We have also compiled these data in a MISFISHIE-compliant format. This is available for both human or mouse experiments, and may be viewed or downloaded via the links below:

• View human data. Download as zip archive of TSV or CSV files.
• View mouse data. Download as zip archive of TSV or CSV files.

In addition, you can download a summary of the staining for various species and cell types directly as a tab-delimited text file.

You may also download all of the IHC images of either human or mouse tissue, or the entire collection as zip archives. Please note that these are large files (between 73 and 659 MB) containing many individual images. The files are named systematically based on the antibody used in staining, the organism, tissue type, tissue block, and magnification. As an example, the file 'CD44 98-395F HP ba 100.jpg' was stained with CD44, is from tissue block 98-395F, is human prostate tissue, and is shot at 100X magnification.

Cytometry Data

The Magnetic and Flow Cytometry data associated with specimens, used in the immunohistochemistry study, can be found in the SBEAMS - Cytommetry database module. Most of the individual Cytometry experiments are linked to the source specimen in the Immunostain database and vice versa. The Cytometry Samples are named systematically based on the specimen, tissue type, sort technique and sort entity. As an example, the sample '99-395p_M_CD44_F_Hoechst' indicates that the prostate (p) tissue specimen '99-395' was first magnetically (M) sorted with 'CD44' and subsequently flow (F) sorted using 'Hoechst' dye.

Cytometry Data Access

Microarray Data

Affymetrix array analysis of prostate cancer cell lines

These experiments were done using Affymetrix chip HG-U133_Plus_2; various data types are available for download. The CEL file is the raw data from the array scan, the RPT file holds the statistical analysis of the chip signal, the XML file is a MAGE-ML description of the experiment, and the Image file is a jpg image of the chip itself. Depending on your browser settings, you may have to select 'save link to disk' in order to save the file rather than having your browser open it for all but the CEL file.

• Data from LNCaP (androgen-dependent) replicate 1 ( CEL   RPT   XML   Image   ).
• Data from LNCaP (androgen-dependent) replicate 2 ( CEL   RPT   XML   Image   ).
• Data from C4-2 (androgen-independent) replicate 1 ( CEL   RPT   XML   Image   ).
• Data from C4-2 (androgen-independent) replicate 2 ( CEL   RPT   XML   Image   ).

Affymetrix array analysis of sorted primary prostate cells

Primary prostate tissue was collagen-digested and the constituent cells were subjected to magnetic activated cell sorting (MACS) based on information from the CD marker survey experiments. The enriched populations were then analyzed using Affymetrix chip HG-U133_Plus_2, typically with 5 biological replicates. A paper describing this work has been accepted for publication, entitled "Transcriptomes of Human Prostate Cells". The raw data can be downloaded by individual cell population or as a single zip archive via the links below. This data can also be searched via the SCGAP consortium portal. Below is a list of CD markers that were used in this experiment, and the cell types for which they are believed to enrich.

MPSS analysis of prostate cancer cell lines

The following results are from MPSS (Massively parallel signature sequencing) experiments on the LNCaP and C4-2 cell lines. This work was published as a paper entitled "Application of Affymetrix array and Massively Parallel Signature Sequencing for identification of genes involved in prostate cancer progression", which can be found here. Data may be downloaded as an excel spreadsheet for each cell type, containing the accession number and experimentally detected TPM (transcripts per million) for each analyzed sequence.

• LNCaP (androgen-dependent) Excel   data.
• C4-2 (androgen-independent) Excel   data.

MPSS vs Affymetrix analysis of prostate cancer cell lines

The following results are a comparison of MPSS and Affymetrix data from LNCaP and C4-2 cell lines. Data may be downloaded as an excel spreadsheet, which contains both transcripts per million (TPM) from MPSS and normalized fluorescent signal from Affymetrix.

• Merged MPSS and Affymetrix data for C4-2 and LNCaP cell lines(Excel).

ISB Human 40k cDNA microarray slide design

• MAGE-ML document (3.5 MB gzipped file).
• Tab-delimited text (2.5 MB gzipped file).

Limited Access Data

Links to datasets for which access is limited and requires authentication are posted here. Please contact Eric Deutsch if you would like to request access to these data.

Two-color microarray Data

The microarray data associated with this NIDDK SCGAP project are currently split between several different SBEAMS projects. Here are links to them (username and password required):