Trim32 expression in rat eye tissue

Browse datasets

datamonger:scheetz2006@1 · Registry 1.2.0. Default version in this registry.

Prepared from the authors' GSE5680 processed RMA expression matrix. Contains 120 F2 rats from an SR/JrHsd x SHRSP intercross, with 18,985 expression predictors and response y (Trim32 probe 1389163_at). Retains GEO numeric precision, sample identifiers, and source sample and probe order, without additional normalization or imputation. After excluding 57 AFFX controls, selection keeps probes whose maximum exceeds the global first quartile and whose range is at least one on the log2 scale, following the paper's rule at full precision. This retains 10 predictors beyond Iowa's rounded export. sample_id is metadata excluded from model features. Added gene annotations and experimental controls are omitted.

Dimensions and tasks

Task

Type

Split

Samples

Predictors

default

regression

—

120

18,985

Predictor counts follow each task's feature selection and exclude targets and identifiers. Sample counts are reported separately for each split.

Retrieve

These examples pin both the dataset version and the registry's exact index. An uncached dataset requires network access to its source. The CLI retrieves verified artifacts. The language clients also decode them.

Python

from datamonger import Registry, fetch_data

registry = Registry(
    release="1.2.0",
    index_sha256="4b4e6aeb71ad7e53c3596a725e62008c76c27a59ac68c53a02432898ec8b6f21",
    index_url="https://github.com/jolars/datamonger/releases/download/registry-v1.2.0/index.json",
)
data = fetch_data("datamonger:scheetz2006@1", registry=registry)

R

library(datamonger)

registry <- registry_selector(
  release = "1.2.0",
  index_sha256 = "4b4e6aeb71ad7e53c3596a725e62008c76c27a59ac68c53a02432898ec8b6f21",
  index_url = "https://github.com/jolars/datamonger/releases/download/registry-v1.2.0/index.json"
)
data <- fetch_data("datamonger:scheetz2006@1", registry = registry)

Julia

using Datamonger

registry = registry_selector(
    "1.2.0",
    "4b4e6aeb71ad7e53c3596a725e62008c76c27a59ac68c53a02432898ec8b6f21",
    "https://github.com/jolars/datamonger/releases/download/registry-v1.2.0/index.json",
)
data = fetch_data("datamonger:scheetz2006@1"; registry=registry)

CLI

cat > datamonger-registry.json <<'JSON'
{
  "index_sha256": "4b4e6aeb71ad7e53c3596a725e62008c76c27a59ac68c53a02432898ec8b6f21",
  "index_url": "https://github.com/jolars/datamonger/releases/download/registry-v1.2.0/index.json",
  "release": "1.2.0",
  "schema_version": 1
}
JSON
datamonger --selector datamonger-registry.json fetch 'datamonger:scheetz2006@1'

Representation and variables

Tabular data with a dense representation. Decoder: delimited-text version 1.

Component

Kind

Type

Shape

sample_id

vector

string

120

1367458_at

vector

float64

120

1367462_at

vector

float64

120

1367467_at

vector

float64

120

1367468_at

vector

float64

120

1367474_at

vector

float64

120

1367478_at

vector

float64

120

1367484_at

vector

float64

120

1367491_at

vector

float64

120

1367494_at

vector

float64

120

1367495_at

vector

float64

120

1367498_at

vector

float64

120

1367499_at

vector

float64

120

1367501_at

vector

float64

120

1367502_at

vector

float64

120

1367505_at

vector

float64

120

1367508_at

vector

float64

120

1367515_at

vector

float64

120

1367517_at

vector

float64

120

1367521_at

vector

float64

120

1367526_at

vector

float64

120

1367527_at

vector

float64

120

1367530_at

vector

float64

120

1367534_at

vector

float64

120

1367537_at

vector

float64

120

1367539_at

vector

float64

120

1367540_at

vector

float64

120

1367541_at

vector

float64

120

1367542_at

vector

float64

120

1367544_at

vector

float64

120

Showing 30 of 18,987 components. The complete registry record contains every variable name and task binding.

Preprocessing

Preprocessing history is not recorded in this registry release.

Provenance and citation

Provider: Datamonger; derived from Scheetz et al. at NCBI GEO. Upstream name: Expression data for an eQTL experiment in rat eye. Retrieved: 2026-10-16.

Original source

Authors: Todd E. Scheetz, Kwang-Youn A. Kim, Ruth E. Swiderski, Alisdair R. Philp, Terry A. Braun, Kevin L. Knudtson, Anne M. Dorrance, Gerald F. DiBona, Jian Huang, Thomas L. Casavant, Val C. Sheffield, Edwin M. Stone.

Scheetz TE, Kim K-YA, Swiderski RE, Philp AR, Braun TA, Knudtson KL, Dorrance AM, DiBona GF, Huang J, Casavant TL, Sheffield VC, and Stone EM (2006). Regulation of gene expression in the mammalian eye and its relevance to eye disease. PNAS 103:14429-14434. https://doi.org/10.1073/pnas.0602562103. GEO accession GSE5680.

License

Known (see terms)

License information

GEO places no restrictions on use or distribution of submitted data, while warning that submitters may retain intellectual property rights. No additional data-specific restriction was found in GSE5680 or its sample records. This review treats GEO's source terms as the redistribution basis for this numeric extract, retaining attribution. No SPDX license or public-domain dedication is inferred. Iowa's RDS, code, and added annotations are not preparation inputs.

Artifacts

Total download: 18.5 MiB. Sizes describe the distributed files, including any compression.

Artifact

Format

Compression

Size

Distribution

Preservation

data

csv

gzip

18.5 MiB

mirror

durable

data: mirror

Preservation deposit

Versions in this registry

1 (default)

Registry record

Download the complete registry record, registry selector, or full registry index.

Index SHA-256: 4b4e6aeb71ad7e53c3596a725e62008c76c27a59ac68c53a02432898ec8b6f21.