Complete profiles are deposited on the GEO website under super-series accession no. GSE9200 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9200).

Raw and normalized microarray expression data are available on the National Center for Biotechnology Information GEO Web site (http://www.ncbi.nih.gov/geo/) under the accession codes GSE3437 for the σ^E overexpression time course (37) and GSE6444 for all other microarray experiments.

Data deposition: The sequences reported in this paper have been deposited in the GEO database (accession no. GSE6708).

The microarray data have been deposited in GEO data bank with accession no.GSE5245.

Supplemental data describing the results of our GeneChip studies are deposited with GEO database at http://www.ncbi.nlm.nih.gov/geo/ (accession GSE4097).

Microarray data accession number. The complete microarray data set used in this study is available under accession number GSE5604 in the Gene Expression Omnibus database.

Microarray data accession numbers. The data discussed in this report have been deposited in the NCBI Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession numbers GSE6319, GSE6326, GSE6327, GSE6328, and GSE6331.

The raw data from all arrays are available online at http://www.ncbi.nlm.nih.gov/project/geo under series GSE6994.

Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE8573).

Microarray data performed in this study can be found in the National Center for Biotechnology Information Gene Expression Omnibus data library under accession number GSE5187.

The entire set of supporting microarray data is available at Gene Expression Omnibus (accession no. GSE7698).

Data deposition: Microarray data have been deposited in the Gene Expression Omnibus repository (accession no. GSE6010).

Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih/gov/geo (accession no. GSE7163).

Summary and raw microarray data are available from the GEO database⁷ (accession number GSE9544).

The data for these experiments have been deposited into the GEO database (accession no. GSE4826).

Data deposition. The CGH data from these experiments is deposited under accession number GSE7695, and transcriptomics data for the nonmotile Δfnr mutant are available under accession number GSE3591, in the gene expression omnibus (GEO) at the National Center for Biotechnology Information (http:www.ncbi.nlm.nih.gov/geo).

Microarray accession number. The transcriptome data have been deposited at http://www.ncbi.nlm.nih.gov/geo under accession number GSE5194.

Data deposition: The microarray data have been deposited in the Gene Expression Omnibus (GEO) Database, www.ncbi.nlm.nih.gov/geo (accession no. GSE10900).

Normalized log₂ ratios as well as raw data sets of this study have been deposited in the NCBI Gene Expression Omnibus (accession numbers GSE8737 and GPL5713).

All RSTs, site coordinates, and associated soil chemical properties were deposited in the Gene Expression Omnibus (GEO) database (10) of the National Center for Biotechnology Information. GEO was designed to hold gene expression data such as those generated by serial analysis of gene expression and microarray analysis, but it also accepts other forms of data such as those generated by SARST. GEO storage is helpful because most RST sequences are too short for GenBank submissions. Within GEO, SARST data are stored in platform GPL919, and the RST libraries from this study are entered in series GSE949. Corresponding sample accession numbers are Nadluardjuk Lake replicates (GSM14854 and GSM14855), Alert (GSM35149), Narrow Hills (GSM35162), Peace River (GSM35163), Montmorency (GSM35161) and Cape Dyer (GSM35159).

 Note not  gene expression microarray data

Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE7345).

The complete set of gene array data has been deposited in the National Center for Biotechnology Information Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under accession no. GSE2052, according to MIAME guidelines.

Compared to control cells (with scrambled siRNAs), global levels of gene expression were unaltered in knockdown cells (mean ratio of p75/PSIP1 siRNA expression to scrambled control expression = 0.96) (http://www.ncbi.nlm.nih.gov/geo/; accession no. GSE3485)

 Reuse.  Note it also includes references to beta-geo!

Prior data from earlier pancreas infiltrate samples (8) (GEO database accession no. GSE1419), was pooled and distilled together with newly generated pancreas samples prepared in parallel with the PLN and MLN samples generated for this study (GSE1419).

 reused their own work

Gene Expression Profiling. The gene expression data for results shown in Fig. 1A were obtained from the National Center for Biotechnology Information Gene Expression Omnibus (GEO; www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO series accession no. GSE4452 (20)

 Data by the same group, has another paper as the primary citation

Dye-coupled cDNAs were purified with a MiniElute PCR purification kit (QIAGEN) and hybridized to the National Cancer Institute in-house–printed oligonucleotide DNA spotted glass slides (Mouse Exotic Evidence Based Oligo­nucleotide [MEEBO] Set; Gene Expression Omnibus [GEO] accession number GPL4200).

 only the platform

Microarray Analysis. Log2-normalized intensities from all experiments were zero centered (Gene Expression Omnibus platform GPL-20) to create an adjusted intensity for the heat diagram, as shown by different colors (24)

 only the platform

PMC1475731

 refers only to GEO platform

All samples were run in duplicate on FHCRC murine 22K cDNA microarrays (GEO accession #GPL2931).

 only refers to the platform, didn't deposit their data

PMC1084298

ran own microarrays, didn't deposit (beta-geo)

We also analyzed two public (GEO) HeLa cDNA array data sets (GSM2145 and GSM2177; http://www.ncbi.nlm.nih.gov/geo/).

 Reused data, though also ran own microarray data

PMC140671

 No depositing.  beta-geo.

All data sets were downloaded from Gene Expression Omnibus (36) in MICROARRAY SUITE software, Version 5 preprocessed format, by using the accession numbers described in SI Table 4

 Reused data

Exemplary Data Analyses. Public data exemplifying clonal and metabolic disease were obtained from the Entrez Gene Expression Omnibus website (www.ncbi.nlm.nih.gov/geo) and were used to explore BPA in the context of additional real-world data, including an example of metabolic disease (accession no. GDS268, skeletal muscle from morbidly obese individuals) and cancer (accession no. GDS760, acute lymphoblastic leukemia). Analysis used eight microarrays per experimental group, chosen randomly in the GDS760 case.

 reuse

Microarray Data. To ensure that our results are not an artifact of how the microarray experiments were carried out, we used two independent datasets [retrieved from the Gene Expression Omnibus (www.ncbi.nih.gov/geo) and the SymAtlas web site (http://symatlas.gnf.org), Gene Expression Omnibus accession numbers GDS594, GDS596, and GSE740]

 Reused data

Microarray data are available in the National Center for Biotechnology Information Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) under accession nos. GSE85, GSE2585, and GSE3023.

 Reused data

Gene tree clustering revealed two major subtrees of genes whose transcript levels increased from 0 to 24 h (Figure 1c), which displayed nonrandom overlap (P = 0.011) with a subset of genes induced upon restoration of GATA-1 activity during differentiation of ESC-derived GATA-1-null G1E erythroid cells (NCBI GEO Accession Number GDS568).

 Must be reuse because the citation in the data submission doesn't match their names

The data set considered here is discussed in detail in Lan et al. (2006) and is available at GEO (Barrett et al. 2007), accession no. GSE3330.

 Reuse.

In addition, IRF5 expression values (probeset 205469_s_at) were obtained from a data set of 233 CEPH EBV-transformed B cell lines (16, 17) (GEO accession no. GSE1485).

 Reuse.

We analyzed a mice data set published by Lan et al. (2006). The data are publicly available at gene expression omnibus (GEO) with accession no. GSE3330.

 Reuse.

PMC2099627

 ran own microarray data but no sharing

Complete MAIME compliant microarray data is available from GEO (accession no. GSE8352 and NCBI tracking no. 15303196).

PMC154527

 own microarrays, but didn't deposit

PMC1140618

 did their own microarrays, but no mention of geo or omnibus

Gene profiles in SYT-SSX2–expressing cells repeatedly showed changes in the expression patterns of key proteins involved in cell cycle control, signal transduction, cytoskeletal organization, extracellular matrix components, and transcriptional regulation (Supplementary Tables 1 and 2; GEO Database Accession Nos. GSM180973 and GSM180974)

Microarray accession number. The microarray data determined in this study have been submitted to the Gene Expression Omnibus at the National Center for Biotechnology Information under series accession number GSE 7555.

Microarray data accession number. DNA microarray data were deposited in the Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo) under the series accession number GSE6289.

Microarray data accession number. The array data determined in this study have been submitted to the GEO data repository (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE5842.

Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE3751).

These data have been submitted to the Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information under series accession number GSE 6371.

PMC1592844

 GEO in a different context beta-geo, did generate microarray data

Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE5795).

PMC1895508

 Used data from GEO

The gene expression data are available at the GEO website under accession number GSE796: http://www.ncbi.nlm.nih.gov/geo/

Microarray data. The microarray data are accessible via GEO accession number GSE3657 at http://www.ncbi.nlm.nih.gov/geo.

Original data for the four expression profiles analyzed are available at the Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo) under accession numbers GSE1232 (light-adapted prors1-1 versus the wild type), GSE1233 (light-adapted prors1-2 versus the wild type), GSE1495 (dark-adapted prors1-1 versus the wild type), and GSE1496 (dark-adapted prors1-2 versus the wild type).

The microarray data were deposited in the Gene Expression Omnibus database at the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov/geo/; accession number GSE8319).

The complete array data are available from GEO (series record number GSE6143).

The microarray data were submitted to the Gene Expression Omnibus and are available under the accession numbers GSM88040 to GSM88042 (wild type of vfb mutant experiment), GSM88046 to GSM88048 (vfb mutant), GSM88055 to GSM88057 (wild type of csn4 experiment), and GSM88049 to GSM88051 (csn4 mutant).

PMC2245850

 No mention of GEO or omnibus, discussed their previous microarray results, beta-geo

p53 conditional knockout mouse aCGH data are under submission at the GEO database, accession number GSE7794. Gene expression data are deposited at the Arrayexpress database accession number E-NCMF-6, details are in the Supplementary Data.

Sequence data from this article have been deposited in the National Center for Biotechnology Information's Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) and are accessible through the GEO Series accession number GSE5806

MA Suite 5.0 expression values have been submitted to the Gene Expression Omnibus (accession no. GSE9338)

The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) and are accessible through GEO Series accession number GSE5249. It can also be accessed at our web site (http://www.ciwemb.edu/brownlab/index.html).

Results from two separate types of tissues and from the five and seven independent donors were clearly separated in the first and second principal component and are uploaded in the Gene Expression Omnibus Repository (GEO accession no. GSE7224)

Data Deposition. The microarray data have been deposited in the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo) (accession no. GSE5428).

Microarray data are available online at NCBI Gene Expression Omnibus (http://www. ncbi.nlm.nih.gov/geo/) accession no. GSE934.

Microarray data accession numbers. Raw microarray data have been deposited into the National Center for Biotechnology Information Gene Expression Omnibus database at http://www.ncbi.nlm.nih.gov/geo under series accession number GSE4681.