cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12875769
title: Additional file 14 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 14:300 housekeeping genes selected. A table listing 300 housekeeping genes (HKGs) with relatively high levels of expression. To identify these HKGs, we first selected genes with an average RPKM-normalized transcript count greater than 10. Next, we selected the top 300 genes from the list with the lowest coefficient of variation (CV = standard deviation/mean). The RPKM-normalized expression counts, MapMan functional class and description for each HKG selected are also presented in the table. (TXT 76 KB)
DOI: 10.6084/m9.figshare.12875772
title: Additional file 15 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 15:Genes differentially expressed between ES and PES internodes of alfalfa genotype 708.A table listing 3,838 genes differentially expressed between ES and PES internodes of alfalfa genotype 708 in MSGI 1.0. We used a MA-plot-based method with random sampling model in a DEGSeq program to select these genes (p-value &lt; 0.001, FDR &lt; 0.025, ≥ 2-fold difference). RPKM-normalized expression counts, log ratios, z-scores, p-values, and q-values for each gene selected are also presented in the table. (TXT 250 KB)
DOI: 10.6084/m9.figshare.12875772.v1
title: Additional file 15 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 15:Genes differentially expressed between ES and PES internodes of alfalfa genotype 708.A table listing 3,838 genes differentially expressed between ES and PES internodes of alfalfa genotype 708 in MSGI 1.0. We used a MA-plot-based method with random sampling model in a DEGSeq program to select these genes (p-value &lt; 0.001, FDR &lt; 0.025, ≥ 2-fold difference). RPKM-normalized expression counts, log ratios, z-scores, p-values, and q-values for each gene selected are also presented in the table. (TXT 250 KB)
DOI: 10.6084/m9.figshare.12875775
title: Additional file 16 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 16:Genes differentially expressed between ES and PES internodes of alfalfa genotype 773. A table listing 4,428 genes differentially expressed between ES and PES internodes of alfalfa genotype 708 in MSGI 1.0. For details, see the description for additional file 11. (TXT 290 KB)
DOI: 10.6084/m9.figshare.12875778
title: Additional file 17 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 17:Genes differentially expressed between alfalfa genotypes 708 and 773 in ES internodes.A table listing 8,883 genes differentially expressed between alfalfa genotypes 708 and 773 in ES internodes in MSGI 1.0. For details, see the description for additional file 11. (TXT 600 KB)
DOI: 10.6084/m9.figshare.12875778.v1
title: Additional file 17 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 17:Genes differentially expressed between alfalfa genotypes 708 and 773 in ES internodes.A table listing 8,883 genes differentially expressed between alfalfa genotypes 708 and 773 in ES internodes in MSGI 1.0. For details, see the description for additional file 11. (TXT 600 KB)
DOI: 10.6084/m9.figshare.12875769.v1
title: Additional file 14 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 14:300 housekeeping genes selected. A table listing 300 housekeeping genes (HKGs) with relatively high levels of expression. To identify these HKGs, we first selected genes with an average RPKM-normalized transcript count greater than 10. Next, we selected the top 300 genes from the list with the lowest coefficient of variation (CV = standard deviation/mean). The RPKM-normalized expression counts, MapMan functional class and description for each HKG selected are also presented in the table. (TXT 76 KB)
DOI: 10.6084/m9.figshare.12875775.v1
title: Additional file 16 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 16:Genes differentially expressed between ES and PES internodes of alfalfa genotype 773. A table listing 4,428 genes differentially expressed between ES and PES internodes of alfalfa genotype 708 in MSGI 1.0. For details, see the description for additional file 11. (TXT 290 KB)
DOI: 10.6084/m9.figshare.12875781
title: Additional file 18 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 18:Genes differentially expressed between alfalfa genotypes 708 and 773 in PES internodes. A table listing 4,799 genes differentially expressed between alfalfa genotypes 708 and 773 in PES internodes in MSGI 1.0. For details, see the description for additional file 11. (TXT 332 KB)
DOI: 10.6084/m9.figshare.12875781.v1
title: Additional file 18 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 18:Genes differentially expressed between alfalfa genotypes 708 and 773 in PES internodes. A table listing 4,799 genes differentially expressed between alfalfa genotypes 708 and 773 in PES internodes in MSGI 1.0. For details, see the description for additional file 11. (TXT 332 KB)
DOI: 10.6084/m9.figshare.12875784.v1
title: Additional file 19 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 19:Genes differentially expressed in ES and PES internodes of alfalfa genotypes 708 and 773. A table listing 13,797 genes differentially expressed in ES and PES internodes of alfalfa genotypes 708 and 773 in MSGI 1.0. Genes selected in additional files 15, 16, 17 and 18 were combined together to produce this table. The RPKM-normalized expression counts, MapMan functional class and description for each gene selected are also presented in the table. (TXT 4 MB)
DOI: 10.6084/m9.figshare.12875784
title: Additional file 19 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 19:Genes differentially expressed in ES and PES internodes of alfalfa genotypes 708 and 773. A table listing 13,797 genes differentially expressed in ES and PES internodes of alfalfa genotypes 708 and 773 in MSGI 1.0. Genes selected in additional files 15, 16, 17 and 18 were combined together to produce this table. The RPKM-normalized expression counts, MapMan functional class and description for each gene selected are also presented in the table. (TXT 4 MB)
DOI: 10.6084/m9.figshare.12875790
title: Additional file 20 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 20:Top 200 most differentially expressed genes in each pair-wise comparison. A table that lists 657 genes that were generated after combining the top 200 most differentially expressed genes selected in each pair-wise comparison of gene expression between ES and PES internodes of genotypes 708 and 773. This table is a data source for Figure 5. The RPKM-normalized expression counts, MapMan functional class and description for each gene selected are also presented in the table. (TXT 130 KB)
DOI: 10.6084/m9.figshare.12875787
title: Additional file 1 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 1:de novo assembly of alfalfa Illumina GA-II EST reads. A fasta file containing a total of 132,153 unique sequences generated after de novo assembly of Illumina GA-II EST reads derived from 4 cDNA libraries developed in this study. The Velvet program [32] with k-mer 61 was used for de novo assembly. (ZIP 13 MB)
DOI: 10.6084/m9.figshare.12875790.v1
title: Additional file 20 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 20:Top 200 most differentially expressed genes in each pair-wise comparison. A table that lists 657 genes that were generated after combining the top 200 most differentially expressed genes selected in each pair-wise comparison of gene expression between ES and PES internodes of genotypes 708 and 773. This table is a data source for Figure 5. The RPKM-normalized expression counts, MapMan functional class and description for each gene selected are also presented in the table. (TXT 130 KB)
DOI: 10.6084/m9.figshare.12875793.v1
title: Additional file 21 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 21:Phenylpropanoid (lignin) pathway genes differentially expressed in ES and PES internodes of alfalfa genotypes 708 and 773. A table listing phenylpropanoid (lignin) pathway genes differentially expressed in ES and PES internodes of alfalfa genotypes 708 and 773 (p-value &lt; 0.001, FDR,0.025, ≥ 2-fold difference). This table is a data source for Figure 6. The log ratios from each pair-wise comparison, EC number, and enzyme ID for each gene selected are also presented in the table. (TXT 6 KB)
DOI: 10.6084/m9.figshare.12875787.v1
title: Additional file 1 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 1:de novo assembly of alfalfa Illumina GA-II EST reads. A fasta file containing a total of 132,153 unique sequences generated after de novo assembly of Illumina GA-II EST reads derived from 4 cDNA libraries developed in this study. The Velvet program [32] with k-mer 61 was used for de novo assembly. (ZIP 13 MB)
DOI: 10.6084/m9.figshare.12875793
title: Additional file 21 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 21:Phenylpropanoid (lignin) pathway genes differentially expressed in ES and PES internodes of alfalfa genotypes 708 and 773. A table listing phenylpropanoid (lignin) pathway genes differentially expressed in ES and PES internodes of alfalfa genotypes 708 and 773 (p-value &lt; 0.001, FDR,0.025, ≥ 2-fold difference). This table is a data source for Figure 6. The log ratios from each pair-wise comparison, EC number, and enzyme ID for each gene selected are also presented in the table. (TXT 6 KB)
DOI: 10.6084/m9.figshare.12875796.v1
title: Additional file 22 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 22:Candidate genes identified in 708 and 773 that may be involved in general stem development independent of genotypic variation in gene expression. A table listing 594 genes potentially involved in general stem development independent of genotypic variation in gene expression in alfalfa (Log2(PES/ES)≥1 or ≤-1 in both genotypes 708 and 773). The RPKM-normalized expression counts, log ratios, MapMan functional class and description for each gene selected are also presented in the table. (TXT 159 KB)
DOI: 10.6084/m9.figshare.12875796
title: Additional file 22 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 22:Candidate genes identified in 708 and 773 that may be involved in general stem development independent of genotypic variation in gene expression. A table listing 594 genes potentially involved in general stem development independent of genotypic variation in gene expression in alfalfa (Log2(PES/ES)≥1 or ≤-1 in both genotypes 708 and 773). The RPKM-normalized expression counts, log ratios, MapMan functional class and description for each gene selected are also presented in the table. (TXT 159 KB)
DOI: 10.6084/m9.figshare.12875802
title: Additional file 24 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 24:Putative transporter genes differentially expressed in ES and PES internodes of alfalfa genotypes 708 and 773. A table listing 478 transporter genes in ES and PES internodes of alfalfa genotypes 708 and 773 in MSGI 1.0. The RPKM-normalized expression counts, log ratios from each pair-wise comparison, MapMan functional class and description for each transporter gene selected are also presented in the table. (TXT 174 KB)
DOI: 10.6084/m9.figshare.12875802.v1
title: Additional file 24 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 24:Putative transporter genes differentially expressed in ES and PES internodes of alfalfa genotypes 708 and 773. A table listing 478 transporter genes in ES and PES internodes of alfalfa genotypes 708 and 773 in MSGI 1.0. The RPKM-normalized expression counts, log ratios from each pair-wise comparison, MapMan functional class and description for each transporter gene selected are also presented in the table. (TXT 174 KB)
DOI: 10.6084/m9.figshare.12875820
title: Additional file 2 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 2:Alfalfa Gene Index 1.0 (MSGI 1.0). A fasta file containing Alfalfa Gene Index 1.0 (MSGI 1.0) sequences. MSGI 1.0 contains a total of 124,025 unique sequences including 22,729 tentative consensus sequences (TCs), 22,315 singletons and 78,981 pseudo-singletons. The average length of the unique sequences in MSGI 1.0 is 384 bp (100 bp minimum and 6,956 bp maximum) with more than 10,000 sequences larger than 800 bp. The total base count of the sequences in MSGI 1.0 is 47,628,953 bp. Unfortunately, the current pipe line of the DFCI gene index database http://compbio.dfci.harvard.edu/tgi/ is not suited for short reads (personal communication with a DFCI Gene Index staff). The Gene Index Project team has indicated that it plans to address this issue soon. When a gene index database is established for alfalfa, MSGI1.0 will be uploaded to the DFCI gene index database. (ZIP 15 MB)
DOI: 10.6084/m9.figshare.12875820.v1
title: Additional file 2 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 2:Alfalfa Gene Index 1.0 (MSGI 1.0). A fasta file containing Alfalfa Gene Index 1.0 (MSGI 1.0) sequences. MSGI 1.0 contains a total of 124,025 unique sequences including 22,729 tentative consensus sequences (TCs), 22,315 singletons and 78,981 pseudo-singletons. The average length of the unique sequences in MSGI 1.0 is 384 bp (100 bp minimum and 6,956 bp maximum) with more than 10,000 sequences larger than 800 bp. The total base count of the sequences in MSGI 1.0 is 47,628,953 bp. Unfortunately, the current pipe line of the DFCI gene index database http://compbio.dfci.harvard.edu/tgi/ is not suited for short reads (personal communication with a DFCI Gene Index staff). The Gene Index Project team has indicated that it plans to address this issue soon. When a gene index database is established for alfalfa, MSGI1.0 will be uploaded to the DFCI gene index database. (ZIP 15 MB)
DOI: 10.6084/m9.figshare.12875832.v1
title: Additional file 3 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 3:Functional classification and annotation of sequences in the Alfalfa Gene Index 1.0 (MSGI 1.0). A table listing Gene ontology (GO), pathway, MapMan functional classes and gene annotation for sequences in the Alfalfa Gene Index 1.0 (MSGI 1.0). (ZIP 6 MB)
DOI: 10.6084/m9.figshare.12875835.v1
title: Additional file 4 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 4:Simple sequence repeats (SSRs) detected in MSGI 1.0. A table listing SSR-containing sequence IDs, SSR types and position, and primers spanning each SSR for the sequences in the Alfalfa Gene Index 1.0 (MSGI 1.0). (TXT 210 KB)
DOI: 10.6084/m9.figshare.12875832
title: Additional file 3 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 3:Functional classification and annotation of sequences in the Alfalfa Gene Index 1.0 (MSGI 1.0). A table listing Gene ontology (GO), pathway, MapMan functional classes and gene annotation for sequences in the Alfalfa Gene Index 1.0 (MSGI 1.0). (ZIP 6 MB)
DOI: 10.6084/m9.figshare.12875838
title: Additional file 5 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 5:Single nucleotide polymorphisms (SNPs) predicted between alfalfa genotypes 708 and 773. A table listing SNPs predicted between alfalfa genotypes 708 and 773 including SNP-containing sequence ID, SNP type, SNP position and depth in each genotype. (TXT 732 KB)
DOI: 10.6084/m9.figshare.12875838.v1
title: Additional file 5 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 5:Single nucleotide polymorphisms (SNPs) predicted between alfalfa genotypes 708 and 773. A table listing SNPs predicted between alfalfa genotypes 708 and 773 including SNP-containing sequence ID, SNP type, SNP position and depth in each genotype. (TXT 732 KB)
DOI: 10.6084/m9.figshare.12875841
title: Additional file 6 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 6:Validation of SNPs predicted between alfalfa genotypes 708 and 773 using RNA-Seq data. A table showing SNP validation results. A total of 55 SNPs were randomly selected to genotype genomic DNAs purified from the genotypes 708 and 773 by MALDI-TOF mass spectrometry using the iPLEX Gold spectrometry system http://www.sequenom.com . In addition to genotypes 708 and 773, we also genotyped 51 additional alfalfa (M. sativa) genotypes selected from different populations of M. sativa ssp. sativa or M. sativa ssp. falcata. (TXT 12 KB)
DOI: 10.6084/m9.figshare.12875841.v1
title: Additional file 6 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 6:Validation of SNPs predicted between alfalfa genotypes 708 and 773 using RNA-Seq data. A table showing SNP validation results. A total of 55 SNPs were randomly selected to genotype genomic DNAs purified from the genotypes 708 and 773 by MALDI-TOF mass spectrometry using the iPLEX Gold spectrometry system http://www.sequenom.com . In addition to genotypes 708 and 773, we also genotyped 51 additional alfalfa (M. sativa) genotypes selected from different populations of M. sativa ssp. sativa or M. sativa ssp. falcata. (TXT 12 KB)
DOI: 10.6084/m9.figshare.12875835
title: Additional file 4 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 4:Simple sequence repeats (SSRs) detected in MSGI 1.0. A table listing SSR-containing sequence IDs, SSR types and position, and primers spanning each SSR for the sequences in the Alfalfa Gene Index 1.0 (MSGI 1.0). (TXT 210 KB)
DOI: 10.6084/m9.figshare.12875847
title: Additional file 8 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 8:Allelic variations (SNPs) detected within genotype 708. A table listing a total of 287,555 allelic variations (SNPs) detected within genotype 708 using minimum SNP depth cutoff of 10. (TXT 6 MB)
DOI: 10.6084/m9.figshare.12875847.v1
title: Additional file 8 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 8:Allelic variations (SNPs) detected within genotype 708. A table listing a total of 287,555 allelic variations (SNPs) detected within genotype 708 using minimum SNP depth cutoff of 10. (TXT 6 MB)
DOI: 10.6084/m9.figshare.12875850
title: Additional file 9 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 9:Allelic variations (SNPs) detected within genotype 773. A table listing a total of 168,966 allelic variations (SNPs) detected within genotype 773 using minimum SNP depth cutoff of 10. (TXT 11 MB)
DOI: 10.6084/m9.figshare.12875850.v1
title: Additional file 9 of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file 9:Allelic variations (SNPs) detected within genotype 773. A table listing a total of 168,966 allelic variations (SNPs) detected within genotype 773 using minimum SNP depth cutoff of 10. (TXT 11 MB)
DOI: 10.5281/zenodo.4727790
title: Structural Mechanism of Transcription Regulation by Histone Variant H2A.Z_supporting data files

description: Supporting data for manuscript review. - PDB validation report (H2A.Z nucleosome): D_1000255453_val-report-full_P1.pdf - Molecular coordinate (H2A.Z nucleosome) : 7M1X.pdb - cryo-EM maps : H2Az-Nuc.mrc, H2A-Nuc.mrc, H2Az_Fiber_Map_Combined.mrc, H2A_Fiber_Map_Combined.mrc
DOI: 10.6084/m9.figshare.14446733.v45
title: Additional file of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

description: Additional file of Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems