cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6627434
title: Additional file 2: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S3. List of significant differentially expressed genes. (XLSX 1396 kb)
DOI: 10.6084/m9.figshare.11870130
title: Additional file 17 of Transcriptional reprogramming strategies and miRNA-mediated regulation networks of Taxus media induced into callus cells from tissues

description: Additional file 17. Co-expression values of TFs with taxol biosynthesis genes The co-expression correlation co-efficiency values were displayed.
DOI: 10.6084/m9.figshare.11870160.v1
title: Additional file 4 of Transcriptional reprogramming strategies and miRNA-mediated regulation networks of Taxus media induced into callus cells from tissues

description: Additional file 4. All expressed miRNAs All expressed miRNAs were listed in sheet (a) including known and novel miRNAs. The sheet (footnotes) provided the information about the table.
DOI: 10.6084/m9.figshare.6627359
title: Additional file 10: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S10. GO analysis of 42 differentially expressed cis-NATs. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6627365.v1
title: MOESM1 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 1. Genomic locations mapped by 8850 FL fusion transcripts.
DOI: 10.6084/m9.figshare.11870163
title: Additional file 5 of Transcriptional reprogramming strategies and miRNA-mediated regulation networks of Taxus media induced into callus cells from tissues

description: Additional file 5. GO annotations and statistics of DEGs GO statistic of DEGs (a) and GO annotation of DEGs (b). The genes with only one specific annotation was counted.
DOI: 10.6084/m9.figshare.11870166
title: Additional file 6 of Transcriptional reprogramming strategies and miRNA-mediated regulation networks of Taxus media induced into callus cells from tissues

description: Additional file 6. GO annotation of DEGs and degraded DEGs Supplement figure compared the GO annotations of DEGs (a and b) with degraded DEGs (c and d). (a) GO annotations of DEGs, (b) GO enrichment analysis of DEGs (first 20 terms). (c) GO annotations of degraded DEGs, (d) GO enrichment analysis of degraded DEGs (first 20 terms). All these results suggested that miRNAs comprehensively regulated in transcriptional reprogramming in callus cells.
DOI: 10.6084/m9.figshare.6627377
title: Additional file 11: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S11. List of 132 differentially expressed TFs. (XLSX 82 kb)
DOI: 10.6084/m9.figshare.6627377.v1
title: Additional file 11: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S11. List of 132 differentially expressed TFs. (XLSX 82 kb)
DOI: 10.6084/m9.figshare.6627380
title: MOESM2 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 2. Genomic locations mapped by 2853 non-FL fusion transcripts.
DOI: 10.6084/m9.figshare.6627413
title: Additional file 1: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S2. Summary of RNA-Seq mapping. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.11870148
title: Additional file 2 of Transcriptional reprogramming strategies and miRNA-mediated regulation networks of Taxus media induced into callus cells from tissues

description: Additional file 2. Information of miRNA-seq The length distribution of miRNAs was showed in (a). Total and first nucleotide bias were showed in (b) and (c) respectively. (d) Pearson relation analysis of all expressed miRNAs between six samples. (e) Venn diagram of miRNAs in callus cells and tissues. (f) Expression patterns of all DE miRNAs (p &lt; 0.05).
DOI: 10.6084/m9.figshare.6627461.v1
title: MOESM6 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 6. Mapping of the genomic coordinates between the same genes in Pvir_3 and v4.
DOI: 10.6084/m9.figshare.11870160
title: Additional file 4 of Transcriptional reprogramming strategies and miRNA-mediated regulation networks of Taxus media induced into callus cells from tissues

description: Additional file 4. All expressed miRNAs All expressed miRNAs were listed in sheet (a) including known and novel miRNAs. The sheet (footnotes) provided the information about the table.
DOI: 10.6084/m9.figshare.6627422
title: MOESM4 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 4. Genomic coordinates of the predicted lncRNA transcripts.
DOI: 10.6084/m9.figshare.6627443.v1
title: MOESM5 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 5. The TF list and matching families.
DOI: 10.6084/m9.figshare.6627434.v1
title: Additional file 2: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S3. List of significant differentially expressed genes. (XLSX 1396 kb)
DOI: 10.6084/m9.figshare.6627473
title: Additional file 4: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S4. GO analysis of DEGs. (XLSX 93 kb)
DOI: 10.6084/m9.figshare.11870076.v1
title: Additional file 10 of Transcriptional reprogramming strategies and miRNA-mediated regulation networks of Taxus media induced into callus cells from tissues

description: Additional file 10. Degradome-seq results All the degraded targets and miRNAs were listed. Y in column (DegradomeDetection) means the degraded fragment was sequenced, while N indicated the target was only predicted by software TargetFinder.
DOI: 10.6084/m9.figshare.6627449
title: Additional file 3: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S1. Primer list used in this study. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.6627449.v1
title: Additional file 3: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S1. Primer list used in this study. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.14490118.v1
title: Additional file 1 of Characteristics and variation of fecal bacterial communities and functions in isolated systolic and diastolic hypertensive patients

description: Additional file 1: Table S1. Data production of fecal samples in control, ISH and IDH.
DOI: 10.6084/m9.figshare.11870103.v1
title: Additional file 13 of Transcriptional reprogramming strategies and miRNA-mediated regulation networks of Taxus media induced into callus cells from tissues

description: Additional file 13. Ten miRNA regulatory networks which targeted to taxol biosynthesis genes.
DOI: 10.6084/m9.figshare.6627473.v1
title: Additional file 4: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S4. GO analysis of DEGs. (XLSX 93 kb)
DOI: 10.6084/m9.figshare.6627398
title: MOESM3 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 3. CW-related transcript list and functional prediction.
DOI: 10.6084/m9.figshare.11870124.v1
title: Additional file 16 of Transcriptional reprogramming strategies and miRNA-mediated regulation networks of Taxus media induced into callus cells from tissues

description: Additional file 16. Degraded transcription factors All degraded transcription factors and related miRNAs were listed in (a). Transcription factors were annotated with plnTFdb database.
DOI: 10.6084/m9.figshare.6627398.v1
title: MOESM3 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 3. CW-related transcript list and functional prediction.
DOI: 10.6084/m9.figshare.6627500
title: Additional file 6: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S6. List of differentially AS events including IR, ES, AltA and AltD. (XLSX 207 kb)
DOI: 10.6084/m9.figshare.23930450
title: Additional file 2 of Predicting response to immunotherapy in gastric cancer via assessing perineural invasion-mediated inflammation in tumor microenvironment

description: Additional file 2: Figure S1. Establishment process and distribution of inflammation score. Figure S2. Establishment, prognostic significance and distribution of NII.cluster subtypes. Figure S3. The noteworthy differentially-expressed genes among NII cluster subtypes. Figure S4. The analyse of NII cluster subtypes and non-PNI in mutational signatures, methylation and CNV. Figure S5. Verification for prognosis of NII score in pan digestive tract cohorts. Figure S6. The verification that NII score serves as an independent prognostic factor using forest plots and subgroup analyses. Figure S7. The immune scores, stromal scores, ESTIMATE scores and potential therapeutic chemicals of NII score subgroups. Figure S8. The supplementary immunotherapy analyses of NII clusters and non-PNI in NII score subgroups. Figure S9. The result of chemosensitivity analyses. Figure S10. VCAM1 RNA expression of shRNA and overexpression cell models.
DOI: 10.6084/m9.figshare.23930450.v1
title: Additional file 2 of Predicting response to immunotherapy in gastric cancer via assessing perineural invasion-mediated inflammation in tumor microenvironment

description: Additional file 2: Figure S1. Establishment process and distribution of inflammation score. Figure S2. Establishment, prognostic significance and distribution of NII.cluster subtypes. Figure S3. The noteworthy differentially-expressed genes among NII cluster subtypes. Figure S4. The analyse of NII cluster subtypes and non-PNI in mutational signatures, methylation and CNV. Figure S5. Verification for prognosis of NII score in pan digestive tract cohorts. Figure S6. The verification that NII score serves as an independent prognostic factor using forest plots and subgroup analyses. Figure S7. The immune scores, stromal scores, ESTIMATE scores and potential therapeutic chemicals of NII score subgroups. Figure S8. The supplementary immunotherapy analyses of NII clusters and non-PNI in NII score subgroups. Figure S9. The result of chemosensitivity analyses. Figure S10. VCAM1 RNA expression of shRNA and overexpression cell models.
DOI: 10.6084/m9.figshare.6627461
title: MOESM6 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 6. Mapping of the genomic coordinates between the same genes in Pvir_3 and v4.
DOI: 10.6084/m9.figshare.6627413.v1
title: Additional file 1: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S2. Summary of RNA-Seq mapping. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.11870181.v1
title: Additional file 8 of Transcriptional reprogramming strategies and miRNA-mediated regulation networks of Taxus media induced into callus cells from tissues

description: Additional file 8. KEGG annotations and statistics of DEGs KEGG statistic of DEGs (a) and KEGG annotation of DEGs (b). The genes with only one specific annotation was counted.
DOI: 10.6084/m9.figshare.6627422.v1
title: MOESM4 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 4. Genomic coordinates of the predicted lncRNA transcripts.
DOI: 10.6084/m9.figshare.11870184.v1
title: Additional file 9 of Transcriptional reprogramming strategies and miRNA-mediated regulation networks of Taxus media induced into callus cells from tissues

description: Additional file 9. DE miRNAs and their expression levels.
DOI: 10.6084/m9.figshare.23930456
title: Additional file 3 of Predicting response to immunotherapy in gastric cancer via assessing perineural invasion-mediated inflammation in tumor microenvironment

description: Additional file 3: Table S1. Clinical and pathologic characteristics of patients with gastric cancer and pan-gastrointestinal tumor. Table S2. 200 genes and their functions of MSigdb Hallmarks inflammatory response. Table S3. 22 genes from MCODE. Table S4. Univariate Cox regreesion of 200 genes with PNI and No PNI. Table S5. High NII score VS Low NII score. Table S6. Go analysis of No PNI and NII.clusterB. Table S7. Description of 47 genes used to construct NII score. Table S8. Multivariable Cox regression analysis of variables of nomogram in training cohort and whole cohort. Table S9. NII.score. Table S10. Subgroup.
DOI: 10.6084/m9.figshare.23930456.v1
title: Additional file 3 of Predicting response to immunotherapy in gastric cancer via assessing perineural invasion-mediated inflammation in tumor microenvironment

description: Additional file 3: Table S1. Clinical and pathologic characteristics of patients with gastric cancer and pan-gastrointestinal tumor. Table S2. 200 genes and their functions of MSigdb Hallmarks inflammatory response. Table S3. 22 genes from MCODE. Table S4. Univariate Cox regreesion of 200 genes with PNI and No PNI. Table S5. High NII score VS Low NII score. Table S6. Go analysis of No PNI and NII.clusterB. Table S7. Description of 47 genes used to construct NII score. Table S8. Multivariable Cox regression analysis of variables of nomogram in training cohort and whole cohort. Table S9. NII.score. Table S10. Subgroup.
DOI: 10.6084/m9.figshare.6627500.v1
title: Additional file 6: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S6. List of differentially AS events including IR, ES, AltA and AltD. (XLSX 207 kb)
DOI: 10.6084/m9.figshare.6627506.v1
title: MOESM8 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 8. The coordinates of 105,419 assembled transcripts in Pvir_v3.
DOI: 10.6084/m9.figshare.6627359.v1
title: Additional file 10: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S10. GO analysis of 42 differentially expressed cis-NATs. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6627515
title: Additional file 7: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S7. List of hormone-related and splicing factor genes, which have different isoforms after GA was applied. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.6627365
title: MOESM1 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 1. Genomic locations mapped by 8850 FL fusion transcripts.
DOI: 10.6084/m9.figshare.6627515.v1
title: Additional file 7: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S7. List of hormone-related and splicing factor genes, which have different isoforms after GA was applied. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.6627392
title: Additional file 12: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S12. List of TFs associated with AS and cis-NATs. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.6627527
title: Additional file 8: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S8. List of cis-NATs in moso bamboo, which were classified into head-to-head (5′-5′), tail-to-tail (3′-3′) and fully overlapping. (XLSX 156 kb)
DOI: 10.6084/m9.figshare.6627530
title: MOESM9 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 9. The coordinates of 105,405 assembled transcripts in Pvir_v4.
DOI: 10.6084/m9.figshare.6627479
title: MOESM7 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 7. Mapping between the corresponding transcripts in Pvir_3 and v4.
DOI: 10.6084/m9.figshare.6627479.v1
title: MOESM7 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 7. Mapping between the corresponding transcripts in Pvir_3 and v4.
DOI: 10.6084/m9.figshare.6627506
title: MOESM8 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 8. The coordinates of 105,419 assembled transcripts in Pvir_v3.
DOI: 10.6084/m9.figshare.6627530.v1
title: MOESM9 of Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing

description: Additional file 9. The coordinates of 105,405 assembled transcripts in Pvir_v4.
DOI: 10.6084/m9.figshare.6627533.v1
title: Additional file 9: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S9. List of 42 differentially expressed cis-NATs upon GA treatment. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.11870406
title: Additional file 1 of Graph regularized L2,1-nonnegative matrix factorization for miRNA-disease association prediction

description: Additional file 1. disease semantic similarity1.txt. This is disease semantic similarity 1, which integrated 383 disease semantic similarities.
DOI: 10.6084/m9.figshare.11870439
title: Additional file 6 of Graph regularized L2,1-nonnegative matrix factorization for miRNA-disease association prediction

description: Additional file 6. miRNAs_list.xlsx. This file lists 495 miRNA names.
DOI: 10.6084/m9.figshare.14490187.v1
title: Additional file 2 of The physiological and molecular mechanisms of N transfer in Eucalyptus and Dalbergia odorifera intercropping systems using root proteomics

description: Additional file 2: Table S2. Summary of the differential expressed proteins (&gt; 1.5 times) in D. odorifera roots (p &lt; 0.05) in this study.
DOI: 10.6084/m9.figshare.6627527.v1
title: Additional file 8: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S8. List of cis-NATs in moso bamboo, which were classified into head-to-head (5′-5′), tail-to-tail (3′-3′) and fully overlapping. (XLSX 156 kb)
DOI: 10.6084/m9.figshare.11870406.v1
title: Additional file 1 of Graph regularized L2,1-nonnegative matrix factorization for miRNA-disease association prediction

description: Additional file 1. disease semantic similarity1.txt. This is disease semantic similarity 1, which integrated 383 disease semantic similarities.
DOI: 10.6084/m9.figshare.11870412
title: Additional file 2 of Graph regularized L2,1-nonnegative matrix factorization for miRNA-disease association prediction

description: Additional file 2. disease semantic similarity2.txt. This is disease semantic similarity 2, which integrated 383 disease semantic similarities.
DOI: 10.6084/m9.figshare.14490418
title: Additional file 3 of The evolution of opsin genes in five species of mirid bugs: duplication of long-wavelength opsins and loss of blue-sensitive opsins

description: Additional file 3. Genomic sequences of LW opsins in Nesidiocoris tenuis and Apolygus lucorum
DOI: 10.5281/zenodo.10678135
title: Supplementary data for "DNA metabarcoding reveals fine scale geographical differences of consumed algae in the Galápagos marine iguanas (Amblyrhynchus cristatus)"

description: Supplementary data for "DNA metabarcoding reveals fine scale geographical differences of consumed algae in the Galápagos marine iguanas (Amblyrhynchus cristatus)" puvlished in Amphibia-Reptilia, 42(4), 471-480
DOI: 10.5281/zenodo.10678136
title: Supplementary data for "DNA metabarcoding reveals fine scale geographical differences of consumed algae in the Galápagos marine iguanas (Amblyrhynchus cristatus)"

description: Supplementary data for "DNA metabarcoding reveals fine scale geographical differences of consumed algae in the Galápagos marine iguanas (Amblyrhynchus cristatus)" puvlished in Amphibia-Reptilia, 42(4), 471-480
DOI: 10.6084/m9.figshare.6627584.v1
title: Additional file 1: of Integration of proteomic and transcriptomic profiles reveals multiple levels of genetic regulation of salt tolerance in cotton

description: Table S6. Primers for miRNA and target genes for qRT-PCR and stem-loop RT-PCR. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.6627608.v1
title: Additional file 3: of Integration of proteomic and transcriptomic profiles reveals multiple levels of genetic regulation of salt tolerance in cotton

description: Table S1. Summary of iTRAQ-based proteomic data. (XLSX 3294 kb)
DOI: 10.6084/m9.figshare.6627620
title: Additional file 4: of Integration of proteomic and transcriptomic profiles reveals multiple levels of genetic regulation of salt tolerance in cotton

description: Table S2. Summary of mRNA-seq data. (XLSX 2064 kb)
DOI: 10.6084/m9.figshare.10297628.v1
title: MOESM1 of The incision strategy for minimizing sural nerve injury in medial displacement calcaneal osteotomy: a cadaveric study

description: Additional file 1: The datasets used and analyzed during the current study.
DOI: 10.6084/m9.figshare.11870412.v1
title: Additional file 2 of Graph regularized L2,1-nonnegative matrix factorization for miRNA-disease association prediction

description: Additional file 2. disease semantic similarity2.txt. This is disease semantic similarity 2, which integrated 383 disease semantic similarities.
DOI: 10.6084/m9.figshare.11870418.v1
title: Additional file 3 of Graph regularized L2,1-nonnegative matrix factorization for miRNA-disease association prediction

description: Additional file 3. miRNA functional similarity.txt. This is the miRNA functional similarity, which integrated 495 miRNA functional semantic similarities.
DOI: 10.6084/m9.figshare.6627533
title: Additional file 9: of Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

description: Table S9. List of 42 differentially expressed cis-NATs upon GA treatment. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.6627608
title: Additional file 3: of Integration of proteomic and transcriptomic profiles reveals multiple levels of genetic regulation of salt tolerance in cotton

description: Table S1. Summary of iTRAQ-based proteomic data. (XLSX 3294 kb)
DOI: 10.6084/m9.figshare.14490184.v1
title: Additional file 1 of The physiological and molecular mechanisms of N transfer in Eucalyptus and Dalbergia odorifera intercropping systems using root proteomics

description: Additional file 1: Table S1. Summary of the differential expressed proteins (&gt; 1.5 times) in E. urophylla × E. grandis roots (p &lt; 0.05) in this study.
DOI: 10.6084/m9.figshare.14490187
title: Additional file 2 of The physiological and molecular mechanisms of N transfer in Eucalyptus and Dalbergia odorifera intercropping systems using root proteomics

description: Additional file 2: Table S2. Summary of the differential expressed proteins (&gt; 1.5 times) in D. odorifera roots (p &lt; 0.05) in this study.
DOI: 10.6084/m9.figshare.6627620.v1
title: Additional file 4: of Integration of proteomic and transcriptomic profiles reveals multiple levels of genetic regulation of salt tolerance in cotton

description: Table S2. Summary of mRNA-seq data. (XLSX 2064 kb)
DOI: 10.5281/zenodo.10658459
title: Tree species root:shoot ratio
DOI: 10.5281/zenodo.10658460
title: Tree species root:shoot ratio