2. Samples. This section parallels the MIAME version 1.1 “Samples” section and describes both the source of the sample and any biological perturbations applied using art-recognized descriptors (e.g. cell line, passage number) derived from well established databases (e.g. ATCC) or literature citations. Treatments are divided into three classes and include those associated with (1) general growth and/or cell culture conditions, (2) pre-siRNA treatments, and (3) post-siRNA treatments. Both pre- and post-treatment categories require a description or reference to the treatment type, the compound used, and the protocol employed
3. Delivery. This section provides details of how the silencing reagent(s) were introduced into the biological sample. In addition to generic descriptors that cover standard methods of delivery (transfection, transduction, electroporation, specific details pertaining to the type and concentration of the delivery reagent, cell density at the time of delivery, the concentration of siRNA, and protocol are included.
4. Assay Plate. The “Assay Plate” section describes conditions of the plates in which the data is acquired. Critical descriptors include the number of cells per well, and the time between silencing reagent delivery and performance of the assay. In addition, details pertaining to media changes and any treatments are also essential.
5. Assay Plate Layout] This section describes the common features of the assay plates used in the experiment. Similar to the equivalent section of MIAME, this section is divided into two parts. The first part includes a description of the assay plate as a whole such as plate type, manufacturer and catalogue number. The second section describes the plate configuration including the well position of each reagent, the reagent type (e.g., experimental siRNA, or shRNA (short hairpin RNA), the target and any controls (positive and negative).
6. Silencing RNA Reagent This section describes the silencing reagents used in the experiment including a description of target genes (e.g., official gene symbol, sequence(s) database accession number), physical descriptions of the siRNA(s) (e.g., sequence(s) if available) and the manufacturer (unique catalog number) or source (if not commercial). In cases where libraries of silencing reagents are used, identification of manufacturer and version of the library are included. Furthermore, as an increasing number of synthetic siRNAs incorporate modifications and/or conjugates that enhance stability, delivery, and/or specificity, descriptions of these features should be included when available. For expressed shRNAs, descriptions and references regarding the vector, the characteristics of the shRNA design (e.g., stem and loop composition), and the method of delivery (e.g., transient expression vs. viral transduction) should be included. In cases where validation studies utilize a second unrelated set of silencing reagents, the unique features (sequence, modification pattern, etc) should be reported.
7. Assay. The Assay section describes critical elements of the assay and data acquisition. Because the effects of RNAi can be measured at the level of the transcriptome, proteome and phenome (phenotypes resulting from knockdown), using a variety of techniques (quantitative RT-PCR, Western blot, apoptosis assay, etc), detailed descriptions of protocols and reagents are imperative. Where guidelines exist for a specific assay or procedure, references should be included. Where guidelines are absent, a detailed set of descriptors including a summary of the assay, protocols, equipment, readout units and other points should be entered into the document. In cases where multiple assays are employed in a single screen, detailed descriptions of each should be included. This would include descriptions of selection-based assays, live/dead assays, modifier assays and validation assays used to verify the readouts (e.g., phenotypes) of hits selected in primary screens to ensure consistency with the original readout.
8. Data Analysis and Output. The Data Analysis section defines the transformation, normalization, and scoring procedures used to filter background effects. Further, this section is used to report data for the specific controls, the statistical procedures employed for hit identification (e.g., z-score), and the quality control steps that are applied to the data (e.g., Z’-factor). Reporting of the Data Output will occur in a separate section dedicated to the raw quantitative or qualitative data. For quantitative data, investigators may provide a brief description of how the data was quantized followed by the raw unprocessed data and reference to a physical map of the actual data (e.g., an assay plate layout). Additionally, reference to an assay plate layout for unprocessed and scored sets will be required to properly orient and evaluate collections. For qualitative data, researchers will be asked to provide a brief description of how the data was acquired and references to assay plate layouts for unprocessed and scored sets. Researchers will also be asked to cite protocols and specifications for data, and will accommodate references to software for data acquisition

Deletions:
~1. Description and Design. This introductory section consists of two elements focusing on experimental description and design. The experimental description provides a broad overview of the experiment and includes key information such as the primary contact, a short description of the biological or technical hypothesis being addressed and the target organism in which the experiments are being performed. The experimental design section provides the context of the experiment including assays conducted, descriptions of the number and type of replicates, details of follow-up confirmation studies, and links to related information.
2. Samples. This section parallels the MIAME version 1.1 “Samples” section and describes both the source of the sample and any biological perturbations applied using art-recognized descriptors (e.g. cell line, passage number) derived from well established databases (e.g. ATCC) or literature citations. Treatments are divided into three classes and include those associated with (1) general growth and/or cell culture conditions, (2) pre-siRNA treatments, and (3) post-siRNA treatments. Both pre- and post-treatment categories require a description or reference to the treatment type, the compound used, and the protocol employed
3. Delivery. This section provides details of how the silencing reagent(s) were introduced into the biological sample. In addition to generic descriptors that cover standard methods of delivery (transfection, transduction, electroporation, specific details pertaining to the type and concentration of the delivery reagent, cell density at the time of delivery, the concentration of siRNA, and protocol are included.
4. Plate. The “Assay Plate” section describes conditions of the plates in which the data is acquired. Critical descriptors include the number of cells per well, and the time between silencing reagent delivery and performance of the assay. In addition, details pertaining to media changes and any treatments are also essential.
5. Plate Layout. This section describes the common features of the assay plates used in the experiment. Similar to the equivalent section of MIAME, this section is divided into two parts. The first part includes a description of the assay plate as a whole such as plate type, manufacturer and catalogue number. The second section describes the plate configuration including the well position of each reagent, the reagent type (e.g., experimental siRNA, or shRNA (short hairpin RNA), the target and any controls (positive and negative).
6. Silencing Reagent. This section describes the silencing reagents used in the experiment including a description of target genes (e.g., official gene symbol, sequence(s) database accession number), physical descriptions of the siRNA(s) (e.g., sequence(s) if available) and the manufacturer (unique catalog number) or source (if not commercial). In cases where libraries of silencing reagents are used, identification of manufacturer and version of the library are included. Furthermore, as an increasing number of synthetic siRNAs incorporate modifications and/or conjugates that enhance stability, delivery, and/or specificity, descriptions of these features should be included when available. For expressed shRNAs, descriptions and references regarding the vector, the characteristics of the shRNA design (e.g., stem and loop composition), and the method of delivery (e.g., transient expression vs. viral transduction) should be included. In cases where validation studies utilize a second unrelated set of silencing reagents, the unique features (sequence, modification pattern, etc) should be reported.
7. Assay. The Assay section describes critical elements of the assay and data acquisition. Because the effects of RNAi can be measured at the level of the transcriptome, proteome and phenome (phenotypes resulting from knockdown), using a variety of techniques (quantitative RT-PCR, Western blot, apoptosis assay, etc), detailed descriptions of protocols and reagents are imperative. Where guidelines exist for a specific assay or procedure, references should be included. Where guidelines are absent, a detailed set of descriptors including a summary of the assay, protocols, equipment, readout units and other points should be entered into the document. In cases where multiple assays are employed in a single screen, detailed descriptions of each should be included. This would include descriptions of selection-based assays, live/dead assays, modifier assays and validation assays used to verify the readouts (e.g., phenotypes) of hits selected in primary screens to ensure consistency with the original readout.
8. Analysis and Output. The Data Analysis section defines the transformation, normalization, and scoring procedures used to filter background effects. Further, this section is used to report data for the specific controls, the statistical procedures employed for hit identification (e.g., z-score), and the quality control steps that are applied to the data (e.g., Z’-factor). Reporting of the Data Output will occur in a separate section dedicated to the raw quantitative or qualitative data. For quantitative data, investigators may provide a brief description of how the data was quantized followed by the raw unprocessed data and reference to a physical map of the actual data (e.g., an assay plate layout). Additionally, reference to an assay plate layout for unprocessed and scored sets will be required to properly orient and evaluate collections. For qualitative data, researchers will be asked to provide a brief description of how the data was acquired and references to assay plate layouts for unprocessed and scored sets. Researchers will also be asked to cite protocols and specifications for data, and will accommodate references to software for data acquisition

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Edited on 2007-02-19 06:13:06 by GraemeGrimes

Additions:
The MIARE reporting guidelines were initiated by members of the RNAi Global∞ in order to facilitate data sharing within the initiative. The guidelines were developed in part by a inter laboratory benchmarking study to identify minimal reporting parameters for high-throughput siRNA screens, and in part by workshops and discussions within the RNAi Global.

Deletions:
The MIARE reporting guidelines were initiated by members of the RNAi Global∞ in order to facilitate data sharing within the initiative. The guidelines were developed in part by a inter laboratory benchmarking study to identify minimal reporting parameters for high-throughput siRNA screens, and in part by workshops and discussions within the RNAi Global.

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Edited on 2007-02-19 06:11:23 by GraemeGrimes

Additions:
The MIARE reporting guidelines were initiated by members of the RNAi Global∞ in order to facilitate data sharing within the initiative. The guidelines were developed in part by a inter laboratory benchmarking study to identify minimal reporting parameters for high-throughput siRNA screens, and in part by workshops and discussions within the RNAi Global.

Deletions:
The MIARE reporting guidelines were initiated by members of the RNAi Global∞ in order to facilitate data sharing within the initiative. The guidelines were developed in part by a inter laboratory benchmarking study to identify minimal reporting parameters for high-throughput siRNA screens, and in part by workshops and discussions within the RNAi Global.

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Edited on 2007-02-19 05:38:49 by GraemeGrimes

Additions:
~-MIARE reporting guidelines MIAREReportingGuidelines065

Deletions:
~-MIARE reporting guidelines MIAREReportingGuidelines0-6-5∞

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Edited on 2007-02-19 05:38:05 by GraemeGrimes

Additions:
~-MIARE reporting guidelines MIAREReportingGuidelines0-6-5∞

Deletions:
~-MIARE reporting guidelines MIAREGuidelines

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Edited on 2007-02-19 05:37:01 by GraemeGrimes

Additions:
~-MIARE reporting guidelines MIAREGuidelines

Deletions:
~-MIARE reporting guidelines MIARE-0-6-5∞

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Edited on 2007-02-19 05:36:22 by GraemeGrimes

Additions:
~-MIARE reporting guidelines MIARE-0-6-5∞

Deletions:
~-MIARE reporting guidelines MIARE-0.6.5∞

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Edited on 2007-02-19 05:35:46 by GraemeGrimes

Additions:
~-MIARE reporting guidelines MIARE-0.6.5∞

Deletions:
~-MIARE reporting guidelines [MIARE-0.6.5]

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Edited on 2007-02-19 05:34:20 by GraemeGrimes

Additions:
~-MIARE reporting guidelines [MIARE-0.6.5]

Deletions:
~-MIARE reporting guidelines MIARE-0-6-5∞

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Edited on 2007-02-19 05:33:45 by GraemeGrimes

Additions:
~-MIARE reporting guidelines MIARE-0-6-5∞

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Edited on 2007-02-07 03:37:48 by JavierSantoyo

Additions:


Deletions:

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Oldest known version of this page was edited on 2007-02-07 03:34:37 by JavierSantoyo []

1. Description and Design. This introductory section consists of two elements focusing on experimental description and design. The experimental description provides a broad overview of the experiment and includes key information such as the primary contact, a short description of the biological or technical hypothesis being addressed and the target organism in which the experiments are being performed. The experimental design section provides the context of the experiment including assays conducted, descriptions of the number and type of replicates, details of follow-up confirmation studies, and links to related information.

2. Samples. This section parallels the MIAME version 1.1 “Samples” section and describes both the source of the sample and any biological perturbations applied using art-recognized descriptors (e.g. cell line, passage number) derived from well established databases (e.g. ATCC) or literature citations. Treatments are divided into three classes and include those associated with (1) general growth and/or cell culture conditions, (2) pre-siRNA treatments, and (3) post-siRNA treatments. Both pre- and post-treatment categories require a description or reference to the treatment type, the compound used, and the protocol employed

3. Delivery. This section provides details of how the silencing reagent(s) were introduced into the biological sample. In addition to generic descriptors that cover standard methods of delivery (transfection, transduction, electroporation, specific details pertaining to the type and concentration of the delivery reagent, cell density at the time of delivery, the concentration of siRNA, and protocol are included.

4. Plate. The “Assay Plate” section describes conditions of the plates in which the data is acquired. Critical descriptors include the number of cells per well, and the time between silencing reagent delivery and performance of the assay. In addition, details pertaining to media changes and any treatments are also essential.

5. Plate Layout. This section describes the common features of the assay plates used in the experiment. Similar to the equivalent section of MIAME, this section is divided into two parts. The first part includes a description of the assay plate as a whole such as plate type, manufacturer and catalogue number. The second section describes the plate configuration including the well position of each reagent, the reagent type (e.g., experimental siRNA, or shRNA (short hairpin RNA), the target and any controls (positive and negative).

6. Silencing Reagent. This section describes the silencing reagents used in the experiment including a description of target genes (e.g., official gene symbol, sequence(s) database accession number), physical descriptions of the siRNA(s) (e.g., sequence(s) if available) and the manufacturer (unique catalog number) or source (if not commercial). In cases where libraries of silencing reagents are used, identification of manufacturer and version of the library are included. Furthermore, as an increasing number of synthetic siRNAs incorporate modifications and/or conjugates that enhance stability, delivery, and/or specificity, descriptions of these features should be included when available. For expressed shRNAs, descriptions and references regarding the vector, the characteristics of the shRNA design (e.g., stem and loop composition), and the method of delivery (e.g., transient expression vs. viral transduction) should be included. In cases where validation studies utilize a second unrelated set of silencing reagents, the unique features (sequence, modification pattern, etc) should be reported.

7. Assay. The Assay section describes critical elements of the assay and data acquisition. Because the effects of RNAi can be measured at the level of the transcriptome, proteome and phenome (phenotypes resulting from knockdown), using a variety of techniques (quantitative RT-PCR, Western blot, apoptosis assay, etc), detailed descriptions of protocols and reagents are imperative. Where guidelines exist for a specific assay or procedure, references should be included. Where guidelines are absent, a detailed set of descriptors including a summary of the assay, protocols, equipment, readout units and other points should be entered into the document. In cases where multiple assays are employed in a single screen, detailed descriptions of each should be included. This would include descriptions of selection-based assays, live/dead assays, modifier assays and validation assays used to verify the readouts (e.g., phenotypes) of hits selected in primary screens to ensure consistency with the original readout.

8. Analysis and Output. The Data Analysis section defines the transformation, normalization, and scoring procedures used to filter background effects. Further, this section is used to report data for the specific controls, the statistical procedures employed for hit identification (e.g., z-score), and the quality control steps that are applied to the data (e.g., Z’-factor). Reporting of the Data Output will occur in a separate section dedicated to the raw quantitative or qualitative data. For quantitative data, investigators may provide a brief description of how the data was quantized followed by the raw unprocessed data and reference to a physical map of the actual data (e.g., an assay plate layout). Additionally, reference to an assay plate layout for unprocessed and scored sets will be required to properly orient and evaluate collections. For qualitative data, researchers will be asked to provide a brief description of how the data was acquired and references to assay plate layouts for unprocessed and scored sets. Researchers will also be asked to cite protocols and specifications for data, and will accommodate references to software for data acquisition