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Matrix Example
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| # Use this template for a NimbleGen gene expression. If your array not represented in GEO. Complete the platform sections, if it is, these sections are optional. | ||||||||||||||||
| # Include descriptive information and protocols for the overall experiment, individual Samples, and Platform in this Metadata worksheet. | ||||||||||||||||
| # Click the Metadata Example tab below to view a completed worksheet. | ||||||||||||||||
| # Field names (in blue on this page) should not be edited. Hover over cells containing field names to view field content guidelines or, | ||||||||||||||||
| # CLICK HERE for Field Content Guidelines Web page. | ||||||||||||||||
| # Include your Platform annotation columns and processed Sample data in the accompanying Matrix worksheet (click Matrix tab below). | ||||||||||||||||
| # NOTE: If your row count exceeds the capacity of Excel, then skip the Matrix worksheet and provide Platform annotation columns and processed data as an external file(s) in plain text, tab-delimited format: | ||||||||||||||||
| # either as a matrix containing both Platform Columns and multiple Samples -or- as individual files for the Platform Columns and each of the Samples. | ||||||||||||||||
| # Any external file(s) must contain an ID_REF column (e.g., based on SEQ_ID column of the .ngd file). | ||||||||||||||||
| # Reference any external file name(s) under the 'processed data file' and 'Platform file' headers below. | ||||||||||||||||
| SERIES | ||||||||||||||||
| # This section describes the overall experiment. | ||||||||||||||||
| title | ||||||||||||||||
| summary | ||||||||||||||||
| summary | ||||||||||||||||
| overall design | ||||||||||||||||
| contributor | ||||||||||||||||
| contributor | ||||||||||||||||
| SEEK Project | Project | |||||||||||||||
| Experiment Class (assay Type) | transcripomics | |||||||||||||||
| Experiment Design type | ExperimentDesignType | |||||||||||||||
| Technology type | microarray | |||||||||||||||
| quality control type | QualityControlDescriptionType | |||||||||||||||
| SAMPLES | ||||||||||||||||
| # The Sample names in the first column are arbitrary but they must match the column headers of the Matrix table (see next worksheet). | ||||||||||||||||
| Sample name | title | raw data file | processed data file | source name | organism | characteristics:NCBI_ID | characteristics:Strain | characteristics:Genotype | characteristics:Phenotype | characteristics: Tag | molecule | label | description | |||
| SAMPLE 1 | organism | MaterialType | LabelCompound | |||||||||||||
| SAMPLE 2 | organism | MaterialType | LabelCompound | |||||||||||||
| SAMPLE 3 | organism | MaterialType | LabelCompound | |||||||||||||
| SAMPLE 4 | organism | MaterialType | LabelCompound | |||||||||||||
| SAMPLE 5 | organism | MaterialType | LabelCompound | |||||||||||||
| SAMPLE 6 | organism | MaterialType | LabelCompound | |||||||||||||
| SAMPLE 7 | organism | MaterialType | LabelCompound | |||||||||||||
| SAMPLE 8 | organism | MaterialType | LabelCompound | |||||||||||||
| SAMPLE 9 | organism | MaterialType | LabelCompound | |||||||||||||
| SAMPLE X | organism | MaterialType | LabelCompound | |||||||||||||
| PROTOCOLS | ||||||||||||||||
| # This section includes protocols and fields which are common to all Samples. | ||||||||||||||||
| # Protocols which are applicable to specific Samples or specific channels should be included in additional columns of the SAMPLES section instead. | ||||||||||||||||
| # You can link to SOPs by SEEK ID (if they have already been submitted), or by name | ||||||||||||||||
| growth protocol | ||||||||||||||||
| treatment protocol | ||||||||||||||||
| extract protocol | ||||||||||||||||
| label protocol | ||||||||||||||||
| hyb protocol | ||||||||||||||||
| scan protocol | ||||||||||||||||
| data processing | ||||||||||||||||
| value definition | ||||||||||||||||
| PLATFORM | ||||||||||||||||
| # If your array is not deposited in GEO, please include platform annotation columns in your Matrix table (see example) and complete the fields below. | ||||||||||||||||
| title | ||||||||||||||||
| technology | in situ oligonucleotide | |||||||||||||||
| distribution | ||||||||||||||||
| organism | ||||||||||||||||
| manufacturer | NimbleGen | |||||||||||||||
| manufacture protocol | ||||||||||||||||
| description | ||||||||||||||||
| native array description file | .ndf | |||||||||||||||
| native array description file | .ngd | |||||||||||||||
| Platform file | ||||||||||||||||
| # Platform Column Definitions: describe the contents of each platform column in the Matrix worksheet or in an external file | ||||||||||||||||
| header 1 | header 1 definition | |||||||||||||||
| header 2 | header 2 definition | |||||||||||||||
| header 3 | header 3 definition | |||||||||||||||
| etc… |
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| # Use this template for a NimbleGen gene expression submission based on an array not represented in GEO. | ||||||||||||||||
| # Include Platform annotation columns (header 1, header 2, etc.) and processed Sample data used to draw the conclusions from your study (e.g., RMA-normalized signal intensities). | ||||||||||||||||
| # The ID_REF column must contain unique identifiers, e.g., based on SEQ_ID column of the .ngd file (SEQ_IDs are used to group the probe pairs for determining gene expression summary values). | ||||||||||||||||
| # The sample header names in the Matrix must match the Sample name in the SAMPLES section of the Metadata file. | ||||||||||||||||
| # Values that should be disregarded may either be left blank or labeled as "null". | ||||||||||||||||
| # NOTE: If your row count exceeds the capacity of Excel, then skip this Matrix worksheet and provide Platform annotation columns and processed data as an external file(s) in plain text, tab-delimited format: | ||||||||||||||||
| # either as a matrix containing Platform Columns and multiple Samples -or- as individual files for the Platform Columns and each of the Samples. | ||||||||||||||||
| # Any external file(s) must contain an ID_REF column (e.g., based on SEQ_ID column of the .ngd file). | ||||||||||||||||
| # Reference the file name(s) under the 'processed data file' and 'Platform Columns file' headers of the Metadata worksheet. | ||||||||||||||||
| ID_REF | header 1 | header 2 | header 3 | SAMPLE 1 | SAMPLE 2 | SAMPLE 3 | SAMPLE 4 | SAMPLE 5 | SAMPLE 6 | SAMPLE 7 | SAMPLE 8 | SAMPLE 9 | SAMPLE X | |||
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| # This is a Metadata example for a NimbleGen gene expression submission based on an array not represented in GEO. | |||||||||||
| SERIES | |||||||||||
| title | Expression analysis of Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH acapsular mutant | ||||||||||
| summary | Investigation of whole genome gene expression level changes in a Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH triple mutant, compared to the wild-type strain. The mutations engineered into this strain render it acapsular. | ||||||||||
| summary | The mutants analyzed in this study are further described in Coyne, M. J., M. Chatzidaki-Livanis, L. C. Paoletti, and L. E. Comstock. 2008. Role of glycan synthesis in colonization of the mammalian gut by the bacterial symbiont Bacteroides fragilis. PNAS 105(35):13098-13103 (PID 18723678). | ||||||||||
| overall design | A six chip study using total RNA recovered from three separate wild-type cultures of Bacteroides fragilis NCTC 9343 and three separate cultures of a triple mutant strain, Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH, in which ungD1 (BF1706), ungD2 (BF2848), and six genes (BF3454 through BF3459) of the PSH capsular polysaccharide locus are truncated or deleted entirely. Each chip measures the expression level of 4,302 genes from Bacteroides fragilis NCTC 9343 and the associated plasmid pBF9343 with fourteen 24-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy. | ||||||||||
| contributor | Jane,Doe | ||||||||||
| contributor | John,A,Smith | ||||||||||
| SAMPLES | |||||||||||
| Sample name | title | raw data file | processed data file | source name | organism | characteristics: Genotype | characteristics: Phenotype | characteristics: Accession | molecule | label | description |
| Sample 1 | BWH_Comstock_B_fragilis_ddungD_dPSH_study_wild-type_rep1 | 90805_532.pair | GEO_sample_wt1.txt | Bacteroides fragilis NCTC 9343 wild-type | Bacteroides fragilis NCTC 9343 | Wild-type | normal | NC_003228 + NC_006873 | total RNA | Cy3 | This sample is of wild-type Bacteroides fragilis NCTC 9343. It is the first of three wild-type biological replicates used in this experiment, each from separate cultures. |
| Sample 2 | BWH_Comstock_B_fragilis_ddungD_dPSH_study_wild-type_rep2 | 91986_532.pair | GEO_sample_wt2.txt | Bacteroides fragilis NCTC 9343 wild-type | Bacteroides fragilis NCTC 9343 | Wild-type | normal | NC_003228 + NC_006873 | total RNA | Cy3 | This sample is of wild-type Bacteroides fragilis NCTC 9343. It is the second of three wild-type biological replicates used in this experiment, each from separate cultures. |
| Sample 3 | BWH_Comstock_B_fragilis_ddungD_dPSH_study_wild-type_rep3 | 94079_532.pair | GEO_sample_wt3.txt | Bacteroides fragilis NCTC 9343 wild-type | Bacteroides fragilis NCTC 9343 | Wild-type | normal | NC_003228 + NC_006873 | total RNA | Cy3 | This sample is of wild-type Bacteroides fragilis NCTC 9343. It is the third of three wild-type biological replicates used in this experiment, each from separate cultures. |
| Sample 4 | BWH_Comstock_B_fragilis_ddungD_dPSH_study_mutant_rep1 | 124726_532.pair | GEO_sample_mut1.txt | Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH | Bacteroides fragilis NCTC 9343 | Triple deletion mutant delta-ungD1 delta-ungD2 delta-PSH | acapsular | NC_003228 + NC_006873 | total RNA | Cy3 | This sample is of Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH, a triple deletion mutant in which ungD1 (BF1706), ungD2 (BF2848), and six genes (BF3454 through BF3459) of the PSH capsular polysaccharide locus are truncated or deleted entirely. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures. |
| Sample 5 | BWH_Comstock_B_fragilis_ddungD_dPSH_study_mutant_rep2 | 125016_532.pair | GEO_sample_mut2.txt | Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH | Bacteroides fragilis NCTC 9343 | Triple deletion mutant delta-ungD1 delta-ungD2 delta-PSH | acapsular | NC_003228 + NC_006873 | total RNA | Cy3 | This sample is of Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH, a triple deletion mutant in which ungD1 (BF1706), ungD2 (BF2848), and six genes (BF3454 through BF3459) of the PSH capsular polysaccharide locus are truncated or deleted entirely. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures. |
| Sample 6 | BWH_Comstock_B_fragilis_ddungD_dPSH_study_mutant_rep3 | 1820602_532.pair | GEO_sample_mut3.txt | Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH | Bacteroides fragilis NCTC 9343 | Triple deletion mutant delta-ungD1 delta-ungD2 delta-PSH | acapsular | NC_003228 + NC_006873 | total RNA | Cy3 | This sample is of Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH, a triple deletion mutant in which ungD1 (BF1706), ungD2 (BF2848), and six genes (BF3454 through BF3459) of the PSH capsular polysaccharide locus are truncated or deleted entirely. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures. |
| PROTOCOLS | |||||||||||
| growth protocol | Bacteroides fragilis NCTC 9343 was grown to mid-log phase (O.D.600nm 0.8) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in basal media (Pantosti et al. Infect. Immun. 59(6):2075). | ||||||||||
| growth protocol | Bacteroides fragilis NCTC 9343 delta-ungD1 delta-ungD2 delta-PSH was grown to mid-log phase (O.D.600nm 0.8) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in basal media (Pantosti et al. Infect. Immun. 59(6):2075). | ||||||||||
| extract protocol | Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA). | ||||||||||
| label protocol | Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com. | ||||||||||
| hyb protocol | Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com. | ||||||||||
| scan protocol | Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com. | ||||||||||
| data processing | The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.). | ||||||||||
| value definition | RMA-normalized, averaged gene-level signal intensity | ||||||||||
| PLATFORM | |||||||||||
| title | BWH_Comstock_Bacteroides fragilis_4.3k array | ||||||||||
| technology | in situ oligonucleotide | ||||||||||
| distribution | custom-commercial | ||||||||||
| organism | Bacteroides fragilis NCTC 9343 | ||||||||||
| manufacturer | NimbleGen | ||||||||||
| manufacture protocol | High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/. | ||||||||||
| description | NimbleGen design name 2005-08-12_B_fragilis_24mer, NimbleGen design ID 2451. A 1:2 expression design for 4,302 genes from Bacteroides fragilis NCTC 9343 and associated plasmid pBF9343 with fourteen 24-mer probe pairs (PM/MM) per gene. Each probe is replicated 3 times. The design includes random GC and other control probes. | ||||||||||
| description | The Platform data table reflects a condensed representation of the expression array's replicate (SEQ_ID) features. The .ndf and .ngd files are linked below as supplementary files. | ||||||||||
| native array description file | 2005-08-12_B_fragilis_24mer.ndf | ||||||||||
| native array description file | 2005-08-12_B_fragilis_24mer.ngd | ||||||||||
| Platform file | GEO_Platform_file.txt | ||||||||||
| # Platform Column Definitions | |||||||||||
| ORF | Entrez locus_tag name of the ORF to which the indicated probe is directed. | ||||||||||
| GENE_ID | Entrez GeneID number for the ORF to which the indicated probe is directed. | ||||||||||
| GENOME_ACC | GenBank accession number of the Bacteroides fragilis NCTC 9343 chromosome or of the resident plasmid pBF9343. |
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| # This is a truncated Matrix worksheet for a NimbleGen gene expression submission based on an array not represented in GEO. | ||||||||||||||||||||||||||
| # Include Platform annotation columns (e.g., ID_REF, ORF, etc.) and processed Sample data (e.g., RMA-normalized signal intensities) used to draw the conclusions from your study. | ||||||||||||||||||||||||||
| # The ID_REF column must contain unique identifiers, e.g., from the SEQ_ID column of the .ngd file. | ||||||||||||||||||||||||||
| # The sample header names in the matrix must match the Sample name in the SAMPLES section of the Metadata file. | ||||||||||||||||||||||||||
| # Values that should be disregarded may either be left blank or labeled as "null". | ||||||||||||||||||||||||||
| ID_REF | ORF | GENE_ID | GENOME_ACC | Sample 1 | Sample 2 | Sample 3 | Sample 4 | Sample 5 | Sample 6 | |||||||||||||||||
| BFRAG050300004255 | pBF9343.01 | 3284946 | NC_006873 | 255.3262 | 183.142 | 378.5431 | 500.067 | 707.5409 | 470.4521 | |||||||||||||||||
| BFRAG050300004256 | pBF9343.02 | 3284935 | NC_006873 | 172.0598 | 135.7478 | 157.5338 | 230.0392 | 302.0056 | 173.5768 | |||||||||||||||||
| BFRAG050300004257 | pBF9343.03 | 3284904 | NC_006873 | 498.864 | 190.6291 | 455.7704 | 515.1519 | 965.7572 | 924.5740 | |||||||||||||||||
| BFRAG050300004258 | pBF9343.04 | 3284931 | NC_006873 | 848.6745 | 588.5652 | 956.8781 | 866.7193 | 1148.627 | 1154.7953 | |||||||||||||||||
| BFRAG050300004259 | pBF9343.05 | 3284918 | NC_006873 | 748.4699 | 464.9425 | 790.6603 | 928.6717 | 1171.4703 | 1144.1228 | |||||||||||||||||
| BFRAG050300004260 | pBF9343.06 | 3284924 | NC_006873 | 420.5154 | 240.9511 | 492.4178 | 474.6811 | 765.6066 | 566.2008 | |||||||||||||||||
| BFRAG050300004261 | pBF9343.07 | 3284900 | NC_006873 | 701.4152 | 355.5406 | 750.49 | 771.4772 | 1072.1554 | 765.4364 | |||||||||||||||||
| BFRAG050300004262 | pBF9343.08 | 3284901 | NC_006873 | 264.0158 | 241.6258 | 296.0301 | 309.0987 | 428.4496 | 312.4879 | |||||||||||||||||
| BFRAG050300004263 | pBF9343.09 | 3284943 | NC_006873 | 300.6331 | 207.4954 | 328.0974 | 533.5214 | 606.3881 | 445.8661 | |||||||||||||||||
| BFRAG050300004264 | pBF9343.10 | 3284923 | NC_006873 | 661.9359 | 492.7845 | 690.5916 | 855.7896 | 1056.799 | 912.8154 | |||||||||||||||||
| BFRAG050300004265 | pBF9343.11 | 3284899 | NC_006873 | 271.3373 | 117.5928 | 445.0274 | 487.0796 | 760.6274 | 829.4079 | |||||||||||||||||
| BFRAG050300004266 | pBF9343.12 | 3284934 | NC_006873 | 623.8344 | 381.0994 | 659.9505 | 867.3932 | 974.7184 | 856.5961 | |||||||||||||||||
| BFRAG050300004267 | pBF9343.13 | 3284920 | NC_006873 | 363.4182 | 218.1653 | 410.3016 | 629.1421 | 776.3666 | 748.5597 | |||||||||||||||||
| BFRAG050300004268 | pBF9343.14 | 3284929 | NC_006873 | 263.011 | 132.066 | 297.0464 | 341.1129 | 493.3506 | 514.0959 | |||||||||||||||||
| BFRAG050300004269 | pBF9343.15 | 3284932 | NC_006873 | 611.9013 | 294.5972 | 757.9686 | 732.5484 | 813.3563 | 778.8423 | |||||||||||||||||
| BFRAG050300004270 | pBF9343.16 | 3284939 | NC_006873 | 849.9622 | 421.0073 | 1079.5544 | 1095.5089 | 1322.6208 | 1589.6975 | |||||||||||||||||
| BFRAG050300004271 | pBF9343.17c | 3284915 | NC_006873 | 333.4997 | 232.627 | 451.9647 | 446.9815 | 559.5529 | 629.0124 | |||||||||||||||||
| BFRAG050300004272 | pBF9343.18c | 3284942 | NC_006873 | 141.1727 | 126.8155 | 191.6323 | 198.0268 | 270.7928 | 218.7605 | |||||||||||||||||
| BFRAG050300004273 | pBF9343.19c | 3284938 | NC_006873 | 136.9939 | 132.4228 | 196.2624 | 211.3621 | 223.1854 | 180.1972 | |||||||||||||||||
| BFRAG050300004274 | pBF9343.20c | 3284908 | NC_006873 | 722.4106 | 579.5368 | 1170.1295 | 1260.0654 | 1195.8899 | 1101.5036 | |||||||||||||||||
