title: Dose 100, 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_100_271_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


title: SHIV_BD04_axillary

status: Public on Sep 01 2016

type: RNA

city: Cleveland

first: Rafick

last: Pierre-Sekaly

state: OH

address: 2103 Cornell Avenue

department: Pathology

country: USA

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

molecule: total RNA

organism: Macaca mulatta

source_name: axillary

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: axillary (LN)

tag: viral status

value: Negative

tag: treatment

tag: timepoint

tag: barcode


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

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

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_22_251_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).

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

organism: Rattus norvegicus

source_name: Dose 22, KO, CV

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: Centrilobular (CV) Hepatocyte

tag: genotype/variation

value: AHR-Knock-out (KO)

tag: agent

value: TCDD

tag: dose

value: 22 ng/kg/day

tag: exposure time

value: 28 days

tag: animal id


title: Dose 22, 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_22_258_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_BC64_PBMC_pre_challenge


title: SHIV_AY56_Splenocytes

source_name: Splenocytes

value: Splenocytes


title: Dose 3, 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_3_239_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 3, KO, CV

value: 3 ng/kg/day


title: Dose 22, 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_22_252_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_Ileum

source_name: Ileum

value: Ileum (GI)


title: SHIV_BD04_Colon

source_name: Colon

value: Colon (GI)


title: SHIV_BC64_Rectum

source_name: Rectum

value: Rectum (GI)

value: Positive


title: Dose 3, 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_3_236_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 3, 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_3_237_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_BB90_axillary


title: SHIV_BB60_Mid_Vagina

value: Mid_Vagina (FRT)


title: Dose 3, 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_3_238_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_Splenocytes


title: SHIV_BB90_Thymus

source_name: Thymus

value: Thymus


title: Dose 3, 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_3_234_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_BD04_pararectal_paracolonic


title: SHIV_AY56_axillary


title: SHIV_BD04_Liver

source_name: Liver

value: Liver


title: SHIV_BB60_Jejunum

source_name: Jejunum

value: Jejunum (GI)


title: SHIV_BC64_Colon


title: SHIV_BC64_genital_pelvic

value: genital_pelvic (LN)


title: SHIV_BB90_Uterus

source_name: Uterus

value: Uterus (FRT)

value: Negative


title: Dose 3, 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_3_233_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

value: AHR-Knock-out (KO)


title: SHIV_BB90_Inguinal

source_name: Inguinal

value: Inguinal (LN)


title: SHIV_BB90_PBMC_pre_challenge


title: Dose 0, 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_0_216_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 0, KO, CV

value: control

value: 0 ng/kg/day

value: 28 days


title: SHIV_BB60_Duodenum

source_name: Duodenum

value: Duodenum (GI)


title: SHIV_AY96_PBMC_pre_challenge


title: SHIV_BB90_Liver


title: SHIV_BC64_Sacral

source_name: Sacral

value: Sacral (LN)


title: SHIV_AY96_Bone_Marrow


title: Dose 3, 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_3_231_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

value: 3 ng/kg/day


title: Dose 3, 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_3_232r_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_Ileum

value: Ileum (GI)


title: Dose 0, 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_0_220_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_BB90_Bone_Marrow


title: SHIV_AY96_pararectal_paracolonic


title: Dose 0, 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_0_219_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_Cecum

source_name: Cecum

value: Cecum (GI)


title: SHIV_BB90_Duodenum


title: SHIV_BB60_Inguinal


title: SHIV_BB60_Sacral


title: Dose 0, 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_0_214_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_Jejunum

value: Jejunum (GI)


title: SHIV_BB60_Lung

source_name: Lung

value: Lung


title: SHIV_BB60_mesenteric

source_name: mesenteric

value: mesenteric (LN)


title: SHIV_AY56_PBMC

source_name: PBMC

value: PBMC (Blood)


title: SHIV_BB60_Cecum

value: Negative


title: Dose 0, 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_0_211_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_BB90_genital_pelvic

value: genital_pelvic (LN)


title: Dose 0, 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_0_213_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: control


title: Dose 0, 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_0_17_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: 0 ng/kg/day

value: 28 days


title: SHIV_AY96_PBMC


title: SHIV_BB90_mesenteric


title: SHIV_BD04_Cecum


title: SHIV_BD04_Inguinal

value: Inguinal (LN)


title: SHIV_BC64_Cecum

value: Positive


title: SHIV_AY56_Jejunum


title: SHIV_BD04_Jejunum


title: SHIV_BC64_mesenteric


title: siZNF25 hMSC-TERT4 at day 14, rep2

city: Sydney

first: Natalie

last: Twine

address: High Street, Kensington

country: Australia

institute: University of New South Wales

hyb_protocol: Following fragmentation, 3ug of biotin labelled ss-cDNA is hybridised for 16 hours at 45C on the HuGene 2.0 ST array. Arrays were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: Arrays  were scanned using an Affymetrix GCS 3000 7G scanner.

data_processing: Data was analysed using the Partek Genomics Suite version 6.6, RMA was used to normalise the data

organism: Homo sapiens

source_name: hMSC_TERT4 cells

label_protocol: 500ng of total RNA from each sample was used for biotin-labelled cRNA

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 and days 14 after induction of osteoblast differentiation total RNA was extracted using TRIzol

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.

tag: cell line

tag: transfection

value: siZNF25, at day 14 post OB induction


title: SHIV_BC64_PBMC


title: SHIV_BB90_Lung


title: control hMSC-TERT4 at day 14, rep1

value: control siRNA, at day 14 post OB induction


title: SHIV_BD04_Splenocytes

source_name: Splenocytes

value: Splenocytes


title: SHIV_AY56_Mid_Vagina

value: Mid_Vagina (FRT)


title: control hMSC-TERT4 at day 14, rep2


title: SHIV_BC64_Bone_Marrow


title: SHIV_BD04_Sacral

value: Sacral (LN)


title: siZNF25 hMSC-TERT4 at day 14, rep3


title: control hMSC-TERT4 at day 0, rep3

value: control siRNA, at day 0 post OB induction


title: SHIV_BC64_Tonsil

source_name: Tonsil

value: Tonsil


title: SHIV_BC64_axillary

source_name: axillary

value: axillary (LN)


title: control hMSC-TERT4 at day 14, rep3


title: SHIV_AY56_Tonsil


title: SHIV_AY56_Duodenum

value: Duodenum (GI)

value: Negative


title: siZNF25 hMSC-TERT4 at day 14, rep1


title: control hMSC-TERT4 at day 0, rep2


title: SHIV_BC64_Ileum

source_name: Ileum

value: Ileum (GI)


title: SHIV_AY56_Cervix

source_name: Cervix

value: Cervix (FRT)


title: control hMSC-TERT4 at day 0, rep1


title: siZNF25 hMSC-TERT4 at day 0, rep1

value: siZNF25, at day 0 post OB induction


title: SHIV_AY56_Colon

source_name: Colon

value: Colon (GI)


title: SHIV_BB60_Rectum

source_name: Rectum

value: Rectum (GI)


title: SHIV_BB90_Sacral


title: SHIV_AY96_Colon


title: siZNF25 hMSC-TERT4 at day 0, rep3


title: SHIV_BB60_Thymus

source_name: Thymus

value: Thymus


title: SHIV_BB60_axillary


title: SHIV_BB60_Tonsil


title: siGLS on stiff matrix, biological replicate 3

city: Nice

first: Thomas

last: BERTERO

address: 28 Av de Valombrose

department: Medical School

country: France

institute: IRCAN, Nice CNRS UMR 7284 - INSERM U1081 - UNS

description: Gene expression data from PAEC transfected with siGLS stiff

hyb_protocol: Following fragmentation, 41 ul of cDNA were hybridized for 16hr at 45 C on the GeneChip Human 2.0 ST Array in an Affymetrix GeneChip Hybridization Oven 645; GeneChips were washed and stained I nthe Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G running affymetrix Gene Command Console ver 3.2

data_processing: The data were analyzed using Affymetrix Expression Console ver 1.3.0.187 via the RMA algorithm

source_name: PAEC siGLS on stiff matrix

label_protocol: Biotinylated cDNA were prepared from 100ng total RNA (WT Plus amplification kit) according to the standard Affymetrix protocol

growth_protocol: PAECs were cultivated in EGM2 (Lonza) on soft (1kPa) or sttiff (50kPa) hydrogel (Matrigen)

extract_protocol: Qiazol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: PAECs were transfected with 10nM of on Target Plus siRNA control (siNC) or siGLS (Dhermacon)

value: pulmonary arterial endothelial cells


title: siGLS on soft matrix, biological replicate 3

description: Gene expression data from PAEC transfected with siGLS soft

source_name: PAEC siGLS on soft matrix


title: siZNF25 hMSC-TERT4 at day 0, rep2


title: SHIV_BB90_Ileum


title: SHIV_BB60_Brain_lymphocytes


title: SHIV_BC64_Jejunum

source_name: Jejunum

value: Jejunum (GI)


title: SHIV_BD04_Ileum


title: SHIV_BB60_Bone_Marrow


title: SHIV_BD04_Lung

value: Lung


title: siNC on stiff matrix, biological replicate 3

description: Gene expression data from PAEC transfected with siNC stiff

source_name: PAEC siNC on stiff matrix


title: SHIV_BC64_Cervix

value: Positive


title: SHIV_BB90_ileocecal

source_name: ileocecal

value: ileocecal (LN)


title: siNC on soft matrix, biological replicate 3

description: Gene expression data from PAEC transfected with siNC soft

source_name: PAEC siNC on soft matrix


title: SHIV_AY56_genital_pelvic

value: genital_pelvic (LN)


title: siGLS on stiff matrix, biological replicate 2


title: Dose 0, 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_0_212_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 0, KO, CV

value: Sprague-Dawley

value: Centrilobular (CV) Hepatocyte

value: AHR-Knock-out (KO)

value: control

value: 0 ng/kg/day

value: 28 days


title: SHIV_BB90_Rectum

value: Negative


title: siNC on stiff matrix, biological replicate 2


title: SHIV_BB90_Tonsil

value: Tonsil


title: siGLS on soft matrix, biological replicate 2


title: SHIV_BB90_Cervix

value: Cervix (FRT)


title: siGLS on stiff matrix, biological replicate 1


title: SHIV_BB90_Cecum

source_name: Cecum

value: Cecum (GI)


title: SHIV_BC64_Uterus

source_name: Uterus

value: Uterus (FRT)


title: SHIV_BC64_Liver

source_name: Liver

value: Liver


title: siNC on stiff matrix, biological replicate 1

value: pulmonary arterial endothelial cells


title: SHIV_BB90_Splenocytes

source_name: Splenocytes

value: Splenocytes


title: SHIV_BB90_Mid_Vagina

value: Mid_Vagina (FRT)

value: Positive


title: siNC on soft matrix, biological replicate 2


title: SHIV_BD04_Duodenum

source_name: Duodenum

value: Duodenum (GI)


title: SHIV_BD04_Bone_Marrow


title: SHIV_BB90_Jejunum

value: Jejunum (GI)


title: SHIV_BB90_pararectal_paracolonic


title: SHIV_BD04_PBMC

source_name: PBMC

value: PBMC (Blood)


title: SHIV_BD04_ileocecal

value: ileocecal (LN)


title: siGLS on soft matrix, biological replicate 1


title: SHIV_AY56_Inguinal

source_name: Inguinal

value: Inguinal (LN)


title: SHIV_BC64_Duodenum


title: SHIV_BC64_Lung

source_name: Lung

value: Lung


title: siNC on soft matrix, biological replicate 1


title: S13

city: Memphis

first: Satya

last: Vemula

state: TN

address: 855 Monroe Avenue, Suite 415 Link Building

department: Neurology

institute: University of Tennessee Health Science Center

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 2.0 ST Arrays (Affymetrix) and scanned at the UTHSC Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Expression console and transcriptome analysis console v3.0. Data was further analyzed using Genespring to identify probsets that were significantly dysregulated at p<0.05

organism: Mus musculus

source_name: KO Female Mouse

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA from mouse cerebellum was isolated from 6 adult (10 mo) Ciz1/mice (3 males and 3 females) and 6 age and gender matched Ciz1+/+ controls (AmbionTM TRI Reagent®, ThermoFisher Scientific).

tag: Sex

value: Female

value: Cerebellum


title: S15


title: S14


title: NHDF treated with conditioned medium from SKBR-3 rep3

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol using an Illumina BeadArray reader.

data_processing: Raw data were log2 transformed and normalized with robust spline normalization using the lumi package from Bioconductor.

source_name: NHDF treated with conditioned medium from SkBr3

label_protocol: Three hundred ng of total RNA were reverse-transcribed, labeled with biotin and amplified overnight with the Illumina RNA TotalPrep Amplification kit by Ambion according to manufacturer’s instructions.

growth_protocol: Human breast cancer cell lines, cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 5% fetal bovine serum (T47D) or with 10% fetal bovine serum (MDA-MB-468) or in McCoy’s medium supplemented with 10% fetal bovine serum (SkBr3), were used to stimulate the normal human fibroblast cell line NHDF cultured in Fibroblast Basal Medium (FBM) supplemented with Fibroblast Growth Medium-2 (FGM-2) Bullet kit containing 2% fetal bovine serum (FBS), 0.1% Insulin, 0.1% GA 1000, 0.1% FGF. All cell lines were cultured at 37 °C in 95% humidified air in the presence of 5% CO2.

extract_protocol: Total RNA was extracted from treated NHDF cells using QIAzol reagent followed by a clean-up treatment with the RNeasy Mini kit by Qiagen according to manufacturer’s recommendations to remove contaminating genomic DNA. RNA integrity and purity were assessed by Bioanalyzer and concentration was evaluated using a NanoDrop 2000c spectrophotometer.

treatment_protocol: Conditioned media (c.m.) were collected from breast cancer cell lines (SkBr3, MDA-MB-468, T47D) separately plated (1.65x10^6cells) in F25 cm2 flasks, in DMEM F/12 5% FBS/FBM 2% FBS (1:1). After cell attachment, the medium was replaced with 7 mL of serum-free MIX medium and collected at 72 hours. After collection, media were clarified by centrifugation (1,400 x g for 3 minutes). Conditioned media produced by SkBr3, MDA-MB-468, T47D were used for the treatment (72 h) of NHDF (NAF) plated in 6-wells plate at a density of 750,000 cells.

value: NHDF

value: normal human dermal fibroblasts

tag: conditioned medium


title: NHDF control cultured in McCoy conditioned medium rep1


title: S11

source_name: KO Male Mouse

value: Male


title: NHDF treated with conditioned medium from MDA468 rep3

source_name: NHDF treated with conditioned medium from MDA-MB-468


title: NHDF control cultured in McCoy conditioned medium rep2


title: NHDF control cultured in DMEM conditioned medium rep1


title: S10


title: S9


title: S7

source_name: Wild Type Female Mouse


title: NHDF control cultured in DMEM conditioned medium rep2


title: NHDF treated with conditioned medium from SKBR-3 rep2


title: S6


title: NHDF control cultured in DMEM conditioned medium rep3


title: NHDF treated with conditioned medium from MDA468 rep2


title: NHDF treated with conditioned medium from SKBR-3 rep1


title: NHDF treated with conditioned medium from T47D rep3


title: NHDF control cultured in McCoy conditioned medium rep3


title: S5


title: NHDF treated with conditioned medium from MDA468 rep1


title: S4

source_name: Wild Type Male Mouse


title: NHDF treated with conditioned medium from T47D rep1


title: GSK8815 rep4

city: Cambridge

first: KA HING

last: CHE

state: Cambridgeshire

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

description: 20 µM

hyb_protocol: Sample processed according to the protocol of Cambridge Genome Service

data_processing: R Bioconductor lumi package

source_name: LNCaP cell

growth_protocol: RPMI 1640 + 10% Fetal Calf Serum

extract_protocol: Qiagen Rneasy Kit

treatment_protocol: Compounds treated for 24 hours

value: LNCaP


title: GSK8815 rep3

description: 20 µM

scan_protocol: Sample processed according to the protocol of Cambridge Genome Service


title: GSK8815 rep1

description: 20 µM

label_protocol: Sample processed according to the protocol of Cambridge Genome Service


title: GSK8815 rep2

description: 20 µM


title: S2


title: GSK8814 rep4

description: 20 µM


title: GSK8814 rep3

description: 20 µM


title: DMSO rep4

value: DMSO


title: S1


title: BMDM infected 24h WT rep3

city: Seattle

first: Ryan

last: McMahan

state: WA

address: 850 Republican, S-320

institute: University of Washington

hyb_protocol: Affymetrix standard protocol

scan_protocol: GeneChip Operating System (GCOS)

data_processing: RMA algorithm with quantile normalization and background correction

source_name: BMDM

label_protocol: Affymetrix standard protocol

growth_protocol: Bone marrow cells were differentiated to macrophages by 7 days of culture in RPMI media supplemented with 10% FBS and 20% conditioned media from L929 cells.

extract_protocol: TRIzol extraction followed by cleanup with RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: BMDM that had been exposed only to standard culture medium for 7 days were designated as M0, and basal expression levels were determined using RNA from these cells. For post-infection transcriptional analysis, M0 cells were exposed to P. aeruginosa strain K at an MOI of 5:1 for 1 h, after which infection media was aspirated, and cells were rinsed twice with PBS. The cells were then cultured in medium containing 75 μg/ml gentamicin, 100 IU/ml penicillin, and 100 μg/ml streptomycin, until RNA was collected at 6 h or  24 h after the end of the infection period.

value: bone marrow

value: macrophages

tag: genotype

value: WT


title: GSK8814 rep1

description: 20 µM


title: DMSO rep3


title: NHDF treated with conditioned medium from T47D rep2


title: DMSO rep2


title: DMSO rep1


title: GLD4 knockdown 3

city: Philadelphia

first: Bin

last: Tian

state: PA

address: 3601 Spruce Street

institute: the wistar institute

description: siGLD4 replicate 3

hyb_protocol: hybridization for 18hours at 58C

scan_protocol: BeadArray reader from illumina

data_processing: A project was created with scan data imported into genomestudio 1.0 (illumina) arrays normalized to the 50th percentile, and individual genes normalized to the median of controls.

source_name: human primary fibroblasts_GLD4 knockdown

label_protocol: biotinylation using Total Prep Amplification kit from ambion

growth_protocol: human primary fibroblasts were culture in DMEM media supplemented with 10% FBS and 1% AA

extract_protocol: RNA was extracted with TRIzol, followed by poly(U) chromatography and Rneasy mini kit (qiagen)

treatment_protocol: Cells were transfected with siRNA (Dharmacon) with DharmafectI

value: human primary fibroblasts

tag: treated with

value: siRNA targeting GLD4


title: Jurkat-76 cell line

city: Leiden

first: Marieke

last: Griffioen

address: Albinusdreef 2

department: Hematology

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized in R

source_name: Cell line from human acute T cell leukemia

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amp kit for Illumina arrays

extract_protocol: RNA was extracted with Ambion RNAqueous isolation kit, followed by DNase I treatment and clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: tissue

value: peripheral blood


title: BMDM infected 24h MMP10KO rep3


title: FB 5852B

source_name: Fibroblasts cultured from a skin derived biopsy in DMEM with low glucose

value: skin

value: Fibroblasts

tag: protocol


title: BMDM infected 24h MMP10KO rep1


title: GLD4 knockdown 1

description: siGLD4 replicate 1


title: GSK8814 rep2

description: 20 µM

tag: treatment


title: BMDM infected 6h MMP10KO rep2


title: BMDM infected 6h MMP10KO rep3


title: Raji cell line

source_name: Cell line from human Burkitt's lymphoma

value: lymphoblast

value: Raji


title: Jurkat cell line 02

value: Jurkat


title: BMDM infected 24h WT rep1


title: BMDM infected 24h MMP10KO rep2


title: BMDM infected 24h WT rep2


title: FB 5852B + T-cell sup

source_name: Fibroblasts cultured from a skin derived biopsy in DMEM with low glucose, cultured with T cell culture supernatant


title: control replicate 2

description: siNT replicate 2

source_name: human primary fibroblasts_control

value: non-targeting siRNA


title: control replicate 3

description: siNT replicate 3


title: GLD4 knockdown 2

description: siGLD4 replicate 2


title: control replicate 1

description: siNT replicate 1


title: Daudi cell line

value: Daudi


title: BMDM untreated MMP10KO rep3


title: BMDM infected 6h MMP10KO rep1


title: BMDM untreated MMP10KO rep1


title: BEC 01

source_name: Intrahepatic biliary epithelial cells isolated from liver

value: bile duct

value: Intrahepatic biliary epithelial cells

value: isolated from liver


title: FB 4766B + T-cell sup

value: cultured from a skin derived biopsy in DMEM with low glucose, cultured with T cell culture supernatant


title: BMDM infected 6h WT rep2

value: bone marrow


title: Jurkat cell line 01


title: HUVEC 01

source_name: Umbilical vein endothelial cells isolated from umbilical cords and cultured in EGM-2 bullit kit supplemented EGM-2 medium

value: umbilical cord

value: Umbilical vein endothelial cells


title: HUVEC 01 + IFN-γ

source_name: Umbilical vein endothelial cells isolated from umbilical cords and cultured in EGM-2 bullit kit supplemented EGM-2 medium and IFN-γ (100 IU/mL) for 4 days


title: Cornea Epithelium 02

source_name: Cornea epithelial cells isolated from cornea and cultured in CnT-20 medium

value: eye

value: Cornea epithelial cells


title: FB 4766B

value: cultured from a skin derived biopsy in DMEM with low glucose


title: BMDM untreated MMP10KO rep2

value: macrophages


title: AML-193 cell line

source_name: Cell line from human acute monocytic leukemia

value: peripheral blood


title: BMDM infected 6h WT rep1

value: WT


title: K562 cell line 02

source_name: Cell line from human chronic myelogenous leukemia


title: BMDM untreated WT rep1


title: BEC 02


title: BMDM untreated WT rep3


title: THP-1 cell line


title: Cornea Stroma 01

source_name: Cornea stroma cells isolated from cornea and cultured in DMEM/HAM-F12

value: Cornea stroma cells


title: Cornea Stroma 03

value: isolated from cornea and cultured in DMEM/HAM-F12


title: Cornea Epithelium 01

value: isolated from cornea and cultured in CnT-20 medium


title: K562 cell line 01


title: HUVEC 02 + IFN-γ

value: isolated from umbilical cords and cultured in EGM-2 bullit kit supplemented EGM-2 medium and IFN-γ (100 IU/mL) for 4 days


title: BMDM infected 6h WT rep3


title: BMDM untreated WT rep2


title: Cornea Stroma 02


title: T2 cell line

source_name: A somatic cell hybrid of human B- and T-lymphoblastoid cell lines


title: HUVEC 03

value: isolated from umbilical cords and cultured in EGM-2 bullit kit supplemented EGM-2 medium


title: PHA-T 2877B

source_name: PHA-T blasts generated by stimulating PBMC with IL-2 and PHA

value: PHA-T blasts


title: AML 4781 (CD33/CD14pos)

source_name: Acute myeloid leukemia cells isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 and CD14 surface expression

value: Acute myeloid leukemia cells


title: AML 2536 (CD33)

source_name: Acute myeloid leukemia cells isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 surface expression


title: MM 5019 (CD38)

source_name: Multiple myeloma cells isolated from samples with >30% plasma cells (range 30-95%) based on CD38 surface expression

value: Multiple myeloma cells


title: MM 6622 (CD38)

value: bone marrow

value: isolated from samples with >30% plasma cells (range 30-95%) based on CD38 surface expression


title: BMMC 650

source_name: Mononuclear cells isolated from bone marrow after Ficoll-Isopaque separation

value: Mononuclear cells


title: GWAT LDLR -/- HFSC, replicate 4

city: Vienna

last: Stulnig

address: Waehringer Guertel 18-20

department: Christian Doppler Laboratory for Cardio-Metabolic Immunotherapy and Clinical Division of Endocrinology and Metabolism, Department of Medicine III

country: Austria

institute: Medical University of Vienna

description:
GWAT Gene expression data from a LDLR KO mouse placed at 9 weeks of age for up to 20 weeks on HFSC
SAMPLE 31

hyb_protocol: Affymetrix GeneChip® Mouse Gene 2.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

source_name: GWAT_LDLR -/- mouse placed at 9 weeks of age for up to 20 weeks on HFSC

label_protocol: 200ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Catalog Number 902281, Affymetrix, Santa Clara, CA)

growth_protocol: At 9 weeks of age WT were placed on HFD  and Ldlr-/- mice were placed on HFSC, both for up to 20 weeks. Their respective controls were kept on NC for up to 20 weeks.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Described above (growth protocol)

tag: strain background

value: LDLR-/-; LDLR KO

tag: diet

value: Sucrose enriched high fat diet (HFSC)

value: gonadal white adipose tissue (GWAT)


title: GWAT LDLR -/- HFSC, replicate 6

description:
GWAT Gene expression data from a LDLR KO mouse placed at 9 weeks of age for up to 20 weeks on HFSC
SAMPLE 33


title: AML 3097 (CD33)

tag: cell type

value: isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 surface expression


title: Macrophage type-1 5932

source_name: Type I macrophages cultured from CD14 isolated monocytes with GM-CSF for 7 days

value: peripheral blood

value: Type I macrophages


title: HUVEC 02

value: umbilical cord

value: Umbilical vein endothelial cells


title: Macrophage type-2 5932

source_name: Type 2 macrophages cultured from CD14 isolated monocytes with M-CSF for 7 days

value: Type 2 macrophages


title: GWAT LDLR -/- HFSC, replicate 1

description:
GWAT Gene expression data from a LDLR KO mouse placed at 9 weeks of age for up to 20 weeks on HFSC
SAMPLE 28

tag: genotype/variation


title: AML 1591 (CD33)


title: GWAT LDLR -/- HFSC, replicate 5

description:
GWAT Gene expression data from a LDLR KO mouse placed at 9 weeks of age for up to 20 weeks on HFSC
SAMPLE 32


title: GWAT LDLR -/- NC, replicate 6

description:
GWAT Gene expression data from a LDLR KO mouse placed for up to 20 weeks on NC
SAMPLE 27

source_name: GWAT_LDLR -/- mouse placed for up to 20 weeks on NC

value: Normal chow (NC)


title: BMMC 3087

value: isolated from bone marrow after Ficoll-Isopaque separation


title: GWAT LDLR -/- HFSC, replicate 3

description:
GWAT Gene expression data from a LDLR KO mouse placed at 9 weeks of age for up to 20 weeks on HFSC
SAMPLE 30


title: AML 1143 (CD33)


title: GWAT LDLR -/- NC, replicate 4

description:
GWAT Gene expression data from a LDLR KO mouse placed for up to 20 weeks on NC
SAMPLE 25


title: BMMC 641


title: Macrophage type-1 7412

value: cultured from CD14 isolated monocytes with GM-CSF for 7 days


title: Lung 03

source_name: Primary bronchial epithelial cells isolated from lung cultured under submerged conditions and mucociliary differentation was achieved by culture at the air-liquid interface

value: lung

value: Primary bronchial epithelial cells


title: EBV-B 5098

source_name: B-cells immortalized by Epstein Barr Virus

value: B-cells

value: immortalized by Epstein Barr Virus


title: Macrophage type-2 7412

value: cultured from CD14 isolated monocytes with M-CSF for 7 days


title: GWAT LDLR -/- NC, replicate 3

description:
GWAT Gene expression data from a LDLR KO mouse placed for up to 20 weeks on NC
SAMPLE 24

value: LDLR-/-; LDLR KO


title: GWAT LDLR -/- NC, replicate 5

description:
GWAT Gene expression data from a LDLR KO mouse placed for up to 20 weeks on NC
SAMPLE 26


title: Macrophage type-1 5800


title: GWAT LDLR -/- HFSC, replicate 2

description:
GWAT Gene expression data from a LDLR KO mouse placed at 9 weeks of age for up to 20 weeks on HFSC
SAMPLE 29

value: Sucrose enriched high fat diet (HFSC)


title: Macrophage type-2 5800


title: C57BL6_Islets_ZT20

city: Rochester

first: Aleksey

middle: V

last: Matveyenko

state: MN

address: 200 First St SW

department: Physiology and Biomedical Engineering

institute: Mayo Clinic

description: Gene expression at ZT 20

hyb_protocol: The labeled cRNAs were hybridized onto the Whole Mouse Genome Oligo Microarray (4 x 44K, Agilent Technologies).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software (Agilent Technologies)
After quantile normalization of the raw data, genes that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen. Finally, Hierarchical Clustering was performed to show the distinguishable gene expression profiling among samples. Results were provided in the Gene Expression Profiling Data.xls file

source_name: islets, ZT20

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies).

growth_protocol: C57BL6 mice fed on rodent chow diet under 12hr light, 12hr dark cycles

extract_protocol: Pancreatic islets were isolated at respective time points around the diurnal cycle using standard collagenase method. Total RNA from each sample was isolated using the RNeasy Kit from Qiagen (Valencia, CA), quantified using the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: strain

tag: gender

value: male

value: pancreatic islets

tag: age

value: 8 weeks


title: Lung 01

value: isolated from lung cultured under submerged conditions and mucociliary differentation was achieved by culture at the air-liquid interface


title: Hepatocytes 03

source_name: Hepatocytes isolated from liver and cultured on collagen I-coated plates in William's Medium E with insulin, transferrin, selenium and hydrocortisone

value: liver

value: Hepatocytes


title: GWAT LDLR -/- NC, replicate 1

description:
GWAT Gene expression data from a LDLR KO mouse placed for up to 20 weeks on NC
SAMPLE 22

value: gonadal white adipose tissue (GWAT)


title: C57BL6_Islets_ZT16

description: Gene expression at ZT 16

source_name: islets, ZT16


title: C57BL6_Islets_ZT12

description: Gene expression at ZT 12

source_name: islets, ZT12


title: AML 6395 (CD33)

value: peripheral blood

value: Acute myeloid leukemia cells

value: isolated from samples with >20% leukemic blasts (range 22%-95%) based on CD33 surface expression


title: GWAT LDLR -/- NC, replicate 2

description:
GWAT Gene expression data from a LDLR KO mouse placed for up to 20 weeks on NC
SAMPLE 23

value: Normal chow (NC)


title: Lung 02

value: lung

value: Primary bronchial epithelial cells


title: C57BL6_Islets_ZT8

description: Gene expression at ZT 8

source_name: islets, ZT8


title: AML 587 (CD33)

value: peripheral blood/bone marrow


title: Small Intestine 03

source_name: Small intestine epithelial cells isolated from small intestine tissue biopsies and cultured in Matrigel and advanced DMEM-F12 with murine EGF, murine noggin, human R-spondin-1, recombinant human Wnt-3A, gastrin, nicotinamide, A83-01, SB202190

value: small intestine

value: Small intestine epithelial cells


title: Small Intestine 05

value: isolated from small intestine tissue biopsies and cultured in Matrigel and advanced DMEM-F12 with murine EGF, murine noggin, human R-spondin-1, recombinant human Wnt-3A, gastrin, nicotinamide, A83-01, SB202190


title: AML 3009 (CD33)

value: bone marrow


title: Small Intestine 04


title: Colon 03

source_name: Colon epithelial cells isolated from colon tissue biopsies and cultured in Matrigel and advanced DMEM-F12 with murine EGF, murine noggin, human R-spondin-1, recombinant human Wnt-3A, gastrin, nicotinamide, A83-01, SB202190

value: colon

value: Colon epithelial cells


title: C57BL6_Islets_ZT0

description: Gene expression at ZT 0

source_name: islets, ZT0

value: male

value: pancreatic islets

value: 8 weeks


title: Hepatocytes 01

value: liver

value: Hepatocytes

value: isolated from liver and cultured on collagen I-coated plates in William's Medium E with insulin, transferrin, selenium and hydrocortisone


title: Hepatocytes 02


title: Colon 01

value: isolated from colon tissue biopsies and cultured in Matrigel and advanced DMEM-F12 with murine EGF, murine noggin, human R-spondin-1, recombinant human Wnt-3A, gastrin, nicotinamide, A83-01, SB202190


title: C57BL6_Islets_ZT4

description: Gene expression at ZT 4

source_name: islets, ZT4


title: Small Intestine 01


title: CLL 1695 (CD19/CD5)

source_name: Chronic lymphoblastic leukemia cells isolated from samples with >90% malignant cells based on CD19 and CD5 surface expression

value: Chronic lymphoblastic leukemia cells


title: MM 5744 (CD38)

source_name: Multiple myeloma cells isolated from samples with >30% plasma cells (range 30-95%) based on CD38 surface expression

value: Multiple myeloma cells


title: Colon 02


title: CLL 5535 (CD19/CD5)

value: peripheral blood

value: isolated from samples with >90% malignant cells based on CD19 and CD5 surface expression


title: MM 5987 (CD38)

value: isolated from samples with >30% plasma cells (range 30-95%) based on CD38 surface expression


title: CLL 2159 (CD19/CD5)


title: MM 4298 (CD38)


title: Small Intestine 02

value: small intestine

value: Small intestine epithelial cells


title: OS3-CD146+

city: Toronto

first: Yuning

middle: Jackie

last: Tang

state: Ontario

address: 686 Bay Street

department: Program in Developmental Biology

country: Canada

institute: Hospital for Sick Children

description:
Replicate3
SAMPLE 9

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Osteosarcoma tumor biopsy

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA and cDNA conversion are performed following manufacteur's protcol provided in the Ovation® RNA Amplification System kit

value: SP


title: CLL 6242 (CD19/CD5)


title: OS3-NSP

description:
Replicate3
SAMPLE 12

value: NSP


title: OS1-CD146+

description:
Replicate1
SAMPLE 1


title: OS3-CD146-

description:
Replicate1
SAMPLE 10


title: OS2-NSP

description:
Replicate2
SAMPLE 8


title: OS2-CD146+

description:
Replicate2
SAMPLE 5


title: OS2-SP

description:
Replicate1
SAMPLE 7


title: OS1-SP

description:
Replicate3
SAMPLE 3


title: OS1-NSP

description:
Replicate1
SAMPLE 4


title: CLL 4725 (CD19/CD5)

value: bone marrow


title: S48hR1

first: Xiaowei

last: Xu

address: 3400 Spruce st

institute: University of Pennsylvania

description: SNS-314 at 48h replicate 1

data_processing: The data were normalised using quantile normalisation with lumi in R

source_name: SNS-314 at 48h replicate 1

growth_protocol: Human melanoma cells were grown in Tu2% medium before they reach the 70% confluency.

extract_protocol: Cells were washed again with HBSS and lysed directly in TRI Reagent® RNA Isolation Reagent (Sigma) and stored at -20°C.

treatment_protocol: Human melanoma cells were treated with AZD1152 at 0.5uM and SNS-314 at 0.05uM, respectively.

tag: cell

value: 1205Lu melanoma cells


title: C00hR1

description: Control at 00h replicate 1

source_name: Control at 00h replicate 1


title: OS3-SP

description:
Replicate2
SAMPLE 11


title: S24hR3

description: SNS-314 at 24h replicate 3

source_name: SNS-314 at 24h replicate 3


title: OS2-CD146-

description:
Replicate3
SAMPLE 6


title: Epidermis Tgm1-/- 19.5 dpc rep 2

city: Nishinomiya

first: Kiyofumi

last: Yamanishi

state: Hyogo

address: 1-1, Mukogawa-cho

department: Department of Dermatology

country: Japan

institute: Hyogo College of Medicine

description: Gene expression of epidermis

hyb_protocol: 0.6 µg Cy3-labelled cRNA was fragmented at 60°C for 30 minutes and hybridized to an SurePrint G3 Mouse GE 8x60K Microarray for 17 hours at 65°C in a rotating hybridization oven, using a Gene Expression Hybridization Kit (Agilent).  After hybridization, microarrays were washed using a Gene Expression Wash Buffers Pack (Agilent).

scan_protocol: Slides were scanned immediately after washing on a SureScan Microarray Scanner (G2600D) using one color scan setting.

data_processing: The scanned images were analyzed using a Feature Extraction Software (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Epidermis from 19.5 dpc Tgm1 -/- mice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using an One-Color Low Input Quick Amp Labeling  Kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA from each specimen was prepared using a RNeasy Fibrous Tissue Kit (Qiagen, Inc., Hilden, Germany) according to the manufacturer’s instructions.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Tgm1 knockout

tag: background


title: OS1-CD146-

description:
Replicate2
SAMPLE 2


title: S24hR2

description: SNS-314 at 24h replicate 2

source_name: SNS-314 at 24h replicate 2


title: C00hR4

description: Control at 00h replicate 4

source_name: Control at 00h replicate 4


title: C00hR3

description: Control at 00h replicate 3

source_name: Control at 00h replicate 3


title: S48hR3

description: SNS-314 at 48h replicate 3

source_name: SNS-314 at 48h replicate 3


title: S48hR4

description: SNS-314 at 48h replicate 4

source_name: SNS-314 at 48h replicate 4


title: S18hR4

description: SNS-314 at 18h replicate 4

source_name: SNS-314 at 18h replicate 4


title: S18hR3

description: SNS-314 at 18h replicate 3

source_name: SNS-314 at 18h replicate 3


title: S24hR1

description: SNS-314 at 24h replicate 1

source_name: SNS-314 at 24h replicate 1


title: S24hR4

description: SNS-314 at 24h replicate 4

source_name: SNS-314 at 24h replicate 4


title: S48hR2

description: SNS-314 at 48h replicate 2

source_name: SNS-314 at 48h replicate 2


title: C00hR2

description: Control at 00h replicate 2

source_name: Control at 00h replicate 2


title: S18hR2

description: SNS-314 at 18h replicate 2

source_name: SNS-314 at 18h replicate 2


title: S18hR1

description: SNS-314 at 18h replicate 1

source_name: SNS-314 at 18h replicate 1


title: Epidermis Tgm1-/- 19.5 dpc rep 1

description: Gene expression of epidermis


title: S12hR1

description: SNS-314 at 12h replicate 1

source_name: SNS-314 at 12h replicate 1


title: S12hR2

description: SNS-314 at 12h replicate 2

source_name: SNS-314 at 12h replicate 2


title: S12hR3

description: SNS-314 at 12h replicate 3

source_name: SNS-314 at 12h replicate 3


title: S06hR3

description: SNS-314 at 06h replicate 3

source_name: SNS-314 at 06h replicate 3


title: G3_010

city: Calgary

first: Mitra

last: Mojtahedi

state: AB

address: 2500 University Dr. NW

institute: University of Calgary

hyb_protocol: An input of 100ng of total RNA was used to generate Cyanine-3 labeled cRNA. 600ng of Cy3-labeled cRNA (specific activity >15 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1ul Agilent fragmentation buffer and 5ul of 10X Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays (Agilent Microarray Design ID #028005) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried for 1min in acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Green processed signal was quantile normalized.

source_name: EPO+GM-CSF/IL-3_d6_replicate 1

label_protocol: Samples were prepared following the protocol of Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0.  Total RNA is initially converted into cDNA using aT7 polymerase dT primed reverse transcriptase reaction to synthesize first and second strand of cDNA. This cDNA then served as a template for cRNA synthesis by T7 RNA polymerase in the presence of Cyanine 3-labeled CTP (Cy3).

growth_protocol: EML-C1 cells (ATCC CRL-11691) were maintained in a condition containing Iscove’s modified Dulbecco’s medium (IMDM), 1% L-glutamine and 20% (vol/vol) horse serum supplemented with a 15% (vol/vol) BHK/MKL conditioned medium. To differentiate the EML cells into the myeloid cells, EML cells were suspended in a growth medium which contained 10 ng/ml IL-3 (Sigma) and 10 μM ATRA (Sigma) at an initial cell density of 2.0×105 cells/ml on day 0. After incubation for 3 days at 37°C in a 5% CO2/95% air environment, cells were re-suspended in IMDM + 20% Donor Horse Serum + 1% glutamine + 2% (v/v) BHK/MKL conditioned medium + 10 ng/ml IL-3 (Sigma) + 10 μM ATRA (Sigma) + 10 ng/ml mGM-CSF (Peprotech). Cells were incubated at 37 °C for two more days after which additional 10 ng/ml mGM-CSF (Peprotech) was added to the medium. To differentiate EML cells into the erythroid cells, the EML cells were resuspended in a growth medium containing 10 ng/ml erythropoietin (Epo) (Sigma) cytokine and at an initial cell density of 2.5×105 cells/ml on day 0. Cells were incubated for 3 days at 37 °C in a 5% CO2/95% air. After this incubation period, cells were re-suspended in IMDM + 20% Donor Horse Serum (DHS) + 1% glutamine + 2% (v/v) BHK/MKL conditioned medium + 10 ng/ml Epo (Sigma). Then they were incubated at 37 °C for two more days, after which another 10 ng/ml Epo (Sigma) was added to the medium. For the COMB treatment, EML cells were suspended in a growth medium which contained 10 ng/ml IL-3 (Sigma),10 μM ATRA (Sigma) and 10 ng/ml Epo (Sigma) at an initial cell density of 2.2×105 cells/ml on day 0. After incubation for 3 days at 37°C in a 5% CO2/95% air environment, cells were re-suspended in IMDM + 20% Donor Horse Serum + 1% glutamine + 2% (v/v) BHK/MKL conditioned medium + 10 ng/ml IL-3 (Sigma) + 10 μM ATRA (Sigma) + 10 ng/ml mGM-CSF (Peprotech) + 10 ng/ml Epo (Sigma). Cells were incubated at 37 °C for two more days after which additional 10 ng/ml mGM-CSF (Peprotech) + 10 ng/ml Epo (Sigma) was added to the medium.

extract_protocol: Total RNA was extracted from 1×106 of sorted subpopulations using mirVana miRNA Isolation Kit (Ambion) as described by manufacturer’s instructions. Genomic DNA was removed from the isolated and purified RNA using DNase I. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: EML cell cultures were incubated for 3 or 6 days at three different conditions (EPO, GM-CSF/IL-3 and EPO+GM-CSF/IL-3) at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line

tag: condition

tag: time period


title: Pb SSPELD KO duplicate

city: Hyderabad

first: Segireddy

middle: Rameswara

last: Reddy

state: Telangana

address: Gachibowli

department: Animal Biology

country: India

institute: University of Hyderabad

description:
Gene expression of PB SSPELD Knock out parasites
FZ KO-2

hyb_protocol: 1650ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to an Agilent Custom Plasmodium berghei Gene Expression Microarray 4x44k designed by Genotypic Technology Private Limited. (AMADID No: 067226). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version  software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Plasmodium berghei

source_name: Plasmodium berghei SSPELD KO infected HepG2 cells

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: HepG2 cells were grown in DMEM medium with 10% FBS and 50 U/ml of  Pencillin and streptomycin, cells were maintained at 37 C and 5% CO2

extract_protocol: RNA was extracted using the Ambion Pure Link RNA Isolation Kit following the manufacturer's recommendations.

treatment_protocol: HepG2 cells were infected with Plasmodium berghei Wild type and SSPELD knock out sporozoites

value: Pb SSPELD KO

tag: infected host cell line


title: A48hR1

description: AZD1152 at 48h replicate 1

source_name: AZD1152 at 48h replicate 1


title: A48hR2

description: AZD1152 at 48h replicate 2

source_name: AZD1152 at 48h replicate 2


title: Epidermis WT 19.5 dpc rep 2

description: Gene expression of epidermis

source_name: Epidermis from 19.5 dpc wild-type mice

value: wild-type


title: S12hR4

description: SNS-314 at 12h replicate 4

source_name: SNS-314 at 12h replicate 4


title: A48hR4

description: AZD1152 at 48h replicate 4

source_name: AZD1152 at 48h replicate 4


title: A24hR4

description: AZD1152 at 24h replicate 4

source_name: AZD1152 at 24h replicate 4


title: Epidermis WT 19.5 dpc rep 1

description: Gene expression of epidermis


title: S06hR1

description: SNS-314 at 06h replicate 1

source_name: SNS-314 at 06h replicate 1


title: G2_HIGH Sca1_005

source_name: GM-CSF/IL-3_HIGH Sca1_d3_replicate 1


title: G2_009

source_name: GM-CSF/IL-3_d6_replicate 1


title: A48hR3

description: AZD1152 at 48h replicate 3

source_name: AZD1152 at 48h replicate 3


title: Pb SSPELD KO

description:
Gene expression of PB SSPELD Knock out parasites
FZ KO-1


title: A24hR2

description: AZD1152 at 24h replicate 2

source_name: AZD1152 at 24h replicate 2


title: S06hR2

description: SNS-314 at 06h replicate 2

source_name: SNS-314 at 06h replicate 2


title: A24hR3

description: AZD1152 at 24h replicate 3

source_name: AZD1152 at 24h replicate 3


title: A24hR1

description: AZD1152 at 24h replicate 1

source_name: AZD1152 at 24h replicate 1


title: G3_LOW Sca1_006

source_name: EPO+GM-CSF/IL-3_LOW Sca1_d3_replicate 1


title: A18hR3

description: AZD1152 at 18h replicate 3

source_name: AZD1152 at 18h replicate 3


title: G1_008

source_name: EPO_d6_replicate 1

value: EPO


title: G2_LOW Sca1_004

source_name: GM-CSF/IL-3_LOW Sca1_d3_replicate 1


title: G1_HIGH Sca1_003

source_name: EPO_HIGH Sca1_d3_replicate 1


title: Pb WT duplicate

description:
Gene expression of PB WT parasites
FZ WT-2

source_name: Plasmodium berghei WT infected HepG2 cells

value: Pb WT


title: G3_HIGH Sca1_007


title: Pb WT

description:
Gene expression of PB WT parasites
FZ WT-1


title: A18hR4

description: AZD1152 at 18h replicate 4

source_name: AZD1152 at 18h replicate 4


title: G1_LOW Sca1_002

source_name: EPO_LOW Sca1_d3_replicate 1


title: A18hR2

description: AZD1152 at 18h replicate 2

source_name: AZD1152 at 18h replicate 2


title: A12hR3

description: AZD1152 at 12h replicate 3

source_name: AZD1152 at 12h replicate 3


title: G0_001

source_name: NoTreatment_d0_replicate 1

value: no treatment


title: A12hR4

description: AZD1152 at 12h replicate 4

source_name: AZD1152 at 12h replicate 4


title: Low-dose group

city: Hangzhou

first: Junli

last: Feng

address: Hangzhou, Jiaogong Road 149#

country: China

institute: Zhejiang Gongshang University

hyb_protocol: The labeled cRNAs were hybridized onto the microarray according to the manufacturer’s standard protocols.

scan_protocol: After washing, arrays were scanned using GenePix 4000B scanner (Molecular Devices) according to the manufacturer’s protocol.

data_processing: Feature Extraction software (GenePix® Pro 7, Axon Instruments, Inc.) was used to analyze array images to get raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 out of all samples have flags in Detected were chosen for further data analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.   expression pattern among samples.

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

growth_protocol: SHRs were housed individually in steel cages with controlled room temperature (23 ± 1℃), humidity (55 ± 5%), and lighting (lights on from 06:00 to 18:00).

extract_protocol: Total RNA from each sample was extracted using TRK1001 (LC Sciences, Cat. TRK-1001, Total RNA Purification Kit)according to the manufacturer’s instructions. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: SHRs were randomly divided into three groups (n=10): control group, rats were orally administered with water (about 3 mL) for 4 weeks; low-dose group, rats were orally administered with HBMP (10 mg/kg/day, about 3 mL) for 4 weeks; high-dose group, rats were orally administered with HBMP (20 mg/kg/day, about 3 mL) for 4 weeks. The HBMP was orally administered at 9:00 every morning.

value: wistar

value: Spontaneously hypertensive rats (SHRs)

value: 8-10 week-old

value: male

tag: body weight (g)

tag: treated with

value: HBMP 10 mg/kg/day for 28days

value: kidney


title: A06hR2

description: AZD1152 at 06h replicate 2

source_name: AZD1152 at 06h replicate 2


title: Heaves_10

city: Ithaca

first: Donald

last: Miller

state: NY

address: Hungerford Hill Rd.

department: Baker Institute for Animal Health

institute: Cornell University

description: Mediastinal lymph node RNA from heaves affected.

hyb_protocol: 825ng per sample of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 11ul 25x Agilent fragmentation buffer and 2.2 ul 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized 100ul to Agilent-021322 Horse Gene Expression Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Red and the Red and PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using parameters (protocol GE1-105_DEC8 and Grid: 021322_D_F_20080905) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Samples were analyzed with GeneSpring GX 11.0. In short, samples were quantile normalized then filtered where at least 100% of the values representing one condition were acceptable.

organism: Equus caballus

source_name: mediastinal lymph node, heaves

label_protocol: 1ug of total RNA from each sample was linearly amplified and Cy3 labeled using the Ambion Amino Allyl MessageAmp™ II kit (Applied Biosystems, Foster City, CA).

extract_protocol: Total RNA was extracted from samples using the Qiagen RNeasy kit following the manufacturer’s protocol. RNA quality and concentration were initially quantified using a Nano-Drop spectrophotometer, and then assayed on an Agilent BioAnalyzer. All samples had a RIN score above 9.0.

treatment_protocol: Mediastinal lymph nodes were aseptically removed from affected and control horses immediately following euthanasia through a sterile thoracotomy site, rinsed with sterile 0.9% NaCl solution and immediately transported in a sterile container on ice to the laboratory for further processing within a laminar flow hood. Ten mm3 samples of mediastinal lymph nodes (containing the cortex and medulla) were snap frozen in an isopentane bath in liquid N2 and stored at -80oC until RNA was extracted.

tag: breed

value: mixed

tag: tissue

value: mediastinal lymph node

tag: disease status

value: heaves


title: High-dose group

tag: strain background

value: HBMP 20 mg/kg/day for 28days


title: A18hR1

description: AZD1152 at 18h replicate 1

source_name: AZD1152 at 18h replicate 1

value: 1205Lu melanoma cells


title: Heaves_06


title: Control_13

description: Mediastinal lymph node RNA from healthy control.

source_name: mediastinal lymph node, control

value: healthy


title: Heaves_14


title: A06hR1

description: AZD1152 at 06h replicate 1

source_name: AZD1152 at 06h replicate 1


title: A12hR2

description: AZD1152 at 12h replicate 2

source_name: AZD1152 at 12h replicate 2


title: Heaves_04


title: Heaves_08


title: OCILY10 Birinapant Treated - 6 hours - mAdbID:128865

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: 128865

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

scan_protocol: Scan_MicronsPerPixelX: 3 Scan_MicronsPerPixelY: 3 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)

source_name: OCILY10 DMSO Treated

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: Agent: DMSO (Dimethyl sulfoxide)

tag: cell type

value: ABC DLBCL cells

tag: disease state

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

source_name: OCILY10 Birinapant Treated - 6 hours

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: compound
Agent: Birinapant (Smac mimetic TL32711)
Treatment dose: 2.5 uM
Treatment time: 6 hours


title: Control group

tag: strain

value: water for 28days


title: Heaves_02


title: A06hR3

description: AZD1152 at 06h replicate 3

source_name: AZD1152 at 06h replicate 3


title: A12hR1

description: AZD1152 at 12h replicate 1

source_name: AZD1152 at 12h replicate 1


title: OCILY10 Birinapant Treated - 24 hours - mAdbID:128866

description: mAdb experiment ID: 128866

source_name: OCILY10 Birinapant Treated - 24 hours

treatment_protocol:
Treatment type: compound
Agent: Birinapant (Smac mimetic TL32711)
Treatment dose: 2.5 uM
Treatment time: 24 hours


title: OCILY10 Birinapant Treated - 2 hours - mAdbID:128863

description: mAdb experiment ID: 128863

source_name: OCILY10 Birinapant Treated - 2 hours

treatment_protocol:
Treatment type: compound
Agent: Birinapant (Smac mimetic TL32711)
Treatment dose: 2.5 uM
Treatment time: 2 hours


title: OCILY3 Birinapant Treated - 24 hours - mAdbID:128862

description: mAdb experiment ID: 128862

source_name: OCILY3 DMSO Treated

source_name: OCILY3 Birinapant Treated - 24 hours


title: OCILY3 Birinapant Treated - 6 hours - mAdbID:128861

description: mAdb experiment ID: 128861

source_name: OCILY3 Birinapant Treated - 6 hours


title: OCILY10 Birinapant Treated - 4 hours - mAdbID:128864

description: mAdb experiment ID: 128864

source_name: OCILY10 Birinapant Treated - 4 hours

treatment_protocol:
Treatment type: compound
Agent: Birinapant (Smac mimetic TL32711)
Treatment dose: 2.5 uM
Treatment time: 4 hours


title: Control_09


title: Control_07


title: Control_11


title: OCILY3 Birinapant Treated - 4 hours - mAdbID:128860

description: mAdb experiment ID: 128860

source_name: OCILY3 Birinapant Treated - 4 hours


title: Control_05


title: Hepatocyte at C3, biological rep3

city: Ningbo

first: Jin

address: 818 Fenghua Road

institute: Ningbo University

description: Human liver cell line

hyb_protocol: 15µg fragmented cRNA  was hybridized to the Affymetrix PrimeView™ Human Gene Expression Arrays at 45℃ for 16 hours

scan_protocol: The microarrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix® GeneChip® Command Console® (AGCC) Software.The Robust Multiarray Averaging (RMA) method was used to correct, normalize and summarize the probe level information

source_name: Human normal hepatocyte treated with 10 μM TBT for 2 h

label_protocol: Biotin-labeled cRNAs was synthesized using an GeneChip IVT Labeling kit

growth_protocol: HL7702 cells were cultured in RPMI 1640 medium supplemented with 10% FBS at 37°C in a humidified incubator containing 5% CO2.

extract_protocol: Total RNA was extracted with a Qiagen RNeasy Mini Kit according to the manufacturer’s instructions

treatment_protocol: The HL7702 cells were treated with 0 μM, 2 μM, 6 μM, and 10 μM TBT for 2 h. Subsequently, the exposure medium was removed, and cells were rinsed with PBS two times.

tag: treatment

value: TBT


title: Control_03


title: TMD8 Birinapant Treated - 24 hours - mAdbID:128800

description: mAdb experiment ID: 128800

source_name: TMD8 DMSO Treated

source_name: TMD8 Birinapant Treated - 24 hours


title: TMD8 Birinapant Treated - 4 hours - mAdbID:128798

description: mAdb experiment ID: 128798

source_name: TMD8 Birinapant Treated - 4 hours


title: HBL1 Birinapant Treated - 6 hours - mAdbID:128795

description: mAdb experiment ID: 128795

source_name: HBL1 DMSO Treated

source_name: HBL1 Birinapant Treated - 6 hours


title: TMD8 Birinapant Treated - 6 hours - mAdbID:128799

description: mAdb experiment ID: 128799

source_name: TMD8 Birinapant Treated - 6 hours


title: HBL1 Birinapant Treated - 24 hours - mAdbID:128796

description: mAdb experiment ID: 128796

source_name: HBL1 Birinapant Treated - 24 hours


title: S09-0463

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

hyb_protocol: Samples that pass the QC for specific activity were taken for hybridization. 600ng of labeled cRNA were hybridized on the array using the Hi-RPM large Hybridization Kit (Part No: 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression Wash Buffers Set (Part No: 5188-5327).  The hybridized, washed microarray slides were then scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 5 micron resolution.

scan_protocol: scanned using the Agilent Microarray Scanner (Agilent Technologies)

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift Method

source_name: Punch biopsies from psoriatic lesions

label_protocol: The samples were labeled using Agilent Low Input Quick Amp Labeling Kit one color (Part number: 5190-02305).30ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using  RNeasy Mini Kit(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

growth_protocol: Skin biopsies from clinical trial

extract_protocol: RNA isolation was performed using Qiagen RNeasy Mini Kit (CAT# 74106 ) following the manufacturer's recommendations.

treatment_protocol: Punch biopsies were collected in RNA later stored at 2-8 degree C. The tissues were cut and frozen at -80 degree C for microarray analysis.

tag: group

value: Non-Responder

value: skin

value: psoriasis

tag: time


title: KYSE150-vector control

city: Shantou

first: Jincheng

last: Guo

address: Xinling Road

department: Medical collage

institute: Shantou University

description: Expression profiling by array

hyb_protocol: After fragmentation of these amplified RNA (aRNA), sample was hybridized to the Affymetrix PrimeViewTM Human Gene Expression Array for 16-18 h at 45°C.

scan_protocol: Following hybridization, the microarrays were washed and stained with Streptavidin Phycoerythrin on the Affymetrix Fluidics Station 450. Microarrays were scanned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using default analysis settings and global scaling as normalization method by Partek® Genomics Suite 6.6. Values presented are log2 RMA signal intensity..

source_name: KYSE150-vector control

label_protocol: After having passed RNA measurement on the Nanodrop ND-1000 and denaturing gel electrophoresis, a total of 500 ng RNA was used for a single round of amplification and simultaneously labeled with biotincongugated nucleotide.

growth_protocol: KYSE150 cells were cultured in RPMI-1640 medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum. All cells were maintained at 37°C in ahumidified 5% CO2 atmosphere.

extract_protocol: Total RNA are harvested using TRIzol (Invitrogen) and the RNeasy kit (Qiagen) according to manufacturer’s instructions, including a DNase digestion step.

treatment_protocol: Chemically modified Stealth siRNAs (5'-agggaugguguccacuucaaatt-3') were purchased from QIAGEN. L1CAM-specific small hairpin RNA lentiviruses (L1CAM shRNA1 and control shRNA) were purchased from GenePharma of China. The shRNA sequences were similar to siRNAs and were ligated into the pGLV3/H1/GFP/+Puro Vector. Two L1CAM lentivirus shRNAs were mixed and used to simultaneously infect KYSE150, following the manufacturer’s instructions, when cells reached 30-40% confluence. Seventy-two hours later, cells were passaged or harvested for further analysis.

value: esophageal squamous carcinoma (ESCC cell line)

tag: genotype/variation

value: KYSE150-vector control


title: HBL1 Birinapant Treated - 4 hours - mAdbID:128794

description: mAdb experiment ID: 128794

tag: cell line

source_name: HBL1 Birinapant Treated - 4 hours


title: Hepatocyte at C2, biological rep1

description: Human liver cell line

source_name: Human normal hepatocyte treated with 6 μM TBT for 2 h


title: Hepatocyte at C1, biological rep2

description: Human liver cell line

source_name: Human normal hepatocyte treated with 2 μM TBT for 2 h


title: Hepatocyte at C1, biological rep3

description: Human liver cell line


title: KYSE150-L1CAM knockdown

description: Expression profiling by array

source_name: KYSE150-L1CAM knockdown

value: KYSE150-L1CAM knockdown


title: OCILY3 Birinapant Treated - 2 hours - mAdbID:128859

description: mAdb experiment ID: 128859

source_name: OCILY3 DMSO Treated

source_name: OCILY3 Birinapant Treated - 2 hours


title: S09-0467


title: HBL1 Birinapant Treated - 2 hours - mAdbID:128793

description: mAdb experiment ID: 128793

source_name: HBL1 Birinapant Treated - 2 hours


title: Control_01

source_name: mediastinal lymph node, control


title: Hepatocyte at C1, biological rep1

description: Human liver cell line


title: TMD8 Birinapant Treated - 2 hours - mAdbID:128797

description: mAdb experiment ID: 128797

source_name: TMD8 DMSO Treated

source_name: TMD8 Birinapant Treated - 2 hours


title: Hepatocyte at C3, biological rep1

description: Human liver cell line

source_name: Human normal hepatocyte treated with 10 μM TBT for 2 h


title: S09-0461

value: Responder


title: S09-0459


title: S09-0468


title: Hepatocyte at C2, biological rep2

description: Human liver cell line


title: Hepatocyte at C2, biological rep3

description: Human liver cell line


title: Hepatocyte at C0, biological rep3

description: Human liver cell line

source_name: Human normal hepatocyte without TBT


title: S09-0441


title: S09-0440


title: S09-0439


title: S09-0434


title: Hepatocyte at C0, biological rep2

description: Human liver cell line


title: S09-0430


title: S09-0431


title: S08-0420


title: S09-0427


title: S08-0417


title: mICSI_BCB-_blast_rep 3

city: Clayton

first: Justin

middle: C

last: St. John

state: Vic

address: 27-31 Wright St

department: Centre for Genetic Diseases

institute: Hudson Institute of Medical Research

description: Gene expression in blastocyst produced from mICSI BCB+ oocyte

hyb_protocol: 1.65 μg of Cy3 labeled antisense RNA (aRNA; DOL 1-3.5%) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 4.4x Agilent blocking agent, according to the manufacturer’s instructions. On completion, 55 μl of 2x Agilent gene expression hybridisation buffer, 3 μl H2O and 27 μl CGH ULS block were added and 100 μl of the mixture was hybridised for 17 hours at 67°C in a rotating Agilent hybridisation oven. After hybridisation, Thethe EmbryoGENE porcine – 4x 44K (ID 031068) microarrays  (Agilent Technologies, CA) were washed for 1 minute at room temperature with GE wash buffer 1 (Agilent) and 1 minute with 37°C GE wash buffer 2 (Agilent, CA).

scan_protocol: Slides were scanned immediately after washing on the Agilent C DNA microarray scanner. The scanned images were analyzed using Feature Extraction Software 11.0.1.1 (Agilent)

data_processing: The scanned images were analyzed using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as not detected  were excluded. Filtered on Expression (20.0 - 100.0)th Percentile in the Raw Data where at least 100.0 percent of samples in any 1 out of 3 conditions have flags in [Detected].

organism: Sus scrofa

source_name: mICSI BCB- blast-rep 3

label_protocol: Quality and concentration of extracted RNA was analyzed before and after T7 RNA amplification (Bio analyzer, Agilent). 1.8 μg amplified RNA was labeled with Cy3-ULS using the Agilent DNA ULS Fluorescent Labeling kit. The Degree of Labeling (DOL) was measured with the Nanodrop ND-1000 Spectrophotometer. (Thermo Scientific).

growth_protocol: After follicule aspiration from pig ovaries, oocyte-cumulus complexes were stained for 60 minute in BCB solution, then separate according to staining outcome (positive vs negative) and then culture for 44h for in vitro maturation in TCM medium supplemented with PVA and FSH+LH. Mature oocytes at metaphase II were inseminated by ICSI or mICSI (ICSI + mitochondrial solution extracted from oocytes) then culture for 7 days in PZM medium. At day 7, blastocysts were harvested and individually stored at -80 degree celcius.

extract_protocol: Before extraction, RNA agilent spike-ins (Agilent) was added to the sample. RNA was extracted from single porcine blastocyst using PicoPure Arcturus RNA extraction kit (Life Technologies), followed by whole RNA population amplification using Arcturus® RiboAmp® HS PLUS Kit (Life Technologies).

treatment_protocol: Oocytes were treated with BCB staining solution to discriminate developmental competency. Moreover, non-competent oocytes were supplemented with mitochondrial solution to enhance blastocyst rate.

value: blastocyst

tag: bcb staininig

value: negative

tag: insemination

value: mICSI


title: S08-0410


title: ICSI_BCB-_blast_rep 3

description: Gene expression in blastocyst produced from ICSI BCB- oocyte

source_name: ICSI BCB- blast-rep 3

value: ICSI


title: Hepatocyte at C0, biological rep1

description: Human liver cell line


title: mICSI_BCB-_blast_rep 2

source_name: mICSI BCB- blast-rep 2


title: mICSI_BCB-_blast_rep 4

source_name: mICSI BCB- blast-rep 4


title: ICSI_BCB-_blast_rep 2

description: Gene expression in blastocyst produced from ICSI BCBi oocyte

source_name: ICSI BCB- blast-rep 2


title: S08-0405

source_name: Punch biopsies from psoriatic lesions


title: S08-0396


title: mICSI_BCB-_blast_rep 1

source_name: mICSI BCB- blast-rep 1


title: ICSI-BCB+_blast_rep 1

description: Gene expression in blastocyst produced from ICSI BCB+ oocyte

source_name: ICSI BCB+ blast-rep 1

value: positive


title: S08-0407


title: ICSI_BCB-_blast_rep 1

source_name: ICSI BCB- blast-rep 1


title: ICSI-BCB+_blast_rep 4

source_name: ICSI BCB+ blast-rep 4


title: ICSI-BCB+_blast_rep 2

source_name: ICSI BCB+ blast-rep 2


title: S08-0394


title: ICSI-BCB+_blast_rep 3

source_name: ICSI BCB+ blast-rep 3


title: Heaves_12

source_name: mediastinal lymph node, heaves

value: mixed

value: mediastinal lymph node

value: heaves


title: tumor galectin-9 treated 4

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: tumor galectin-9

label_protocol: Extracted total RNA was labeled with Hy3 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Tumor (mouse): Each mouse was inoculated with TFK-1 cells (5×106cells/animal) subcutaneously on the flank regions of the mouse.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: The galectin-9-treated group was injected 3 times a week subcutaneously at 30 μg/body or 90 μg/body per day for 7 weeks.

value: tumor

tag: disease type

value: cholangiocarcinoma


title: tumor galectin-9 treated 3


title: tumor galectin-9 treated 1


title: tumor galectin-9 treated 2


title: tumor control 5

source_name: tumor control


title: S08-0379

value: Non-Responder


title: tumor control 4


title: S08-0384

value: skin


title: tumor control 2


title: tumor control 3


title: S08-0382

value: psoriasis


title: S08-0383


title: tumor control 1


title: S08-0385


title: S08-0377


title: S08-0378


title: S08-0372


title: S08-0358


title: S08-0359


title: S08-0352


title: S08-0363


title: S08-0365


title: S08-0392


title: S08-0370


title: S08-0351


title: S08-0341


title: S08-0350


title: S08-0337


title: S08-0339


title: fibroblast_ERT2-TRF2dB_36hr_rep1

city: Nankang

first: Liuh-Yow

last: Chen

state: Taipei

address: 128, Section 2, Academia Rd,

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description:
Gene expression after 36hr in 1 µM of  4-hydroxytamoxifen in immortalized fibroblast transduced with ERT2-TRF2dB
EXP-36

hyb_protocol: The fluorochrome-labeled cDNAs were hybridized on Agilent human GE array 8x60K using Agilent Gene Expression Hybridization Kit. After hybridization, sildes were wased sequential.

scan_protocol: Scanned on an Agilent G2565CA Microarray Scanner. Images were then quantified using Agilent Feature Extraction Software (version A.10.5.1.1, protocol GE1_105_Dec08)

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.5.11 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 039494_D__F20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Raw intensity is normalized at 75th percentile and  log2 transformed to untreated samples of corresponding cells.

label_protocol: The cDNAs of vector control and ERT2-TRF2dB cells were reverse transcribed from 10 microgram of total RNAs and labeled with Alexa Fluor 555 647, respectively, by SuperScript® Indirect cDNA Labeling System (Life Technologies) following manufacturer's instructions.

growth_protocol: All human cell lines were maintained in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, 2.5 mM of L-glutamine and 5 U/ml of penicillin/streptomycin (Life Technology) at 37°C with 5% CO2.

extract_protocol: Total RNA was isolated from 4-OHT-treated and non-treated BJTL/ERT2-TRF2dB or BJTL/Vec cells using RNeasy Mini Kit (QIAGEN, Germany). RNA quality was determined using Agilent RNA 6000 Nano kit (Agilent Technology, USA)

treatment_protocol: Global gene expression in immortalized human fibroblast transduced with ERT2-TRF2dB gene was measured at 0, 12, 24, 36, 48 and 60 hours of 1 µM  4-hydroxytamoxifen (4-OHT).  Gene expression in immortalized human fibrobblast transduced with vector was measured at 0 and 48 hrs of 1 µM  4-hydroxytamoxifen (4-OHT) as controls. Three independent experiments were performed at each time using different donors for each experiment.

value: BJ-5ta fibroblast immortalized with hTERT

tag: transduced with


title: fibroblast_ERT2-TRF2dB_48hr_rep1

description:
Gene expression after 48hr in 1 µM of  4-hydroxytamoxifen in immortalized fibroblast transduced with ERT2-TRF2dB
EXP-48


title: fibroblast_ERT2-TRF2dB_60hr_rep1

description:
Gene expression after 60hr in 1 µM of  4-hydroxytamoxifen in immortalized fibroblast transduced with ERT2-TRF2dB
EXP-60


title: S08-0329


title: S08-0334


title: S08-0322


title: fibroblast_ERT2-TRF2dB_0hr_rep1

description:
Gene expression in ERT2-TRF2dB fibroblast without 4-OHT treatment
EXP-0


title: S08-0326


title: S08-0328


title: fibroblast_vector control_48hr_rep1

description:
Gene expression after 48hr in 1 µM of  4-hydroxytamoxifen in immortalized fibroblast vector
Ctrl-48

source_name: fibroblast_vector control_48hr

value: vector control


title: fibroblast_ERT2-TRF2dB_24hr_rep1

description:
Gene expression after 24hr in 1 µM of  4-hydroxytamoxifen in immortalized fibroblast transduced with ERT2-TRF2dB
EXP-24


title: S08-0308


title: S08-0300


title: Hepatocyte at C3, biological rep2

description: Human liver cell line

source_name: Human normal hepatocyte treated with 10 μM TBT for 2 h

value: TBT


title: NB4 cell line in co-culture rep3

description: Gene expression after 48 hours of co-culture

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Agilent Human Gene Expression Microarray 8x60K (AMADID No: 39494) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX  software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

source_name: cell line

growth_protocol: The cells were grown in 10% RPMI and were maintained at a density between 0.5x10^6 cells/ml and 1x10^6cells/m

extract_protocol: RNA was extracted using the Qiagen Rneasy Mini kit with Dnase tre atment  following the manufacturer's recommendations.

treatment_protocol: The cells were co-cultured with HS-5 cells for 48 hours and the NB4 cells were taken back for RNA isolation

value: promyelocytic leukemic cell line

tag: morphology

value: single cells in suspension, round and polymorphic cells

value: 48 hours of co-culture


title: NB4 cell line in co-culture rep3a


title: fibroblast_vector control_0hr_rep1

description:
Gene expression immortalized fibroblast vector without 4-OHT treatment
Ctrl-0

source_name: fibroblast_vector control_0hr


title: NB4 cell line in co-culture rep1