Additional File 1:

promoter::GFP fusions Strain names, source and references for GFP reporters used to validate microarray data.

Format: XLS Size: 18KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 2:

Intensity Values Following Global Normalization (Affymetrix MAS 5.0) Raw intensity values were scaled against a global average intensity value calculated for each chip using Affymetrix MAS 5.0. Column A lists Affymetrix IDs for 22,548 features on the chip. These are indexed by rows with normalized intensity values for each independent hybridization and its Present/Absent (P/A) call. Columns labeled DMR 28, 30, 32, 34 include intensity values for hybridizations using RNA from all N2 (wildtype) cells. Columns labeled DM39, 51, 59 include the experimental hybridizations using RNA from FACS-isolated unc-4::GFP neurons.

Format: XLS Size: 5.3MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 3:

Intensity values after RMA normalization. Raw data from 2 were normalized with Robust Multi-array Analysis (RMA) (GeneTraffic, version 2.8) (Iobion). Normalized values are listed for the 22,548 features on the Affymetrix C. elegans chip. Affy IDs are listed in column A. Columns C-I show RMA normalized values for individual replicates. DMR 28, 30, 32, 34 are the baseline hybridizations using RNA from all N2 (wildtype) cells. DM39, 51, 59 are the experimental hybridizations using RNA from FACS-isolated unc-4::GFP neurons.

Format: XLS Size: 3.8MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 4:

N2 (wildtype) Expressed Genes (EGs) 9103 genes were called "Present" by MAS 5.0 in 3 out of 4 N2 hybridizations and are listed here as EGs. Affymetrix ID, Cosmid Name and common names (Columns A-C respectively) are given for each gene. Column D contains KOG descriptions and Column E indicates the dataset in which an individual gene is present.

Format: XLS Size: 960KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 5:

unc-4::GFP Present Genes 6828 genes were called "Present" by MAS 5.0 in 2 out of 3 unc-4::GFP hybridizations and are listed here.

Format: XLS Size: 746KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 6:

unc-4::GFP Present Genes minus N2 Enriched Genes The list of unc-4::GFP "present" calls in 5 is likely to include transcripts that are highly expressed in the small fraction of contaminating non-GFP cells (~10%). These transcripts were removed from the list of unc-4::GFP Present calls (5) by subtracting genes that are highly enriched in N2 cells (10). The balance of 6099 genes is listed here with Affy ID, Cosmid Name, Common Name and KOG description.

Format: XLS Size: 661KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 7:

unc-4::GFP Expressed Genes (EGs) RMA normalization ignores the MAS 5.0 P/A calls and therefore does not discard some of the "absent" genes that are excluded from 6 (unc-4::GFP Present Genes). As a result, the unc-4::GFP enriched genes (9) identified by SAM statistics actually includes 118 genes that are not listed in Additional Files 5 and 6. These 118 additional unc-4::GFP enriched genes were therefore restored to the list of unc-4::GFP Present Genes in 6 to provide a more accurate list of genes (6217) that are actually expressed in unc-4::GFP cells. These unc-4::GFP Expressed Genes (EGs) are listed with Affy ID, Cosmid Name, Common Name and KOG description.

Format: XLS Size: 682KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 8:

Expressed Genes (EGs) EGs from N2 (4) and from unc-4::GFP (7) cells were combined to detect a total of 10,071 unique EGs.

Format: XLS Size: 1.2MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 9:

unc-4::GFP Enriched Genes Transcripts elevated 1.7 fold above baseline at a False Discovery Rate (FDR) ≤1% were considered enriched. 1012 transcripts met these criteria and are listed according to statistical rank (Column A). Annotation includes Affy ID, Cosmid Name, Common Name and KOG description (Columns B-E); SAM score, Fold Change and q-value are listed (Columns F-H). We attribute the high ranking (2) of dpy-20 (T22B3.1) to its use as a coselectable marker in the generation of the unc-4::GFP transgenic line [104].

Format: XLS Size: 186KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 10:

N2 Enriched Genes 1586 genes are enriched 1.7 fold (FDR ≤1%) in N2 cells compared to unc-4::GFP neurons. These are listed according to statistical rank (Column A). Annotation includes Affy ID, Cosmid Name, Common Name and KOG description (Columns B-E); SAM score, Fold Change and q-value are listed (Columns F-H).

Format: XLS Size: 324KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 11:

Genes previously known to be expressed in unc-4::GFP neurons. Published literature and wormbase http://www.wormbase.org webcite were searched to identify 27 genes that are expressed in embryonic neurons that also express unc-4::GFP (I5, DA, SAB).

Format: XLS Size: 24KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 12:

unc-4::GFP motor neuron enriched genes with human homologs. 537 Enriched genes (9) and human genes listed here have BLAST scores ≤ e^-10.

Format: XLS Size: 251KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 13:

unc-4::GFP EGs with human homologs. 4050 Expressed genes (8) and human genes listed here have BLAST scores ≤ e^-10.

Format: XLS Size: 3.2MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 14:

Summary of unc-4::GFP enriched and expressed (EGs) transcripts in selected categories. This file is an expanded version of Table 2 (see text) in which EGs are added to the list of enriched genes. Genes are organized as in Table 2 according to molecular function (KOG description, other description http://www.wormbase.org webcite). Statistical rank is indicated for each enriched transcript and "EG" designates transcripts that are EGs.

Format: XLS Size: 84KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 15:

Genes Expressed only in unc-4::GFP neurons. Affy ID, Cosmid Name, Common Name and KOG description for 968 genes that are expressed in unc-4::GFP neurons. These genes are not detected in the reference (N2) dataset.

Format: XLS Size: 113KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional File 16:

Gene families represented in unc-4::GFP neurons. A comprehensive description of neuronal transcripts organized according to gene family.

Format: DOC Size: 316KB Download file

This file can be viewed with: Microsoft Word Viewer

Additional File 17:

Logic tree of data analysis methods.

Format: PDF Size: 2.9MB Download file

This file can be viewed with: Adobe Acrobat Reader