1. Analysis
    1. AGR SOP WGBS AgR data analysis
      Last updated: 2020-06-10 (PDF)
    2. FBNGenomePhysiology SOP RNAseqDataProcessing
      Last updated: 2019-09-18 (PDF)
    3. ROSLIN SOP CAGE analysis pipeline
      Last updated: 2019-10-29 (PDF)
    4. ROSLIN SOP RNA-Seq analysis pipeline
      Last updated: 2020-06-10 (PDF)
    5. UCD SOP processing and analyzing equine ChIP data
      Last updated: 2019-10-30 (PDF)
    6. ULE SOP RNA-Seq Analysis
      Last updated: 2017-05-04 (TXT)
    7. Roslin SOP Alignment-based RNA-Seq-Processing
      Last updated: 2017-09-17 (PDF)
    8. WSU SOP ChIP-seq Bioinformatic Analysis Protocol 2020.pdf
  2. Assays
    1. AGR SOP WGBS AgR Libary prep
      Last updated: 2020-06-10 (PDF)
    2. DEDJTR SOP SamplingMilkForRNA
      Last updated: 2016-03-01 (PDF)
    3. EHU SOP sheep encephalon RNA extraction
      Last updated: 2019-04-23 (PDF)
    4. INRA SOP ATAC-seq AG v1
      Last updated: 2016-08-05 (PDF)
    5. INRA SOP Hi-C HA v1
      Last updated: 2016-06-10 (PDF)
    6. INRA SOP RNA extraction
      Last updated: 2016-05-04 (PDF)
    7. INRA SOP mRNA-seq long protocol
      Last updated: 2016-09-08 (PDF)
    8. ISU SOP ChIP swine immune cells
      Last updated: 2019-01-24 (PDF)
    9. ISU SOP Fetalliver
      Last updated: 2018-09-15 (PDF)
    10. ISU SOP Macrophage isolation stimulation
      Last updated: 2019-02-12 (PDF)
    11. ROSLIN SOP CAGE-library-preparation
      Last updated: 2019-09-03 (PDF)
    12. ROSLIN SOP Chromatin Immunoprecipitation of Histone Marks
      Last updated: 2016-11-17 (PDF)
    13. ROSLIN SOP DNA Purification Nasal Swabs
      Last updated: 2014-07-29 (PDF)
    14. ROSLIN SOP Isolation of Total RNA from Cells With DNAse Treatment
      Last updated: 2016-11-16 (PDF)
    15. ROSLIN SOP Isolation of Total RNA from Cells Without DNAse Treatment
      Last updated: 2016-11-16 (PDF)
    16. ROSLIN SOP Tissue Fixation and Sonication of Chromatin for ChIP
      Last updated: 2016-11-15 (PDF)
    17. UCD SOP ATAC-Seq Animal tissue
      Last updated: 2020-02-12 (PDF)
    18. UCD SOP ChIP-Seq Animal tissue
      Last updated: 2016-11-01 (PDF)
    19. UCD SOP ChIP-seq for Histone Marks
      Last updated: 2019-11-01 (PDF)
    20. UCD SOP ChIP-seq for Histone Marks AdiposeTissue
      Last updated: 2019-11-02 (PDF)
    21. UCD SOP RNA-Seq Library Prep
      Last updated: 2015-05-10 (PDF)
    22. UCD SOP RNAIsolationNon-fiberousTissues
      Last updated: 2018-04-04 (PDF)
    23. UCD SOP RNAIsolationTendon
      Last updated: 2018-04-05 (PDF)
    24. UIUC SOP Complete Bisulfite Conversion and cleanup of DNA for Methylation Analysis
      Last updated: 2017-05-23 (PDF)
    25. UIUC SOP PCR Product Isolation Protocol
      Last updated: 2017-05-23 (PDF)
    26. UIUC SOP Simultaneous Purification of Genomic DNA and Total RNA
      Last updated: 2017-05-23 (PDF)
    27. UIUC SOP Targeted Control Library Production Protocol
      Last updated: 2017-06-09 (PDF)
    28. ULE SOP RNA-Seq Library Preperation
      Last updated: 2017-06-05 (PDF)
    29. USDA SOP DNA Extraction From WholeBloodandLiver
      Last updated: 2020-06-11 (PDF)
    30. USDA SOP RNA Extraction From Tissue
      Last updated: 2018-06-26 (PDF)
    31. FBNGenomePhysiology SOP total RNALibraryPreparation
      Last updated: 2019-09-18 (PDF)
    32. INRAE SOP Hi-C pig muscle tissue
      Last updated: 2020-08-12 (PDF)
    33. INRA SOP GENESWITCH WP1 PIG EXTRACTION DNA RNA
      Last updated: 2020-11-11 (PDF)
    34. ROSLIN SOP GENESWITCH WP1 CHICK EXTRACTION DNA RNA
      Last updated: 2020-11-11 (PDF)
    35. WSU SOP Native ChIP-seq Protocol 2019.pdf
  3. Samples
    1. AGS SOP Sample collection RNAseq
      Last updated: 2019-05-08 (PDF)
    2. DEDJTR SOP CryofreezingTissue
      Last updated: 2016-03-17 (PDF)
    3. EHU SOP sheep encephalon Tissue collection
      Last updated: 2019-04-22 (PDF)
    4. FBNGenomePhysiology SOP CryofreezingTissueSsamples
      Last updated: 2016-03-31 (PDF)
    5. FBNGenomePhysiology SOP RNAPreparation
      Last updated: 2019-09-05 (PDF)
    6. INRA SOP GENESWITCH D30 FETUS POOLING
      Last updated: 2020-02-21 (PDF)
    7. INRA SOP GENESWITCH D30 FETUS SAMPLING
      Last updated: 2020-02-21 (PDF)
    8. INRA SOP GENESWITCH D70 FETUS SAMPLING
      Last updated: 2020-02-21 (PDF)
    9. INRA SOP GENESWITCH PIGLET SAMPLING
      Last updated: 2020-02-21 (PDF)
    10. INRA SOP PBMC purification cattle caprine
      Last updated: 2016-05-04 (PDF)
    11. INRA SOP PBMC seperation swine blood
      Last updated: 2016-05-04 (PDF)
    12. INRA SOP alveolar macrophages mammals sampling
      Last updated: 2016-07-21 (PDF)
    13. INRA SOP chicken splenocytes sampling
      Last updated: 2016-07-21 (PDF)
    14. INRA SOP liver spleen mammarygland forHiC sampling
      Last updated: 2016-07-21 (PDF)
    15. INRA SOP oocytes granulosa mammals sampling
      Last updated: 2016-07-21 (PDF)
    16. INRA SOP sorting caprine CD cells
      Last updated: 2017-12-01 (PDF)
    17. INRA SOP sorting cattle CD cells
      Last updated: 2017-12-01 (PDF)
    18. INRA SOP sorting chicken CD cells
      Last updated: 2018-02-13 (PDF)
    19. INRA SOP sorting swine CD cells
      Last updated: 2016-05-04 (PDF)
    20. INRA SOP testis forHiC sampling
      Last updated: 2016-07-21 (PDF)
    21. INRA SOP tissue aliquots sampling 1b
      Last updated: 2016-07-21 (PDF)
    22. INRA SOP tissue sampling 1a
      Last updated: 2016-07-21 (PDF)
    23. INRA SOP tracheal epithelium mammals sampling
      Last updated: 2016-07-21 (PDF)
    24. KU Pool creation protocol
      Last updated: 2017-05-23 (PDF)
    25. KU SOP Preperation of Genomic DNA from Small Samples
      Last updated: 2017-05-16 (PDF)
    26. NMBU SOP Isolation of Monocyte-derived Macrophages from Blood of Norwegian Red Cattle
      Last updated: 2017-12-19 (PDF)
    27. ROSLIN SOP Blood Leukocyte Isolation
      Last updated: 2016-05-03 (PDF)
    28. ROSLIN SOP Collection of Blood or Nasal Swabs or Ear Tissue for Animal Genotyping
      Last updated: 2016-10-19 (PDF)
    29. ROSLIN SOP Collection of tissue samples for ATAC-Seq and RNA-Seq from large animals
      Last updated: 1806-20-20 (PDF)
    30. ROSLIN SOP Cryopreservation of Nuclei for ATACSeq using GentleMACS
      Last updated: 1806-20-20 (PDF)
    31. ROSLIN SOP Culturing macrophages from bone marrow PBMCs and bronchoalveolar lavage
      Last updated: 2016-07-15 (PDF)
    32. ROSLIN SOP Dissection of Brain Tissue from Large Animals
      Last updated: 2016-04-13 (PDF)
    33. ROSLIN SOP Dissection of Cardiovascular Tissues from Large Animals
      Last updated: 2016-04-13 (PDF)
    34. ROSLIN SOP Dissection of Embryonic and Female Reproductive Tissues from Large Animals
      Last updated: 2016-04-17 (PDF)
    35. ROSLIN SOP Harvest of Large Animal Tissues
      Last updated: 2016-05-16 (PDF)
    36. ROSLIN SOP Isolation of Macrophages from Lungs Blood and Bone Marrow of Large Animals
      Last updated: 2016-05-16 (PDF)
    37. ROSLIN SOP Isolation of Ovine Embryonic Fibroblasts
      Last updated: 2016-05-03 (PDF)
    38. ROSLIN SOP Isolation of RNA from RNAlater preserved tissue
      Last updated: 2016-11-08 (PDF)
    39. ROSLIN SOP Isolation of RNA from frozen tissue
      Last updated: 2016-11-08 (PDF)
    40. ROSLIN SOP Nasal Swabs Large Animals
      Last updated: 2014-07-29 (PDF)
    41. TAMU SOP Cattle Mammary Gland Sample Collection Protocol
      Last updated: 2018-02-22 (PDF)
    42. UCD SOP 50 TissueCollection
      Last updated: 2016-05-20 (PDF)
    43. UCD SOP Equine whole animal collection
      Last updated: 2018-01-05 (PDF)
    44. UIC SOP Tissue Collection Protocol
      Last updated: 2017-04-12 (PDF)
    45. UIUC SOP Targeted Control Pool Creation Protocol
      Last updated: 2017-05-17 (PDF)
    46. USU SOP Ovine Benz2616 Cell Isolation
      Last updated: 2016-04-26 (PDF)
    47. USU SOP Ovine Benz2616 Tissue Collection
      Last updated: 2016-04-26 (PDF)
    48. WUR SOP animal sampling
      Last updated: 2016-04-05 (PDF)
    49. DIAGENODE SOP sorting chicken CD cells
      Last updated: 2018-02-18 (PDF)
    50. DIAGENODE SOP sorting chicken CD cells
      Last updated: 2018-02-19 (PDF)
    51. DIAGENODE SOP sorting chicken CD cells
      Last updated: 2018-02-20 (PDF)
    52. DIAGENODE SOP sorting chicken CD cells
      Last updated: 2018-02-22 (PDF)
    53. FBN SOP Milk Sampling & Milk Cell Isolation
      Last updated: 2020-11-24 (PDF)
    54. FBN SOP pbMEC Isolation
      Last updated: 2020-11-24 (PDF)
    55. INRAE SOP pig muscle tissue sampling
      Last updated: 2020-08-12 (PDF)
    56. INRA SOP cartilage-sampling
      Last updated: 2017-11-17 (PDF)
    57. INRA SOP FRAGENCODE mRNA-seq library preparation
      Last updated: 2021-01-11 (PDF)
    58. INRA SOP alveolar-macrophages mammals sampling
      Last updated: 2016-07-21 (PDF)
    59. INRA SOP cattlebrain sampling
      Last updated: 2017-11-04 (PDF)
    60. INRA SOP mammarygland sampling
      Last updated: 2017-11-04 (PDF)
    61. INRA SOP oocytes-granulosa mammals sampling
      Last updated: 2016-07-21 (PDF)
    62. INRA SOP sorting chicken CD cells
      Last updated: 2018-02-14 (PDF)
    63. INRA SOP sorting chicken CD cells
      Last updated: 2018-02-15 (PDF)
    64. INRA SOP sorting chicken CD cells
      Last updated: 2018-02-16 (PDF)
    65. INRA SOP sorting chicken CD cells
      Last updated: 2018-02-17 (PDF)
    66. INRA SOP sorting chicken CD cells
      Last updated: 2018-02-18 (PDF)
    67. INRA SOP tissue sampling protocol 6
      Last updated: 2018-04-26 (PDF)
    68. ISU SOP sorting swine immune cells
      Last updated: 2021-01-13 (PDF)
    69. NMBU SOP Tissue sampling and freezing Ssal
      Last updated: 2020-06-23 (PDF)
    70. QAAFI-UQ SOP CryofreezingTissue
      Last updated: 2016-10-21 (PDF)
    71. QAAFI-UQ SOP sorting fake fake fake fake
      Last updated: 2016-05-04 (PDF)
    72. ROSLIN SOP ATAC-Seq DNAIsolationandTagmentation Cryopreserved Muscle Nuclei Preparations
      Last updated: 2020-07-20 (PDF)
    73. ROSLIN SOP ATAC-Seq LibraryPreparationandSizeSelection
      Last updated: 2020-07-20 (PDF)
    74. ROSLIN SOP ATAC Seq DNAIsolationandTagmentation Frozen Muscle Tissue
      Last updated: 2020-07-20 (PDF)
    75. ROSLIN SOP Collection of tissue samples for ATAC-Seq and RNA-Seq from large animals
      Last updated: 2020-06-18 (PDF)
    76. ROSLIN SOP Cryopreservation of Nuclei for ATACSeq using GentleMACS
      Last updated: 2020-11-19 (PDF)
    77. ROSLIN SOP GENESWITCH E15 EMBRYO SAMPLING
      Last updated: 2020-09-15 (PDF)
    78. ROSLIN SOP GENESWITCH E8 EMBRYO POOLING
      Last updated: 2020-09-15 (PDF)
    79. ROSLIN SOP GENESWITCH E8 EMBRYO SAMPLING
      Last updated: 2020-09-15 (PDF)
    80. ROSLIN SOP GENESWITCH HATCHED CHICK SAMPLING
      Last updated: 2020-09-15 (PDF)
    81. ROSLIN SOP GENESWITCH WP1 TeloPrime cDNA amplification
      Last updated: 2020-11-16 (PDF)
    82. ROSLIN SOP RNA IsolationoftotalRNAfromfrozentissuesamples
      Last updated: 2020-07-20 (PDF)
    83. UAL SOP CollectionAndTransportTissueCattleSampling
      Last updated: 2021-01-18 (PDF)
    84. UAL SOP fakecollection
      Last updated: 2021-01-18 (PDF)
    85. UIDAHO SOP Bovine FAANG fetal tissue collection
      Last updated: 2018-11-28 (PDF)
    86. WSU SOP Pilot sheep tissue collection-Ovine FAANG Project
      Last updated: 2020-08-13 (PDF)
    87. WU SOP GENESWITCH WP1 RRBS library preparation
      Last updated: 2020-12-01 (PDF)
    88. ABDN SOP ATAC
      Last updated: 2021-05-07 (PDF)
    89. ABDN SOP FAKEPROTOCOL
      Last updated: 2021-05-10 (PDF)
    90. ABDN SOP Leukcoytes ext
      Last updated: 2021-05-20 (PDF)
    91. ABDN SOP cell rna ext
      Last updated: 2021-05-07 (PDF)
    92. ABDN SOP cell rna extraction
      Last updated: 2021-05-07 (PDF)
    93. ABDN SOP tissue rna ext
      Last updated: 2021-05-07 (PDF)
    94. INRAE SOP GENESWITCH POOLING CHICKEN ISO
      Last updated: 2021-06-04 (PDF)
    95. INRAE SOP GENESWITCH POOLING ISO
      Last updated: 2021-06-01 (PDF)
    96. ROSLIN SOP Specimen collection protocol
      Last updated: 2021-06-07 (PDF)
    97. ROSLIN SOP uChIPmentation ChIPseq of histone marks using fish embryos
      Last updated: 2021-05-26 (PDF)
    98. UNIPD SOP FAKE
      Last updated: 2021-06-03 (PDF)
    99. UNIPD SOP Leucocytes Isolation and Stimulation Dlab
      Last updated: 2020-05-18 (PDF)
    100. USC SOP embryo isolation ChIPseq
      Last updated: 2021-06-02 (PDF)
    101. USC SOP embryonic cell isolation ATACseq
      Last updated: 2021-06-02 (PDF)
    102. USC SOP turbot egg preservation RNAseq
      Last updated: 2021-06-02 (PDF)
  4. Analyses
    1. ROSLIN SOP ATAC-Seq analysis pipeline
      Last updated: 2020-11-13 (PDF)
    2. ROSLIN SOP RNA-Seq analysis pipeline
      Last updated: 2020-11-13 (PDF)
    3. UCD SOP processing and analyzing equine PE ChIP data
      Last updated: 2020-12-30 (PDF)
  5. Experiments
    1. DIAGENODE SOP GENESWITCH ATAC-SEQ
      Last updated: 2020-11-18 (PDF)
    2. FBN SOP 10xGenomics CG000204 ChromiumNextGEMSingleCell3 v3.1 Rev B
      Last updated: 2020-11-24 (PDF)
    3. FBN SOP 10xGenomics CG00053 SingleCellPrepGuide RevC
      Last updated: 2020-11-24 (PDF)
    4. INRAE SOP FRAGENCODE DNA extraction
      Last updated: 2021-04-16 (PDF)
    5. INRAE SOP FRAGENCODE WGS library preparation
      Last updated: 2021-04-16 (PDF)
    6. INRAE SOP GENESWITCH CaptureHiC Cell Dissociation
      Last updated: 2021-03-24 (PDF)
    7. INRAE SOP GENESWITCH WP1 PROMOTER CAPTURE HI-C
      Last updated: 2021-03-25 (PDF)
    8. INRA SOP FRAGENCODE RNA extraction
      Last updated: 2021-01-11 (PDF)
    9. ROSLIN SOP ATAC-Seq Cryopreservednucleisamplesfrompigmuscletissue Experimental Protocol
      Last updated: 2020-07-20 (PDF)
    10. ROSLIN SOP ATAC-Seq Frozenpigmuscletissuesamples Experimental Protocol
      Last updated: 2020-07-20 (PDF)
    11. ROSLIN SOP GENESWITCH WP1 PIG CHICK mRNAseq library preparation
      Last updated: 2020-11-23 (PDF)
    12. ROSLIN SOP GENESWITCH WP1 mRNAseq library preparation
      Last updated: 2020-11-23 (PDF)
    13. ROSLIN SOP GENESWITCH WP1 smallRNA-seq library preparation
      Last updated: 2020-11-23 (PDF)
    14. ROSLIN SOP RNA RNAIsolationandSequencingofPigMuscleTissues Experimental Protocol
      Last updated: 2020-07-20 (PDF)
    15. UCD SOP ChIP-seq for Histone Marks Bone
      Last updated: 2020-12-18 (PDF)
    16. UCD SOP ChIP-seq for Histone Marks Skin
      Last updated: 2020-12-18 (PDF)
    17. WU SOP GENESWITCH WP1 RRBS library preparation
      Last updated: 2020-12-01 (PDF)
    18. WU SOP GENESWITCH WP1 WGBS library preparation
      Last updated: 2021-01-27 (PDF)
    19. ABDN SOP ChIP
      Last updated: 2021-05-19 (PDF)
    20. ABDN SOP ChIP
      Last updated: 2021-05-20 (PDF)
    21. ABDN SOP cell rna ext
      Last updated: 2021-05-07 (PDF)
    22. ABDN SOP cell rna ext
      Last updated: 2021-05-17 (PDF)
    23. ABDN SOP fresh ATAC
      Last updated: 2021-05-07 (PDF)
    24. ABDN SOP fresh ATAC
      Last updated: 2021-05-17 (PDF)
    25. ABDN SOP fresh ATAC
      Last updated: 2021-05-18 (PDF)
    26. ABDN SOP tissue rna ext
      Last updated: 2021-05-07 (PDF)
    27. ABDN SOP tissue rna ext
      Last updated: 2021-05-17 (PDF)
    28. INRA SOP invivo.invitro.challenges
      Last updated: 2020-01-31 (PDF)
    29. NMBU SOP ChIP protocol
      Last updated: 2021-05-04 (PDF)
    30. NMBU SOP Microchipmentation for histones Diagenode
      Last updated: 2021-05-18 (PDF)
    31. NMBU SOP Microplex library preparation v3 Diagenode
      Last updated: 2021-05-18 (PDF)
    32. NMBU SOP OmniATAC protocol
      Last updated: 2020-04-29 (PDF)
    33. NMBU SOP POOL INPUT
      Last updated: 2021-05-14 (PDF)
    34. NMBU SOP RNAextraction protocol
      Last updated: 2020-05-03 (PDF)
    35. ROSLIN SOP ATACseq protocol part1
      Last updated: 2021-05-27 (PDF)
    36. ROSLIN SOP ATACseq protocol part2
      Last updated: 2021-05-27 (PDF)
    37. ROSLIN SOP GENESWITCH WP1 TeloPrime cDNA amplification
      Last updated: 2021-02-25 (PDF)
    38. ROSLIN SOP RNAseq protocol
      Last updated: 2021-05-27 (PDF)
    39. UNIPD SOP NucleoSpin-miRNA extraction
      Last updated: 2021-06-03 (PDF)
    40. USC SOP RNAextraction protocol DevMap
      Last updated: 2021-06-02 (PDF)
    41. USC SOP RNAextraction protocol ImmunoMap
      Last updated: 2021-06-02 (PDF)
    42. USC SOP nuclei isolation tissue ATACseq
      Last updated: 2021-06-02 (PDF)