cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4880405.v1
title: K-2237_T_fossilibus_holotype_dors40xZeiss_p1

description: Original image stacks and layered images of the holotype specimens of fossil Acari: Trombidiformes: Tetranychoidea: Tuckerellidae: (1) Tuckerella fossilibus Khaustov, Sergeyenko & Perkovsky, 2014, deutonymph, ength of idiosoma – 245 μm, width – 165 μm, specimen deposited in I.I. Schmalhausen Institute of Zoology, National Academy of Science, Kiev (SIZK), collection number KF-2237; (2) new species of Tuckerella, Female. Length of idiosoma – 274, width – 155, height – 55 μm, originates from collection of Mr. Thomas Weiterschan (TW), original number TW 1288, and is transferred to the collection of the Geological-Paleontological Museum and University Hamburg (GPIH).<br>Image stacks were obtained with Zeiss AxioImager A2 compound microscope with dry lenses and differential interference contrast (DIC) illumination with AxioCam 506 color digital camera. Bright field and polarized light micrographs were obtained with Nikon Eclipse 800 microscope with 60x water immersion lens, Nikon DS-Fi1 and Nikon D7000 digital cameras. All images were corrected for light, color, noise and sharpness using Adobe Lightroom, then processed with Helicon Focus algorithm A, always with some detail manually transferred from the individual focal planes to the resulting images. These images are further referred to as "comb" in the file names.
DOI: 10.6084/m9.figshare.4880432.v1
title: Pulmonary exposure to metallic nanomaterials during pregnancy irreversibly impairs lung development of the offspring

description: Due to the growing commercial applications of manufactured nanoparticles (NPs), toxicological studies on NPs, especially during the critical window of development, are of major importance. The aim of the study was to assess the impact of respiratory exposure to metallic and metal oxide NPs during pregnancy on lung development of the offspring and to determine the key parameters involved in lung alterations. Pregnant mice were exposed to weekly doses of 100 μg (total dose 300 μg) of titanium dioxide (TiO<sub>2</sub>), cerium oxide (CeO<sub>2</sub>), silver (Ag) NPs or saline solution by nonsurgical intratracheal instillation. The offspring lungs were analyzed at different stages of lung development: fetal stage (gestational day 17.5), pulmonary alveolarization (post-delivery day 14.5) and lung maturity (post-delivery day 49.5). Regardless of the type of NP, maternal exposure during gestation induced long-lasting impairment of lung development of the offspring. This effect was accompanied by: i) decreased placental efficiency together with the presence of NPs in placenta, ii) no increase of inflammatory mediators present in amniotic fluid, placenta or offspring lungs and iii) decreased pulmonary expression of vascular endothelial growth factor-α (VEGF-α) and matrix metalloproteinase 9 (MMP-9) at the fetal stage, and fibroblast growth factor-18 (FGF-18) at the alveolarization stage. Respiratory exposure to metallic NPs during pregnancy induces stereotyped impairment of lung development with a lasting effect in adult mice, independently of the chemical nature of the NP.
DOI: 10.6084/m9.figshare.4880381
title: K-2237_T_fossilibus_holotype_ventr40xZeiss_p2

description: Original image stacks and layered images of the holotype specimens of fossil Acari: Trombidiformes: Tetranychoidea: Tuckerellidae: (1) Tuckerella fossilibus Khaustov, Sergeyenko & Perkovsky, 2014, deutonymph, ength of idiosoma – 245 μm, width – 165 μm, specimen deposited in I.I. Schmalhausen Institute of Zoology, National Academy of Science, Kiev (SIZK), collection number KF-2237; (2) new species of Tuckerella, Female. Length of idiosoma – 274, width – 155, height – 55 μm, originates from collection of Mr. Thomas Weiterschan (TW), original number TW 1288, and is transferred to the collection of the Geological-Paleontological Museum and University Hamburg (GPIH).<br>Image stacks were obtained with Zeiss AxioImager A2 compound microscope with dry lenses and differential interference contrast (DIC) illumination with AxioCam 506 color digital camera. Bright field and polarized light micrographs were obtained with Nikon Eclipse 800 microscope with 60x water immersion lens, Nikon DS-Fi1 and Nikon D7000 digital cameras. All images were corrected for light, color, noise and sharpness using Adobe Lightroom, then processed with Helicon Focus algorithm A, always with some detail manually transferred from the individual focal planes to the resulting images. These images are further referred to as "comb" in the file names.
DOI: 10.6084/m9.figshare.4880399.v1
title: K-2237_T_fossilibus_holotype_ventr40xZeiss_p1

description: Original image stacks and layered images of the holotype specimens of fossil Acari: Trombidiformes: Tetranychoidea: Tuckerellidae: (1) Tuckerella fossilibus Khaustov, Sergeyenko & Perkovsky, 2014, deutonymph, ength of idiosoma – 245 μm, width – 165 μm, specimen deposited in I.I. Schmalhausen Institute of Zoology, National Academy of Science, Kiev (SIZK), collection number KF-2237; (2) new species of Tuckerella, Female. Length of idiosoma – 274, width – 155, height – 55 μm, originates from collection of Mr. Thomas Weiterschan (TW), original number TW 1288, and is transferred to the collection of the Geological-Paleontological Museum and University Hamburg (GPIH).<br>Image stacks were obtained with Zeiss AxioImager A2 compound microscope with dry lenses and differential interference contrast (DIC) illumination with AxioCam 506 color digital camera. Bright field and polarized light micrographs were obtained with Nikon Eclipse 800 microscope with 60x water immersion lens, Nikon DS-Fi1 and Nikon D7000 digital cameras. All images were corrected for light, color, noise and sharpness using Adobe Lightroom, then processed with Helicon Focus algorithm A, always with some detail manually transferred from the individual focal planes to the resulting images. These images are further referred to as "comb" in the file names.
DOI: 10.6084/m9.figshare.4880402.v1
title: Experimental data file

description: Experimental data file for DMSP, DMSO, FV/FM, Chlorophyll a fluorescence and ROS fluorescence
DOI: 10.6084/m9.figshare.4880381.v1
title: K-2237_T_fossilibus_holotype_ventr40xZeiss_p2

description: Original image stacks and layered images of the holotype specimens of fossil Acari: Trombidiformes: Tetranychoidea: Tuckerellidae: (1) Tuckerella fossilibus Khaustov, Sergeyenko & Perkovsky, 2014, deutonymph, ength of idiosoma – 245 μm, width – 165 μm, specimen deposited in I.I. Schmalhausen Institute of Zoology, National Academy of Science, Kiev (SIZK), collection number KF-2237; (2) new species of Tuckerella, Female. Length of idiosoma – 274, width – 155, height – 55 μm, originates from collection of Mr. Thomas Weiterschan (TW), original number TW 1288, and is transferred to the collection of the Geological-Paleontological Museum and University Hamburg (GPIH).<br>Image stacks were obtained with Zeiss AxioImager A2 compound microscope with dry lenses and differential interference contrast (DIC) illumination with AxioCam 506 color digital camera. Bright field and polarized light micrographs were obtained with Nikon Eclipse 800 microscope with 60x water immersion lens, Nikon DS-Fi1 and Nikon D7000 digital cameras. All images were corrected for light, color, noise and sharpness using Adobe Lightroom, then processed with Helicon Focus algorithm A, always with some detail manually transferred from the individual focal planes to the resulting images. These images are further referred to as "comb" in the file names.
DOI: 10.6084/m9.figshare.4880321
title: Egg capsules and veligers of the corallivorous muricid gastropod <i>Drupella rugosa</i> (Born, 1778)

description: Population outbreaks of the corallivorous muricid gastropod <i>Drupella</i> can cause significant coral mortality but our current understanding of their early life history, recruitment mechanisms and behaviour is limited. In this study, we observed the deposition of <i>D. rugosa</i> (Born, 1778) egg capsules on bare skeletal surfaces of the scleractinian coral <i>Pocillopora acuta</i> Lamarck, 1816. Each egg capsule measured 2.43 by 2.39 mm and contained an average of 67 embryos. Intracapsular development lasted 15 days post-oviposition, after which free-swimming veliger larvae emerged from the capsule. The larval shells of these veligers with 1⅓ whorls averaged 328 by 245 μm in size. Compared to its congeners, <i>D. rugosa</i> veliger larvae were the largest at hatching. Detailed descriptions of <i>D. rugosa</i> egg capsules and early veligers are provided to supplement current knowledge on reproductive biology and early life history of the species. Such data will provide more insights into understanding and modelling the population dynamics of <i>D. rugosa</i>.
DOI: 10.6084/m9.figshare.4880318
title: CAGE peaks expression (mm10 v3)

description: <pre>This folder contains CAGE peaks expression tables for the robust set of peaks. mm10.fair+new_CAGE_peaks_phase1and2_ann.txt.gz - CAGE peak based table with annotated peaks for mouse samples (fairly remapped) mm10.fair+new_CAGE_peaks_phase1and2_liftover_ann.txt.gz - CAGE peak based table with annotated peaks for mouse samples (all liftover) mm10.fair+new_CAGE_peaks_phase1and2_tpm.osc.txt.gz - CAGE peak based expression table (RLE normalized) for mouse samples [see edgeR documentation for further details about normalization method] mm10.fair+new_CAGE_peaks_phase1and2_counts.osc.txt.gz - CAGE peak based expression table for mouse samples mm10.fair+new_CAGE_peaks_phase1and2_tpm_ann.osc.txt.gz - CAGE peak based expression table (RLE normalized) for mouse with annotation mm10.fair+new_CAGE_peaks_phase1and2_counts_ann.osc.txt.gz - CAGE peak based expression table for mouse with annotation </pre>
DOI: 10.6084/m9.figshare.4880321.v1
title: Egg capsules and veligers of the corallivorous muricid gastropod <i>Drupella rugosa</i> (Born, 1778)

description: Population outbreaks of the corallivorous muricid gastropod <i>Drupella</i> can cause significant coral mortality but our current understanding of their early life history, recruitment mechanisms and behaviour is limited. In this study, we observed the deposition of <i>D. rugosa</i> (Born, 1778) egg capsules on bare skeletal surfaces of the scleractinian coral <i>Pocillopora acuta</i> Lamarck, 1816. Each egg capsule measured 2.43 by 2.39 mm and contained an average of 67 embryos. Intracapsular development lasted 15 days post-oviposition, after which free-swimming veliger larvae emerged from the capsule. The larval shells of these veligers with 1⅓ whorls averaged 328 by 245 μm in size. Compared to its congeners, <i>D. rugosa</i> veliger larvae were the largest at hatching. Detailed descriptions of <i>D. rugosa</i> egg capsules and early veligers are provided to supplement current knowledge on reproductive biology and early life history of the species. Such data will provide more insights into understanding and modelling the population dynamics of <i>D. rugosa</i>.
DOI: 10.6084/m9.figshare.4880312
title: CAGE peaks (mm10 v3)

description: <pre>CAGE peaks === This directory contains the CAGE peaks defined in the FANTOM5 project as a robust set, where genomic coordinates originally defined on mm9 are lifted to mm10 by liftOver tool. By following the update, their annotations are also updated - see “CAGE_peaks_annotation” directory in the parent directory. - Inquiries: fantom-help@gsc.riken.jp - Update: 2015-09-18 initial release 2016-07-22 ver.2 release 2017-04-14 ver.3 release Data files --- - mm10_liftover_CAGE_peaks_phase1and2.bed.gz : all lifted-over CAGE peaks using UCSC Lift-over - mm10_fair_CAGE_peaks_phase1and2.bed : fairly remapped CAGE peaks. - mm10_problematic_CAGE_peaks_phase1and2.bed : problematic CAGE peaks that were filtered out by QC - mm10_new_CAGE_peaks_phase1and2.bed : newly identified CAGE peaks in mm10 DPI clustering - mm9_droppped_CAGE_peaks_phase1and2.bed : unmapped CAGE peaks (in mm9 coordination) Description of the columns in CAGE peaks coordinates files --- This is baed on BED9 format, where the thickStart and thickEnd position represent representative TSS positions. (https://genome.ucsc.edu/FAQ/FAQformat.html#format1) - chromosome - start of CAGE peak region - end of CAGE peak region - name (ID) of the CAGE peak - score - strand of the CAGE peak - start of the representative TSS position - end of the representative TSS position (Note: end is always start+1) - rgb string for color coding (plus or minus strand only) </pre>
DOI: 10.6084/m9.figshare.4880315
title: CAGE peaks annotation (mm10 v3)

description: <pre>Annotation files = Transcript association * (Human phase1+2 set) hg38_liftover+new_CAGE_peaks_phase1and2_trans.txt * (Mouse phase1+2 set) mm10_liftover+new_CAGE_peaks_phase1and2_trans.txt (Format) 1) CAGE peak ID "(Old FANTOM5 CAGE Peak ID);(new TSS ID)" 2) Associated transcript ID 3) Distance between CAGE peak and associated transcript 4) Number of transcripts within 500bp (polII transcripts) or 50bp (non-polII transcripts) 5) All transcripts within the above cutoffs (500bp or 50bp) (Transcript ID:distance) = Gene/protein association * (Human phase1+2 set) hg38_liftover+new_CAGE_peaks_phase1and2_annot.txt * (Mouse phase1+2 set) mm10_liftover+new_CAGE_peaks_phase1and2_annot.txt (Format) 1) CAGE peak ID "(Old FANTOM5 CAGE Peak ID);(new TSS ID)" 2) Associated transcript ID 3) Distance between CAGE peak and associated transcript 4) EntrezGene GeneID 5) HGNC/MGI ID 6) UniProt ID 7) Associated gene name 8) Associated gene symbol 9) Associated gene synonym 10) Source of associated gene = CAGE peak name * (Human phase1+2 set) human_phase1and2_CAGE_Peak_name.txt * (Mouse phase1+2 set) mouse_phase1and2_CAGE_Peak_name.txt (Format) 1) CAGE peak ID "(Old FANTOM5 CAGE Peak ID);(new TSS ID)" 2) New CAGE peak name 3) Old (Obsoleted) CAGE peak name = Annotation sources Jun. 16th, 2015 snapshots of the following databases * EntrezGene * Gencode (Human v22, Mouse vM4) * HGNC * MGI * UCSC Genome Browser (hg38/mm10) * UniProt </pre>
DOI: 10.6084/m9.figshare.4880318.v1
title: Re-processing of the data generated by the FANTOM5 project (mm10 v3)_CAGE_peaks_expression

description: <pre>This folder contains CAGE peaks expression tables for the robust set of peaks. mm10.fair+new_CAGE_peaks_phase1and2_ann.txt.gz - CAGE peak based table with annotated peaks for mouse samples (fairly remapped) mm10.fair+new_CAGE_peaks_phase1and2_liftover_ann.txt.gz - CAGE peak based table with annotated peaks for mouse samples (all liftover) mm10.fair+new_CAGE_peaks_phase1and2_tpm.osc.txt.gz - CAGE peak based expression table (RLE normalized) for mouse samples [see edgeR documentation for further details about normalization method] mm10.fair+new_CAGE_peaks_phase1and2_counts.osc.txt.gz - CAGE peak based expression table for mouse samples mm10.fair+new_CAGE_peaks_phase1and2_tpm_ann.osc.txt.gz - CAGE peak based expression table (RLE normalized) for mouse with annotation mm10.fair+new_CAGE_peaks_phase1and2_counts_ann.osc.txt.gz - CAGE peak based expression table for mouse with annotation </pre>
DOI: 10.6084/m9.figshare.4880312.v1
title: Re-processing of the data generated by the FANTOM5 project (mm10 v3)_CAGE_peaks_expression

description: <pre>CAGE peaks === This directory contains the CAGE peaks defined in the FANTOM5 project as a robust set, where genomic coordinates originally defined on mm9 are lifted to mm10 by liftOver tool. By following the update, their annotations are also updated - see “CAGE_peaks_annotation” directory in the parent directory. - Inquiries: fantom-help@gsc.riken.jp - Update: 2015-09-18 initial release 2016-07-22 ver.2 release 2017-04-14 ver.3 release Data files --- - mm10_liftover_CAGE_peaks_phase1and2.bed.gz : all lifted-over CAGE peaks using UCSC Lift-over - mm10_fair_CAGE_peaks_phase1and2.bed : fairly remapped CAGE peaks. - mm10_problematic_CAGE_peaks_phase1and2.bed : problematic CAGE peaks that were filtered out by QC - mm10_new_CAGE_peaks_phase1and2.bed : newly identified CAGE peaks in mm10 DPI clustering - mm9_droppped_CAGE_peaks_phase1and2.bed : unmapped CAGE peaks (in mm9 coordination) Description of the columns in CAGE peaks coordinates files --- This is baed on BED9 format, where the thickStart and thickEnd position represent representative TSS positions. (https://genome.ucsc.edu/FAQ/FAQformat.html#format1) - chromosome - start of CAGE peak region - end of CAGE peak region - name (ID) of the CAGE peak - score - strand of the CAGE peak - start of the representative TSS position - end of the representative TSS position (Note: end is always start+1) - rgb string for color coding (plus or minus strand only) </pre>
DOI: 10.6084/m9.figshare.4880315.v1
title: Re-processing of the data generated by the FANTOM5 project (mm10 v3)_CAGE_peaks_annotation

description: <pre>Annotation files = Transcript association * (Human phase1+2 set) hg38_liftover+new_CAGE_peaks_phase1and2_trans.txt * (Mouse phase1+2 set) mm10_liftover+new_CAGE_peaks_phase1and2_trans.txt (Format) 1) CAGE peak ID "(Old FANTOM5 CAGE Peak ID);(new TSS ID)" 2) Associated transcript ID 3) Distance between CAGE peak and associated transcript 4) Number of transcripts within 500bp (polII transcripts) or 50bp (non-polII transcripts) 5) All transcripts within the above cutoffs (500bp or 50bp) (Transcript ID:distance) = Gene/protein association * (Human phase1+2 set) hg38_liftover+new_CAGE_peaks_phase1and2_annot.txt * (Mouse phase1+2 set) mm10_liftover+new_CAGE_peaks_phase1and2_annot.txt (Format) 1) CAGE peak ID "(Old FANTOM5 CAGE Peak ID);(new TSS ID)" 2) Associated transcript ID 3) Distance between CAGE peak and associated transcript 4) EntrezGene GeneID 5) HGNC/MGI ID 6) UniProt ID 7) Associated gene name 8) Associated gene symbol 9) Associated gene synonym 10) Source of associated gene = CAGE peak name * (Human phase1+2 set) human_phase1and2_CAGE_Peak_name.txt * (Mouse phase1+2 set) mouse_phase1and2_CAGE_Peak_name.txt (Format) 1) CAGE peak ID "(Old FANTOM5 CAGE Peak ID);(new TSS ID)" 2) New CAGE peak name 3) Old (Obsoleted) CAGE peak name = Annotation sources Jun. 16th, 2015 snapshots of the following databases * EntrezGene * Gencode (Human v22, Mouse vM4) * HGNC * MGI * UCSC Genome Browser (hg38/mm10) * UniProt </pre>
DOI: 10.6084/m9.figshare.4880318.v2
title: Reprocessed CAGE peaks generated by FANTOM5 (mm10 v3)_CAGE_peaks_expression

description: <pre>This folder contains CAGE peaks expression tables for the robust set of peaks. mm10.fair+new_CAGE_peaks_phase1and2_ann.txt.gz - CAGE peak based table with annotated peaks for mouse samples (fairly remapped) mm10.fair+new_CAGE_peaks_phase1and2_liftover_ann.txt.gz - CAGE peak based table with annotated peaks for mouse samples (all liftover) mm10.fair+new_CAGE_peaks_phase1and2_tpm.osc.txt.gz - CAGE peak based expression table (RLE normalized) for mouse samples [see edgeR documentation for further details about normalization method] mm10.fair+new_CAGE_peaks_phase1and2_counts.osc.txt.gz - CAGE peak based expression table for mouse samples mm10.fair+new_CAGE_peaks_phase1and2_tpm_ann.osc.txt.gz - CAGE peak based expression table (RLE normalized) for mouse with annotation mm10.fair+new_CAGE_peaks_phase1and2_counts_ann.osc.txt.gz - CAGE peak based expression table for mouse with annotation </pre>
DOI: 10.6084/m9.figshare.4880315.v2
title: Reprocessed CAGE peaks generated by FANTOM5 (mm10 v3)_CAGE_peaks_annotation

description: <pre>Annotation files = Transcript association * (Human phase1+2 set) hg38_liftover+new_CAGE_peaks_phase1and2_trans.txt * (Mouse phase1+2 set) mm10_liftover+new_CAGE_peaks_phase1and2_trans.txt (Format) 1) CAGE peak ID "(Old FANTOM5 CAGE Peak ID);(new TSS ID)" 2) Associated transcript ID 3) Distance between CAGE peak and associated transcript 4) Number of transcripts within 500bp (polII transcripts) or 50bp (non-polII transcripts) 5) All transcripts within the above cutoffs (500bp or 50bp) (Transcript ID:distance) = Gene/protein association * (Human phase1+2 set) hg38_liftover+new_CAGE_peaks_phase1and2_annot.txt * (Mouse phase1+2 set) mm10_liftover+new_CAGE_peaks_phase1and2_annot.txt (Format) 1) CAGE peak ID "(Old FANTOM5 CAGE Peak ID);(new TSS ID)" 2) Associated transcript ID 3) Distance between CAGE peak and associated transcript 4) EntrezGene GeneID 5) HGNC/MGI ID 6) UniProt ID 7) Associated gene name 8) Associated gene symbol 9) Associated gene synonym 10) Source of associated gene = CAGE peak name * (Human phase1+2 set) human_phase1and2_CAGE_Peak_name.txt * (Mouse phase1+2 set) mouse_phase1and2_CAGE_Peak_name.txt (Format) 1) CAGE peak ID "(Old FANTOM5 CAGE Peak ID);(new TSS ID)" 2) New CAGE peak name 3) Old (Obsoleted) CAGE peak name = Annotation sources Jun. 16th, 2015 snapshots of the following databases * EntrezGene * Gencode (Human v22, Mouse vM4) * HGNC * MGI * UCSC Genome Browser (hg38/mm10) * UniProt </pre>
DOI: 10.6084/m9.figshare.4880312.v2
title: Reprocessed CAGE peaks generated by FANTOM5 (mm10 v3)_CAGE_peaks_expression

description: <pre>CAGE peaks === This directory contains the CAGE peaks defined in the FANTOM5 project as a robust set, where genomic coordinates originally defined on mm9 are lifted to mm10 by liftOver tool. By following the update, their annotations are also updated - see “CAGE_peaks_annotation” directory in the parent directory. - Inquiries: fantom-help@gsc.riken.jp - Update: 2015-09-18 initial release 2016-07-22 ver.2 release 2017-04-14 ver.3 release Data files --- - mm10_liftover_CAGE_peaks_phase1and2.bed.gz : all lifted-over CAGE peaks using UCSC Lift-over - mm10_fair_CAGE_peaks_phase1and2.bed : fairly remapped CAGE peaks. - mm10_problematic_CAGE_peaks_phase1and2.bed : problematic CAGE peaks that were filtered out by QC - mm10_new_CAGE_peaks_phase1and2.bed : newly identified CAGE peaks in mm10 DPI clustering - mm9_droppped_CAGE_peaks_phase1and2.bed : unmapped CAGE peaks (in mm9 coordination) Description of the columns in CAGE peaks coordinates files --- This is baed on BED9 format, where the thickStart and thickEnd position represent representative TSS positions. (https://genome.ucsc.edu/FAQ/FAQformat.html#format1) - chromosome - start of CAGE peak region - end of CAGE peak region - name (ID) of the CAGE peak - score - strand of the CAGE peak - start of the representative TSS position - end of the representative TSS position (Note: end is always start+1) - rgb string for color coding (plus or minus strand only) </pre>
DOI: 10.6084/m9.figshare.4880312.v3
title: Reprocessed CAGE peaks generated by FANTOM5 (mm10 v3)_CAGE_peaks

description: <pre>CAGE peaks === This directory contains the CAGE peaks defined in the FANTOM5 project as a robust set, where genomic coordinates originally defined on mm9 are lifted to mm10 by liftOver tool. By following the update, their annotations are also updated - see “CAGE_peaks_annotation” directory in the parent directory. - Inquiries: fantom-help@gsc.riken.jp - Update: 2015-09-18 initial release 2016-07-22 ver.2 release 2017-04-14 ver.3 release Data files --- - mm10_liftover_CAGE_peaks_phase1and2.bed.gz : all lifted-over CAGE peaks using UCSC Lift-over - mm10_fair_CAGE_peaks_phase1and2.bed : fairly remapped CAGE peaks. - mm10_problematic_CAGE_peaks_phase1and2.bed : problematic CAGE peaks that were filtered out by QC - mm10_new_CAGE_peaks_phase1and2.bed : newly identified CAGE peaks in mm10 DPI clustering - mm9_droppped_CAGE_peaks_phase1and2.bed : unmapped CAGE peaks (in mm9 coordination) Description of the columns in CAGE peaks coordinates files --- This is baed on BED9 format, where the thickStart and thickEnd position represent representative TSS positions. (https://genome.ucsc.edu/FAQ/FAQformat.html#format1) - chromosome - start of CAGE peak region - end of CAGE peak region - name (ID) of the CAGE peak - score - strand of the CAGE peak - start of the representative TSS position - end of the representative TSS position (Note: end is always start+1) - rgb string for color coding (plus or minus strand only) </pre>