title: Dose 300, KO, PP, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_293_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 100, KO, PP, biological replicate 2

status: Public on Sep 01 2016

type: RNA

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

country: USA

institute: Scitovation, LLC.

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_272_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

hyb_protocol: 1.6ug of labeled cDNA was added to Gene Titan Hybridization Cocktail formulation for 3’ Array plates (Affymetrix, Santa Clara, CA) as described in appendix VI of the Ovation® PicoSL WTA system V2 user manual (Nugen, San Carlos, CA).  Finally, the samples were hybridized onto a HT RG-230 PM Array Plate (96 or 16 plate, Affymetrix) and analyzed using the Gene Titan microarray system (Affymetrix) according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan array scanner to generate CEL files with corresponding intensity values.

data_processing: Affymetrix CEL files were normalized by RMA using Partek Genomic's Suite 6.6

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: Dose 100, KO, PP

label_protocol: The RNA was amplified to cDNA using the Ovation Pico WTA system V2 (Nugen, San Carlos, CA) and purified using a QIAquick PCR Purification kit (Qiagen) according to the manufacturer’s protocol.  The cDNA was quantified using a nanodrop (model ND-1000, ThermoFisher Scientific, Waltham, MA).  5ug of each sample was biotin-labeled using the Encore Biotin Module (Nugen) according to the manufacturer’s protocol.

growth_protocol: Adult male Sprague-Dawley rats purchased from Charles Rivers Laboratories, Inc (Raleigh, NC).  Animals kept in a humidity- and temperature-controlled, HEPA-filtered, mass air-displacement room.  The room maintained on a 12-hr light-dark cycle (7 AM – 7 PM) at approximately 68-79°F with a relative humidity of approximately 30-70%. All animals allowed access to NIH-07 standard diet and reverse osmosis water ad libitum.

extract_protocol: A 4 mm by 10 mm section from the center of the left liver lobe will be collected,preserved in O.C.T. compound, frozen on dry ice and stored at -80°C.  12micron thick slices were sectioned from the preserved tissue using a cryostat and placed onto membrane slides.  The sections were immediately fixed and stained using the following steps

treatment_protocol: Animals 1 – 56 will be weighed and vehicle or chemical treatment will be administered by oral gavage for 4 days.  No other procedures will be performed on these animals until day 5.  On day 5 (24 hr after the final dose), animals will be euthanized by isoflurane anesthesia and exsanguination.  Doses

tag: strain

value: Sprague-Dawley

tag: cell type

value: Periportal (PP) Hepatocyte

tag: genotype/variation

value: AHR-Knock-out (KO)

tag: agent

value: TCDD

tag: dose

value: 100 ng/kg/day

tag: exposure time

value: 28 days

tag: animal id


title: Dose 100, KO, PP, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_276_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: HBL1 shcIAP1/2 - 4 days - mAdbID:129701

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 129701

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 2 Scan_MicronsPerPixelY: 2 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

organism: Homo sapiens

source_name: HBL1 shControl - 4 days

label_protocol:
Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol:
TRIzol Extraction Protocol
Other: Total RNA was prepared by the TRIzol method (Invitrogen) and purified using RNeasy Mini columns (Qiagen).

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 4 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 4 days.

tag: cell line

value: ABC DLBCL cells

tag: disease state

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: HBL1 shcIAP1/2 - 4 days

label_protocol:
Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 4 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shcIAP1 and shcIAP2. shRNA expression was induced with doxycycline for 4 days.


title: TMD8 shcIAP1/2 - 4 days - mAdbID:129699

description: mAdb experiment ID: 129699

source_name: TMD8 shControl - 4 days

source_name: TMD8 shcIAP1/2 - 4 days


title: HBL1 shcIAP1/2 - 3 days - mAdbID:129700

description: mAdb experiment ID: 129700

source_name: HBL1 shControl - 3 days

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 3 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 3 days.

source_name: HBL1 shcIAP1/2 - 3 days

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 3 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shcIAP1 and shcIAP2. shRNA expression was induced with doxycycline for 3 days.


title: Dose 100, KO, PP, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_273_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: hMSC-TERT4 at day 13, rep2

city: Sydney

first: Natalie

last: Twine

address: High Street, Kensington

country: Australia

institute: University of New South Wales

description: replicate 2

hyb_protocol: Hybridization, washing, Cy3-streptavidin staining and scanning were performed on the Illumina BeadStation 500 platform (Illumina) according to the manufacturer’s instruction.

data_processing: Raw data were normalized using the quantile normalisation and then filtered for significant expression on the basis of negative control beads. A p-value of < 0.01 was used as a cut-off for detection of significance.

source_name: hMSC-TERT4 at day 13 post OB induction

label_protocol: 500 ng of total RNA from each sample was used for biotin-labeled cRNA production using a linear amplification kit (Ambion).

growth_protocol: hMSC-TERT4 cells were used as a model for primary hMSC. hMSC-TERT cells were routinely cultured in standard media (MEM) with 10% v/v FBS.

extract_protocol: At days 0, 1, 7 and 13 after induction of osteoblast differentiation total RNA was extracted using highly purified total cellular RNA was isolated using an RNeasy Kit (QIAGEN Nordic, West Sussex, UK)

treatment_protocol: Ex vivo osteoblast differentiation in hMSC-TERT4 cells was performed using osteoblast induction medium containing containing β-glycerophosphate (10mM), L-ascorbic acid-2-phosphate (50µg/ml), dexamathasone (10nM) and calcitriol (10nM) in standard medium (SM). Media were changed every 3 days until day 15.


title: hMSC-TERT4 at day 7, rep3

description: replicate 3

scan_protocol: Hybridization, washing, Cy3-streptavidin staining and scanning were performed on the Illumina BeadStation 500 platform (Illumina) according to the manufacturer’s instruction.

source_name: hMSC-TERT4 at day 7 post OB induction


title: hMSC-TERT4 at day 13, rep3

description: replicate 3


title: hMSC-TERT4 at day 13, rep1

description: replicate 1


title: hMSC-TERT4 at day 7, rep2

description: replicate 2


title: Dose 100, KO, PP, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_271_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: hMSC-TERT4 at day 1, rep3

description: replicate 3

source_name: hMSC-TERT4 at day 1 post OB induction


title: TMD8 shcIAP1/2 - 3 days - mAdbID:129698

description: mAdb experiment ID: 129698

source_name: TMD8 shControl - 3 days

source_name: TMD8 shcIAP1/2 - 3 days


title: Dose 22, KO, PP, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_257_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 22, KO, PP

value: 22 ng/kg/day


title: Dose 22, KO, PP, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_256_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: hMSC-TERT4 at day 1, rep2

description: replicate 2


title: hMSC-TERT4 at day 0, rep2

description: replicate 2

source_name: hMSC-TERT4 at day 0 post OB induction


title: Dose 22, KO, PP, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_258_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 22, KO, PP, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_259_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: hMSC-TERT4 at day 7, rep1

description: replicate 1


title: hMSC-TERT4 at day 0, rep3

description: replicate 3


title: SHIV_BD66_Tonsil

city: Cleveland

first: Rafick

last: Pierre-Sekaly

state: OH

address: 2103 Cornell Avenue

department: Pathology

institute: Case Western Reserve University

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

label: Biotin

organism: Macaca mulatta

source_name: Tonsil

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: 24 outbred, Indian-origin female rhesus monkeys (Macaca mulatta) were genotyped and selected as negative for the protective MHC class I alleles Mamu-A*01, Mamu-B*08, and Mamu-B*17.  TRIM5 polymorphisms were balanced equally among groups, and animals were otherwise randomly allocated.  All monkeys were housed at Bioqual, Rockville, MD

extract_protocol: Plasma SIV RNA levels were measured using a gag targeted quantitative real-time RT-PCR assay, and tissue levels of SIV RNA and DNA were measured using gag targeted, nested quantitative hybrid real time/digital RT-PCR and PCR assays. SIV Gag-specific cellular immune responses in blood and tissues were assessed by multiparameter ICS assays.  9-color ICS assays were performed with predetermined titers of mAbs against CD3 (SP34; Alexa700), CD4 (L200; AmCyan), CD8 (SK1; allophycocyanin-cyanine 7 [APC-Cy7]), CD28 (L293; peridinin chlorophyll-A-cyanine 5.5 [PerCP-Cy5.5]), CD95 (DX2; phycoerythrin [PE]), CD69 (TP1.55.3; phycoerythrin-Texas Red [energy coupled dye; ECD]; Beckman Coulter), IFN-γ (B27; phycoerythrin-cyanine 7 [PE-Cy7]), IL-2 (MQ1-17H12; allophycocyanin [APC]) and TNF-α (Mab11; fluorescein isothiocya [FITC]). IFN-γ backgrounds were consistently <0.01% in PBMC and <0.05% in tissues

treatment_protocol: Animals received 2 mg/kg PGT121 or an isotype matched sham control antibody DEN3 by the intravenous route on day -1 and were infected with 5x104 TCID50 of our SHIV-SF162P3 stock by the intravaginal route on day 0.  Animals were necropsied on day 1, 3, 7, or 10 following infection, and multiple samples of 30 independent tissues were obtained for virologic, immunologic, and transcriptomic analyses.  12 additional rhesus monkeys were utilized for the initial PGT121 protection study, and 3 additional rhesus monkeys were utilized for the adoptive transfer study.  All animal studies were approved by the appropriate Institutional Animal Care and Use Committee (IACUC).

tag: subject

tag: label

tag: tissue

value: Tonsil

tag: viral status

tag: treatment

tag: timepoint

tag: barcode


title: hMSC-TERT4 at day 0, rep1

description: replicate 1


title: hMSC-TERT4 at day 1, rep1

description: replicate 1


title: Dose 22, KO, PP, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_254_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 22, KO, PP, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_253_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 22, KO, PP, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_251_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_CP20_Duodenum

source_name: Duodenum

value: Duodenum (GI)

value: Negative


title: SHIV_MKO_ileocecal

source_name: ileocecal

value: MKO

value: ileocecal (LN)


title: Dose 22, KO, PP, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_252_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_PL9_genital_pelvic

value: genital_pelvic (LN)

value: Positive


title: SHIV_CP20_ileocecal


title: SHIV_MKO_PBMC

source_name: PBMC

value: PBMC (Blood)


title: Dose 3, KO, PP, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_239_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 3, KO, PP

value: Sprague-Dawley

value: 3 ng/kg/day


title: Dose 3, KO, PP, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_238_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Periportal (PP) Hepatocyte

value: AHR-Knock-out (KO)


title: Dose 3, KO, PP, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_237_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: TCDD


title: SHIV_CP20_Splenocytes

source_name: Splenocytes

value: Splenocytes


title: SHIV_E41_Uterus

source_name: Uterus

value: Uterus (FRT)


title: SHIV_CP20_Tonsil


title: SHIV_MKO_PBMC_pre_challenge


title: SHIV_BD66_Duodenum


title: SHIV_E41_Splenocytes


title: Dose 3, KO, PP, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_234_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: 28 days


title: Dose 3, KO, PP, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_236_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_BD66_PBMC


title: SHIV_MKO_Sacral

source_name: Sacral

value: Sacral (LN)


title: SHIV_CP20_mesenteric

source_name: mesenteric

value: mesenteric (LN)


title: SHIV_BD66_mesenteric


title: SHIV_E41_Tonsil

value: Tonsil


title: Dose 3, KO, PP, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_232_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_MKO_mesenteric

value: Negative


title: SHIV_BD66_pararectal_paracolonic


title: Dose 0, KO, PP, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_220_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 0, KO, PP

value: control

value: 0 ng/kg/day


title: SHIV_MKO_Splenocytes

value: MKO


title: SHIV_E41_Cecum

source_name: Cecum

value: Cecum (GI)


title: SHIV_E41_mesenteric


title: Dose 3, KO, PP, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_233_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_PL9_Thymus

source_name: Thymus

value: Thymus


title: Dose 3, KO, PP, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_231_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Sprague-Dawley


title: Dose 0, KO, PP, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_219_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 0, KO, PP, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_213_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_BE34_Inguinal

source_name: Inguinal

value: Inguinal (LN)


title: SHIV_PL9_Bone_Marrow


title: SHIV_BE34_Uterus

value: Positive


title: Dose 0, KO, PP, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_212_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Periportal (PP) Hepatocyte

value: AHR-Knock-out (KO)


title: SHIV_E41_Bone_Marrow


title: SHIV_MKO_Lung

source_name: Lung

value: Lung


title: SHIV_CP20_axillary

source_name: axillary

value: axillary (LN)


title: SHIV_BE34_PBMC_pre_challenge


title: SHIV_BE34_Tonsil


title: SHIV_CP20_Rectum

source_name: Rectum

value: Rectum (GI)


title: SHIV_BE34_Thymus


title: Dose 0, KO, PP, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_214_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: 28 days


title: Dose 1000, WT, CV, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_119_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 1000, WT, CV

value: Centrilobular (CV) Hepatocyte

value: Wild type (WT)

value: TCDD

value: 1000 ng/kg/day


title: SHIV_MKO_Duodenum

value: Duodenum (GI)

value: Negative


title: Dose 0, KO, PP, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_17_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: control

value: 0 ng/kg/day


title: SHIV_MKO_Bone_Marrow

value: MKO


title: Dose 1000, WT, CV, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_118_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Sprague-Dawley


title: SHIV_MKO_genital_pelvic

value: genital_pelvic (LN)


title: Dose 0, KO, PP, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_211_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Periportal (PP) Hepatocyte


title: SHIV_CP20_Colon

source_name: Colon

value: Colon (GI)


title: Dose 1000, WT, CV, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_117_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_BE34_Duodenum

source_name: Duodenum


title: SHIV_MKO_Inguinal

value: Inguinal (LN)


title: SHIV_PL9_pararectal_paracolonic


title: SHIV_BE34_Cervix

source_name: Cervix

value: Cervix (FRT)

value: Positive


title: SHIV_CP20_Ileum

source_name: Ileum

value: Ileum (GI)


title: SHIV_BD66_Mid_Vagina

value: Mid_Vagina (FRT)


title: SHIV_E41_Ileum


title: Dose 0, KO, PP, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_216_KO_PP
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: AHR-Knock-out (KO)

value: 28 days


title: Dose 1000, WT, CV, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_116_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Centrilobular (CV) Hepatocyte

value: Wild type (WT)

value: TCDD

value: 1000 ng/kg/day


title: SHIV_BD66_Sacral

value: Sacral (LN)


title: SHIV_BE34_Jejunum

source_name: Jejunum

value: Jejunum (GI)

value: Negative


title: SHIV_BE34_axillary

value: axillary (LN)


title: SHIV_MKO_Liver

source_name: Liver

value: MKO

value: Liver


title: Dose 1000, WT, CV, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_113_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Sprague-Dawley


title: SHIV_PL9_Mid_Vagina


title: SHIV_E41_pararectal_paracolonic


title: Dose 1000, WT, CV, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_112_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_E41_Mid_Vagina


title: SHIV_PL9_Cervix

value: Cervix (FRT)


title: SHIV_E41_Rectum

value: Rectum (GI)


title: Dose 1000, WT, CV, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_111_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_BD66_Cervix

value: Positive


title: Dose 1000, WT, CV, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_114_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_CP20_Thymus

value: Thymus


title: Dose 300, WT, CV, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_99_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 300, WT, CV

value: 300 ng/kg/day


title: SHIV_PL9_Sacral

source_name: Sacral


title: SHIV_BE34_Ileum

value: Ileum (GI)


title: Dose 300, WT, CV, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_97_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Centrilobular (CV) Hepatocyte

value: 28 days


title: SHIV_PL9_PBMC_pre_challenge


title: SHIV_E41_axillary


title: SHIV_BE34_Cecum

value: Cecum (GI)


title: Dose 300, WT, CV, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_98_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Wild type (WT)

value: TCDD


title: SHIV_BD66_Jejunum

value: Jejunum (GI)


title: Dose 300, WT, CV, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_96_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 300, WT, CV, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_94_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 300, WT, CV, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_92_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 300, WT, CV, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_93_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_PL9_Colon

value: Colon (GI)


title: SHIV_BE34_PBMC

source_name: PBMC

value: PBMC (Blood)


title: SHIV_MKO_Cecum

value: MKO

value: Negative


title: SHIV_BE34_genital_pelvic

value: genital_pelvic (LN)


title: SHIV_CP20_Cervix

value: Cervix (FRT)


title: SHIV_PL9_Ileum


title: SHIV_BE34_Rectum

value: Rectum (GI)


title: SHIV_E41_ileocecal

source_name: ileocecal

value: ileocecal (LN)


title: Dose 300, WT, CV, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_91_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Sprague-Dawley


title: SHIV_E41_Sacral

value: Sacral (LN)


title: Dose 100, WT, CV, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_77_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 100, WT, CV

value: 100 ng/kg/day


title: Dose 100, WT, CV, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_79_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Centrilobular (CV) Hepatocyte


title: Dose 100, WT, CV, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_76_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: 28 days


title: SHIV_E41_Cervix

value: Positive


title: SHIV_MKO_axillary

value: axillary (LN)


title: SHIV_BE34_ileocecal


title: SHIV_E41_Colon


title: Dose 100, WT, CV, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_78_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Wild type (WT)

value: TCDD


title: SHIV_E41_Jejunum

value: Jejunum (GI)


title: SHIV_BE34_Colon

value: Colon (GI)


title: SHIV_PL9_ileocecal


title: Dose 100, WT, CV, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_75_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 100, WT, CV, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_71_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_BE34_Splenocytes

source_name: Splenocytes

value: Splenocytes


title: SHIV_BD66_Colon

value: Negative


title: SHIV_E41_genital_pelvic

value: genital_pelvic (LN)


title: SHIV_E41_Lung

value: Lung


title: SHIV_MKO_pararectal_paracolonic

value: MKO


title: Dose 100, WT, CV, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_73_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 100, WT, CV, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_72_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 22, WT, CV, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_59_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 22, WT, CV

value: 22 ng/kg/day


title: SHIV_MKO_Rectum

value: Rectum (GI)


title: SHIV_CP20_Sacral

value: Sacral (LN)


title: SHIV_MKO_Thymus

source_name: Thymus

value: Thymus


title: SHIV_CP20_Cecum

source_name: Cecum

value: Cecum (GI)


title: SHIV_E41_PBMC

value: PBMC (Blood)


title: SHIV_PL9_Lung

source_name: Lung


title: SHIV_CP20_Jejunum


title: Dose 22, WT, CV, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_58_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Sprague-Dawley

value: Centrilobular (CV) Hepatocyte

value: 28 days


title: SHIV_BD66_Rectum

source_name: Rectum

value: Positive


title: Dose 22, WT, CV, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_56_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Wild type (WT)

value: TCDD


title: SHIV_BE34_pararectal_paracolonic


title: SHIV_BD66_Ileum

value: Ileum (GI)


title: Dose 22, WT, CV, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_54_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_BD66_Cecum

value: Negative


title: Dose 22, WT, CV, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_53_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_BD66_axillary

source_name: axillary

value: axillary (LN)


title: SHIV_BE34_Lung

value: Lung


title: SHIV_MKO_Tonsil

source_name: Tonsil

value: MKO

value: Tonsil


title: SHIV_CP20_PBMC_pre_challenge


title: SHIV_MKO_Jejunum

value: Jejunum (GI)


title: SHIV_PL9_PBMC


title: SHIV_PL9_Jejunum


title: Dose 22, WT, CV, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_51_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: 22 ng/kg/day


title: Dose 3, WT, CV, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_38_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 3, WT, CV

value: 3 ng/kg/day


title: SHIV_BE34_Sacral

value: Sacral (LN)


title: Dose 22, WT, CV, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_57_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 3, WT, CV, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_37_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_CP20_pararectal_paracolonic


title: SHIV_MKO_Uterus

source_name: Uterus

value: Uterus (FRT)


title: SHIV_PL9_Rectum

value: Rectum (GI)


title: SHIV_PL9_Liver

value: Liver


title: SHIV_CP20_Lung


title: Dose 22, WT, CV, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_52_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Sprague-Dawley

value: Centrilobular (CV) Hepatocyte

value: 28 days


title: SHIV_E41_Liver


title: Dose 3, WT, CV, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_36_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Wild type (WT)

value: TCDD


title: Dose 3, WT, CV, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_39_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_PL9_Duodenum

source_name: Duodenum

value: Duodenum (GI)

value: Positive


title: Dose 3, WT, CV, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_34_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_PL9_Cecum

value: Cecum (GI)


title: Dose 3, WT, CV, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_32_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_MKO_Ileum

source_name: Ileum

value: MKO

value: Ileum (GI)

value: Negative


title: SHIV_E41_Thymus

value: Thymus


title: SHIV_E41_Inguinal

source_name: Inguinal

value: Inguinal (LN)


title: SHIV_PL9_mesenteric

source_name: mesenteric

value: mesenteric (LN)


title: SHIV_MKO_Colon

source_name: Colon

value: Colon (GI)


title: Dose 3, WT, CV, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_31r_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: 3 ng/kg/day


title: SHIV_BD66_Bone_Marrow


title: SHIV_BD66_Uterus

value: Uterus (FRT)


title: SHIV_E41_PBMC_pre_challenge


title: SHIV_PL9_Inguinal


title: Dose 3, WT, CV, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_3_33_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Sprague-Dawley


title: SHIV_BD66_Splenocytes

value: Splenocytes


title: SHIV_MKO_Cervix

source_name: Cervix

value: Cervix (FRT)


title: Dose 0, WT, CV, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_18_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 0, WT, CV

value: Centrilobular (CV) Hepatocyte

value: Wild type (WT)

value: control

value: 0 ng/kg/day

value: 28 days


title: SHIV_BD66_Liver

source_name: Liver

value: Liver


title: CD44+ HuH7

city: Yonago

first: Tomohiko

last: Sakabe

state: Tottori

address: Nishi-cho 86

country: Japan

institute: Tottori University

hyb_protocol: Fragmented RNA was hybridized on the Oligo chip for 16 hour at 37˚C.

scan_protocol: Human Oligo chip was scanned by a ProScanArray scanner.

data_processing: To generate the normalized data, the raw signal intensity were subtracted with the Background mean and normalized to the value in which the median intensity was 25.

source_name: CSC

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (thermo fisher scientific). CyeDye coupling was performed according to the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA was extracted with TRIzol Reagent

value: CD44+ HuH7


title: SHIV_BE34_Liver


title: Dose 0, WT, CV, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_14_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_CP20_Liver


title: SHIV_CP20_Bone_Marrow


title: SHIV_PL9_Tonsil

value: Tonsil


title: Dose 0, WT, CV, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_13_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_BD66_genital_pelvic

value: genital_pelvic (LN)

value: Positive


title: Dose 0, WT, CV, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_17_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 0, WT, CV, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_12_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_CP20_PBMC

source_name: PBMC

value: PBMC (Blood)


title: CD44- HuH7

source_name: non-CSC

value: CD44- HuH7


title: SHIV_BD66_Inguinal

value: Inguinal (LN)

value: Negative


title: SHIV_PL9_axillary

value: axillary (LN)


title: hNHeps

source_name: Normal

value: human normal hepatocytes


title: SHIV_CP20_genital_pelvic


title: SHIV_BD66_ileocecal

source_name: ileocecal

value: ileocecal (LN)


title: Dose 0, WT, CV, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_16_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Sprague-Dawley

value: Centrilobular (CV) Hepatocyte


title: SHIV_BE34_Bone_Marrow


title: SHIV_BD66_Thymus

source_name: Thymus

value: Thymus


title: SHIV_CP20_Inguinal


title: Dose 0, WT, CV, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_11r_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Wild type (WT)

value: control

value: 0 ng/kg/day


title: SHIV_BD66_PBMC_pre_challenge


title: SHIV_BD66_Lung

source_name: Lung

value: Lung


title: SHIV_CP20_Uterus

value: Uterus (FRT)


title: Dose 1000, KO, CV, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_319_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 1000, KO, CV

value: AHR-Knock-out (KO)

value: TCDD

value: 1000 ng/kg/day

value: 28 days


title: Dose 1000, KO, CV, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_318_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_BE34_mesenteric

value: mesenteric (LN)


title: Dose 1000, KO, CV, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_317_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_AY96_Duodenum

value: Duodenum (GI)

value: Negative


title: SHIV_AY96_Liver

value: Liver


title: SHIV_BB90_Colon

value: Colon (GI)


title: SHIV_BD04_mesenteric

value: Positive


title: SHIV_AY96_Rectum

source_name: Rectum

value: Rectum (GI)


title: SHIV_PL9_Splenocytes

source_name: Splenocytes

value: Splenocytes


title: SHIV_AY56_Liver


title: Dose 1000, KO, CV, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_311_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Sprague-Dawley

value: Centrilobular (CV) Hepatocyte


title: Dose 1000, KO, CV, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_314_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_AY56_Rectum


title: SHIV_BB90_PBMC

value: PBMC (Blood)


title: SHIV_BB60_ileocecal

value: ileocecal (LN)


title: SHIV_BD04_Tonsil

source_name: Tonsil

value: Tonsil


title: Dose 1000, KO, CV, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_313_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: AHR-Knock-out (KO)


title: Dose 1000, KO, CV, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_316_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: TCDD


title: SHIV_BC64_Thymus

value: Thymus


title: SHIV_BD04_genital_pelvic

value: genital_pelvic (LN)


title: Dose 300, KO, CV, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_299_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 300, KO, CV

value: 300 ng/kg/day

value: 28 days


title: Human intestinal epithelial cells: Control vs. MIC-1 Transfected

city: Yangsan

first: YUSEOK

last: MOON

state: (Select)

address: Rm 704 PNU Med School

country: South Korea

institute: PUSAN NATIONAL UNIV. med school

description: HCT vs. MIC-1 overepxression HCT-8 cells

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: HCT-8 intestinal epithelial cells

label_protocol: 2 µg of total RNA were primed with 2 µl of 100 µM random primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3(Cy5)-labeled dCTP

growth_protocol: 10% FBS 1% P/S RPMI media

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: protocol

value: control

source_name: HCT-8 MIC-1 transfected intestinal epithelial cells

value: MIC-1 overepxression


title: SHIV_AY56_Cecum

source_name: Cecum

value: Cecum (GI)

value: Negative


title: Dose 1000, KO, CV, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_1000_312_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

tag: strain

value: 1000 ng/kg/day


title: SHIV_BC64_Mid_Vagina

value: Mid_Vagina (FRT)

value: Positive


title: SHIV_AY56_PBMC_pre_challenge


title: SHIV_BC64_pararectal_paracolonic


title: Dose 300, KO, CV, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_296_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Sprague-Dawley

tag: cell type

value: Centrilobular (CV) Hepatocyte


title: SHIV_AY96_Thymus


title: Dose 100, KO, CV, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_279_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 100, KO, CV

tag: genotype/variation

value: 100 ng/kg/day


title: SHIV_BC64_Splenocytes

value: Splenocytes


title: Dose 300, KO, CV, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_294_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: AHR-Knock-out (KO)

tag: agent


title: SHIV_AY96_Inguinal

source_name: Inguinal

value: Inguinal (LN)


title: Dose 300, KO, CV, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_298_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: TCDD

tag: dose


title: SHIV_BD04_Cervix

source_name: Cervix

value: Cervix (FRT)


title: SHIV_AY56_Thymus

value: Thymus


title: SHIV_BD04_PBMC_pre_challenge


title: Dose 300, KO, CV, biological replicate 1

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_282_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: 300 ng/kg/day

tag: exposure time

value: 28 days


title: SHIV_BC64_Brain_lymphocytes


title: Dose 300, KO, CV, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_293_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

tag: animal id


title: Dose 300, KO, CV, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_297_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_AY96_Lung

value: Lung


title: SHIV_AY96_ileocecal

value: ileocecal (LN)


title: SHIV_AY96_axillary

source_name: axillary

value: axillary (LN)

value: Negative


title: SHIV_BB60_genital_pelvic

value: genital_pelvic (LN)


title: SHIV_BC64_Inguinal

value: Positive


title: SHIV_BB60_Colon

source_name: Colon

value: Colon (GI)


title: Dose 300, KO, CV, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_300_291_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Sprague-Dawley

value: Centrilobular (CV) Hepatocyte


title: SHIV_AY56_Uterus

source_name: Uterus

value: Uterus (FRT)


title: SHIV_AY56_ileocecal

source_name: ileocecal


title: SHIV_AY96_Tonsil

value: Tonsil


title: SHIV_BB60_Liver

source_name: Liver

value: Liver


title: Dose 100, KO, CV, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_277_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: AHR-Knock-out (KO)

value: TCDD

value: 100 ng/kg/day


title: Dose 100, KO, CV, biological replicate 7

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_278_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_BB60_PBMC_pre_challenge


title: Dose 100, KO, CV, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_274_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: SHIV_AY96_Ileum

source_name: Ileum

value: Ileum (GI)


title: SHIV_AY96_Cervix

value: Cervix (FRT)


title: SHIV_BB60_pararectal_paracolonic


title: SHIV_BB60_Cervix


title: Dose 0, WT, CV, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_0_19_WT_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 0, WT, CV

value: Wild type (WT)

value: control

value: 0 ng/kg/day

value: 28 days


title: Dose 22, KO, CV, biological replicate 8

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_259_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

source_name: Dose 22, KO, CV

value: 22 ng/kg/day


title: SHIV_AY96_Sacral

source_name: Sacral

value: Sacral (LN)

value: Negative


title: Dose 100, KO, CV, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_276_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Sprague-Dawley


title: SHIV_AY96_mesenteric

source_name: mesenteric

value: mesenteric (LN)


title: SHIV_AY96_Uterus

value: Uterus (FRT)


title: Dose 100, KO, CV, biological replicate 2

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_272_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Centrilobular (CV) Hepatocyte


title: SHIV_BC64_ileocecal

value: ileocecal (LN)

value: Positive


title: SHIV_AY96_genital_pelvic

value: genital_pelvic (LN)


title: SHIV_BB60_PBMC

source_name: PBMC

value: PBMC (Blood)


title: Dose 100, KO, CV, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_100_273_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: AHR-Knock-out (KO)

value: TCDD

value: 100 ng/kg/day


title: SHIV_AY56_Lung

source_name: Lung

value: Lung


title: SHIV_BB60_Splenocytes

source_name: Splenocytes

value: Splenocytes


title: SHIV_BD04_Thymus

source_name: Thymus

value: Thymus


title: SHIV_BD04_Rectum

source_name: Rectum

value: Rectum (GI)


title: SHIV_AY56_pararectal_paracolonic


title: SHIV_AY56_Bone_Marrow


title: Dose 22, KO, CV, biological replicate 5

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_256_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: 22 ng/kg/day

value: 28 days


title: SHIV_AY56_Sacral

value: Sacral (LN)

value: Negative


title: SHIV_BD04_Uterus

value: Uterus (FRT)


title: Dose 22, KO, CV, biological replicate 4

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_254n_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).

value: Sprague-Dawley

value: Centrilobular (CV) Hepatocyte


title: SHIV_AY56_mesenteric

value: mesenteric (LN)


title: Dose 22, KO, CV, biological replicate 3

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_253_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).


title: Dose 22, KO, CV, biological replicate 6

description:
Gene Expression data from rat livers, laser dissected for discrete periportal or central lobular cellular populations
Laser capture micro-dissection sample
BP_22_257_KO_CV
Description of "animal id" suffixes: n = indicates a sample where the initial NuGen amplification did not produce a suitable array scan and fresh total RNA was isolated from Laser Capture Micro-dissection tissue to produce a new sample for NuGen amplification, labeling and array scanning; r = refers to a re-scanned Titan array starting from the original labeled RNA when there was an issue with the initial scan (often a bubble or some such artifact).