbal

Datasets needed to run the Galaxy training:  miRNA target finder in Arabidopsis thaliana

Files (13.4 GB)
Name Size
annotation_AtRTD2_19April2016.gtf.gz
md5:8d64d472daf45bfebdf4d00717dec101
6.1 MB Download
downregulated_mRNA_complete_dataset.fasta
md5:bf0d73e742832b605b9ff7e39d98e379
60.1 kB Download
Galaxy15-[BRL3_mRNA_drought__SRR7779222].fastqsanger.gz
md5:a0b2f76ba665d8144e9f814461751ad8
1.2 GB Download
Galaxy15-[BRL3_mRNA_drought__SRR7779223].fastqsanger.gz
md5:43d936ddeab66dbf16a4da3e2025e9cf
1.1 GB Download
Galaxy15-[BRL3_mRNA_drought__SRR7779224].fastqsanger.gz
md5:941f6a094821d71d4b2f319c883a826a
1.1 GB Download
Galaxy19-[BRL3_mRNA_control__SRR7779228].fastqsanger.gz
md5:795a460befd31ba7c8a72a22812ebee4
956.2 MB Download
Galaxy19-[BRL3_mRNA_control__SRR7779229].fastqsanger.gz
md5:d83940952a379bf886def2ce9b20dea8
1.1 GB Download
mature_miRNA_AT.fasta
md5:abaa12d0072baabe8a7957f4cfd17246
7.7 kB Download
miRNA_stem-loop_seq.fasta
md5:8956c11d5176e661f47140ad49676689
27.7 kB Download
PmiREN_miRNA_database.fasta
md5:abaa12d0072baabe8a7957f4cfd17246
7.7 kB Download
SRR1019436_RNASEQ_CTL.fastqsanger.gz
md5:860343e34ff5842d9aa7368e4b521e01
22.0 MB Download
SRR1019437_RNASEQ_CTL.fastqsanger.gz
md5:8cb65af3e9a616abb8414cdf96e4ca82
24.0 MB Download
SRR1019438_RNASEQ_BL.fastqsanger.gz
md5:f782ef2368345699fe74bfce374c62a6
23.8 MB Download
SRR1019439_RNASEQ_BL.fastqsanger.gz
md5:cff8b700b7b2706af7f619ce352d212e
23.8 MB Download
SRR11611349_MIRNASEQ_CTL.fastqsanger.gz
md5:53250a1fe8c7da369e031bace9ba17a1
18.8 MB Download
SRR11611350_MIRNASEQ_CTL.fastqsanger.gz
md5:27a619a2cd301732be894d7cb6f37723
15.7 MB Download
SRR11611351.MIRNASEQ_CTLfastqsanger.gz
md5:37181d275ba214b65fe5c3a0836fff40
17.1 MB Download
SRR11611352_MIRNASEQ_BL.fastqsanger.gz
md5:351c959aebe763c7b95dc1288999ad5a
17.7 MB Download
SRR11611353_MIRNASEQ_BL.fastqsanger.gz
md5:860d15dde59624c870c0731e66346016
19.2 MB Download
SRR11611354_MIRNASEQ_BL.fastqsanger.gz
md5:1210b3ab28e3d8f057b47cb63c648359
10.5 MB Download
SRR7779219_WT_Drought.fastqsanger.gz
md5:e90a75a5be17b142198e91c5abdcde0c
9.8 MB Download
SRR7779220_WT_Drought.fastqsanger.gz
md5:719f54e189af1b19065d96fb6d5cfa49
9.9 MB Download
SRR7779221_WT_Drought.fastqsanger.gz
md5:3d8082eac05dc9ae35552593a6f9198d
9.8 MB Download
SRR7779222_BLR3_Drought.fastqsanger.gz
md5:3ae8716b00c01743c550a0843e6739d5
10.8 MB Download
SRR7779222_BRL3_mRNA_drought.fastqsanger.gz
md5:a0b2f76ba665d8144e9f814461751ad8
1.2 GB Download
SRR7779223_BLR3_Drought.fastqsanger.gz
md5:3227b62e12f641d4f04609905640d01d
10.4 MB Download
SRR7779223_BRL3_mRNA_drought.fastqsanger.gz
md5:43d936ddeab66dbf16a4da3e2025e9cf
1.1 GB Download
SRR7779224_BLR3_Drought.fastqsanger.gz
md5:4dda63f86d6d3f08efa55dca1d5d0f78
10.6 MB Download
SRR7779224_BRL3_mRNA_drought.fastqsanger.gz
md5:941f6a094821d71d4b2f319c883a826a
1.1 GB Download
SRR7779225_WT_Watered.fastqsanger.gz
md5:06f382054475d4f81e399e2cf7469684
9.0 MB Download
SRR7779226_WT_Watered.fastqsanger.gz
md5:cde72de70f8118389ece01b46a2d65db
9.8 MB Download
SRR7779227_WT_Watered.fastqsanger.gz
md5:04d10703adb4ffc207b9b27499fcfc1e
8.9 MB Download
SRR7779228_BLR3_Watered.fastqsanger.gz
md5:aa8d3c372ebdf2018105240a4140ca79
8.9 MB Download
SRR7779228_BRL3_mRNA_drought.fastqsanger.gz
md5:795a460befd31ba7c8a72a22812ebee4
956.2 MB Download
SRR7779228_BRL3_mRNA_watered.fastqsanger.gz
md5:fc9c855b72df04e165939200e53066bb
955.2 MB Download
SRR7779229_BLR3_Watered.fastqsanger.gz
md5:8b464701a003de77f96891a22c6fe2a1
10.4 MB Download
SRR7779229_BRL3_mRNA_drought.fastqsanger.gz
md5:d83940952a379bf886def2ce9b20dea8
1.1 GB Download
SRR7779229_BRL3_mRNA_watered.fastqsanger.gz
md5:322730c80edefd0c2e8b6fddea365dbc
1.1 GB Download
star_miRNA_seq.fasta
md5:93c352ffb59b95b919d0f7cb1c302dfa
7.9 kB Download
transcriptome_AtRTD2_12April2016.fasta.gz
md5:4f2561c0b800a0e2466dcfca93a123f1
26.4 MB Download
upregulated_miRNA_BR_complete_dataset.fasta
md5:99ff1d82f862a04778ddbcfef7c64563
942 Bytes Download
  • Park, S. Y., Choi, J. H., Oh, D. H., Johnson, J. C., Dassanayake, M., Jeong, D. H., & Oh, M. H. (2020). Genome-wide analysis of brassinosteroid responsive small RNAs in Arabidopsis thaliana. Genes & Genomics, 42(8), 957-969.

  • Oh, Eunkyoo, et al. "Cell elongation is regulated through a central circuit of interacting transcription factors in the Arabidopsis hypocotyl." elife 3 (2014): e03031.

  • Zhang, R., Calixto, C.P.G., Marquez, Y., Venhuizen, P., Tzioutziou, N.A., Guo, W., Spensley, M., Frei dit Frey, N., Hirt, H., James, A.B., Nimmo, H.G., Barta, A., Kalyna, M., Brown, J.W.S (2016) AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data. bioRxiv doi: http://dx.doi.org/10.1101/051938

  • PmiREN: a comprehensive encyclopedia of plant miRNAs. Z Guo, Z Kuang, Y Wang, Y Zhao, Y Tao, C Cheng, J Yang, X Lu, C Hao, T Wang, X Cao, J Wei, L Li, and X Yang. Nucleic Acids Res. 2019. doi: 10.1093/nar/gkz894.

  • Lamesch, P., Berardini, T. Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., ... & Huala, E. (2012). The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic acids research, 40(D1), D1202-D1210.

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