title: TOV-21G rep1

city: Torino

first: Raffaele

last: Calogero

address: Via Nizza 52

institute: University of Torino

hyb_protocol: Standard Illumina ibridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: data were analysed using BeadStudio version 1.5.1.3;  rank invariant normalization was performed

label_protocol: Biotilinated cRNA were prepared with the Ambion messageAmp for Illumina array

extract_protocol: Total RNA was extracted using the SV total RNA Isolation System (Promega,USA).

treatment_protocol: Exponentially growing cells were cultured for 24 hours and then treated with 10 microM cisplatin for 6, 12 and 24 hours

tag: cell type

value: ovarian cancer cells


title: TOV-21G treated with CDDP 12h rep1

status: Public on Dec 31 2013

type: RNA

middle: A

state: To

department: Molecular Biotechnology Center

country: Italy

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: TOV-21G_10µM CDDP_12hr

tag: cell line

tag: treated with

value: 10µM CDDP for 12hr


title: Colon_M

city: Tokyo

first: Fuyuki

last: Miya

state: Tokyo

address: 35 Shinanomachi, Shinjuku-ku

department: School of Medicine

country: Japan

institute: Keio University

description: colon Human Tiling 1.0R chip M

hyb_protocol: Approximately 6.0μg of DNA was hybridized per array using the Affymetrix hybridization kit. For these 14 array sets, 7 arrays were hybridized for 16 hours at 45°C at 60rpm using an Affymetrix hybridization oven. The hybridized solution was removed from these arrays and reused to hybridize the remaining seven arrays.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G. Images were quantified using GCOS software (Affymetrix). Signal values ware exported to text files using GCOS Manager software (Affymetrix).

data_processing:
The ".CEL" files are raw data. The "normalized.txt" files (supplementary data linked to GSE18490) are data normalized as follows.

1) To exclude potential low quality probes, we excluded probes that corresponded to the following conditions: A) probes for which either the Perfect Match (PM) or Miss Match (MM) probe perfectly match more than once in the genome, B) probes which contain SNPs, C) probes located on sex chromosomes.
2) To reduce inter-chip differences, we equalized the mean and variance of probe intensities among all chips in each tissue. Note that the intensities were converted to a logarithmic scale (base 2).
3) To reduce background noise, we subtracted the intensity of each MM probe from the PM probe in each probe set. If the value was negative, zero was assigned as the value.
4) To adjust for GC content of probes, we calculated normalized intensities by each GC content.
5) To equalize the distribution of signals in each chip, we performed quantile normalization for each chip
6) To smooth the probe intensities with neighboring probes, we calculated Hodges-Lehmann statistics. The size of each sliding window was 101bp.
7) All probes that ranked higher than the top 15% signal threshold were selected and those with an inter-probe distance less than a maximum gap threshold of 25bp were concatenated. Then, the concatenated probes with length longer than a minimum run threshold of 101bp were defined as transfrags. Finally, we performed BLAST to exclude probes that mapped to multiple locations.

label: biotin

source_name: pooled Human colon total RNA

label_protocol: Reverse transcription, amplification, fragmentation and labeling steps were performed according to Affymetrix protocol using WT Amplified Double-Strand cDNA Synthesis Kit (Affymetrix) and WT Double-Strand DNA Terminal Labeling Kit (Affymetrix).

extract_protocol: Samples of total RNA from Human tissues were purchased from several companies (Clontech, Ambion, Stratagene, Cell Applications). HeLa and SH-SY5Y cells were cultured in standard DMEM / 10% FBS medium. Total RNA was extracted from cells with TRIzol regent (Invitrogen). Additionally, total RNA was purified with Rneasy Mini Kit (Qiagen) and treated with RNase-free DNase Set (Qiagen) to remove any contaminating genomic DNA.

tag: tissue

value: colon

tag: race

value: caucasian


title: Cortex-PC-24h-Rep2

city: Hobart

first: Minghui Jessica

last: Chen

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

country: Australia

institute: Menzies Research Institute

description:
Replicate 2
4514990042_C

hyb_protocol: Standard Illumina hybridization protocol with a hybridization duration of 17h.

scan_protocol: Standard Illumina scanning protocol with a pmt value=478

data_processing: The data were normalised using median normalisation with GeneSpring Ver 7.3

organism: Mus musculus

source_name: Infarct Cortex

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

growth_protocol: All animal work conducted in this study was approved by the University of New South Wales (UNSW) Animal Ethics and Experimentation Committee and performed in accordance with the guidelines of the National Health and Medical Research Council (Australia). C57 Black 6 mouse pups were obtained from Animal Resources Centre (Perth, WA) and were housed under standard housing conditions in the UNSW Biological Resources Centre animal facility throughout experiments.

extract_protocol: RNA was extracted and cleaned up with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with E-gene HDA-GT12 genetic analyzer.

treatment_protocol: Pups were anesthetized with 1.5% isoflurane in 30% O2/70% N2 mixture and underwent unilateral HI. The right common carotid artery was exposed through a ventral midline neck incision and permanently occluded by electrocoagulation (Aaron Medical Industries Inc, Florida, USA), where the occlusion was verified The wound was sutured and mouse pups were returned to their mother for 1.5–2 h. Sham control rats (n = 4) underwent the identical procedure, without carotid artery occlusion.  Pups were then placed in an 8% O2/92% N2 humidified chamber at 37°C for 1 h. This combined procedure results in select neuronal damage or infarction in the hemisphere ipsilateral to the carotid occlusion, whereas hypoxia alone (contralateral hemisphere) does not produce any significant brain injury (reference). Following the HI or sham surgery procedure, all pups were returned to their dam and kept under standard housing conditions for the remainder of the study.

tag: strain

tag: age

value: 8 days

tag: treatment

value: Hypoxic pre-conditioning

tag: time point

value: brain cortex


title: Cortex-PC-24h-Rep3

description:
Replicate 3
4514990040_D


title: TOV-21G treated with CDDP 6h rep1

source_name: TOV-21G_10µM CDDP_6h

value: 10µM CDDP for 6h


title: TOV-21G rep2


title: Cortical neurons-AMPA-15h-Rep 2

description:
4068838002_E
Replicate 2

source_name: Murine primary cortical neurons

growth_protocol: Neocortical neurons (gestational days 15 or 16) obtained from foetal cortices of Swiss albino mice were used to prepare the primary cultures employing previous described procedures with modifications [Cheung NS, Beart PM, Pascoe CJ, John CA, Bernard O. Human Bcl-2 protects against AMPA receptor-mediated apoptosis. J Neurochem. 2000; 74: 1613-1620.].

extract_protocol: RNA was extracted and cleaned up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with E-gene HDA-GT12 genetic analyzer.

treatment_protocol: AMPA (Sigma- Aldrich) was dissolved in 100mM NaOH to give a 55mM stock concentration which was stored at -20°C. The stock solution was further diluted down to 300uM in NeuroBasal medium for drug treatment on neuron cultures. Neuronal samples then collected for global gene expression analyses.

value: Swiss Albino mice

value: Gestation day 15-16

value: Primary cortical neurons

tag: age of  culture

value: Day 5

tag: agent

value: 300uM AMPA

tag: treatment time-point


title: 1 dpf-DMSO-rep1

city: houston

first: Ruixin

last: Hao

state: TX

address: 3605 Cullen Blvd, Room 3005

department: Department of biology and biochemistry

country: USA

institute: University of Houston

description:
Gene expression of 1 dpf embryos after 1 day  of 0.1% DMSO treatment
Sample name: 24979

hyb_protocol: The Agilent’s Hybridization Kit was used for the hybridization. After Cy3 labeling, the samples were fragmented and 1.65 µg of sample and hybridization mix was loaded onto each of the 4x44K Expression arrays. The slide was hybridized in Agilent Hybridization Chamber at 65C at a 10rpm rotation for 17 hours. The slide was washed using the Agilent Expression Wash Buffer Set 1 and 2 as per the Agilent protocol. Performed by Performed by Genomic and RNA Profiling Core, Baylor College of Medicine.

scan_protocol: The slides were scanned with the Agilent Scanner (G2565BA) using Scanner Version C. Performed by Genomic and RNA Profiling Core, Baylor College of Medicine.

data_processing: The Agilent Feature Extraction Software Version 11.0.1.1 was used to analyze the scanned images and processed Signal intensities were obtained after background substraction. Performed by Genomic and RNA Profiling Core, Baylor College of Medicine.

organism: Danio rerio

source_name: Whole embryo, 1 dpf, 0.1% DMSO control treatment, replicate 1

label_protocol: The Agilent Quick Amp Labeling Kit (for one-color) Protocol Version 6.5 was used.  The Labeling Kit (Agilent p/n 5190-0442) was used along with Agilent’s RNA Spike-In Kit and Agilent’s Wash Buffers 1 and 2. The RNA Spike-Ins was added to the sample. The sample was simultaneously amplified and Cy3 dye labeled as cRNA was generated using T7 RNA Polymerase. The cRNA was purified using Qiagen RNeasy mini spin columns. Samples were then measured again on the Nanodrop for yield and dye incorporation. Performed by Genomic and RNA Profiling Core, Baylor College of Medicine.

growth_protocol: Zebrafish embryos were collected after spawning and allowed to develop in a Petri dish in embryo medium (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4) at 28.5˚C with 14:10 LD (14:10 LD; lights on 8 AM; lights off 10 PM.) .

extract_protocol: Total RNA from pooled embryos was extracted using Trizol (Invitrogen Corporation, Carlsbad, CA) and RNeasy spin columns (Qiagen, Chatsworth, CA) according to the manufacturer’s protocols. On-column DNase I (Qiagen, Chatsworth, CA) digestion was performed to remove remaining DNA. RNA concentrations were measured with NanoDrop 1000 spectrophotometer (Agilent Technologies, Palo Alto, CA) and RNA integrity was analyzed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: 17β-estradiol (E2) at a 1 mM stock solution in 100% dimethylsulfoxide (DMSO) was diluted in embryo medium to obtain 1 μM concentrations. A clutch of zebrafish embryos from several pairs of adult fish were divided and transferred into 6 well plates. 30 embryos were pooled as one sample and exposed to 3 ml 1 μM E2 or vehicle (0.1% DMSO) at approximately 3 hours post fertilization (hpf). Embryo media containing E2 were changed every day. At different time points, 1 dpf (24 hpf), 2 dpf (48 hpf), 3 dpf (72 hpf) and 4 dpf (104 hpf), embryos were collected for RNA extractions.

value: DMSO

tag: time

value: 1 day

tag: developmental stage

value: 1 dpf embryo

value: Whole embryo


title: Cerebellum_M

description: cerebellum Human Tiling 1.0R chip M

source_name: pooled Human cerebellum total RNA

value: cerebellum


title: Cortical neurons-AMPA-24h-Rep 2

description:
4068838002_G
Replicate 2


title: Cortical neurons-AMPA-24h-Rep 1

description:
4068838001_G
Replicate 1


title: NIH:OVCAR-3 treated with CDDP 12h rep3

source_name: NIH:OVCAR-3_10µM CDDP_12hr

value: ovarian cancer cells

value: 10µM CDDP for 12hr


title: Cortical neurons-AMPA-15h-Rep 3

description:
4068838003_E
Replicate 3


title: TOV-21G treated with CDDP 12h rep2


title: NIH:OVCAR-3 treated with CDDP 6h rep3

source_name: NIH:OVCAR-3_10µM CDDP_6h


title: Cortex-PC-24h-Rep1

description:
Replicate 1
4514990042_D


title: NIH:OVCAR-3 rep3


title: Cortex-Sham-24h-Rep2

description:
Replicate 2
4514990042_A

value: Ctrl


title: Cortex-Sham-24h-Rep3

description:
Replicate 3
4514990040_B

value: 8 days


title: BoneMarrow_M

description: bone marrow Human Tiling 1.0R chip M

source_name: pooled Human bone marrow total RNA

value: bone marrow

value: caucasian


title: Cortical neurons-AMPA-24h-Rep 3

description:
4068838003_G
Replicate 3


title: SHSY5Y_F

description: SH-SY5Y cells Human Tiling 1.0R chip F

source_name: pooled Human SH-SY5Y cells total RNA


title: NIH:OVCAR-3 treated with CDDP 6h rep2

value: 10µM CDDP for 6h


title: Cortex-Sham-24h-Rep1

description:
Replicate 1
4514990155_B

value: brain cortex


title: Cortical neurons-AMPA-5h-Rep 3

description:
4068838003_C
Replicate 3

value: Swiss Albino mice

value: Gestation day 15-16


title: HeLa_F

description: HeLa cells Human Tiling 1.0R chip F

source_name: Human HeLa cells total RNA

value: HeLa


title: Cortex-HI+PC-8h-Rep3

description:
Replicate 3
4514990041_H

value: Pre-conditioning+Hypoxic ischemia


title: Uterus_F

description: uterus Human Tiling 1.0R chip F

source_name: pooled Human uterus total RNA

value: uterus


title: Trachea_F

description: trachea Human Tiling 1.0R chip F

source_name: pooled Human trachea total RNA

value: trachea


title: Thyroid_F

description: thyroid Human Tiling 1.0R chip F

source_name: pooled Human thyroid total RNA

value: thyroid


title: Cortex-Sham-24h-Rep4

description:
Replicate 4
4514990040_A


title: Cortical neurons-AMPA-15h-Rep 1

description:
4068838001_E
Replicate 1

value: Primary cortical neurons

value: Day 5

value: 300uM AMPA


title: Cortex-HI+PC-8h-Rep2

description:
Replicate 2
4514990043_H


title: Cortical neurons-AMPA-5h-Rep 2

description:
4068838002_C
Replicate 2


title: Cortical neurons-AMPA-5h-Rep 1

description:
4068838001_C
Replicate 1


title: Cortical neurons-Ctrl-Rep 6 [AMPA, KA]

description:
4068838003_B
Replicate 6

value: none, control


title: NIH:OVCAR-3 treated with CDDP 6h rep1

value: ovarian cancer cells


title: Thymus_F

description: thymus Human Tiling 1.0R chip F

source_name: pooled Human thymus total RNA

value: thymus


title: Cortical neurons-Ctrl-Rep 5 [AMPA, KA]

description:
4068838003_A
Replicate 5


title: Cortex-HI-8h-Rep2

description:
Replicate 2
4514990043_G

value: 8 days

value: Hypoxic ischemia


title: Cortex-HI-8h-Rep1

description:
Replicate 1
4514990159_G


title: Cortex-HI-8h-Rep3

description:
Replicate 3
4514990041_G


title: NIH:OVCAR-3 treated with CDDP 12h rep1

value: 10µM CDDP for 12hr


title: NIH:OVCAR-3 rep2


title: Stomach_F

description: stomach Human Tiling 1.0R chip F

source_name: pooled Human stomach total RNA

value: stomach

value: caucasian


title: SK-OV-3 treated with CDDP 24h rep3

source_name: SK-OV-3_10µM CDDP_24h

value: 10µM CDDP for 24h


title: TOV-21G treated with CDDP 6h rep2

value: 10µM CDDP for 6h


title: SK-OV-3 treated with CDDP 6h rep3

source_name: SK-OV-3_10µM CDDP_6h


title: NIH:OVCAR-3 rep1


title: Spleen_F

description: spleen Human Tiling 1.0R chip F

source_name: pooled Human spleen total RNA

value: spleen


title: Cortical neurons-Ctrl-Rep 2 [AMPA, KA]

description:
4068838001_B
Replicate 2

value: Swiss Albino mice

value: Gestation day 15-16


title: Cortical neurons-Ctrl-Rep 3 [AMPA, KA]

description:
4068838002_A
Replicate 3


title: Testes_F

description: testes Human Tiling 1.0R chip F

source_name: pooled Human testes total RNA

value: testes


title: SK-OV-3 rep3


title: SK-OV-3 treated with CDDP 6h rep2


title: Cortex-PC-8h-Rep3

description:
Replicate 3
4514990043_F

source_name: Infarct Cortex

value: Hypoxic pre-conditioning

value: brain cortex


title: SpinalCord_F

description: spinal cord Human Tiling 1.0R chip F

source_name: pooled Human spinal cord total RNA

value: spinal cord


title: SmallIntestine_F

description: small intestine Human Tiling 1.0R chip F

source_name: pooled Human small intestine total RNA

value: small intestine


title: SK-OV-3 treated with CDDP 24h rep2

value: ovarian cancer cells


title: Cortex-PC-8h-Rep2

description:
Replicate 2
4514990155_F


title: Cortex-HI+PC-8h-Rep1

description:
Replicate 1
4514990159_H

value: Pre-conditioning+Hypoxic ischemia


title: Cortex-PC-8h-Rep1

description:
Replicate 1
4514990159_F

value: 8 days


title: SkeletalMuscle_F

description: skeletal muscle Human Tiling 1.0R chip F

source_name: pooled Human skeletal muscle total RNA

value: skeletal muscle


title: Cortex-Sham-8h-Rep4

description:
Replicate 4
4514990041_E

value: Ctrl


title: SalivaryGland_F

description: salivary gland Human Tiling 1.0R chip F

source_name: pooled Human salivary gland total RNA

value: salivary gland


title: Cortical neurons-Ctrl-Rep 1 [AMPA, KA]

description:
4068838001_A
Replicate 1

source_name: Murine primary cortical neurons

value: Primary cortical neurons

value: Day 5

value: none, control


title: SK-OV-3 treated with CDDP 24h rep1

value: 10µM CDDP for 24h


title: Prostate_F

description: prostate Human Tiling 1.0R chip F

source_name: pooled Human prostate total RNA

value: prostate

value: caucasian


title: Pancreas_F

description: pancreas Human Tiling 1.0R chip F

source_name: pooled Human pancreas total RNA

value: pancreas


title: Lung_F

description: lung Human Tiling 1.0R chip F

source_name: pooled Human lung total RNA

value: lung


title: Liver_F

description: liver Human Tiling 1.0R chip F

source_name: pooled Human liver total RNA

value: liver


title: Cortex-PC-8h-Rep4

description:
Replicate 4
4514990041_F

value: Hypoxic pre-conditioning

value: brain cortex


title: Cortex-Sham-8h-Rep2

description:
Replicate 2
4514990155_E


title: SK-OV-3 rep2

value: ovarian cancer cells


title: Cortical neurons-Glutamate-24h-Rep 1

description: Replicate 1

treatment_protocol: Anydrous form of L-Glutamate  (Sigma, Louis, MO) were freshly prepared in water upon usage to get a stock concentration of 100 mM respectively. Desired concentrations were achieved through dilution with NB medium. Day 7 cultured murine cortical neurons were treated with 250μM Glutamate respectively over a time course of 5h, 15h and 24h. Neuronal samples then collected for global gene expression analyses.

value: Swiss Albino mice

value: Gestation day 15-16

tag: tissue type

tag: age of culture

value: Day 7

value: Glutamate


title: Cortical neurons-Glutamate-24h-Rep 3

description: Replicate 3


title: SK-OV-3 treated with CDDP 6h rep1

value: 10µM CDDP for 6h


title: Cortex-Sham-8h-Rep1

description:
Replicate 1
4514990159_E

value: 8 days

value: Ctrl


title: Kidney_F

description: kidney Human Tiling 1.0R chip F

source_name: pooled Human kidney total RNA

value: kidney


title: Cortical neurons-Glutamate-15h-Rep 1

description: Replicate 1

value: Primary cortical neurons


title: Cortical neurons-Ctrl-Rep 4 [AMPA, KA]

description:
4068838002_B
Replicate 4

value: Day 5

value: none, control


title: Cortical neurons-Glutamate-24h-Rep 2

description: Replicate 2


title: Cortex-HI+PC-3h-Rep3

description:
Replicate 3
4625024048_H

value: Pre-conditioning+Hypoxic ischemia


title: SK-OV-3 rep1


title: Heart_F

description: heart Human Tiling 1.0R chip F

source_name: pooled Human heart total RNA

value: heart

value: caucasian


title: Cortical neurons-Glutamate-15h-Rep 2

description: Replicate 2


title: Cortical neurons-Glutamate-15h-Rep 3

description: Replicate 3


title: FetalBrain_F

description: fetal brain Human Tiling 1.0R chip F

source_name: pooled Human fetal brain total RNA

value: fetal brain


title: Cortex-HI+PC-3h-Rep1

description:
Replicate 1
4625024059_H

value: brain cortex


title: Cortex_F

description: cortex Human Tiling 1.0R chip F

source_name: pooled Human cortex total RNA

value: cortex


title: Cortical neurons-Glutamate-5h-Rep 2

description: Replicate 2

value: Swiss Albino mice


title: Cortex-HI+PC-3h-Rep2

description:
Replicate 2
4625024054_H


title: Cortex-Sham-8h-Rep3

description:
Replicate 3
4514990043_E


title: Cortical neurons-Ctrl-Rep 6

description: Replicate 6

value: Gestation day 15-16

value: vehicle control


title: Cortex-HI-3h-Rep4

description:
Replicate 4
4625024047_G

value: Hypoxic ischemia


title: SHSY5Y_L

description: SH-SY5Y cells Human Tiling 1.0R chip L

source_name: pooled Human SH-SY5Y cells total RNA


title: Cortical neurons-Glutamate-5h-Rep 3

description: Replicate 3

value: Day 7

value: Glutamate


title: Cerebellum_F

description: cerebellum Human Tiling 1.0R chip F

source_name: pooled Human cerebellum total RNA

value: cerebellum


title: HeLa_L

description: HeLa cells Human Tiling 1.0R chip L

source_name: Human HeLa cells total RNA

value: HeLa


title: Cortex-HI+PC-3h-Rep4

description:
Replicate 4
4625024047_H

source_name: Infarct Cortex

value: 8 days


title: BoneMarrow_F

description: bone marrow Human Tiling 1.0R chip F

source_name: pooled Human bone marrow total RNA

value: bone marrow


title: Cortex-HI-3h-Rep2

description:
Replicate 2
4625024054_G


title: Cortical neurons-Glutamate-5h-Rep 1

description: Replicate 1

value: Primary cortical neurons


title: Cortical neurons-Ctrl-Rep 4

description: Replicate 4


title: Trachea_L

description: trachea Human Tiling 1.0R chip L

source_name: pooled Human trachea total RNA

value: trachea


title: Cortex-HI-3h-Rep1

description:
Replicate 1
4625024059_G


title: Colon_F

description: colon Human Tiling 1.0R chip F

source_name: pooled Human colon total RNA

value: colon


title: Cortical neurons-Ctrl-Rep 3

description: Replicate 3


title: Thyroid_L

description: thyroid Human Tiling 1.0R chip L

source_name: pooled Human thyroid total RNA

value: thyroid

value: caucasian


title: Cortical neurons-Ctrl-Rep 2

description: Replicate 2

source_name: Murine primary cortical neurons


title: 8 uM Salinomycin JLO-1

city: La Jolla

first: Alan

last: Kiang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

description: microRNA profiling

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were analyzed using Multiexperiment Viewer

source_name: JLO-1 (Laryngeal Cancer Stem Cell)

growth_protocol: JLO-1 cells are grown in keratinocyte serum free medium supplemented with EGF and bFGF.

extract_protocol: RNA was extracted with Applied Biosystems miRvana Isolation Kit following manufacturer's instructions.

treatment_protocol: JLO-1 Cells were treated with the indicated doses of salinomycin for 48 hours prior to microRNA extraction.

value: JLO-1 Laryngeal Cancer Stem Cell line

value: Salinomycin

tag: concentration

value: 8 uM


title: 4 uM Salinomycin JLO-1

description: microRNA profiling

value: 4 uM


title: Thymus_L

description: thymus Human Tiling 1.0R chip L

source_name: pooled Human thymus total RNA

value: thymus


title: Cortical neurons-Ctrl-Rep 5

description: Replicate 5

value: Swiss Albino mice

value: Gestation day 15-16

value: vehicle control


title: Cortex-PC-3h-Rep2

description:
Replicate 2
4625024054_F

value: Hypoxic pre-conditioning

value: brain cortex


title: 2 uM Salinomycin JLO-1

description: microRNA profiling

value: 2 uM


title: Uterus_L

description: uterus Human Tiling 1.0R chip L

source_name: pooled Human uterus total RNA

value: uterus


title: Testes_L

description: testes Human Tiling 1.0R chip L

source_name: pooled Human testes total RNA

value: testes


title: 1 uM Salinomycin JLO-1

description: microRNA profiling

value: 1 uM


title: 0.5 uM Salinomycin JLO-1

description: microRNA profiling


title: Cortex-Sham-3h-Rep3

description:
Replicate 3
4625024047_E

value: 8 days

value: Ctrl


title: Cortical neurons-Ctrl-Rep 1

description: Replicate 1

value: Primary cortical neurons

value: Day 7


title: Stomach_L

description: stomach Human Tiling 1.0R chip L

source_name: pooled Human stomach total RNA

value: stomach

value: caucasian


title: Spleen_L

description: spleen Human Tiling 1.0R chip L

source_name: pooled Human spleen total RNA

value: spleen


title: Cortex-PC-3h-Rep4

description:
Replicate 4
4625024047_F


title: Cortex-Sham-3h-Rep2

description:
Replicate 2
4625024048_E


title: 0 uM Salinomycin JLO-1

description: microRNA profiling

value: JLO-1 Laryngeal Cancer Stem Cell line

value: Untreated (Ethanol vehicle used)

value: 0 uM


title: Cortex-PC-3h-Rep3

description:
Replicate 3
4625024048_F


title: SpinalCord_L

description: spinal cord Human Tiling 1.0R chip L

source_name: pooled Human spinal cord total RNA

value: spinal cord


title: Cortex-Sham-3h-Rep1

description:
Replicate 1
4625024054_E


title: SkeletalMuscle_L

description: skeletal muscle Human Tiling 1.0R chip L

source_name: pooled Human skeletal muscle total RNA

value: skeletal muscle


title: Cortex-HI+PC-0h-Rep3

description:
Replicate 3
4625024017_H

value: Pre-conditioning+Hypoxic ischemia

value: brain cortex


title: SalivaryGland_L

description: salivary gland Human Tiling 1.0R chip L

source_name: pooled Human salivary gland total RNA

value: salivary gland


title: Cortex-HI+PC-0h-Rep1

description:
Replicate 1
4625024032_H


title: SmallIntestine_L

description: small intestine Human Tiling 1.0R chip L

source_name: pooled Human small intestine total RNA

value: small intestine


title: Cortex-HI-0h-Rep2

description:
Replicate 2
4625024023_G

value: Hypoxic ischemia


title: HT1080-ING2_6K-DMSO-02

city: Stanford

first: Dennis

middle: Jacob

last: Bua

address: Gilbert Building, Room 109, 371 Serra Mall

department: Biology

institute: Stanford University

description: replicate 2

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: GeneSpring rank invariant

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion)

growth_protocol: HT1080 cell lines (ATCC) were cultured in Advanced DMEM (Invitrogen) supplemented with penicillin-streptomycin (Invitrogen), glutamine (Invitrogen), and 10% newborn calf serum (Atlanta).

extract_protocol: Rneasy Plus mini kit (Qiagen)

treatment_protocol: HT1080 cells were treated with Etoposide (100 uM) or vehicle (DMSO) for 16hrs, then they were collected for subsequent RNA extraction.

value: DMSO


title: Cortex-PC-3h-Rep1

description:
Replicate 1
4625024059_F

value: 8 days

value: Hypoxic pre-conditioning


title: HT1080-ING2_6K-DMSO-03

description: replicate 3


title: HT1080-ING2_WT-DMSO-03

description: replicate 3


title: Cortex-HI+PC-0h-Rep2

description:
Replicate 2
4625024023_H


title: Prostate_L

description: prostate Human Tiling 1.0R chip L

source_name: pooled Human prostate total RNA

value: prostate


title: HT1080-ING2_6K-ETOPO-03

description: replicate 3

value: Etoposide (100uM)


title: Cortex-HI-0h-Rep1

description:
Replicate 1
4625024032_G

source_name: Infarct Cortex


title: kaiA-overexpressor at LL36 +IPTG (hour 12)

first: Hideo

last: Iwasaki

address: TWIns 1F 2-2 Wakamatsu-cho, Shinjuku

department: Electrical Engineering & Bioscience

institute: Waseda University

description:
Gene expression data from Synechococcus elongatus PCC 7942
oxA LL36 +IPTG

hyb_protocol: Following fragmentation, 1.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Synechococcus Custom Arrays (Syel6301a520114F). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) ver 1.2.1.001 using Affymetrix default analysis settings to obtain raw data.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: Synechococcus Ptrc::kaiA cells at LL36 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture with 1 mM IPTG (hour 12 after IPTG-induction)

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix prokaryotic protocol from 10 ug total RNA (Expression Analysis Technical Manual)

growth_protocol: Synechococcus cells were grown in continuous culture systems in any conditions at 30C under the light (40 micromol/m^2/sec)

extract_protocol: Total RNAs were extracted with a modified hot-phenol extraction method

treatment_protocol: Cells were collected at indicated times and stored at -80C until use

tag: genotype

value: IPTG-inducible kaiA overexpressor strain containing PpsbAI::luxAB construct with a spectinomycin-resistance gene at the neutral site I (NSI) and Ptrc::kaiA construct with a kanamycin-resistance gene at the neutral site II (NSII)

value: IPTG

value: LL36 (hour 12)


title: Cortex-HI-0h-Rep3

description:
Replicate 3
4625024017_G


title: kaiA-overexpressor at LL42 -IPTG (hour 18)

description:
Gene expression data from Synechococcus elongatus PCC 7942
oxA LL42 -IPTG

source_name: Synechococcus Ptrc::kaiA cells at LL42 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture without IPTG (control)

value: without IPTG (control)

value: LL42 (hour 18)


title: HT1080-ING2_6K-DMSO-01

description: replicate 1

tag: cell line


title: kaiA-overexpressor at LL48 +IPTG (hour 24)

description:
Gene expression data from Synechococcus elongatus PCC 7942
oxA LL48 +IPTG

source_name: Synechococcus Ptrc::kaiA cells at LL48 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture with 1 mM IPTG (hour 24 after IPTG-induction)

value: LL48 (hour 24)


title: HT1080-ING2_WT-ETOPO-03

description: replicate 3


title: Pancreas_L

description: pancreas Human Tiling 1.0R chip L

source_name: pooled Human pancreas total RNA

value: pancreas

value: caucasian


title: kaiA-overexpressor at LL36 -IPTG (hour 12)

description:
Gene expression data from Synechococcus elongatus PCC 7942
oxA LL36 -IPTG

source_name: Synechococcus Ptrc::kaiA cells at LL36 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture without IPTG (control)


title: kaiA-overexpressor at LL48 -IPTG (hour 24)

description:
Gene expression data from Synechococcus elongatus PCC 7942
oxA LL48 -IPTG

source_name: Synechococcus Ptrc::kaiA cells at LL48 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture without IPTG (control)


title: Cortex-PC-0h-Rep4

description:
Replicate 4
4625024017_F

value: brain cortex


title: kaiA-overexpressor at LL30 +IPTG (hour 6)

description:
Gene expression data from Synechococcus elongatus PCC 7942
oxA LL30 +IPTG

source_name: Synechococcus Ptrc::kaiA cells at LL30 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture with 1 mM IPTG (hour 6 after IPTG-induction)

value: LL30 (hour 6)


title: Cortex-PC-0h-Rep3

description:
Replicate 3
4625024023_F


title: Lung_L

description: lung Human Tiling 1.0R chip L

source_name: pooled Human lung total RNA

value: lung


title: HT1080-ING2_6K-ETOPO-02

description: replicate 2


title: kaiA-overexpressor at LL42 +IPTG (hour 18)

description:
Gene expression data from Synechococcus elongatus PCC 7942
oxA LL42 +IPTG

source_name: Synechococcus Ptrc::kaiA cells at LL42 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture with 1 mM IPTG (hour 18 after IPTG-induction)


title: Liver_L

description: liver Human Tiling 1.0R chip L

source_name: pooled Human liver total RNA

value: liver


title: Kidney_L

description: kidney Human Tiling 1.0R chip L

source_name: pooled Human kidney total RNA

value: kidney


title: SHSY5Y_A

description: SH-SY5Y cells Human Tiling 1.0R chip A

source_name: pooled Human SH-SY5Y cells total RNA


title: HT1080-ING2_6K-ETOPO-01

description: replicate 1


title: Heart_L

description: heart Human Tiling 1.0R chip L

source_name: pooled Human heart total RNA

value: heart


title: HT1080-ING2_WT-DMSO-02

description: replicate 2

value: DMSO


title: kaiA-overexpressor at LL30 -IPTG (hour 6)

description:
Gene expression data from Synechococcus elongatus PCC 7942
oxA LL30 -IPTG

source_name: Synechococcus Ptrc::kaiA cells at LL30 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture without IPTG (control)


title: HeLa_A

description: HeLa cells Human Tiling 1.0R chip A

source_name: Human HeLa cells total RNA

value: HeLa


title: FetalBrain_L

description: fetal brain Human Tiling 1.0R chip L

source_name: pooled Human fetal brain total RNA

value: fetal brain


title: kaiA-overexpressor at LL24 -IPTG (hour 0)

description:
Gene expression data from Synechococcus elongatus PCC 7942
oxA LL24 -IPTG

source_name: Synechococcus Ptrc::kaiA cells at LL24 under continuous light (LL) after two 12-h:12-h light/dark cycles from a continuous culture without IPTG (control)

value: IPTG-inducible kaiA overexpressor strain containing PpsbAI::luxAB construct with a spectinomycin-resistance gene at the neutral site I (NSI) and Ptrc::kaiA construct with a kanamycin-resistance gene at the neutral site II (NSII)

value: LL24 (hour 0)


title: HT1080-ING2_WT-DMSO-01

description: replicate 1


title: Uterus_A

description: uterus Human Tiling 1.0R chip A

source_name: pooled Human uterus total RNA

value: uterus


title: HT1080-ING2_WT-ETOPO-02

description: replicate 2

value: Etoposide (100uM)


title: Cortex-PC-0h-Rep2

description:
Replicate 2
4625024032_F

source_name: Infarct Cortex

value: 8 days

value: Hypoxic pre-conditioning


title: Cortex-PC-0h-Rep1

description:
Replicate 1
4625024044_F


title: Cortex_L

description: cortex Human Tiling 1.0R chip L

source_name: pooled Human cortex total RNA

value: cortex


title: HT1080-ING2_WT-ETOPO-01

description: replicate 1


title: Trachea_A

description: trachea Human Tiling 1.0R chip A

source_name: pooled Human trachea total RNA

value: trachea

value: caucasian


title: Cortex-Sham-0h-Rep3

description:
Replicate 3
4625024023_E

value: Ctrl

value: brain cortex


title: Cerebellum_L

description: cerebellum Human Tiling 1.0R chip L

source_name: pooled Human cerebellum total RNA

value: cerebellum


title: Thymus_A

description: thymus Human Tiling 1.0R chip A

source_name: pooled Human thymus total RNA

value: thymus


title: 6983-10

city: San Francisco

first: Stephanie

last: Christenson

state: California

address: 513 PARNASSUS AVENUE, HSE1305

department: Pulmonary and Critical Care

institute: University of California, San Francisco

description: Low molecular weight RNA was hybridized to Invitrogen NCode microRNA microarrays, containing 1053 microRNAs across 6 species, including 467 human microRNAs. All microRNA spots were printed in triplicate. Blank spots containing no printed sequence served as background. Data was quantile normalized and log transformed. Only miRNA replicates 2 standard deviations above background were considered for further analysis

hyb_protocol: 5uL of 10% BSA and 28.5uL of 2X enhanced hybridization buffer (Genisphere, Hatfield, PA) were added to the sample to make the hybridization mix. This was applied to Invitrogen NCode miRNA microarrays containing 1053 miRNAs from 6 species (467 human miRNAs) printed in triplicate. The arrays incubated overnight (18 hours) in a humidified chamber at 52oC and the following morning, serial 15 minute washes were done with 2x SSC/0.2% SDS at 52oC, 2x SSC at room temperature and 0.2X SSC at room temperature.

scan_protocol: After drying, the arrays were scanned on a GenePix 4000 scanner (Axon/Molecular Devices, Sunnyvale CA).

data_processing: Raw data was extracted using GenePix Pro 4.0 (Molecular Devices Corporation, Sunnyvale, CA), quantile normalized and log transformed using the limma package for R (http://www.r-project.org/). Only miRNA replicates that were detected at levels two standard deviations above the average background in at least 80% of samples were considered for further analysis. The median of the remaining replicates for each miRNA was then taken to obtain a single expression value for each miRNA.

label: fluorescent dendrimer with approximately 15 molecules of Oyster®-550 dye

source_name: Whole lung tissue

label_protocol: 300 ng of LMW RNA were labeled using the FlashTag labeling kit (Genisphere, Inc., Hatfield, PA). MicroRNA were first poly-A tailed and then directly ligated to a fluorescent dendrimer (a branched DNA structure carrying approximately 15 molecules of Oyster®-550 dye (DeNovo Biolabels GmBH, Munster, Germany)).

extract_protocol: Low molecular weight RNA was isolated from tissue cores using the miRNeasy Mini Kit (Qiagen). The RNA integrity was assessed using an Agilent 2100 Bioanalyzer and RNA purity was assessed using a NanoDrop spectrophotometer. 300 ng of low molecular weight RNA was processed and used as starting material for the microarray studies

tag: copd status

value: Donor

tag: slice

tag: lm

tag: Sex

value: Male

tag: pack years

tag: notes

tag: disease state

value: control

value: lung


title: Testes_A

description: testes Human Tiling 1.0R chip A

source_name: pooled Human testes total RNA

tag: tissue

value: testes

tag: race


title: Cortex-Sham-0h-Rep4

description:
Replicate 4
4625024017_E

tag: strain

tag: age

tag: treatment

tag: time point


title: Cortex-Sham-0h-Rep2

description:
Replicate 2
4625024032_E


title: Day 13

city: Los Angeles

first: Minhyung

last: Kim

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

scan_protocol: Illumina BeadScan 500 System

data_processing: The data were normalised using quantile normalization method with BeadArray version 1.10 and lumi version 1.8.3 in R/Bioconductor package.

source_name: Human cord blood-derived EPCs, day 13

label_protocol: Refer to the Illumina Gene Expression System Manual

growth_protocol: Cord blood-derived EPCs isolated by using Ficoll-Paque density gradient centrifugation system. EPCs cultured under endothelial differentiation conditions.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: partially differentiated EPCs

value: day 13


title: 6983-7


title: 6983-6


title: Day 7

source_name: Human cord blood-derived EPCs, day 7

value: early EPCs

value: day 7


title: Day 17

source_name: Human cord blood-derived EPCs, day 17

value: finally differentiated OECs

value: day 17


title: Day 5

source_name: Human cord blood-derived EPCs, day 5

value: day 5


title: 6983-5


title: 6983-9


title: Cortex-Sham-0h-Rep1

description:
Replicate 1
4625024044_E

value: 8 days


title: 6983-4


title: Colon_L

description: colon Human Tiling 1.0R chip L

source_name: pooled Human colon total RNA

value: colon

value: caucasian


title: HeLa_G

description: HeLa cells Human Tiling 1.0R chip G

value: HeLa


title: Spleen_A

description: spleen Human Tiling 1.0R chip A

source_name: pooled Human spleen total RNA

value: spleen


title: Uterus_G

description: uterus Human Tiling 1.0R chip G

value: uterus


title: SpinalCord_A

description: spinal cord Human Tiling 1.0R chip A

source_name: pooled Human spinal cord total RNA

value: spinal cord


title: SmallIntestine_A

description: small intestine Human Tiling 1.0R chip A

source_name: pooled Human small intestine total RNA

value: small intestine


title: Thyroid_G

description: thyroid Human Tiling 1.0R chip G

source_name: pooled Human thyroid total RNA

value: thyroid


title: Day 9

source_name: Human cord blood-derived EPCs, day 9

value: EPCs start to differentiation into EC

value: day 9


title: SkeletalMuscle_A

description: skeletal muscle Human Tiling 1.0R chip A

source_name: pooled Human skeletal muscle total RNA

value: skeletal muscle


title: Thymus_G

description: thymus Human Tiling 1.0R chip G

value: thymus


title: Cortex-HI-3h-Rep3

description:
Replicate 3
4514990160_A

source_name: Infarct Cortex

value: Hypoxic ischemia

value: brain cortex


title: FT-285

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

data_processing: Array data were analyzed for quality control, quantile normalized, and multiple probes for each gene were averaged.

source_name: ARMS

label_protocol: Biotinylated cDNA was synthesized from 100 ng of total RNA from each sample using mixed poly-T and random nonamer primers.

extract_protocol: Total RNA was isolated from fresh frozen tumor and normal tissue samples

value: Alveolar Rhabdomyosarcoma


title: Prostate_A

description: prostate Human Tiling 1.0R chip A

source_name: pooled Human prostate total RNA

value: prostate


title: Testes_G

description: testes Human Tiling 1.0R chip G

value: testes


title: SalivaryGland_A

description: salivary gland Human Tiling 1.0R chip A

source_name: pooled Human salivary gland total RNA

value: salivary gland


title: 6982-12

source_name: Whole lung tissue

value: Donor

value: Male

value: Non-Smoker

value: Hypertension

value: control

value: lung


title: FT-284


title: 6982-11


title: 6983-3


title: 6982-9


title: 6983-2


title: Trachea_G

description: trachea Human Tiling 1.0R chip G

source_name: pooled Human trachea total RNA

value: trachea

value: caucasian


title: FT-286


title: FT-267


title: FT-301


title: Stomach_G

description: stomach Human Tiling 1.0R chip G

source_name: pooled Human stomach total RNA

value: stomach


title: Pancreas_A

description: pancreas Human Tiling 1.0R chip A

source_name: pooled Human pancreas total RNA

value: pancreas


title: FT-276


title: 6982-7


title: FT-278


title: Spleen_G

description: spleen Human Tiling 1.0R chip G

value: spleen


title: Lung_A

description: lung Human Tiling 1.0R chip A

source_name: pooled Human lung total RNA


title: 6982-6


title: Liver_A

description: liver Human Tiling 1.0R chip A

source_name: pooled Human liver total RNA

value: liver


title: SmallIntestine_G

description: small intestine Human Tiling 1.0R chip G

value: small intestine


title: Kidney_A

description: kidney Human Tiling 1.0R chip A

source_name: pooled Human kidney total RNA

value: kidney


title: SkeletalMuscle_G

description: skeletal muscle Human Tiling 1.0R chip G

value: skeletal muscle


title: Heart_A

description: heart Human Tiling 1.0R chip A

source_name: pooled Human heart total RNA

value: heart


title: FT-261

value: Alveolar Rhabdomyosarcoma


title: SpinalCord_G

description: spinal cord Human Tiling 1.0R chip G

source_name: pooled Human spinal cord total RNA

value: spinal cord


title: FT-266


title: 6982-4

value: Donor

value: Male


title: SalivaryGland_G

description: salivary gland Human Tiling 1.0R chip G

value: salivary gland


title: 6982-2

value: Non-Smoker

value: Hypertension

value: control


title: FT-260


title: 6982-3

value: lung


title: FetalBrain_A

description: fetal brain Human Tiling 1.0R chip A

source_name: pooled Human fetal brain total RNA

value: fetal brain

value: caucasian


title: 6971-11

value: COPD


title: Cortex_A

description: cortex Human Tiling 1.0R chip A

source_name: pooled Human cortex total RNA

value: cortex


title: Prostate_G

description: prostate Human Tiling 1.0R chip G

value: prostate


title: FT-281

source_name: ERMS

value: Endothelial Rhabdomyosarcoma


title: Thyroid_A

description: thyroid Human Tiling 1.0R chip A

source_name: pooled Human thyroid total RNA

value: thyroid


title: Cerebellum_A

description: cerebellum Human Tiling 1.0R chip A

source_name: pooled Human cerebellum total RNA

value: cerebellum


title: Colon_A

description: colon Human Tiling 1.0R chip A

source_name: pooled Human colon total RNA

value: colon


title: Pancreas_G

description: pancreas Human Tiling 1.0R chip G

value: pancreas


title: FT-273


title: 6971-8


title: 6971-6


title: FT-268


title: FT-271


title: 6971-7


title: Lung_G

description: lung Human Tiling 1.0R chip G


title: Liver_G

description: liver Human Tiling 1.0R chip G

value: liver


title: 6971-5

value: Male


title: FT-270


title: BoneMarrow_A

description: bone marrow Human Tiling 1.0R chip A

source_name: pooled Human bone marrow total RNA

value: bone marrow


title: 6971-4


title: Kidney_G

description: kidney Human Tiling 1.0R chip G

value: kidney


title: SHSY5Y_C

description: SH-SY5Y cells Human Tiling 1.0R chip C

source_name: pooled Human SH-SY5Y cells total RNA


title: FT-263


title: FT-269


title: 6971-3

source_name: Whole lung tissue


title: Heart_G

description: heart Human Tiling 1.0R chip G

value: heart


title: HeLa_C

description: HeLa cells Human Tiling 1.0R chip C

source_name: Human HeLa cells total RNA

value: HeLa


title: FT-259


title: FetalBrain_G

description: fetal brain Human Tiling 1.0R chip G


title: Uterus_C

description: uterus Human Tiling 1.0R chip C

source_name: pooled Human uterus total RNA

value: uterus


title: Trachea_C

description: trachea Human Tiling 1.0R chip C

source_name: pooled Human trachea total RNA

value: trachea


title: FT-272

source_name: tumor adjacent skeletal muscle

value: tumor adjacent skeletal muscle


title: Cortex_G

description: cortex Human Tiling 1.0R chip G

value: caucasian


title: Colon_G

description: colon Human Tiling 1.0R chip G


title: FT-282


title: Thyroid_C

description: thyroid Human Tiling 1.0R chip C


title: Cerebellum_G

description: cerebellum Human Tiling 1.0R chip G


title: Thymus_C

description: thymus Human Tiling 1.0R chip C

source_name: pooled Human thymus total RNA

value: thymus


title: 6970-9

value: COPD

value: alpha1-antitrypsin deficiency

value: lung


title: 6971-2


title: 6970-7


title: 6970-6-


title: BoneMarrow_G

description: bone marrow Human Tiling 1.0R chip G


title: Testes_C

description: testes Human Tiling 1.0R chip C

source_name: pooled Human testes total RNA

value: testes


title: FT-262


title: SHSY5Y_N

description: SH-SY5Y cells Human Tiling 1.0R chip N


title: Stomach_C

description: stomach Human Tiling 1.0R chip C

source_name: pooled Human stomach total RNA

value: stomach


title: FT-104

source_name: skeletal muscle

value: skeletal muscle


title: HeLa_N

description: HeLa cells Human Tiling 1.0R chip N


title: Spleen_C

description: spleen Human Tiling 1.0R chip C

source_name: pooled Human spleen total RNA

value: spleen


title: FT-103


title: FT-105


title: Stomach_A

description: stomach Human Tiling 1.0R chip A


title: SHSY5Y_G

description: SH-SY5Y cells Human Tiling 1.0R chip G


title: 6970-2

value: Male


title: 6970-10


title: Uterus_N

description: uterus Human Tiling 1.0R chip N


title: SpinalCord_C

description: spinal cord Human Tiling 1.0R chip C

source_name: pooled Human spinal cord total RNA

value: spinal cord


title: Trachea_N

description: trachea Human Tiling 1.0R chip N


title: Thyroid_N

description: thyroid Human Tiling 1.0R chip N

value: thyroid


title: macular_outer_3

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

description: Eyes 6.CEL

hyb_protocol: The cRNA samples were then fragmented and hybridised onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 arrays (Affymetrix, High Wycombe, Bucks, UK) by incubating at 45°C for 16 hours. Washing and staining of the arrays were carried out following Affymetrix GeneChip® protocols using a Fluidics Station 450.

scan_protocol: Arrays were scanned using an Affymetrix Scanner 3000. GCOS software (Affymetrix) was used to monitor scanning and to convert the raw image files into cell intensity files (.CEL).

data_processing: CEL files were processed with the BioConductor gcrma function from the simpleaffy package.

source_name: Macular Outer Choroidal Endothelial Cells

label_protocol: Biotinylated cRNA probes were prepared from the total RNA samples (1µg) using the microarray target amplification kit and the microarray target RNA synthesis kit (both Roche Applied Sciences) following the manufacturer's instructions.

growth_protocol: Cells were seeded onto fibronectin-coated 35mm culture dishes (Beckton Dickinson, Oxford, UK), and incubated at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol: The total RNA was extracted from primary cultures of unpassaged endothelial cells when they had reached approximately 80% confluence, using the Qiagen  RNeasy minikit as directed (Qiagen, Crawley, UK). Approximately 5Î¼g of total RNA was obtained from each 35mm culture plate. RNA integrity and quality was assessed using an Agilent 2100 Bioanalyser and RNA 6000 Nano kit (Agilent Technologies).

treatment_protocol: Matched human macular inner and outer and peripheral inner choroidal vascular endothelia cells were isolated from anonymised paired human globes, enucleated within 24 hours of death and free of any known ocular disease. Isolation and culture of the human choroidal endothelial cells was carried out with anti-CD31-coated Dynabeads (Dynal Ltd, Wirral, UK). PMID 16170129; http://www.ncbi.nlm.nih.gov/pubmed/16170129

value: Choroidal Endothelium

tag: location

value: Macular Outer


title: 6970-4


title: BoneMarrow_L

description: bone marrow Human Tiling 1.0R chip L

value: bone marrow


title: SkeletalMuscle_C

description: skeletal muscle Human Tiling 1.0R chip C

source_name: pooled Human skeletal muscle total RNA


title: 6969-9

value: Female

value: von Willebrand disease; Hypertension


title: 6969-8


title: Testes_N

description: testes Human Tiling 1.0R chip N

value: caucasian


title: 6970-3-


title: SalivaryGland_C

description: salivary gland Human Tiling 1.0R chip C

source_name: pooled Human salivary gland total RNA

value: salivary gland


title: Stomach_N

description: stomach Human Tiling 1.0R chip N


title: macular_outer_2

description: Eyes 5.CEL


title: 6969-11

value: COPD


title: SmallIntestine_C

description: small intestine Human Tiling 1.0R chip C

source_name: pooled Human small intestine total RNA

value: small intestine


title: Pancreas_C

description: pancreas Human Tiling 1.0R chip C

source_name: pooled Human pancreas total RNA

value: pancreas


title: 6969-3

value: lung


title: 6969-7


title: peripheral_inner_3

description: Eyes 23.CEL

source_name: Peripheral Inner Choroidal Endothelial Cells

value: Peripheral Inner


title: Lung_C

description: lung Human Tiling 1.0R chip C

source_name: pooled Human lung total RNA


title: Thymus_N

description: thymus Human Tiling 1.0R chip N

value: thymus


title: Prostate_C

description: prostate Human Tiling 1.0R chip C

source_name: pooled Human prostate total RNA

value: prostate


title: SpinalCord_N

description: spinal cord Human Tiling 1.0R chip N


title: Spleen_N

description: spleen Human Tiling 1.0R chip N

value: spleen


title: macular_inner_3

description: Eyes 22.CEL

source_name: Macular Inner Choroidal Endothelial Cells

value: Macular Inner


title: macular_outer_1

description: Eyes 4.CEL


title: 6968-11

source_name: Whole lung tissue


title: peripheral_inner_2

description: Eyes 19.CEL


title: Kidney_C

description: kidney Human Tiling 1.0R chip C

source_name: pooled Human kidney total RNA

value: kidney


title: macular_inner_1

description: Eyes 15.CEL

value: Choroidal Endothelium


title: SkeletalMuscle_N

description: skeletal muscle Human Tiling 1.0R chip N

value: skeletal muscle


title: 6968-9


title: SalivaryGland_N

description: salivary gland Human Tiling 1.0R chip N


title: FetalBrain_C

description: fetal brain Human Tiling 1.0R chip C

source_name: pooled Human fetal brain total RNA

value: fetal brain


title: macular_inner_2

description: Eyes 21.CEL


title: 6968-12

value: Female


title: Cortex_C

description: cortex Human Tiling 1.0R chip C

source_name: pooled Human cortex total RNA

value: cortex


title: peripheral_inner_1

description: Eyes 18.CEL


title: MHH-ES-1 transfected with miR-scrambled control

city: Charlestown

first: Mingzhu

last: Liu

state: MA

address: 149 13th street

institute: MGH cancer center

hyb_protocol: Hybridization were performed with Affymetrix GeneChip human HG-U133ver2+ 3’-mRNA expression microarray chips using protocol EukGEs2v4 on the GeneChip Fluidic Station.

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

data_processing: Data was analyzed using GCOS, Partek Genomics Suite and Geospiza GeneSifter using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol, using the BioArray High Yield Transcript Labeling Kit (ENZO diagnostics).

growth_protocol: MHH-ES-1 cell were grown in RMPI 1640 medium supplemented with 5% fetal bovine serum (FBS) and antibiotics.

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

treatment_protocol: We used lipofectamine 2000 reagent (Invitrogen) to transfect cells with in vitro synthesized miRNA mimic (Dharmacon) at a final concentration of 50 nM.

value: transfected with miR-scrambled control


title: 6969-2

value: von Willebrand disease; Hypertension


title: SmallIntestine_N

description: small intestine Human Tiling 1.0R chip N

value: caucasian


title: 6968-8

value: COPD


title: 6968-6


title: repeat of miR-483-5p-1.

description: repeat of miR-483-5p-1.

source_name: repeat of miR-483-5p-1.

value: transfected with miR-483-5p


title: Colon_C

description: colon Human Tiling 1.0R chip C

source_name: pooled Human colon total RNA

value: colon


title: Pancreas_N

description: pancreas Human Tiling 1.0R chip N

value: pancreas


title: Heart_C

description: heart Human Tiling 1.0R chip C

source_name: pooled Human heart total RNA

value: heart


title: MHH-ES-1 transfected with miR-483-3p.

description: MHH-ES-1 transfected with miR-483-3p.

source_name: MHH-ES-1 transfected with miR-483-3p.

value: transfected with miR-483-3p


title: repeat of Control-2.

description: repeat of Control-2.

source_name: repeat of Control-2.


title: Lung_N

description: lung Human Tiling 1.0R chip N

value: lung


title: Prostate_N

description: prostate Human Tiling 1.0R chip N

value: prostate


title: Kidney_N

description: kidney Human Tiling 1.0R chip N

value: kidney


title: MHH-ES-1 transfected with miR-483-5p

description: MHH-ES-1 transfected with miR-483-5p

source_name: MHH-ES-1 transfected with miR-483-5p


title: endothelial cell - sorted-replicate3

city: Doha

first: Najeeb

last: Halabi

address: Education City

country: Qatar

institute: Weill Cornell Medicine in Qatar

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on  GeneChip  Hybridization Oven 645. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Chip  Scanner 3000 7G.

data_processing: Data was processed with Affymetrix Expression Console (Build 1.2.1.20) using GC-RMA  to obtain log2 normalized expression values for each probe.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip 3'IVT Express Kit Assay, Affymetrix).

growth_protocol: E4-EC controls (CTR) were grown in M199 media with no additional supplementaion. The co-cultures were grown in 1:1 ratio of M199 and DMEM high/glucose without any supplementation.

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

value: HUVEC

value: Human umbilical vein endothelial cells

tag: co-cultured with

value: MDA-MB231 breast cancer cells


title: 6968-2

value: Female


title: BoneMarrow_C

description: bone marrow Human Tiling 1.0R chip C

source_name: pooled Human bone marrow total RNA

value: bone marrow


title: 6967-13


title: SHSY5Y_B

description: SH-SY5Y cells Human Tiling 1.0R chip B

source_name: pooled Human SH-SY5Y cells total RNA

tag: cell line


title: Heart_N

description: heart Human Tiling 1.0R chip N


title: FetalBrain_N

description: fetal brain Human Tiling 1.0R chip N

value: fetal brain


title: 6967-11

tag: copd status


title: 6968-4

tag: slice


title: Liver_N

description: liver Human Tiling 1.0R chip N

source_name: pooled Human liver total RNA

value: liver


title: Cortex_N

description: cortex Human Tiling 1.0R chip N

value: cortex

value: caucasian


title: Cerebellum_C

description: cerebellum Human Tiling 1.0R chip C

source_name: pooled Human cerebellum total RNA

value: cerebellum


title: 6967-10

value: COPD

tag: lm


title: Thyroid_B

description: thyroid Human Tiling 1.0R chip B

source_name: pooled Human thyroid total RNA

value: thyroid


title: endothelial cell - control-replicate3

value: none (control)


title: Trachea_B

description: trachea Human Tiling 1.0R chip B

source_name: pooled Human trachea total RNA

value: trachea


title: HeLa_B

description: HeLa cells Human Tiling 1.0R chip B

source_name: Human HeLa cells total RNA

value: HeLa


title: endothelial cell - control-replicate2


title: endothelial cell - sorted-replicate1


title: Cerebellum_N

description: cerebellum Human Tiling 1.0R chip N


title: Thymus_B

description: thymus Human Tiling 1.0R chip B

source_name: pooled Human thymus total RNA

value: thymus


title: Colon_N

description: colon Human Tiling 1.0R chip N

value: colon


title: endothelial cell - sorted-replicate2

value: HUVEC


title: Uterus_B

description: uterus Human Tiling 1.0R chip B

source_name: pooled Human uterus total RNA

value: uterus


title: BoneMarrow_N

description: bone marrow Human Tiling 1.0R chip N


title: 6967-2

source_name: Whole lung tissue

tag: Sex

value: lung


title: 6967-4

value: Female

tag: pack years


title: 6967-8

tag: notes


title: 6967-5

tag: disease state


title: Testes_B

description: testes Human Tiling 1.0R chip B

source_name: pooled Human testes total RNA

tag: tissue

value: testes


title: Skin_osteoma_area_control2

city: Oulu

first: Jussi

last: Vuoristo

address: Aapistie 5

department: Biocenter Oulu

country: Finland

institute: University of Oulu

description: RM C2 O

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed with dChip software.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: Skin biopsies were taken from upper chest (osteoma area) and lower abdomen (unaffected area)

tag: gender

value: male

value: skin

tag: disease status

value: osteoma area


title: 6965-10-COPD

value: Male

tag: age


title: Skin_osteoma_area_patient2

description: RM P2 O


title: Skin_unaffected_area_control2

description: RM C2 K

value: unaffected area


title: Stomach_B

description: stomach Human Tiling 1.0R chip B

source_name: pooled Human stomach total RNA

value: stomach

tag: race

value: caucasian


title: endothelial cell - control-replicate1

value: Human umbilical vein endothelial cells

value: none (control)


title: Skin_osteoma_area_patient3

description: RM P3 O


title: Spleen_B

description: spleen Human Tiling 1.0R chip B

source_name: pooled Human spleen total RNA

value: spleen


title: Skin_unaffected_area_patient3

description: RM P3 K


title: SpinalCord_B

description: spinal cord Human Tiling 1.0R chip B

source_name: pooled Human spinal cord total RNA

value: spinal cord


title: 6965-9-COPD

value: COPD


title: 6965-8-COPD


title: SmallIntestine_B

description: small intestine Human Tiling 1.0R chip B

source_name: pooled Human small intestine total RNA

value: small intestine


title: 6965-6-COPD


title: 6965-7-COPD


title: Skin_unaffected_area_patient4

description: RM P4 K


title: SkeletalMuscle_B

description: skeletal muscle Human Tiling 1.0R chip B

source_name: pooled Human skeletal muscle total RNA

value: skeletal muscle


title: Skin_unaffected_area_patient2

description: RM P2 K


title: SalivaryGland_B

description: salivary gland Human Tiling 1.0R chip B

source_name: pooled Human salivary gland total RNA

value: salivary gland


title: Skin_osteoma_area_patient4

description: RM P4 O


title: Prostate_B

description: prostate Human Tiling 1.0R chip B

source_name: pooled Human prostate total RNA

value: prostate


title: Skin_osteoma_area_control1

description: RM C1 O


title: Pancreas_B

description: pancreas Human Tiling 1.0R chip B

source_name: pooled Human pancreas total RNA

value: pancreas


title: PHEO X_50

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing: Data were processed using Affymetrix Expression Console software. Gene level expression were summarized using RMA quantile normalization method.

source_name: Adrenal

label_protocol: 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.

growth_protocol: Tissue samples collected on the day of surgery for each patient

extract_protocol: Extraction of RNA from normal and tumor tissue was performed following a protocol that combines separation of the RNA fraction of tissue homogenized in TRIZOL with subsequent column-based RNA purification.

value: Adrenal

tag: sample type

value: PHEO

tag: age at diagnosis(yrs)

tag: age at surgery(yrs)

value: f

tag: genotype/variation


title: Lung_B

description: lung Human Tiling 1.0R chip B

source_name: pooled Human lung total RNA

value: lung


title: monocyte from donor 4 stimulated with 1,25D

first: Philip

middle: T.

address: 615 Charles E Young Drive South, 410 OHRC

department: Department of Orthopaedic Surgery

institute: University of California at Los Angeles

hyb_protocol: Standard Affymetrix protocol by UCLA Clinical microarray core facility

data_processing: UCLA DNA microarray core facility, normalized using MAS5

source_name: primary human monocytes isolated via plastic aherence from peripheral blood mononuclear cells.

label_protocol: Standard labeling protocol by UCLA Clinical microarray core facility

growth_protocol: primary human monocytes enriched via plastic adherence from peripherial blood mononuclear cells derived from whole blood of healthy donors

extract_protocol: total RNA was extracted using Trizol reagent based on the manufacturer's recommended protocol, and purified using RNAeasy RNA cleanup protocol according to the manufacturer's recommended protocol

treatment_protocol: enriched monocytes were treated with ATRA or 1,25D3 for 18hours at 10-8M

value: healthy

tag: cell type

value: monocyte

tag: individual

value: donor 4

tag: treatment

value: 1,25a-dihydroxyvitamin D3


title: PGL H_48.6

source_name: Extra-adrenal

value: Extra-adrenal

value: PGL


title: monocyte from donor 2 stimulated with 1,25D

scan_protocol: Standard Affymetrix protocol by UCLA Clinical microarray core facility

value: donor 2


title: PHEO H_49.1


title: Liver_B

description: liver Human Tiling 1.0R chip B

source_name: pooled Human liver total RNA

value: liver

value: caucasian


title: PHEO H_49.2


title: monocyte from donor 3 stimulated with 1,25D

value: donor 3


title: monocyte from donor 3 stimulated with ATRA

value: all-trans retinoic acid


title: PGL H_48.4


title: Patient 10, before CCR treatment

city: Lodz

first: Ida

last: Franiak-Pietryga

address: Pabianicka 62

country: Poland

institute: Copernicus Memorial Hospital in Lodz

description: control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://appliedbiosystems.com
For the normalization it uses the average of housekeeping gene: 18S
Target gene signals normalized to housekeeping gene; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: FAM

source_name: B-CLL cells

label_protocol: PCR assays were performed using the 384 TaqMan Low Density Array (Human Apoptosis Panel) (Applied Biosystems, USA).

extract_protocol: Total RNA was extracted with the RiboPure Blood Kit (Ambion, USA). RNA was reversed transcribed to cDNA using High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, USA).

treatment_protocol: All the patients received CCR treatment by intravenous infusion according to the schedule: rituximab 375mg/m2-day 1, cladribine 0.12mg/kg-days 1-3, cyclophosphamide 600mg/m2- days 1-3. The regimen was repeated every 4 weeks until 6 courses.

value: lymphocytes B

tag: time

value: 0 days

value: male

tag: rai stage before treatment

tag: zap70 status

value: negative

tag: ighv mutation status

value: unmutated

tag: treatment response

value: NR

tag: cytogenetic abnormalities


title: Patient 10, after 2 weeks of CCR treatment

description: test

tag: activation agent

value: cladribine, cyclophosphamide, rituximab

value: 14 days

tag: gender


title: monocyte from donor 4 stimulated with ATRA

tag: disease state

value: healthy

value: monocyte

value: donor 4


title: PGL H_48.5

tag: tissue

value: Extra-adrenal

value: PGL

tag: disease status

value: f


title: monocyte from donor 1 stimulated with 1,25D

value: donor 1

value: 1,25a-dihydroxyvitamin D3


title: PGL H_48.1

tag: sample type

tag: age at diagnosis(yrs)


title: Skin_unaffected_area_control1

description: RM C1 K

value: skin

value: unaffected area


title: monocyte from donor 2 stimulated with ATRA

value: donor 2

value: all-trans retinoic acid


title: Heart_B

description: heart Human Tiling 1.0R chip B

source_name: pooled Human heart total RNA

value: heart

tag: race

value: caucasian


title: Patient 9, after 2 weeks of CCR treatment

description: test

tag: cell type

value: lymphocytes B

value: male


title: FetalBrain_B

description: fetal brain Human Tiling 1.0R chip B

source_name: pooled Human fetal brain total RNA

value: fetal brain


title: Kidney_B

description: kidney Human Tiling 1.0R chip B

source_name: pooled Human kidney total RNA

value: kidney


title: Normal PKh_43

description: NORMAL

value: Normal

value: M

tag: genotype/variation

value: NORMAL

tag: original geo sample id


title: Normal PKh_42

description: NORMAL


title: Patient 8, after 2 weeks of CCR treatment

description: test

value: cladribine, cyclophosphamide, rituximab

tag: time

value: 14 days

value: female


title: monocyte from donor 1 stimulated with ATRA

value: healthy

value: monocyte

tag: individual

value: donor 1

tag: treatment


title: Normal PKh_06

description: NORMAL

value: F


title: Cortex_B

description: cortex Human Tiling 1.0R chip B

source_name: pooled Human cortex total RNA

value: cortex


title: monocyte from donor 2 stimulated with CTRL

value: donor 2

value: control


title: Normal PKh_44

description: NORMAL


title: FLAG-ING2-Etoposide-01

type: genomic

description: Comparison of ING2-ChIP to input chromatin

hyb_protocol: Followed manufacturer's protocol (www.nimblegen.com)

data_processing: Scanned images were analyzed with Nimblescan using the standard protocol

molecule: genomic DNA

source_name: FLAG-ING2 ChIP from HT1080 cells treated with Etoposide

label_protocol: ING2 IP samples were labeled with Cy5 and input chromatin samples were labeled with Cy3 using a NimbleGen Dual-Color DNA labeling kit according to manufacturer's protocol.

extract_protocol: Ht1080 cells were fixed with formaldehyde (1%), then the reaction was quenched with 125mM glycine.  Cells were washed 3X with PBS then snap frozen.  Frozen cell pellets were resuspended in Swelling buffer (0.1M Tris pH 7.5, 10mM KOAc, 15mM MgOAc, 1% NP-40, with protease inhibitors) and dounced.  Nuclei were resuspended in Nuclei Lysis Buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and chromatin was sonicated to ~200bp size.  Sonicated chromatin was IPed with anti-FLAG M2 overnight and purified DNA was collected using a PCR purification kit (Qiagen).

treatment_protocol: Etoposide (100uM) for 1 hour

tag: cell line

tag: chip antibody

value: anti-FLAG M2

value: none, input DNA

source_name: Input chromatin from HT1080 cells treated with Etoposide


title: 6968-10

source_name: Whole lung tissue

tag: copd status

value: COPD

tag: slice

tag: lm

tag: Sex

value: Female

tag: age

tag: pack years

tag: notes

value: lung


title: Cerebellum_B

description: cerebellum Human Tiling 1.0R chip B

data_processing:
The ".CEL" files are raw data. The "normalized.txt" files (supplementary data linked to GSE18490) are data normalized as follows.

1) To exclude potential low quality probes, we excluded probes that corresponded to the following conditions: A) probes for which either the Perfect Match (PM) or Miss Match (MM) probe perfectly match more than once in the genome, B) probes which contain SNPs, C) probes located on sex chromosomes.
2) To reduce inter-chip differences, we equalized the mean and variance of probe intensities among all chips in each tissue. Note that the intensities were converted to a logarithmic scale (base 2).
3) To reduce background noise, we subtracted the intensity of each MM probe from the PM probe in each probe set. If the value was negative, zero was assigned as the value.
4) To adjust for GC content of probes, we calculated normalized intensities by each GC content.
5) To equalize the distribution of signals in each chip, we performed quantile normalization for each chip
6) To smooth the probe intensities with neighboring probes, we calculated Hodges-Lehmann statistics. The size of each sliding window was 101bp.
7) All probes that ranked higher than the top 15% signal threshold were selected and those with an inter-probe distance less than a maximum gap threshold of 25bp were concatenated. Then, the concatenated probes with length longer than a minimum run threshold of 101bp were defined as transfrags. Finally, we performed BLAST to exclude probes that mapped to multiple locations.

source_name: pooled Human cerebellum total RNA

extract_protocol: Samples of total RNA from Human tissues were purchased from several companies (Clontech, Ambion, Stratagene, Cell Applications). HeLa and SH-SY5Y cells were cultured in standard DMEM / 10% FBS medium. Total RNA was extracted from cells with TRIzol regent (Invitrogen). Additionally, total RNA was purified with Rneasy Mini Kit (Qiagen) and treated with RNase-free DNase Set (Qiagen) to remove any contaminating genomic DNA.

tag: tissue

value: cerebellum

value: caucasian


title: Normal PKh_07

description: NORMAL

tag: sample type

value: Normal

tag: disease status

tag: age at diagnosis(yrs)

tag: gender

value: NORMAL


title: Colon_B

description: colon Human Tiling 1.0R chip B

source_name: pooled Human colon total RNA

value: colon

tag: race


title: Patient 8, before CCR treatment

description: control

tag: cell type

value: lymphocytes B

tag: time

value: 0 days

value: female

tag: rai stage before treatment

tag: zap70 status

value: negative

tag: ighv mutation status

value: unmutated

tag: treatment response

value: NR, died

tag: cytogenetic abnormalities


title: Patient 9, before CCR treatment

description: control

value: male

value: mutated

value: CR MRD+


title: Patient 7, after 2 weeks of CCR treatment

description: test

tag: activation agent

value: cladribine, cyclophosphamide, rituximab

value: 14 days


title: monocyte from donor 4 stimulated with CTRL

tag: disease state

value: healthy

value: monocyte

tag: individual

value: donor 4

tag: treatment

value: control


title: Patient 7, before CCR treatment

description: control

value: CR

value: trisomy 12


title: FLAG-ING2-Etoposide-02

scan_protocol: Followed manufacturer's protocol (www.nimblegen.com)

tag: cell line

tag: chip antibody

value: anti-FLAG M2

value: none, input DNA


title: monocyte from donor 3 stimulated with CTRL

value: donor 3


title: Patient 6, after 2 weeks of CCR treatment

description: test

value: lymphocytes B


title: Normal PKh_05

description: NORMAL

tag: tissue

tag: sample type

value: Normal

tag: disease status

value: F

tag: genotype/variation

value: NORMAL

tag: original geo sample id


title: BoneMarrow_B

description: bone marrow Human Tiling 1.0R chip B

source_name: pooled Human bone marrow total RNA

value: bone marrow

tag: race

value: caucasian


title: Normal PKh_04

description: NORMAL

tag: age at diagnosis(yrs)

tag: gender


title: FLAG-ING2-Vehicle-02

source_name: FLAG-ING2 ChIP from HT1080 cells treated with DMSO

treatment_protocol: DMSO for 1 hour

source_name: Input chromatin from HT1080 cells treated with DMSO


title: monocyte from donor 1 stimulated with CTRL

tag: cell type

value: donor 1


title: FLAG-ING2-Vehicle-01


title: Patient 5, before CCR treatment

description: control

tag: time

value: 0 days

value: male

tag: rai stage before treatment

tag: zap70 status

value: negative

tag: ighv mutation status

value: mutated

tag: treatment response


title: Patient 4, after 2 weeks of CCR treatment

description: test

tag: activation agent

value: cladribine, cyclophosphamide, rituximab

value: 14 days


title: Patient 4, before CCR treatment

description: control

value: CR

tag: cytogenetic abnormalities

value: normal


title: Patient 6, before CCR treatment

description: control

value: unmutated

value: NR


title: Normal PKh_03

description: NORMAL

value: M


title: Patient 3, after 2 weeks of CCR treatment

description: test

value: lymphocytes B


title: Patient 3, before CCR treatment

description: control

value: complete remission (CR)


title: SW480-siRNA treated replicate1

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilian University

description: colorectal cancer cell line, siRNA against beta-catenin

hyb_protocol: Fluidics station FS450

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: The software package R (version 2.14.1) was used for the statistical analysis of the microarray data. Microarray data were preprocessed using the rma function from the R package “affy”. Two sets with different cell lines(DLD1 and SW480) were normalized separately. The function nsFilter from the package 'genefilter' was used to exclude all probeset that were not associated with a gene name.

source_name: colorectal cancer cell line

label_protocol: Affymentrix kits for 3'IVT cDNAsynthesis, amplification and  labeling

growth_protocol: The colon carcinoma cell lines DLD1 and SW480 were obtained from ATCC (Manassas, VA, USA) and were cultured in DMEM medium supplemented with 10% calf serum (PAA, Pasching, Austria). Short interfering RNAs targeting β-catenin (cat. no. D-003482-04) and β-Galactosidase (cat. no. D-012539-01) were purchased from Dharmacon (Lafayette, CO, USA) as siGenome siRNAs. Cells were transfected with these siRNAs using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA).

extract_protocol: Trizol method

treatment_protocol: DLD1 and SW480 cells were harvested 48h after siRNA transfection

tag: cell line

tag: treatment

value: siRNA beta-catenin


title: SW480-siRNA treated replicate3


title: SW480-siRNA mock treated replicate1

description: colorectal cancer cell line, mock-siRNA treated

value: siRNA beta-galactosidase


title: Patient 5, after 2 weeks of CCR treatment

description: test


title: CGC-β4e-rep2

city: Innsbruck

first: Daniel

last: Bindreither

state: Tirol

address: Innrain 82

department: Division of Molecular Pathophysiology

country: Austria

institute: Medical University Innsbruck

description: Gene expression data from cultured cerebellar granule cells reconstituted with the β4e splice variant of the voltage-gated calcium channel

hyb_protocol: Resulting targets, in total 12.5 5 µg of fragmented and labeled RNA, were hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 in an Affymetrix fluidic station 450

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000

data_processing: Quality assessment and preprocessing of the microarrays was done in R by utilizing the Bioconductor packages affyPLM and GCRMA respectively

source_name: mRNA extracts from lethargic cultured cerebellar granule cells reconstituted with the β4e splice variant of the voltage-gated calcium channel

label_protocol: 500 ng of RNA per sample were processed to generate biotinylated hybridization targets using the Affymetrix GeneChip 3′ IVT Express kit and the Affymetrix GeneChip hybridization, wash, and stain kit

growth_protocol: Cultures from cerebellar granule cells were grown from postnatal day 7 (P7) BALB/c or lethargic (129/SvJ background) mice. Neurons were plated on poly-L-lysine-coated coverslips and kept in basal Eagle’s medium (Gibco) supplemented with 10% FCS, 5mM KCl, 2mM glutamine, and 50 g/ml gentamycin. Ara-C final concentration of 10mM (Sigma-Aldrich, St. Louis, MO, USA) was added 24 h after plating to the neurons to prevent proliferation of non-neuronal cells. RNA was extracted from granule cells differentiating after 9 days in vitro.

extract_protocol: RNA was extracted with Trizol RNA isolation reagent (Life technologies) the protocol was exactly the same as provided by life technologies, http://tools.lifetechnologies.com/content/sfs/manuals/trizol_reagent.pdf . Further RNA were cleaned with Rneasy MinElute cleanup kit ( Qiagen).

treatment_protocol: Cultured cerebellar granule cells were transfected with the lentiviral constructs with either (bA-4a, bA-4b or A-4e or A-eGFP ) immediately after plating for 12 hours.

tag: background strain

tag: phenotype

value: lethargic

value: cerebellar granule cells


title: CGC-β4e-rep1


title: SW480-siRNA mock treated replicate3


title: CGC-β4b-rep1

description: Gene expression data from cultured cerebellar granule cells reconstituted with the β4b splice variant of the voltage-gated calcium channel

source_name: mRNA extracts from lethargic cultured cerebellar granule cells reconstituted with the β4b splice variant of the voltage-gated calcium channel


title: Patient 2, after 2 weeks of CCR treatment

description: test


title: CGC-β4b-rep3


title: DLD1-siRNA treated replicate1


title: CGC-β4e-rep3


title: DLD1-siRNA treated replicate3


title: SW480-siRNA treated replicate2


title: Patient 2, before CCR treatment

description: control

value: 0 days

value: partial remission (PR)


title: CGC-β4b-rep2


title: DLD1-siRNA mock treated replicate3


title: Patient 1, after 2 weeks of CCR treatment

description: test

value: female


title: SW480-siRNA mock treated replicate2


title: DLD1-siRNA mock treated replicate2


title: Patient 1, before CCR treatment

description: control

value: negative

value: mutated

value: no response (NR), died


title: CGC-β4a-rep1

description: Gene expression data from cultured cerebellar granule cells reconstituted with the β4a splice variant of the voltage-gated calcium channel

source_name: mRNA extracts from lethargic cultured cerebellar granule cells reconstituted with the β4a splice variant of the voltage-gated calcium channel


title: CGC-β4a-rep2


title: CGC-β4a-rep3


title: DLD1-siRNA mock treated replicate1


title: Liver_C

first: Fuyuki

last: Miya

address: 35 Shinanomachi, Shinjuku-ku

institute: Keio University

description: liver Human Tiling 1.0R chip C

source_name: pooled Human liver total RNA

label_protocol: Reverse transcription, amplification, fragmentation and labeling steps were performed according to Affymetrix protocol using WT Amplified Double-Strand cDNA Synthesis Kit (Affymetrix) and WT Double-Strand DNA Terminal Labeling Kit (Affymetrix).

tag: tissue

value: liver

value: caucasian


title: CGC-eGFP-rep3

description: Gene expression data from cultured cerebellar granule cells transfected with eGFP

source_name: mRNA extracts from lethargic cultured cerebellar granule cells transfected with eGFP


title: siBRCA1_TotalRNA_2

city: LYON

first: Estelle

last: DACHEUX

address: 28 rue Laennec

country: France

institute: Centre de Recherche en Cancérologie de Lyon

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000. Then CEL files were generated using the Affymetrix GeneChip Command Console software (AGCC) 3.0

data_processing: CHP files were processed using MAS 5.0 analysis algorithm with Affymetrix Expression Console software 1.1

source_name: MCF7 breast cancer cell line

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: MCF7 cells were plated at 1,8x10^6 cells per 10 cm diameter dish 24h before transfection. Cells were transfected with 200 pmol/dish of siRNA against BRCA1 or Control and 16 µL/dish of Lipofectamine 2000 (Life Technologies) using the protocol of the supplier. Cells were harvested 72 hours after transfection.

extract_protocol: Approximately 20% of the total volume of the cytoplasmic fraction was used as a source for total cytoplasmic RNA by using Trizol (Life Technologies) extraction and isopropanol precipitation. Polysomal RNA was recovered from individual fractions 12 to 18 by Trizol extraction and isopropanol precipitation. Then 100 ng of RNA was amplified using GeneChip 3' IVT Express Kit from Affymetrix.

treatment_protocol: Extracts from MCF7 cells were prepared by lysis at 4°C in extraction buffer (50 mM Tris-HCl, pH 7.4, 25 mM KCl, 5 mM MgCl2, 250 mM sucrose, 0.7 % Nonidet-P40) and nuclei were removed by centrifugation (800 g, 10 min, 4°C). The supernatant was centrifuged (12 000 g, 10 min, 4°C) to eliminate mitochondria. The supernatant (cytoplasmic fraction) was layered onto a 11 ml linear sucrose gradient (10-40% sucrose supplemented with 50 mM Tris-HCl, pH 7.4, 25 mM KCl, 5 mM MgCl2, 10 mM DTE and 100µg/ml cycloheximide). After 2h of centrifugation at 250 000 g and at 4°C in a SW41Ti rotor (Beckman), 18 fractions of 600 µl were manually collected.

tag: transfection

tag: fraction

value: total RNA


title: siBRCA1_PolysomalRNA_2

value: polysomal RNA


title: Nicd vs control rep1

city: Cambridge

first: Sarah

last: Bray

address: Downing Street

department: PDN

institute: University  of Cambridge

description:
biological replicate 1
S109623

hyb_protocol: Add 140 µl of Ocimum hybridisation buffer to the labelled mixture and heat at 100 °C for 2 minutes on a hot-block. Centrifuge for 3 minutes at 13,000 rpm. Load 140 µl of the labelled sample to the microarray, and hybridise for 16 hours at 51 °C. Perform post-hybridisation washes as per PowerMatrix slides protocol (FMB). Pre-heat wash solution 1 (0.2 x SSC; 0.2% SDS) and wash solution 2 (0.2 x SSC) to 55 °C using a water bath. Incubate slides in a slide staining dish with pre-heated wash solution 1 on an orbital shaker at 50 rpm for 20 minutes. Transfer the slides to a staining trough containing pre-heated wash solution 2. Gently dip the slides up and down for 1 minute in wash solution 2. Repeat step in fresh wash solution 2 twice. Rinse the slides 3 times with fresh deionized water at room temperature (dip the rack in MilliQ water for 3 seconds). Transfer the slides to a clean microscope slide box with tissue at the base and centrifuge at 1000 rpm for 5 minutes. The slides are now ready to be scanned.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains selected by the Auto-PMT function (0.005% saturation tolerance). Images are saved as Single-image TIFF.

data_processing: Images are processed and spot quantified by the Dapple software (http://www.cs.wustl.edu/~jbuhler/research/dapple/). The R package limma (SMYTH and SPEED 2003) was used to normalize the arrays. For each array, the background intensity level of the array image was first adjusted before loess normalization was applied to the MA values of the array. The intensities of the two channels of all 3 arrays were then quantile normalized, such that the intensities all had the same empirical distribution. Missing values (i.e. reduced data set) arise because genes are not expressed or there is poor quality on the array. The resulting ratios are log2 ratio of sample/control.

organism: Drosophila melanogaster

source_name: control

label_protocol: To 3 to 5 µg of total RNA, add 1 µl 500 ng/ µl of Oligo(dT)23 anchored primer (Sigma) and adjust volume to 5 µl with DEPC- water. Incubate at 65 °C for 10 min, then snap cool on ice. Add 4 µl 5x First Strand Buffer (Invitrogen), 2 µl 0.1M DTT (Invitrogen), 1 µl 10 mM dNTP mix, 0.25 µl 40 U/µl RNasin (Promega) and 0.75 µl 200 U/µl Superscript III (Invitrogen). Incubate at 46 °C for 2 hours, then at 65 °C for 15 minutes, snap cool on ice. For second strand synthesis: Add 7.5 µl Second Strand Buffer (Invitrogen), 0.75 µl 10 mM dNTP mix, 2 µl 10 U/µl DNA Polymerase I (Invitrogen), 0.1 µl 5 U/µl RnaseH (Promega), 0.5 µl 10 U/µl E. coli Ligase (NEB) adjust volume to 40 µl with DEPC-water. Incubate at 16 °C for 2 hours, then purification using QIAquick PCR Purification Kit. To label take up to 1 µg double stranded DNA and make up to a total volume of 25 µl with DEPC-water. Add 20 µl 2.5x Random Primer Reaction Buffer (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 100 °C for 5 minutes, snap cool on ice. Add 1 µl 10 X low-C dNTP mix (5mM dATP,dGTP,dTTP, 2 mM dCTP), 2 µl 1 mM Cy3 or Cy5 dCTP (GE Healthcare) and 1 µl 40U/µl Klenow (Invitrogen – BioPrime DNA Labelling Kit). Incubate at 37°C for 2 to 3 hours. Stop the reaction by adding 5 µl Stop Buffer (Invitrogen – BioPrime DNA Labelling Kit). Resuspend the resin in the AutoSeq G-50 column (GE Healthcare) by vortexing gently. Loosen the cap a quarter turn and snap off the bottom closure. Place the column in a collection tube. Pre-spin column at 5,000 rpm for 1 minute to remove the buffer. Remove the top cap and place column in a new 1.5 ml tube. Pipette half of the sample onto the centre of the angled surface of the compacted resin bed being careful not to disturb the resin. Spin for 1 minute at 5,000 rpm. Discard the column. Place a second column into the same 1.5 ml microfuge tube and then add the second half of the sample. Spin for 1 minute and 5,000 rmp. Reduce volume of probe to between 2 to 5 µl by placing in a speed vac with medium heat. Add 2 µl of 10 mg / ml sonicated salmon sperm DNA (Invitrogen).

growth_protocol: Larvae grown at 25C.

extract_protocol: Wing imaginal discs form 60 third instar larvea were dissected for each RNA isolation using Trizol (Sigma).

tag: strain/genotype

value: abxUbxFLPase; Act>y>Gal4, UAS GFP; FRT82B tubGal80 with FRT82B

tag: developmental stage

value: third instar lavae

value: Wing imaginal discs

source_name: Nicd giants

tag: strain

value: abxUbxFLPase; Act>y>Gal4, UAS GFP; FRT82B tubGal80 with UAS-Nicd; FRT82B


title: 20 weeks tumor Mammary31

city: Rochester

first: Hu

last: Li

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

description: Gene expression data obtained from mouse whole mammary gland tissue

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix MG 430 2.0 array for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: RMA

source_name: transgenic FVB C3(1)-SV40Tag mouse whole mammary gland

label_protocol: Preparation of biotinylated cDNA was performed according to the standard Nugen amplification sample preparation protocol, starting with 100ng of total RNA

growth_protocol: All animal experimental protocols were approved by the Institutional Animal Care and Use Committee of Children’s Hospital Boston

extract_protocol: Trizol isolation followed by Rneasy (Qiagen) column purification were performed according to manufacturer's specifications

tag: age

value: 20 weeks

tag: genotype

value: mammary tumor


title: Nicd vs control rep2

description:
biological replicate 2, dye-swap
S109624


title: siControl_PolysomalRNA_1

value: control


title: Giant disc vs control rep2

description:
biological replicate 2
S109515

value: UAS-NLS-GFP expressed by the patched[559.1]-Gal4 driver

source_name: Giant disc

value: UAS-GFP:Su(H) expressed by the patched[559.1]-Gal4 driver


title: CGC-eGFP-rep1

value: lethargic

tag: cell type

value: cerebellar granule cells


title: CGC-eGFP-rep2


title: siBRCA1_TotalRNA_1


title: siBRCA1_PolysomalRNA_1


title: Giant disc vs control rep3

description:
biological replicate 3, dye-swap
S109516

source_name: contro


title: siControl_TotalRNA_2


title: DLD1-siRNA treated replicate2

value: siRNA beta-catenin


title: Nicd vs control rep3

description:
biological replicate 3
S109636


title: Nicd vs control rep4

description:
biological replicate 4
S109625


title: 20 weeks tumor Mammary23

value: transgenic FVB C3(1)-SV40Tag mouse whole mammary gland


title: siControl_PolysomalRNA_2


title: 20 weeks tumor Mammary22


title: siControl_TotalRNA_1


title: 20 weeks tumor Mammary24


title: Giant disc vs control rep1

description:
biological replicate 1
S109514


title: 8399 E ductus arteriosus SMC 18.5 days

city: Leiden

first: Regina

last: Bokenkamp

address: Albinusdreef 2

department: Dept of Pediatric Cardiology

country: Netherlands

institute: LUMC

hyb_protocol: Labeled RNA was hybridized to GeneChip Rat Genome 230 2.0 Array. Hybridization was performed using 12.5 μg of biotin-labeled RNA at 45°C for 16 hours under continuous rotation.

scan_protocol: Gene Chips were scanned using the Affymetrix Gene Chip Scanner 3000

data_processing: The Affymetrix probe level data were summarized using FARMS (Factor Analysis for Robust Microarray Summarization - http://www.bioinf.jku.at/software/farms/farms.html). Raw intensities were log2 transformed to get data normally distributed.

organism: Rattus norvegicus

source_name: ductus arteriosus SMC 18.5 days

label_protocol: Two rounds of linear mRNA amplification were performed (modified Eberwine protocol). The second round of amplification, starting from 100 ng of first round aRNA, was finalised during the IVT labelling.

growth_protocol: Pups from 6 timed–pregnant Wistar rats were delivered after respectively 18 and 21 days of gestation (spontaneous birth occurs at 22 days of gestation) by hysterotomy through a median abdominal incision

extract_protocol: RNA from microdissected cells was isolated using the RNeasy Minelute protocol.

treatment_protocol: Isolation of the fetal thorax was carefully performed in RNase free conditions, frozen in tissue tek, and stored at -80 C.

value: smooth muscle cell

value: embryo 18.5 days

value: ductus arteriosus

value: wistar


title: 16 weeks tumor Mammary14

value: 16 weeks


title: NOF151-TGF-beta2-rep2

city: Houston

first: Tsz-Lun

last: Yeung

address: 1515 Holcombe Blvd. Unit 1362

department: Gynecologic Oncology and Reproductive Medicine

institute: University of Texas MD Anderson Cancer Center

description:
NOF151_TGFB2#2
Gene expression data from TGF-beta-2-treated NOF151 cell line.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: Ovarian fibroblast NOF151, TGF-beta-2-treated sample

label_protocol: Biotinylated cRNA were prepared using the MessageAmp Premier RNA Amplification Kit (Ambion) according to the manufacturer's instructions from 100ng total RNA.

growth_protocol: The NOF151 ovarian fibroblast cell line was cultured in a humidified incubator at 37C and 5% carbon dioxide. Culture medium M105/199 supplemented with 10% Fetal bovine serum and 1ng/mL Epidermal growth factor was used as growth medium.

extract_protocol: Total RNA extraction was performed using the Purelink RNA Mini Kit (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Prior to treatment, cells were trypsinized, counted and seeded in 60mm cell culture dishes. 24 hours after cell seeding, the cell culture medium of the control group was replaced with fresh medium without TGF-beta, while the cell culture medium of the two TGF-beta treatment groups was replaced with fresh medium containing either 5ng/mL of TGF-beta-1 or TGF-beta-2. At 48 hours post treatment, cells were harvested and total RNA was extracted.

value: normal ovarian fibroblasts cells


title: 16 weeks tumor Mammary32


title: 16 weeks tumor Mammary15


title: 8462 C Aorta SMC 21 days

source_name: Aorta SMC 21 days

value: embryo 21 days

value: Aorta


title: 8462 A Aorta endo 21 days

source_name: Aorta endo 21 days

value: endothelial cell


title: 12 weeks tumor Mammary10

value: 12 weeks

value: mammary tumor


title: NOF151-TGF-beta2-rep3

description:
NOF151_TGFB2#3
Gene expression data from TGF-beta-2-treated NOF151 cell line.


title: 16 weeks tumor Mammary11


title: 8469 B ductus arteriosus SMC 18.5 days


title: NOF151-TGF-beta2-rep1

description:
NOF151_TGFB2#1
Gene expression data from TGF-beta-2-treated NOF151 cell line.


title: 8399 E ductus arteriosus endo 18.5 days

source_name: ductus arteriosus endo 18.5 days


title: NOF151-TGF-beta1-rep3

description:
NOF151_TGFB1#3
Gene expression data from TGF-beta-1-treated NOF151 cell line.

source_name: Ovarian fibroblast NOF151, TGF-beta-1-treated sample


title: 16 weeks tumor Mammary13


title: NOF151-TGF-beta1-rep2

description:
NOF151_TGFB1#2
Gene expression data from TGF-beta-1-treated NOF151 cell line.


title: NOF151-control-rep3

description:
NOF151_CTL#3
Gene expression data from control NOF151 cell line.

source_name: Ovarian fibroblast NOF151, control sample

value: control


title: 12 weeks tumor Mammary9


title: 8399 H Aorta SMC 18.5 days

source_name: Aorta SMC 18.5 days


title: 8399 H ductus arteriosus SMC 18.5 days


title: 12 weeks tumor Mammary7


title: 12 weeks tumor Mammary8


title: 8462 A Aorta SMC 21 days


title: 12 weeks tumor Mammary6


title: 8399 H ductus arteriosus endo 18.5 days


title: NOF151-control-rep2

description:
NOF151_CTL#2
Gene expression data from control NOF151 cell line.


title: NOF151-control-rep1

description:
NOF151_CTL#1
Gene expression data from control NOF151 cell line.


title: 8462 C ductus arteriosus endo 21 days

source_name: ductus arteriosus endo 21 days


title: OVCA433-VCAN-rep3

description: Gene expression data from versican treated OVCA433 cell line

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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: Ovarian cancer cell line OVCA433 treated with exogenous versican (VCAN)

label_protocol: Biotinylated cRNA were prepared using the MessageAmp Premier RNA Amplification Kit (Ambion) according to the manufacturer's instruction from 100ng total RNA.

growth_protocol: OVCA433 ovarian cancer cell line was cultured in humidified incubator at 37C and 5% carbon dioxide. Culture medium RPMI1640 supplemented with 10% Fetal bovine serum was used as growth medium.

extract_protocol: Total RNA extraction was performed using the Purelink RNA mini kit (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: prior to treatment, cells were trypsinized, counted and seeded in 60mm cell culture dishes. 24 hours after cell seeding, the control group has cell culture medium replaced with fresh medium without versican, while the versican treatment group has cell culture medium replace with fresh medium containing versican. At 48 hours post transfection, transfected cells were harvested and total RNA was extracted.

value: treated with exogenous versican (VCAN)


title: 8 weeks tumor Mammary5

value: 8 weeks


title: NOF151-TGF-beta1-rep1

description:
NOF151_TGFB1#1
Gene expression data from TGF-beta-1-treated NOF151 cell line.


title: 8412 A ductus arteriosus endo 21 days


title: 8 weeks tumor Mammary3


title: 8 weeks tumor Mammary4


title: 8412 D Aorta SMC 21 days


title: OVCA433-VCAN-rep2


title: OVCA433-VCAN-rep1


title: OVCA433-control-rep3

description: Gene expression data from control OVCA433 cell line

source_name: Ovarian cancer cell line OVCA433-Control sample


title: 8 weeks tumor Mammary2


title: OVCA433-control-rep1


title: 8 weeks tumor Mammary1


title: 8 weeks wild type Mammary35

source_name: wild type FVB mouse whole mammary gland

value: wild type FVB mouse whole mammary gland

value: whole mammary gland tissue


title: 8412 A ductus arteriosus SMC 21 days

source_name: ductus arteriosus SMC 21 days


title: 8 weeks wild type Mammary36


title: 8462 M ductus arteriosus SMC 21 days


title: 8412 D Aorta endo 21 days