3adc092b4cf3f9bf509edaf6f20a8cf0 pmc_34350225.pdf 1383860487de930ced5d627d21f8fe12e8b00628 pmc_34350225.pdf 92c2181df74364d81fdfc9c47b9d3cdfe6fd3f6b99125fc488b243ddb78fe878 pmc_34350225.pdf Title: Characterization of the Impact of Density Gradient Centrifugation on the Profile of the Pig Sperm Transcriptome by RNA-Seq Subject: RNA-Seq data from human semen suggests that the study of the sperm transcriptome requires the previous elimination from the ejaculates of somatic cells carrying a larger load of RNA. Semen purification is also carried to study the sperm transcriptome in other species including swine and it is often done by density gradient centrifugation to obtain viable spermatozoa from fresh ejaculates or artificial insemination doses, thereby limiting the throughput and remoteness of the samples that can be processed in one study. Keywords: sperm RNA, RNA-Seq, sperm purification, differentially abundant gene, somatic cell, germline cell, exosome Author: Alex Clop Creator: LaTeX with hyperref package + hypdvips Producer: dvips + MiKTeX GPL Ghostscript 9.0 CreationDate: Mon Jul 12 18:25:41 2021 CEST ModDate: Mon Jul 12 18:38:00 2021 CEST Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 12 Encrypted: no Page size: 595.26 x 779.52 pts Page rot: 0 File size: 731368 bytes Optimized: no PDF version: 1.6 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- ILVUME+HelveticaNeueLTStd-Bd Type 1C Custom yes yes no 32 0 ZPSZTI+HelveticaNeueLTStd-Lt Type 1C Custom yes yes no 37 0 MISMEX+HelveticaNeueLTStd-BdIt Type 1C WinAnsi yes yes no 50 0 WRNDUA+HelveticaNeueLTStd-LtIt Type 1C Custom yes yes no 52 0 NYFJDY+HelveticaNeueLTStd-MdIt Type 1C WinAnsi yes yes no 57 0 PUYGUJ+MinionPro-Regular Type 1C Custom yes yes no 65 0 INTRRM+MTSY Type 1C Custom yes yes yes 74 0 KSJLQD+MinionPro-Bold Type 1C Custom yes yes no 83 0 YODSOG+MTGU Type 1C Custom yes yes no 88 0 SMAQZM+MinionPro-It Type 1C WinAnsi yes yes no 90 0 CVJJBP+RMTMI Type 1C Custom yes yes yes 102 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2023-05-27 02:42:29 CEST RepresentationInformation: pmc_34350225.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2023-03-31 12:14:43 CEST Size: 731368 Format: PDF Version: 1.6 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 335 FreeObjects: 17 IncrementalUpdates: 0 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: true CenterWindow: false DisplayDocTitle: false NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseOutlines Language: en Outlines: Item: Title: Characterization of the Impact of Density Gradient Centrifugation on the Profile of the Pig Sperm Transcriptome by RNA-Seq Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4d3167f4 Children: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@ed9d034 Item: Title: Materials and Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6121c9d6 Children: Item: Title: Sample Collection Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@87f383f Item: Title: Sample Processing and RNA Extraction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4eb7f003 Item: Title: RNA-Seq Library Preparation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@eafc191 Item: Title: RNA-Seq Mapping and Analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@612fc6eb Item: Title: Evaluation of the Potential Tissue of Origin of the Differentially Abundant Genes Between Purified and Non-purified Samples Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1060b431 Item: Title: Results and Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@612679d6 Children: Item: Title: RNA Extraction and qPCR Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@11758f2a Item: Title: Sequencing Metrics Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@e720b71 Item: Title: Description and General Comparison of the P and NP Transcriptomes Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1b26f7b2 Item: Title: Differential RNA Abundance Analysis Between P and NP Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@491cc5c9 Item: Title: Conclusion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@74ad1f1f Item: Title: Data Availability Statement Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6a1aab78 Item: Title: Ethics Statement Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@462d5aee Item: Title: Author Contributions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@69b0fd6f Item: Title: Funding Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@757942a1 Item: Title: Supplementary Material Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4a87761d Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@66d1af89 Info: Title: Characterization of the Impact of Density Gradient Centrifugation on the Profile of the Pig Sperm Transcriptome by RNA-Seq Author: Alex Clop Subject: RNA-Seq data from human semen suggests that the study of the sperm transcriptome requires the previous elimination from the ejaculates of somatic cells carrying a larger load of RNA. Semen purification is also carried to study the sperm transcriptome in other species including swine and it is often done by density gradient centrifugation to obtain viable spermatozoa from fresh ejaculates or artificial insemination doses, thereby limiting the throughput and remoteness of the samples that can be processed in one study. Keywords: sperm RNA, RNA-Seq, sperm purification, differentially abundant gene, somatic cell, germline cell, exosome Creator: LaTeX with hyperref package + hypdvips Producer: dvips + MiKTeX GPL Ghostscript 9.0 CreationDate: Mon Jul 12 18:55:41 CEST 2021 ModDate: Mon Jul 12 19:08:00 CEST 2021 ID: 0x4d35a5cdd4f81d0399317ddd6a5b6d1b, 0x30ca6f7bff28b048962c439ee6054189 Filters: FilterPipeline: FlateDecode FilterPipeline: DCTDecode Images: Image: NisoImageMetadata: FormatName: image/png ImageWidth: 279 ImageHeight: 279 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Filter: FlateDecode Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 2008 ImageHeight: 1730 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Interpolate: true Image: NisoImageMetadata: FormatName: image/jpg CompressionScheme: JPEG ImageWidth: 2008 ImageHeight: 1146 ColorSpace: RGB BitsPerSample: 8 BitsPerSampleUnit: integer Interpolate: true Fonts: Type1: Font: BaseFont: ILVUME+HelveticaNeueLTStd-Bd FontSubset: true FirstChar: 0 LastChar: 124 FontDescriptor: FontName: ILVUME+HelveticaNeueLTStd-Bd Flags: Symbolic FontBBox: -9, -214, 848, 786 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true Font: BaseFont: PUYGUJ+MinionPro-Regular FontSubset: true FirstChar: 2 LastChar: 246 FontDescriptor: FontName: PUYGUJ+MinionPro-Regular Flags: Symbolic FontBBox: -26, -257, 956, 713 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true Font: BaseFont: MISMEX+HelveticaNeueLTStd-BdIt FontSubset: true FirstChar: 42 LastChar: 135 FontDescriptor: FontName: MISMEX+HelveticaNeueLTStd-BdIt Flags: Nonsymbolic FontBBox: -63, -182, 717, 731 FontFile3: true Encoding: WinAnsiEncoding Font: BaseFont: KSJLQD+MinionPro-Bold FontSubset: true FirstChar: 3 LastChar: 121 FontDescriptor: FontName: KSJLQD+MinionPro-Bold Flags: Symbolic FontBBox: -8, -245, 823, 703 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true Font: BaseFont: WRNDUA+HelveticaNeueLTStd-LtIt FontSubset: true FirstChar: 0 LastChar: 242 FontDescriptor: FontName: WRNDUA+HelveticaNeueLTStd-LtIt Flags: Symbolic FontBBox: -137, -206, 978, 729 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true Font: BaseFont: ZPSZTI+HelveticaNeueLTStd-Lt FontSubset: true FirstChar: 0 LastChar: 151 FontDescriptor: FontName: ZPSZTI+HelveticaNeueLTStd-Lt Flags: Serif, Symbolic FontBBox: -30, -214, 904, 786 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true Font: BaseFont: CVJJBP+RMTMI FontSubset: true FirstChar: 49 LastChar: 62 FontDescriptor: FontName: CVJJBP+RMTMI Flags: Symbolic FontBBox: 0, 0, 735, 657 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true Font: BaseFont: YODSOG+MTGU FontSubset: true FirstChar: 97 LastChar: 109 FontDescriptor: FontName: YODSOG+MTGU Flags: Symbolic FontBBox: 0, -196, 607, 683 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true Font: BaseFont: NYFJDY+HelveticaNeueLTStd-MdIt FontSubset: true FirstChar: 42 LastChar: 242 FontDescriptor: FontName: NYFJDY+HelveticaNeueLTStd-MdIt Flags: Symbolic FontBBox: -70, -205, 891, 731 FontFile3: true Encoding: WinAnsiEncoding Font: BaseFont: SMAQZM+MinionPro-It FontSubset: true FirstChar: 40 LastChar: 242 FontDescriptor: FontName: SMAQZM+MinionPro-It Flags: Symbolic FontBBox: -142, -257, 903, 712 FontFile3: true Encoding: WinAnsiEncoding Font: BaseFont: INTRRM+MTSY FontSubset: true FirstChar: 0 LastChar: 68 FontDescriptor: FontName: INTRRM+MTSY Flags: Symbolic FontBBox: 0, -209, 944, 679 FontFile3: true EncodingDictionary: BaseEncoding: WinAnsiEncoding Differences: true ToUnicode: true XMP: 2021-07-12T21:55:41+05:30 LaTeX with hyperref package + hypdvips 2021-07-12T22:08+05:30 2021-07-12T22:08+05:30 application/pdf RNA-Seq data from human semen suggests that the study of the sperm transcriptome requires the previous elimination from the ejaculates of somatic cells carrying a larger load of RNA. Semen purification is also carried to study the sperm transcriptome in other species including swine and it is often done by density gradient centrifugation to obtain viable spermatozoa from fresh ejaculates or artificial insemination doses, thereby limiting the throughput and remoteness of the samples that can be processed in one study. Alex Clop Characterization of the Impact of Density Gradient Centrifugation on the Profile of the Pig Sperm Transcriptome by RNA-Seq sperm RNA RNA-Seq sperm purification differentially abundant gene somatic cell germline cell exosome sperm RNA, RNA-Seq, sperm purification, differentially abundant gene, somatic cell, germline cell, exosome dvips + MiKTeX GPL Ghostscript 9.0 uuid:17a2655d-d1ae-4202-bb1b-5fec6eb14ed5 uuid:944f184f-55bf-43ae-9289-157a77a0f97f Pages: Page: Label: 1 Annotations: Annotation: Subtype: Link Rect: 43, 719, 192, 755 Annotation: Subtype: Link Rect: 474, 736, 551, 744 Annotation: Subtype: Link Rect: 477, 728, 520, 736 Annotation: Subtype: Link Rect: 520, 728, 533, 736 Annotation: Subtype: Link Rect: 533, 728, 551, 736 Annotation: Subtype: Link Rect: 452, 720, 551, 728 Annotation: Subtype: Link Rect: 521, 678, 551, 709 Annotation: Subtype: Link Rect: 43, 30, 135, 38 Annotation: Subtype: Link Rect: 139, 30, 199, 38 Annotation: Subtype: Link Rect: 437, 29, 551, 38 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