title: lc_281


title: lc_287

status: Public on Jan 22 2013

type: RNA

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina whole-genome DASL Assay System Manual.

data_processing: For each probe, replicate mesurements were averaged after removing outliers. Data were were then normalized using the cubic spline algorithm.

molecule: total RNA

organism: Homo sapiens

source_name: liver cirrhosis

extract_protocol: Using 10µm sections taken from formalin-fixed paraffin-embeded tissue blocks, total RNA was extracted using TRIzol LS (Invitrogen).

tag: tissue

value: liver biopsy specimen

tag: prediction

value: Good prognosis

tag: prediction confidence p-value

tag: prediction (p<0.05)

tag: presence of varices

tag: bilirubin ≥ 1.0mg/dl

tag: platelet < 100,000/mm3

tag: days to death

tag: death

tag: days to decomp

tag: decomp

tag: days to child

tag: child

tag: days to hcc

tag: hcc


title: lc_282

scan_protocol: Refer to the Illumina whole-genome DASL Assay System Manual.


title: lc_279

label_protocol: Refer to the Illumina whole-genome DASL Assay System Manual


title: lc_285

value: Intermediate prognosis


title: lc_276


title: lc_300


title: lc_293


title: lc_278


title: lc_280


title: lc_274


title: lc_273


title: lc_272


title: lc_266

value: Poor prognosis


title: lc_270


title: lc_265


title: lc_283


title: lc_268


title: lc_269


title: lc_267


title: lc_260


title: lc_263


title: lc_277


title: lc_261


title: lc_255


title: lc_258


title: lc_256


title: lc_249


title: lc_248


title: lc_242


title: lc_259


title: lc_252


title: lc_240


title: lc_245


title: lc_251


title: lc_241


title: lc_246


title: lc_254


title: lc_247


title: lc_238


title: lc_243


title: lc_235


title: lc_244


title: lc_231


title: lc_239


title: lc_233


title: lc_236


title: lc_229


title: lc_228


title: lc_221


title: lc_234


title: lc_232


title: lc_225


title: lc_253


title: lc_237


title: lc_222


title: lc_227


title: lc_214


title: lc_210


title: lc_213


title: lc_218


title: lc_220


title: lc_208


title: lc_211


title: lc_202


title: lc_217


title: lc_215


title: lc_207


title: lc_216


title: lc_205


title: lc_212


title: lc_199


title: lc_198


title: lc_206


title: lc_194


title: lc_192


title: lc_197


title: lc_200


title: lc_224


title: lc_203


title: lc_175


title: lc_187


title: lc_195


title: lc_186


title: lc_189


title: lc_190


title: lc_184


title: lc_196


title: lc_193


title: lc_170


title: lc_173


title: lc_169


title: lc_168


title: lc_188


title: lc_172


title: lc_171


title: lc_167


title: lc_174


title: lc_166


title: lc_164


title: lc_165


title: lc_162


title: lc_154


title: lc_149


title: lc_153


title: lc_160


title: lc_145


title: lc_142


title: lc_144


title: lc_161


title: lc_135


title: lc_156


title: lc_150


title: lc_148


title: lc_155


title: lc_158


title: lc_139


title: lc_151


title: lc_141


title: lc_152


title: lc_134


title: lc_163


title: lc_157


title: lc_129


title: lc_146


title: lc_140


title: lc_133


title: lc_136


title: lc_124


title: lc_127


title: lc_204


title: lc_115


title: lc_122


title: lc_112


title: lc_110


title: lc_121


title: lc_117


title: lc_095


title: lc_118


title: lc_104


title: lc_101


title: lc_094


title: lc_093


title: lc_105


title: lc_088


title: lc_077


title: lc_096


title: lc_097


title: lc_092


title: lc_070


title: lc_069


title: lc_068


title: lc_075


title: lc_080


title: lc_082


title: lc_076


title: lc_067


title: lc_065


title: lc_064


title: lc_062


title: lc_058


title: lc_063


title: lc_054


title: lc_043


title: lc_056


title: lc_028


title: lc_057


title: lc_052


title: lc_022


title: lc_047


title: lc_040


title: lc_015


title: lc_010


title: lc_004


title: lc_020


title: lc_024


title: lc_055


title: lc_034


title: lc_016


title: lc_030


title: lc_039


title: Father_rep1

status: Public on Oct 30 2012

city: Worcester

first: Rachel

middle: Patton

last: McCord

state: MA

address: 364 Plantation St. LRB 570M

department: Program in Gene Function and Expression

institute: University of Massachusetts Medical School

description:
KC_10-1 patient168
Patient's healthy father.

hyb_protocol: The hybridization cocktail containing the fragmented and biotin-labeled cDNAs were hybridized to an Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. The chips were washed and stained by the Affymetrix Fluidics Station using the standard format and protocols as described by Affymetrix. The probe arrays were stained with streptavidin phycoerythrin solution (Molecular Probes, Carlsbad, CA) and enhanced by using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: An Affymetrix GeneChip Scanner 3000 was used to scan the probe arrays. Gene expression intensities were calculated using the Affymetrix Expression Console software and the CEL files generated.

data_processing: CEL files were processed with RMAExpress using Background Adjustment, Quantile Normalization, and Median Polish.

label: biotin

source_name: normal forearm skin biopsy

label_protocol: For RNA labeling, 1 microgram of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip® WT Sense Target Labeling. The total RNA was first subjected to a ribosomal RNA reduction using the Invitrogen RiboMinus Transcriptome Isolation Kit. The remaining RNA was then reverse transcribed in the presence of dT7N6 primers to generate cDNA. An in vitro transcription was then performed and the resulting cRNA was purified. A first strand cDNA was generated from the cRNA in the presence of dUTPs. After RNA hydrolysis, the single-stranded cDNA was fragmented and end labeled with biotin.

growth_protocol: Cells were grown under 5% CO2 in MEM supplied by 15% FBS.

extract_protocol: RNA was isolated from 1 million cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. Total RNAs were prepared according to Affymetrix protocols (Affymetrix, Inc). RNA quality and quantity were ensured using the Bioanalyzer (Agilent, Inc.) and NanoDrop (Thermo Scientific, Inc.), respectively.

tag: disease status

value: normal

value: forearm skin biopsy

tag: cell type

value: fibroblasts

tag: gender

value: male

tag: cell line

tag: passage


title: HPDE-2D monolayer-1

status: Public on Nov 15 2012

city: Tainan City

first: Wei-Yu

last: Wang

address: 2F., No. 367, Shengli Road

country: Taiwan

institute: National Health Research Institutes

description: HPDE,2D,duplicate data,01

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133A 2.0 Plus GeneChip. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip®Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: HPDE-2D monolayer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Genechip 3'-IVT express kit, Affymetrix).

growth_protocol: HPDE cells were maintained in Keratinocyte-SFM (Sigma-Aldrich); PANC-1 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and antibiotics

extract_protocol: Total RNA samples were extracted from cells or organoids using TRIZOL (Sigma) and then purified using an RNeasy mini-kit and a DNase treatment (Qiagen).

treatment_protocol: no treatment

value: HPDE

value: immortalized pancreatic epithelial cells

tag: culture type

value: 2D monolayer


title: HGPS_rep2

description:
KC_9-2 patient167
HGPS patient.

source_name: patient forearm skin biopsy

value: Hutchinson-Gilford Progeria Syndrome

tag: tissue


title: parotid tissue from control 14

status: Public on Sep 06 2012

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

hyb_protocol: 15μg of labeled cRNA was fragmented into 50- to 200-bp fragments and assessed for quality with a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing: Microarray data were processed and normalized using MAS5.

source_name: parotid tissue from control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA

growth_protocol: parotid tissue from humans

extract_protocol: Total RNAs were extracted using mirVana PARIS Kit (Ambion/Applied Biosystems).

value: Control

tag: batch


title: parotid tissue from control 16


title: Father_rep2

description:
KC_10-2 patient168
Patient's healthy father.


title: Human Conjunctiva Donor 15 OD (Right Eye)

status: Public on Jan 01 2013

first: Martin

last: Nakatsu

address: 200 Stein Plaza

institute: Jules Stein Eye Institute

hyb_protocol: Affymetrix GeneChip Hybridization Protocol

scan_protocol: Affymetrix GeneChip 3000 Scanner Protocol

data_processing: All Affymetrix data were normalized with Robust Multichip Average (RMA) algorithm using Affymetrix Expression Console.

label: Biotin

source_name: Conjunctiva

label_protocol: Affymetrix Gene Expression Protocol for Biotin Labeling

extract_protocol: Each sample was resuspended in a Qiagen lysis buffer provided in w/ β-mercaptoethanol (1:100). In between homogenizations, the blade was rinsed subsequently twice in filtered ddI water, 70% ethanol, and twice again in fresh Millipore ddI water. All samples are kept on dry ice before homogenization. Total RNA was isolated using the Qiagen’s RNA easy mini columns.

value: Conjunctiva


title: parotid tissue from control 17


title: HGPS_rep1

description:
KC_9-1 patient167
HGPS patient.


title: parotid tissue from control 20


title: parotid tissue from control 19


title: HPDE-2D monolayer-2

description: HPDE,2D,duplicate data,02


title: parotid tissue from control 18


title: parotid tissue from control 2


title: parotid tissue from control 13


title: parotid tissue from control 15


title: parotid tissue from control 8


title: parotid tissue from control 10


title: parotid tissue from control 3


title: lc_079

tag: prediction

tag: prediction confidence p-value

tag: prediction (p<0.05)

tag: presence of varices

tag: bilirubin ≥ 1.0mg/dl

tag: platelet < 100,000/mm3


title: parotid tissue from control 12


title: parotid tissue from control 4


title: parotid tissue from control 9


title: parotid tissue from control 5


title: parotid tissue from control 1


title: parotid tissue from control 7


title: lc_085

tag: days to death

tag: death

tag: days to decomp

tag: decomp

tag: days to child

tag: child


title: Normal Sample 1

status: Public on Mar 27 2012

city: Frederick

first: Sudhir

middle: R

last: Chowbina

state: MD

address: Frederick

department: Advanced Biomedical Computing Center

institute: SAIC-Frederick

description:
07-28_N1
Gene expression data from normal human salivary gland.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the EukGE-WS2v5 fluidics protocol.

scan_protocol: Affymetrix scanner 3000 using manufacturer settings.

data_processing: The images generated in the scanning were acquired to make the .DAT files, which in turn were converted to probe-intensity coordinated .CEL files, using the GCOS software package (Affymetrix).

source_name: normal human salivary gland

label_protocol: Affymetrix p/n 900493 GeneChip® Expression 3' Amplification One-Cycle Target Labeling and Control Reagents.

growth_protocol: Xenograft tumors were grown subcutaneously in nude mice.

extract_protocol: Isolation of total RNA was performed using RNeasy spin columns according to the manufacturer's protocol (Qiagen).

treatment_protocol: None.

value: non-neoplastic salivary gland

tag: organ site at which tumor arose

value: submandibular salivary gland

tag: donor sex

value: unknown


title: Normal Sample 3

description:
07-28_N4
Gene expression data from normal human salivary gland.


title: Normal Sample 2

description:
07-28_N2
Gene expression data from normal human salivary gland.


title: Keratinocytes_untreated_replicate3

status: Public on Mar 07 2012

city: Boston

first: William

last: Swindell

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University

description: primary human keratinocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray TM Scanner 3000.

data_processing: Robust Multichip Average (RMA)

source_name: primary keratinocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Monolayer NHK cultures were established and used in the second or third passage (Elder 1991, J. Invest. Dermatol. 96: 425-433). Cultures were grown to 40 or 80% confluence, or maintained to 4 days postconfluency.

extract_protocol: RNA was extracted using QIAGEN RNEasy mini kits

treatment_protocol: Cultures were starved of growth factors in unsupplemented M154 medium (Invitrogen/Cascade Biologics, Portland, OR) for 24 hours before use. Cultures were stimulated 24 hours with recombinant human cytokines and growth factors from R&D Systems (Minneapolis, MN).

value: primary keratinocytes

tag: treatment

value: untreated control


title: Keratinocytes_untreated_replicate1

description: primary human keratinocytes

tag: tissue


title: mammary_epithelium_vehicle_rep4

status: Public on Feb 29 2012

city: West Lafayette

first: Sophie

last: Lelievre

state: IN

address: 625 Harrison St

department: Basic Medical Sciences

institute: Purdue University

description: Vehicle Control 4

hyb_protocol: Following fragmentation, 6.5 ug of cRNA was hybridized with a GeneChip Hybridization Oven 640 for 16 hr at 45C on GeneChip Human Genome U133A 2.0 Arrays.  This included the Affymetrix Hybridization Controls.  GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 400 with fluidics protocol Midi_euk2v3 and user prepared solutions (buffers and stains), as per protocols provided by Affymetrix in the GeneChip Expression Analysis Technical Manual, 2004 (Affymetrix, Inc.  Santa Clara, California).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G enabled for High-Resolution Scanning.  The instruments were controlled using GCOS version 1.4 software.  Library files HG_U133A 2.0 were used to generate CHP data.

data_processing: The image acquisition protocols are set by the instrument based on the type of GeneChip used.  Thus, these were determined by the manufacturer. Chip images as DAT files were generated by the scanner.  The GCOS software and chip-specific library files (in this case HG_U133A 2.0) were used to create CEL files,  generate CHP data (like probe counts, Algorithm: ExpressionStat 5.0) and RPT files (information about internal controls as well as sample and array processing).

label_protocol: Biotin (as a biotinylated ribonucleotide) was used to label the extract. Biotinylated cRNA were prepared from 2.25 ug total RNA utilizing Affymetrix Poly-A RNA Control and Oligo T7 Promoter Primer Kits, as well as the One-Cycle cDNA Synthesis Kit,  GeneChip Sample Cleanup Module and IVT Labeling Kit, according to the Affymetrix GeneChip Expression Analysis Technical Manual, 2004. (Affymetrix, Inc.  Santa Clara, California).

growth_protocol: Non-neoplastic human mammary HMT-3522 epithelial cells, previously established from adult tissue (S1 passage 55 to 60) were propagated as monolayers on plastic surface (2-D culture), in 75-cm2 Falcon flasks (BD Biosciences, Bedford, MA), at 37°C in 5% CO2, in chemically defined H14 medium consisting of DMEM:F12 medium (GIBCO BRL, St. Louis, MO), containing 250 ng/ml insulin (Boehringer Mannheim, Indianapolis, IN), 10 μg/ml transferrin (Sigma, St Louis, MO), 2.6 ng/ml sodium selenite (BD Biosciences), 10−10 M estradiol (Sigma), 1.4 μM hydrocortisone (BD Biosciences), 5 μg/ml prolactin (Sigma), and 10 ng/ml epidermal growth factor (EGF; BD Biosciences). H14 medium was routinely changed every 2-3 days. S1 cells were induced to recapitulate the formation of polarized glandular structures (acini) when cultured in the presence of exogenous ECM-enriched in laminin (Matrigel™, BD Biosciences), a technique called three-dimensional (3-D) culture. Briefly, S1 cells (35,000 cells/cm2) were plated on 41 μl/cm2 matrigel-coated surfaces and cultured in H14 medium containing 5% matrigel. Following 8 days of 3-D culture, cells were induced to exit the cell cycle upon incubation in H14 medium without EGF for 48 h. Acinar morphogenesis, characterized by the formation of a single layer of cells surrounding a lumen and delineated by an endogenous basement membrane, was routinely observed by days 9-10. Usually, at the end of the differentiation process, well-formed acini represent 80–90% of the total acini population.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturers instructions. Briefly, cells at 70-80% were collected in 1ml Trizol and froze at -80C until extraction. The day of extraction 200ul Chloroform was added for phase separation and RNA extracted by isopropanol and ethanol precipitation. Samples were resuspended in DEPC water

treatment_protocol: For treatment of S1 cells cultured under 3-D conditions with 10 μM 5-aza-2' deoxycytidine (Sigma), or 10µM of 18α-glycerrhitinic acid (AGA) (Sigma Aldrich),  H14 medium containing one of the drugs was changed every 2 days for 10 days, starting the day of plating.

tag: cell line

tag: cell type

value: non-neoplastic human mammary epithelium cells

tag: cell culture medium

value: 5% Matrigel H14

tag: cell apical polarity

value: polarized


title: mammary_epithelium_vehicle_rep2

description: Vehicle Control 2


title: mammary_epithelium_5Aza_d1-10_rep2

description: 5-aza-2'-deoxycytidine 2

value: not polarized


title: mammary_epithelium_5Aza_d1-10_rep3

description: 5-aza-2'-deoxycytidine 3


title: mammary_epithelium_vehicle_rep3

description: Vehicle Control 3


title: Keratinocytes_untreated_replicate2

description: primary human keratinocytes


title: mammary_epithelium_aga_d1-10_rep2

description: 18-alpha-glycyrrhetinic acid 2


title: mammary_epithelium_5Aza_d1-10_rep4

description: 5-aza-2'-deoxycytidine 4


title: mammary_epithelium_5Aza_d1-10_rep1

description: 5-aza-2'-deoxycytidine 1


title: mammary_epithelium_aga_d1-10_rep1

description: 18-alpha-glycyrrhetinic acid 1


title: mammary_epithelium_aga_d1-10_rep3

description: 18-alpha-glycyrrhetinic acid 3


title: mammary_epithelium_aga_d1-10_rep4

description: 18-alpha-glycyrrhetinic acid 4


title: mammary_epithelium_vehicle_rep1

description: Vehicle Control 1


title: Human Cornea Donor 1

status: Public on Jun 09 2011

data_processing: All Affymetrix data were normalized with Robust Multichip Average (RMA) algorithm using RMAExpress software.

source_name: Cornea

extract_protocol: Each sample was resuspended in a Qiagen lysis buffer provided in w/ β-mercaptoethanol (1:100). In between homogenizations, the blade was rinsed subsequently twice in filtered ddI water, 70% ethanol, and twice again in fresh Millipore ddI water. All samples are kept on dry ice before homogenization

value: Cornea


title: Human Cornea Donor 2


title: Perio_gingiva_CP3

status: Public on Aug 13 2010

city: Niigata

first: Takehiko

last: Kubota

address: 2-5274, Gakkou-cho

department: Periodontology

country: Japan

institute: Niigata University Graduate School of Medical and Dental Sciences

description: Homo sapiens_EA0530_02

hyb_protocol: Following fragmentation, 10μg of cRNA were hybridized at 45°C for 16h on GeneChip® Human Genome U133 Plus 2.0 Array® (Affymetrix).

scan_protocol: Fluorescence intensities for chips were captured on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Periodontitis affected gingival tissue of patients 3.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.0 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using the RNAiso® reagent (TaKaRa Bio Inc., Otsu, Japan).

tag: Sex

value: male

value: Periodontitis

tag: age (yrs)


title: Healthy_gingiva_CP3

description: Homo sapiens_EA0530_01

source_name: Healthy gingival tissue of patient 3.

value: Healthy


title: Human Conjunctiva Donor 15 OS (Left Eye)


title: Human Conjunctiva Donor 2


title: Naive, donor 12405

status: Public on Jul 07 2009

city: South San Francisco

first: Alex

last: Abbas

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description: Gene expression data on Naive cells from donor 12405

hyb_protocol: cRNA was hybridized on GeneChip HGU133 plus v2.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

source_name: Naive, donor 12405

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNeasy Mini Kit (Qiagen)

value: Naive

tag: sample type

value: purified cells

tag: fractional abundance


title: PBMCs, donor 11405

description: Gene expression data on PBMCs from donor 11405

source_name: PBMCs, donor 11405

value: PBMCs

value: mixed cells


title: Human Cornea Donor 15 OS (Left Eye)


title: Effector memory, donor 121704

description: Gene expression data on Effector memory cells from donor 121704

source_name: Effector memory, donor 121704

value: Effector memory


title: Effector memory, donor 12805

description: Gene expression data on Effector memory cells from donor 12805

source_name: Effector memory, donor 12805


title: Healthy_gingiva_CP1

description: Homo sapiens_EA0432_01

source_name: Healthy gingival tissue of patient1.


title: PBMCs, donor 12805

description: Gene expression data on PBMCs from donor 12805

source_name: PBMCs, donor 12805


title: Central memory, donor 12805

description: Gene expression data on Central memory cells from donor 12805

source_name: Central memory, donor 12805

value: Central memory


title: Naive, donor 11405

description: Gene expression data on Naive cells from donor 11405

source_name: Naive, donor 11405


title: Perio_gingiva_CP1

description: Homo sapiens_EA0432_02

source_name: Periodontitis affected gingival tissue of patients 1.


title: PBMCs, donor 121704

description: Gene expression data on PBMCs from donor 121704

source_name: PBMCs, donor 121704


title: Naive, donor 121704

description: Gene expression data on Naive cells from donor 121704

source_name: Naive, donor 121704


title: Central memory, donor 12405

description: Gene expression data on Central memory cells from donor 12405

source_name: Central memory, donor 12405


title: Effector memory, donor 12405

description: Gene expression data on Effector memory cells from donor 12405

source_name: Effector memory, donor 12405


title: Central memory, donor 121704

description: Gene expression data on Central memory cells from donor 121704

source_name: Central memory, donor 121704


title: Healthy_gingiva_CP2

description: Homo sapiens_EA0432_03

source_name: Healthy gingival tissue of patient 2.

value: female


title: PBMCs, donor 12405

description: Gene expression data on PBMCs from donor 12405

source_name: PBMCs, donor 12405


title: Effector memory, donor 11405

description: Gene expression data on Effector memory cells from donor 11405

source_name: Effector memory, donor 11405


title: Naive, donor 12805

description: Gene expression data on Naive cells from donor 12805

source_name: Naive, donor 12805


title: Perio_gingiva_CP2

description: Homo sapiens_EA0432_04

source_name: Periodontitis affected gingival tissue of patients 2.


title: Central memory, donor 11405

description: Gene expression data on Central memory cells from donor 11405

source_name: Central memory, donor 11405


title: Central memory, donor 120604

description: Gene expression data on Central memory cells from donor 120604

source_name: Central memory, donor 120604


title: Complex I RNAi Mutant 5

status: Public on Feb 14 2008

city: Philadelphia

first: Marni

middle: J

last: Falk

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics/ Human Genetics

institute: CHOP

description: Gene expression data from mutant C. elegans

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G.

data_processing: Probe-level measurements were normalized, summarized and log2-transformed by dCHIP software using perfect-match-only and invariant-set methods.

organism: Caenorhabditis elegans

source_name: C. elegans young adult whole worms complex RNAi mutant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Revision 5, Affymetrix).

growth_protocol: C. elegans were grown for 2 generations on NGM agar 10 cm plates, spread with OP50, HT115, or RNAi-specific E. coli, as indicated in the description for each strain above.  Worms were then transferred for 3rd generation growth in liquid culture in either

extract_protocol: Trizol reagent was used according to the manufacturer's instructions to extract total RNA from approximately 0.2-2.0 g of C. elegans whole worms grown in liquid culture.  Following extraction, RNA from 3 biological replicates of each strain were combined

treatment_protocol: Liquid cultures of each strain were washed free of bacteria and subjected to sucrose centrifugation to enrich for Adult-stage animals.

tag: Genotype

value: ETC complex I mutant generated by feeding RNAi for D2030.4 allele (MRC GeneService clone ID I-3B20) to N2 larvae for 2 generations on plates, then 3rd generation in liquid culture, all in presence of 5 mM IPTG.

tag: Age

value: predominantly young adults (collected by sucrose gradient centrifugation)


title: Complex I missense mutant

source_name: C. elegans young adult whole worms with complex missense mutant

value: gas-1 (fc21) ETC Complex I missense mutation (allele = K09A9.5) - grown on OP50 plates, then K12 liquid culture


title: Wildtype, biological rep4

description: Gene expression data from wildtype C. elegans

source_name: Wildtype C. elegans young adult whole worms

growth_protocol: C. elegans were grown on NGM agar 10 cm plates spread with standard OP50 E. coli.  Synchrony was obtained by bleaching gravid adults, plating the recovered eggs on unspread NGM plates overnight, after which L1-stage arrested animals were transferred to NGM plates spread with standard OP50 E. coli.

extract_protocol: Trizol reagent was used according to the manufacturer's instructions to extract total RNA from aliquots of 500 to 1,000 sorted adult worms

treatment_protocol: Adult animals of each strain were sorted based on time of flight gated by size using an automated sorter (COPAS Biosort, Union Biometrica) to collect 5 biological replicates each consisteing of 1000 living adult worms.

value: N2 (Bristol) wildtype

value: young adults (confirmed by Biosort sorting)


title: Wildtype, biological rep3


title: Complex I RNAi Mutant 3

value: ETC complex I mutant generated by feeding RNAi for C34B2.8 allele (MRC GeneService clone ID I-5K22) to N2 larvae for 2 generations on plates, then 3rd generation in liquid culture, all in presence of 5 mM IPTG.


title: Wildtype (control for missense)

value: N2 (Bristol) wildtype - grown on OP50 plates, then K12 liquid culture


title: Complex II missense mutant

value: mev-1(kn1) ETC Complex II missense mutation (allele = T07C4.7) - grown on OP50 plates, then K12 liquid culture


title: Complex I RNAi Mutant 2

value: ETC complex I mutant generated by feeding RNAi for Y45G12B.1 allele (MRC GeneService clone ID V-2O04)) to N2 larvae for 2 generations on plates, then 3rd generation in liquid culture, all in presence of 5 mM IPTG.


title: Mutant, biological rep5

source_name: C. elegans young adult whole worms with mutation

value: gas-1 (fc21) ETC Complex missense mutation (allele = K09A9.5)


title: Wildtype, biological rep2


title: Complex I RNAi Mutant 1

source_name: C. elegans young adult whole worms with complex RNAi mutant

value: ETC complex I mutant generated by feeding RNAi for F22D6.4 allele (MRC GeneService clone ID I-3O24) to N2 larvae for 2 generations on plates, then 3rd generation in liquid culture, all in presence of 5 mM IPTG.


title: Wildtype (control for RNAi)

value: N2 (Bristol) wildtype - grown on HT115 both on plates and then in liquid culture


title: Mutant, biological rep4


title: Wildtype, biological rep1


title: Complex III missense mutant

value: isp-1(qm150) ETC Complex III missense mutation (allele = T07C4.7) - grown on OP50 plates, then K12 liquid culture


title: Mutant, biological rep3


title: Mutant, biological rep1


title: Complex I RNAi Mutant 4

value: ETC complex I mutant generated by feeding RNAi for Y56A3A.19 allele (MRC GeneService clone ID III-6K15) to N2 larvae for 2 generations on plates, then 3rd generation in liquid culture, all in presence of 5 mM IPTG.


title: Mutant, biological rep2


title: jzo024-rp1-v5-u74av2-met

status: Public on Apr 15 2004

city: Memphis

first: Jiewu

last: Liu

state: TN

address: 332 N. Lauderdale St.

department: Department of Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description: Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P18, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.

organism: Mus musculus

source_name: retina


title: jzo028-rp1-v5-u74av2-met

description: Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P14, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.


title: jzo018-rp1-v5-u74av2-met


title: jzo012-rp1-v5-u74av2-met


title: Wildtype, biological rep5


title: Pancreatic Sample 9-Normal

status: Public on Jun 10 2009

city: Rochester

first: Liewei

state: MN

address: 200 First street SW

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic

description: Gene expression of -PancreaticSample9-Normal

hyb_protocol: The targets for Affymetrix DNA microarray analysis were prepared according to the manufacturer’s instructions. Biotin-labeled cRNA, produced by in vitro transcription, was fragmented and hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays at 45°C for 16 hr and then washed and stained using the GeneChip Fluidics.

scan_protocol: The arrays were scanned by a GeneArray Scanner and patterns of hybridization detected as light emitted from the fluorescent reporter groups incorporated into the target and hybridized to oligonucleotide probes.

data_processing: The data were analyzed with Agilent Gene Spring GX 7.3 version using Affymetrix default analysis settings and GC-RMA as normalization method.

label_protocol: Lableing was performed according to Affymetrix Gene Chip technical manual

extract_protocol: RNA extraction was performed as Affymetrix GeneChip expression technical manual (Affymetrix, Inc., Santa Clara, CA). Briefly, total RNA samples were extracted, followed by measurement of the A2260/a280 ratio with at least 1.8 for pure RNA. Quality of the RNA was checked by an Agilent 2100 Bioanalyzer.  The Bioanalyzer gel profile exhibited a 28S band that is 2 times more intense than 18S ribosomal RNA. The quality of RNA was assessed by agarose gel electrophoresis.

value: Normal Tissue in Pancreatic Cancer Sample

tag: sex

value: Male

tag: age


title: jzo020-rp1-v5-u74av2-met.TXT

description: Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P21, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.


title: jzo032-rp1-v5_u74av2-met


title: jzo030-rp1-v5_u74av2-met


title: jzo014-rp1-v5-u74av2-met

description: Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P10, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.


title: jzo010-rp1-v5-u74av2-met


title: jzo034-rp1-v5_u74av2-met


title: jzo004-v5-u74av2-met


title: jzo026-rp1-v5-u74av2-met

description: Mice used were in a mixed background between 129/SvEv and C57BL/6. They were Rp1 knockout mice (Rp1-/-). At P7, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.


title: jzo022-rp1-v5-u74av2-met


title: jzo008-rp1-v5-u74av2-met


title: YRV_N99

status: Public on Apr 30 2008

city: Cambridge

first: Bernardo

last: Lemos

address: 16 Divinity Avenue, Room 2105

description: Y-chromosome substitution line

hyb_protocol: Genisphere 3DNA system

scan_protocol: Axon Scanner and Genepix

data_processing: The ratios were taken from the Limma package after loess normalization of the raw intensities data originally obtained in Genepix.

organism: Drosophila melanogaster

source_name: Ycongo

label_protocol: Genisphere 3DNA system

extract_protocol: Standard total RNA preps with Trizol

tag: Line

value: Ycongo; Sex:male; Temperature:25'C

source_name: Ymass

value: Ymass; Sex:male; Temperature:25'C


title: jzo016-rp1-v5-u74av2-met


title: jzo017-rp1-v5-u74av2-met

description: Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P18, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.


title: jzo019-rp1-v5-u74av2-met.TXT

description: Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P21, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.


title: jzo027-rp1-v5_u74av2-met

description: Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P14, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.


title: jzo033-rp1-v5_u74av2-met


title: jzo013-rp1-v5-u74av2-met

description: Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P10, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.


title: jzo031-rp1-v5_u74av2-met


title: jzo011-rp1-v5-u74av2-met


title: jzo023-rp1-v5-u74av2-met


title: jzo007-rp1-v5-u74av2-met


title: jzo029-rp1-v5_u74av2-met


title: Human Conjunctiva Donor 1

source_name: Conjunctiva

value: Conjunctiva


title: jzo009-rp1-v5-u74av2-met


title: jzo021-rp1-v5-u74av2-met

description: Mice used were in a mixed background between 129/SvEv and C57BL/6. They were wildtype littermates of Rp1-/- mice used in parallel experiments. At P7, mice were sacrificed, followed by removal of retinal. Each RNA sample included a pool of neural retinas from 3-4 mice. Retinas were all collected at 1-2 pm of the day.

source_name: retinal


title: jzo025-rp1-v5-u74av2-met


title: jzo015-rp1-v5-u74av2-met


title: jzo003-v5-u74av2-met