title: fhm F Liver recovery DES 100-5


title: fhm F Liver recovery DES 1-3

status: Public on Sep 20 2012

type: RNA

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

country: USA

institute: US EPA

hyb_protocol: The Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies, Palo Alto, CA) was used for microarray hybridizations following the manufacturer’s protocol and recommendations.

scan_protocol: An Axon GenePix® 4000B Microarray Scanner (Molecular Devices Inc.) was used to scan microarray images at 5 μm resolution

data_processing: Microarray image processing and data pre-processing were performed Agilent's Feature Extraction software v 9.5 following the manufacturer’s protocol and recommendations.

molecule: total RNA

organism: Pimephales promelas

source_name: liver from female fish exposed to 1 ng DES/L for 96 h, followed by an additional 96 h in control water

label_protocol: cDNA synthesis, cRNA labeling, amplification and hybridization were performed following the manufacturer's kits and protocols (Quick Amp Labeling Kit; Agilent, Palo Alto, CA)

growth_protocol: The fish were held at 25+1ºC under a 16:8 L:D photoperiod and were fed frozen adult brine shrimp twice daily (San Francisco Bay Brand, Newark, CA, USA).  Fish used for the experiment were from an on-site culture, and all procedures involving animals conformed to guidelines approved by the local Animal Care and Use Committee.

extract_protocol: Total RNA was isolated from liver tissue with Tri Reagent (Sigma, St. Louis, MO) according to the manufacturer’s protocol. RNA quality was verified using an Agilent 2100 bioanalyzer (Agilent, Palo Alto, CA) and concentration was quantified spectrophotometrically using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE).

treatment_protocol: Fish were exposed to 0, 1, 10, or 100 ng DES/L delivered in a continuous flow (45 ml/min) of sand filtered, UV treated, Lake Superior Water, without the use of carrier solvents for a total of 96 h.  Delivery of DES then ceased and fish were held in a continuous flow (45 ml/min) of control water for an additional 96 h (4 d depuration).

tag: ctid

tag: treatment

value: 1.0 ng DES/L for 4 days then recovery for another 4 days

tag: tank

tag: Sex

value: F

tag: FISH wet wt (g)

tag: gonad wt (g)

tag: time sampled

tag: gsi

tag: liver vtg mrna

tag: liver esr1 mrna

tag: ex vivo e2 (ng/ml/12h)

tag: ex vivo t (ng/ml/12h)

tag: plasma e2 (ng/ml)

tag: plasma vtg

tag: tissue

value: liver


title: fhm F Liver recovery CON-5

source_name: liver from female fish exposed to control water for 8d

value: con


title: fhm F Liver recovery DES 100-4

source_name: liver from female fish exposed to 100 ng DES/L for 96 h, followed by an additional 96 h in control water

value: 100 ng DES/L for 4 days then recovery for another 4 days


title: fhm F liver exposure des100-6

source_name: liver from female fish exposed to 100 ng DES/L for 96 h

treatment_protocol: Fish were exposed to 0, 1, 10, or 100 ng DES/L delivered in a continuous flow (45 ml/min) of sand filtered, UV treated, Lake Superior Water, without the use of carrier solvents. Total exposure time was 4 d (96 h).

value: 100 ng DES/L for 4 days


title: fhm F liver exposure des100-2


title: fhm F liver exposure des10-5

source_name: liver from female fish exposed to 10 ng DES/L for 96 h

value: 10 ng DES/L for 4 days


title: fhm F liver exposure des100-3


title: fhm F liver exposure des10-1


title: fhm F liver exposure des10-2


title: fhm F liver exposure des1-5

source_name: liver from female fish exposed to 1 ng DES/L for 96 h

value: 1.0 ng DES/L for 4 days


title: fhm F Liver recovery DES 1-6


title: SUM149 cell line, replicate 2

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

description: Gene expression data from metastatic cells of breast cancer.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Arrays. The arrays were then washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Quality check and Robust Multichip Normalization using the R/Bioconductor affy package. The probe set intensities were derived from RMA normalization.

label: biotin

organism: Homo sapiens

source_name: SUM149, adhesive growth

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Dulbecco's Modified Eagle's Medium (DMEM) with high glucose, 1.5 g/l NaHCO3, 10% fetal bovine serum (FBS), 1 mM MEM Na-pyruvate, 100 units/ml penicillin and 100 units/ml streptomycin (Gibco, Life Technologies). Cells were incubated at 37°C under 5% CO2.

extract_protocol: RNeasy kit (Qiagen, Hilden, Germany).

tag: cell line

tag: cell type

value: metastatic cells of breast cancer

tag: growth type

value: adhesive

tag: source

value: pleural effusion


title: MDA-MB231 cell line, replicate 2

source_name: MDA-MB231, adhesive growth


title: SUM149 cell line, replicate 1


title: SUM190 cell line, replicate 1

source_name: SUM190, adhesive growth


title: fhm F liver exposure des1-2

tag: ctid

tag: treatment

tag: tank


title: fhm F liver exposure con-3

source_name: liver from female fish exposed to control water for 96 h

value: control

tag: Sex

tag: FISH wet wt (g)

tag: gonad wt (g)


title: SUM190 cell line, replicate 2


title: sg3 6 dpi 2

first: Stephen

last: Turner

address: 1670 Discovery Drive

institute: Signature Science, LLC

hyb_protocol: For hybridization, cDNA was prepared according to the protocol provided by Roche (Roche Applied Science, Indianapolis, IN). cDNA quality control and hybridization to the 385K arrays were performed at Nimblegen.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Statistical analysis of Nimblegen microarray data was performed using software from the Bioconductor project [39] and implemented in the R environment for statistical computing and graphics (R Development Core Team, 2009), version 2.10.1. RMA background subtraction and normalization were applied to the microarray set. The experiment was performed using three biological replicates.

organism: Vigna unguiculata

source_name: Vigna unguiculata L. Walp., sg3 6 dpi

label_protocol: A 385,000 feature microarray was fabricated (Nimblegen Inc., Madison, WI) using 60-nucleotide long oligonucleotide synthesized based upon the nucleotide sequence of 43,253 cowpea unigenes of known and unknown function previously identified in a gene-space sequencing study. On the fabricated microarray, each predicted gene coding region is represented by six to eight 60-mer oligonucleotide probes.

growth_protocol: Cowpea cultivar B301 seeds were surface-sterilized with 1% hypochlorite for 5 min. They were then placed between two sheets of moist glass fiber filter paper (GF/A Whatman, Piscataway, NJ), held between two blocks of moistened rockwool (Grodan Inc., Milton, ON) for 5 days and then transferred to a growth chamber, which consists of a 24cm x 24cm x 3cm Petri dish containing rockwool with a 100 μm mesh separating the cowpea roots from the rockwool [14]. The chamber was covered with aluminum foil to keep light away from the roots. Cowpea seedlings were grown for another 7 days in a controlled environment growth room under a 12 H light-dark photoperiod at 30o C.

extract_protocol: Root material was collected 6 and 13 days post-inoculation (dpi). The infected areas on the roots were cut (±0.5 around the infection site) and rinsed in distilled water to remove the attached Striga seeds and Striga seedlings. Control roots were cut into 1cm pieces and collected in the same manner. Root material was collected from three cowpea plants per replicate and each treatment was done in triplicate. Samples were frozen using liquid nitrogen and stored in a -80o C freezer. Total RNA was isolated from frozen, finely ground root tissues. RNA samples were treated with DNase (Roche Applied Science, Indianapolis, IN) and repurified using Qiagen RNeasy kit (Qiagen, Valencia, CA) according to the manufacturers’ instructions. RNA concentration and quality was determined using an Experion (Bio-Rad, Hercules, CA).

treatment_protocol: Seeds of S. gesnerioides races SG3 and SG4z were surface sterilized and pre-conditioned for 9 days as previously described [13]. The germination of Striga seeds was triggered using root exudates from cowpea cultivar B301. The roots of each cowpea seedling were inoculated with 15 mg of pre-germinated S. gesnerioides using a paintbrush.

value: S. gesnerioides races SG3

tag: time

value: 6 dpi

value: root

tag: cultivar


title: fhm F liver exposure des1-1

tag: time sampled

tag: gsi

tag: liver vtg mrna

tag: liver esr1 mrna

tag: ex vivo e2 (ng/ml/12h)


title: MDA-MB468 cell line, replicate 1

source_name: MDA-MB468, adhesive growth

tag: cell line


title: IBC3 cell line, replicate 2

source_name: IBC3, adhesive growth

tag: cell type


title: control 3

source_name: Vigna unguiculata L. Walp., control

tag: tissue


title: fhm F liver exposure con-1

tag: notes

value: Immature

tag: ex vivo t (ng/ml/12h)

tag: plasma e2 (ng/ml)

tag: plasma vtg


title: fhm F liver exposure con-6

tag: ctid

tag: treatment

tag: tank

tag: Sex


title: MDA-MB468 cell line, replicate 2

tag: growth type

tag: source


title: sg4z 13 dpi 3

source_name: Vigna unguiculata L. Walp., sg4z 13 dpi

value: S. gesnerioides races SG4z

tag: time

value: 13 dpi

tag: cultivar


title: sg3 6 dpi 1


title: IBC-02 cell line, replicate 1

source_name: IBC-02, adhesive growth

value: pleural effusion from patient with metastatic secondary inflammatory breast cancer (IBC)


title: IBC-02 cell line, mammosphere, replicate 2

source_name: IBC-02, mammosphere growth

value: mammosphere


title: IBC-02 cell line, replicate 2


title: MDA-MB231 cell line, replicate 1


title: IBC-02 cell line, mammosphere, replicate 1


title: sg4z 13 dpi 2


title: IBC3 cell line, replicate 1


title: sg3 6 dpi 3


title: sg3 13 dpi 3

source_name: Vigna unguiculata L. Walp., sg3 13 dpi


title: sg3 13 dpi 1


title: sg4z 13 dpi 1


title: control 2


title: control 1


title: Biceps, control, cohort 22, subject 22U

status: Public on Sep 19 2012

city: Boston

first: Fedik

last: Rahimov

state: MA

address: 3 Blackfan Circle, CLS 15030.4

department: Genetics

institute: Boston Children's Hospital

description: Gene expression data from Biceps, control, cohort 22, subject 22U

hyb_protocol: Hybridization was performed using 5 micrograms of biotinylated target, which was incubated with the GeneChip Human Gene 1.0 ST array (Affymetrix) at 45°C for 16–20 hours. Following hybridization, non-specifically bound material was removed by washing and detection of specifically bound target was performed using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix GeneChip Command Console Software (Affymetrix).

data_processing: Array data were preprocessed using RMA  (apt-1.14.2 and HuGene-1_0-st-v1.r4.analysis-lib-files) and analyzed using the limma package (version 3.8.2, R version 2.11.1, and hugene10sttranscriptcluster.db_7.0.1). Note that arrays were scanned on several different dates (indicated by batch number in sample description), and when computing expression differences it is advisable to include a factor to correct for the batch effects, either directly of with a factor for cohort (as samples within each cohort were scanned on the same date).

source_name: Biceps, control, cohort 22, subject 22U

label_protocol: Biotin-labeled target for the microarray experiment was prepared using 100 ng of total RNA and cDNA was synthesized using the GeneChip WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix). The sense cDNA was then fragmented by UDG (uracil DNA glycosylase) and APE 1 (apurinic/apyrimidic endonuclease 1) and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labelling kit (Affymetrix).

extract_protocol: A portion of each biopsy sample (ranging between 50-200mg) was snap frozen in liquid nitrogen immediately after procurement and stored at -80°C for RNA extraction. Total RNA was isolated from frozen muscle tissues using TRIzol reagent (Invitrogen).

tag: subject

tag: cohort

value: Biceps

tag: disease state

tag: ecori/blni allele length

tag: age (y)

value: F

tag: batch


title: DC_IFNα21_3days_rep1

city: Montpellier

first: Geneviève

last: Garcin

address: UM2. Place Eugene Bataillon. Bat 24.

country: France

institute: CNRS UMR5235

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with HWS kit.

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

data_processing: The values from the data matrix are MAS5 values and derived from affymetrix expression console software.

source_name: IFNα21-DC at 3 days of differentiation

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix IVT Express protocol from 200 ng total RNA (3'IVT ExpressTechnical Manual, 2009, P/N702646 Rev1 Affymetrix).

extract_protocol: Total RNA were extracted with the High Pure RNA isolation Kit from Roche and according to manufacturer's instructions.

tag: ifn type1

tag: Stage

value: 3 days of differentiation


title: Biceps, FSHD, cohort 22, subject 22A

description: Gene expression data from Biceps, FSHD, cohort 22, subject 22A

source_name: Biceps, FSHD, cohort 22, subject 22A

tag: tissue

value: FSHD


title: Deltoid, FSHD, cohort 21, subject 21A

description: Gene expression data from Deltoid, FSHD, cohort 21, subject 21A

source_name: Deltoid, FSHD, cohort 21, subject 21A

value: Deltoid


title: Biceps, control, cohort 21, subject 21U

description: Gene expression data from Biceps, control, cohort 21, subject 21U

source_name: Biceps, control, cohort 21, subject 21U


title: Deltoid, FSHD, cohort 20, subject 20A

description: Gene expression data from Deltoid, FSHD, cohort 20, subject 20A

source_name: Deltoid, FSHD, cohort 20, subject 20A

value: M


title: Deltoid, FSHD, cohort 22, subject 22A

description: Gene expression data from Deltoid, FSHD, cohort 22, subject 22A

source_name: Deltoid, FSHD, cohort 22, subject 22A


description: Gene expression data from Deltoid, control, cohort 15, subject 15V


title: Biceps, FSHD, cohort 21, subject 21B

description: Gene expression data from Biceps, FSHD, cohort 21, subject 21B

source_name: Biceps, FSHD, cohort 21, subject 21B


description: Gene expression data from Deltoid, control, cohort 20, subject 20U


title: Biceps, FSHD, cohort 20, subject 20A

description: Gene expression data from Biceps, FSHD, cohort 20, subject 20A

source_name: Biceps, FSHD, cohort 20, subject 20A


title: Biceps, FSHD, cohort 21, subject 21A

description: Gene expression data from Biceps, FSHD, cohort 21, subject 21A

source_name: Biceps, FSHD, cohort 21, subject 21A


title: Biceps, control, cohort 20, subject 20U

description: Gene expression data from Biceps, control, cohort 20, subject 20U

source_name: Biceps, control, cohort 20, subject 20U


title: Deltoid, FSHD, cohort 21, subject 21B

description: Gene expression data from Deltoid, FSHD, cohort 21, subject 21B

source_name: Deltoid, FSHD, cohort 21, subject 21B


description: Gene expression data from Deltoid, control, cohort 21, subject 21U


title: Biceps, control, cohort 15, subject 15V

description: Gene expression data from Biceps, control, cohort 15, subject 15V

source_name: Biceps, control, cohort 15, subject 15V


title: sg3 13 dpi 2


title: Biceps, control, cohort 19, subject 19U

description: Gene expression data from Biceps, control, cohort 19, subject 19U

source_name: Biceps, control, cohort 19, subject 19U


title: Deltoid, FSHD, cohort 19, subject 19A

description: Gene expression data from Deltoid, FSHD, cohort 19, subject 19A

source_name: Deltoid, FSHD, cohort 19, subject 19A


title: Biceps, FSHD, cohort 19, subject 19A

description: Gene expression data from Biceps, FSHD, cohort 19, subject 19A

source_name: Biceps, FSHD, cohort 19, subject 19A


description: Gene expression data from Deltoid, control, cohort 18, subject 18U


title: Biceps, control, cohort 18, subject 18U

description: Gene expression data from Biceps, control, cohort 18, subject 18U

source_name: Biceps, control, cohort 18, subject 18U


title: Biceps, FSHD, cohort 15, subject 15A

description: Gene expression data from Biceps, FSHD, cohort 15, subject 15A

source_name: Biceps, FSHD, cohort 15, subject 15A


description: Gene expression data from Deltoid, control, cohort 12, subject 12V


title: Biceps, FSHD, cohort 13, subject 13B

description: Gene expression data from Biceps, FSHD, cohort 13, subject 13B

source_name: Biceps, FSHD, cohort 13, subject 13B


title: Deltoid, FSHD, cohort 13, subject 13B

description: Gene expression data from Deltoid, FSHD, cohort 13, subject 13B

source_name: Deltoid, FSHD, cohort 13, subject 13B


title: Deltoid, FSHD, cohort 15, subject 15A

description: Gene expression data from Deltoid, FSHD, cohort 15, subject 15A

source_name: Deltoid, FSHD, cohort 15, subject 15A


description: Gene expression data from Deltoid, control, cohort 13, subject 13U


description: Gene expression data from Deltoid, control, cohort 19, subject 19U


title: Deltoid, FSHD, cohort 18, subject 18A

description: Gene expression data from Deltoid, FSHD, cohort 18, subject 18A

source_name: Deltoid, FSHD, cohort 18, subject 18A


title: Biceps, FSHD, cohort 18, subject 18A

description: Gene expression data from Biceps, FSHD, cohort 18, subject 18A

source_name: Biceps, FSHD, cohort 18, subject 18A


title: Biceps, control, cohort 12, subject 12U

description: Gene expression data from Biceps, control, cohort 12, subject 12U

source_name: Biceps, control, cohort 12, subject 12U


title: Biceps, control, cohort 12, subject 12V

description: Gene expression data from Biceps, control, cohort 12, subject 12V

source_name: Biceps, control, cohort 12, subject 12V


title: Biceps, control, cohort 13, subject 13U

description: Gene expression data from Biceps, control, cohort 13, subject 13U

source_name: Biceps, control, cohort 13, subject 13U


title: Deltoid, FSHD, cohort 12, subject 12B

description: Gene expression data from Deltoid, FSHD, cohort 12, subject 12B

source_name: Deltoid, FSHD, cohort 12, subject 12B


description: Gene expression data from Deltoid, control, cohort 12, subject 12U


title: Biceps, FSHD, cohort 12, subject 12A

description: Gene expression data from Biceps, FSHD, cohort 12, subject 12A

source_name: Biceps, FSHD, cohort 12, subject 12A


title: Biceps, control, cohort 09, subject 09U

description: Gene expression data from Biceps, control, cohort 09, subject 09U

source_name: Biceps, control, cohort 09, subject 09U


title: Biceps, FSHD, cohort 12, subject 12B

description: Gene expression data from Biceps, FSHD, cohort 12, subject 12B

source_name: Biceps, FSHD, cohort 12, subject 12B


description: Gene expression data from Deltoid, control, cohort 09, subject 09U


title: Biceps, FSHD, cohort 09, subject 09A

description: Gene expression data from Biceps, FSHD, cohort 09, subject 09A

source_name: Biceps, FSHD, cohort 09, subject 09A


title: Deltoid, FSHD, cohort 12, subject 12A

description: Gene expression data from Deltoid, FSHD, cohort 12, subject 12A

source_name: Deltoid, FSHD, cohort 12, subject 12A


title: Deltoid, FSHD, cohort 07, subject 07A

description: Gene expression data from Deltoid, FSHD, cohort 07, subject 07A

source_name: Deltoid, FSHD, cohort 07, subject 07A


description: Gene expression data from Deltoid, control, cohort 07, subject 07U


title: Biceps, FSHD, cohort 07, subject 07A

description: Gene expression data from Biceps, FSHD, cohort 07, subject 07A

source_name: Biceps, FSHD, cohort 07, subject 07A


title: Deltoid, FSHD, cohort 09, subject 09A

description: Gene expression data from Deltoid, FSHD, cohort 09, subject 09A

source_name: Deltoid, FSHD, cohort 09, subject 09A


title: Biceps, control, cohort 03, subject 03U

description: Gene expression data from Biceps, control, cohort 03, subject 03U

source_name: Biceps, control, cohort 03, subject 03U


title: Deltoid, FSHD, cohort 03, subject 03A

description: Gene expression data from Deltoid, FSHD, cohort 03, subject 03A

source_name: Deltoid, FSHD, cohort 03, subject 03A


title: si-miR-20a at T60, biological rep1

city: Rehovot

first: Noa

last: Bossel Ben-Moshe

address: Hertzl Street

country: Israel

institute: Weizmann

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-20a, stimulated with EGF.
si20_60_a

hyb_protocol: RNA was hybridized to Affymetrix GeneChip Human Gene 1.0 ST arrays

scan_protocol: According to Affymetrix manual

data_processing: Affymetrix Expression Console was used, followed by normalization of all arrays together using a Lowess multi-array algorithm and signal-dependent noise estimation

source_name: MCF10A cells transfected with si-miR-20a and stimulated with EGF

label_protocol: According to Affymetrix manual

growth_protocol: MCF10A cells were grown in Dulbecco’s modified Eagle’s medium–F12 (DMEM-F12) supplemented with antibiotics, 10 mg/ml insulin, 0.1 mg/ml cholera toxin, 0.5 mg/ml hydrocortisone and heat-inactivated horse serum (5% (vol/vol), and 10 ng/ml EGF).

extract_protocol: RNA was isolated using Qiagen's microRNA isolation kit (Valencia, CA)

treatment_protocol: MCF10A cells were transfected using Oligofectamine transfection reagent (Invitrogen), with siRNA oligonucleotides directed at hsa-miR-20a, hsa-miR-671-5p and hsa-miR-212 and a non-targeting control. MCF10A cells were stimulated with EGF

tag: cell line

value: non-tumorigenic epithelial cell line MCF 10A

tag: time (min.)

tag: sirna transfection


title: si-miR-20a at T60, biological rep2

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-20a, stimulated with EGF.
si20_60_b


title: si-miR-20a at T120, biological rep2

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-20a, stimulated with EGF.
si20_120_b


title: si-miR-20a at T30, biological rep1

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-20a, stimulated with EGF.
si20_30_a


title: si-miR-20a at T0, biological rep2

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-20a, stimulated with EGF.
si20_0_b


title: si-miR-671 at T60, biological rep2

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-671-5p, stimulated with EGF.
si671_60_b

source_name: MCF10A cells transfected with si-miR-671-5p and stimulated with EGF


title: si-miR-671 at T120, biological rep2

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-671-5p, stimulated with EGF.
si671_120_b


title: si-miR-671 at T60, biological rep1

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-671-5p, stimulated with EGF.
si671_60_a


title: si-miR-20a at T120, biological rep1

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-20a, stimulated with EGF.
si20_120_a


title: si-miR-671 at T30, biological rep2

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-671-5p, stimulated with EGF.
si671_30_b


title: si-miR-671 at T30, biological rep1

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-671-5p, stimulated with EGF.
si671_30_a


title: si-miR-20a at T30, biological rep2

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-20a, stimulated with EGF.
si20_30_b


title: si-control at T120, biological rep2

description:
Gene expression data from MCF10A cells transfected with non-targeting control, stimulated with EGF.
con_120_b

source_name: MCF10A cells transfected with si-control and stimulated with EGF

value: si-control


title: si-miR-671 at T0, biological rep1

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-671-5p, stimulated with EGF.
si671_0_a


title: si-control at T0, biological rep2

description:
Gene expression data from MCF10A cells transfected with non-targeting control, stimulated with EGF.
con_0_b


title: si-control at T60, biological rep1

description:
Gene expression data from MCF10A cells transfected with non-targeting control, stimulated with EGF.
con_60_a


title: si-control at T30, biological rep2

description:
Gene expression data from MCF10A cells transfected with non-targeting control, stimulated with EGF.
con_30_b


title: si-control at T120, biological rep1

description:
Gene expression data from MCF10A cells transfected with non-targeting control, stimulated with EGF.
con_120_a


title: si-control at T60, biological rep2

description:
Gene expression data from MCF10A cells transfected with non-targeting control, stimulated with EGF.
con_60_b


title: si-miR-671 at T0, biological rep2

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-671-5p, stimulated with EGF.
si671_0_b


title: Biceps, FSHD, cohort 03, subject 03A

description: Gene expression data from Biceps, FSHD, cohort 03, subject 03A

source_name: Biceps, FSHD, cohort 03, subject 03A

tag: Sex


title: si-control at T30, biological rep1

description:
Gene expression data from MCF10A cells transfected with non-targeting control, stimulated with EGF.
con_30_a


title: si-miR-20a at T0, biological rep1

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-20a, stimulated with EGF.
si20_0_a


description: Gene expression data from Deltoid, control, cohort 03, subject 03U

value: control


title: si-control at T0, biological rep1

description:
Gene expression data from MCF10A cells transfected with non-targeting control, stimulated with EGF.
con_0_a


title: si-miR-671 at T120, biological rep1

description:
Gene expression data from MCF10A cells transfected with siRNA oligonucleotides directed at hsa-miR-671-5p, stimulated with EGF.
si671_120_a


title: +Al/-Al star1 basal roots Replicate 1

city: Bunkyo-ku

first: Tomokazu

last: Tsutsui

state: Tokyo

address: Room 02 (BF), Faculty of Science Building 2, 7-3-1 Hongo

department: Biological Sciences

country: Japan

institute: The university of tokyo

description: Biological replicate 1 of 4.

hyb_protocol: Microarray analysis was performed according to Agilent Oligo DNA Microarray Hybridization protocols using the Agilent 44K Rice Oligo DNA Microarray RAP-DB (Agilent Technologies; G2519F#15241)

scan_protocol: The hybridized slides were scanned using a DNA microarray scanner (Agilent Technologies).

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

organism: Oryza sativa

source_name: star1 basal roots

label_protocol: Fluorescent probe labeling using the oligo-dT-T7 strand-specific amplification method according to the manufacturer's instructions (Agilent Technologies)

growth_protocol: Seeds of wild-type rice (Oryza sativa cv. Koshihikari) and an Al-sensitive mutant, star1, were germinated for 2 days at 30ºC.

extract_protocol: Root tips (0-1 cm) and basal region (1-2 cm) of the roots (20-30 plants per sample) were excised from the seedlings of both wild-type rice and star1 mutant which had been exposed to 20 µM AlCl3 for 6 h and immediately frozen in liquid nitrogen.  Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen, Germany).

treatment_protocol: The seedlings were then transferred to a plastic net floating on a 0.5 mM CaCl2 solution in a 1.5 L plastic box.  At day 4, the seedlings were exposed to a 0.5 mM CaCl2 solution (pH 4.5) containing 0 or 20 µM AlCl3.

tag: age

value: day 4

value: 1-2 cm root (basal roots)

tag: treatment

value: +Al

value: 1-2 cm root (basal root)

value: -Al


title: +Al/-Al star1 root tips Replicate 3

description: Biological replicate 3 of 4.

source_name: star1 root tips

value: 0-1 cm root (root tips)

value: 0-1 cm root (root tip)


title: +Al/-Al star1 basal roots Replicate 3

description: Biological replicate 3 of 4.


title: +Al/-Al star1 basal roots Replicate 2

description: Biological replicate 2 of 4.


title: +Al/-Al star1 basal roots Replicate 4

description: Biological replicate 4 of 4.


title: +Al/-Al star1 root tips Replicate 4

description: Biological replicate 4 of 4.


title: +Al/-Al star1 root tips Replicate 2

description: Biological replicate 2 of 4.


title: +Al/-Al WT basal roots Replicate 4

description: Biological replicate 4 of 4.

source_name: Koshihikari basal roots

value: Koshihikari


title: +Al/-Al WT basal roots Replicate 1

description: Biological replicate 1 of 4.


title: +Al/-Al star1 root tips Replicate 1

description: Biological replicate 1 of 4.


title: +Al/-Al WT basal roots Replicate 3

description: Biological replicate 3 of 4.


title: +Al/-Al WT root tips Replicate 4

description: Biological replicate 4 of 4.

source_name: Koshihikari root tips


title: +Al/-Al WT basal roots Replicate 2

description: Biological replicate 2 of 4.


title: +Al/-Al WT root tips Replicate 3

description: Biological replicate 3 of 4.


title: +Al/-Al WT root tips Replicate 2

description: Biological replicate 2 of 4.


title: +Al/-Al WT root tips Replicate 1

description: Biological replicate 1 of 4.


title: 156_Rep1

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

country: United Kingdom

institute: The University of York

hyb_protocol: Standard Illumina protocol

scan_protocol: Arrays were scanned on a BeadArray reader

data_processing: Data were quantile normalised using Lumi for R.

label: Biotin

source_name: Biopsy

label_protocol: Standard Illumina protocol

extract_protocol: Total RNA was extracted from 5mm paraffin sections using the Ambion RecoverAll kit standard protocol, with the exception of a 16-hour protease digestion. These were routinely collected tissue samples and no attempt was made to standardise fixation or processing protocols

value: diffuse large b-cell lymphoma (DLBCL)

tag: predicted class

value: ABC

tag: class confidence

value: female

tag: treated status

tag: follow-up status

value: Dead

tag: follow-up years

tag: replicate


title: 1_Rep12

value: Alive


description: Gene expression data from Deltoid, control, cohort 22, subject 22U

tag: subject

tag: cohort

value: Deltoid

tag: disease state

tag: ecori/blni allele length

tag: age (y)

value: F


title: 135_Rep2

tag: tissue

value: GCB

value: male


title: 172


title: 53_Rep2


title: 171

value: TypeIII


title: 2_Rep7


title: Biceps, control, cohort 07, subject 07U

description: Gene expression data from Biceps, control, cohort 07, subject 07U

source_name: Biceps, control, cohort 07, subject 07U

value: Biceps

value: control

tag: batch


title: 3_Rep11


title: 44_Rep1


title: 53_Rep3


title: 135_Rep1


title: 3_Rep10


title: 5_Rep6


title: 3_Rep8


title: 170


title: 1_Rep8


title: 5_Rep7


title: 1_Rep11


title: 3_Rep7


title: 1_Rep10


title: 2_Rep6


title: 2_Rep5


title: 3_Rep6


title: 3_Rep5


title: 1_Rep9


title: 3_Rep9


title: 101_Rep1


title: 169


title: 166


title: 168


title: 165


title: 161


title: 162


title: 163


title: 157


title: 159


title: 167


title: 164


title: 158


title: 155


title: 154


title: 149


title: 151


title: 153


title: 156


title: 150


title: 160


title: 145


title: 143


title: 146


title: 33_Rep1


title: 108_Rep1


title: 123_Rep1


title: 148


title: 86_Rep1


title: 147


title: 128_Rep1


title: 152


title: 41_Rep1


title: 53_Rep1


title: 5_Rep5


title: 22_Rep1


title: 1_Rep7


title: 144


title: 10_Rep2


title: 142


title: 3_Rep4


title: 51_Rep1


title: 38_Rep1


title: 141


title: 49_Rep1


title: 137


title: 8_Rep1


title: 126_Rep1


title: 128


title: 135


title: 132


title: 138


title: 56_Rep1


title: 136


title: 129


title: 96_Rep1


title: 125


title: 134


title: 126_Rep2


title: 139


title: 140


title: 133


title: 131


title: 115_Rep1


title: 124


title: 129_Rep1


title: 127


title: 126


title: 123


title: 122


title: 138_Rep1


title: 121


title: 130


title: 120


title: 119


title: 115


title: 117


title: 118


title: 116


title: 113


title: 104


title: 95


title: 111


title: 101


title: 114


title: 107


title: 112


title: 90


title: 103


title: 97


title: 109


title: 98


title: 99


title: 96


title: 110


title: 108


title: 105


title: 88


title: 92


title: 91


title: 106


title: 89


title: 85


title: 87


title: 102


title: 93


title: 86


title: 100


title: 94


title: 84


title: 81


title: 77


title: 83


title: 80


title: 72


title: 67


title: 76


title: 71


title: 82


title: 61


title: 59


title: 63


title: 60


title: 65


title: 73


title: 58


title: 78


title: 56


title: 70


title: 75


title: 57


title: 64


title: 69


title: 79


title: 74


title: 62


title: 66


title: 68


title: 55


title: 51


title: 47


title: 53


title: 49


title: 52


title: 45


title: 48


title: 43


title: 54


title: 44


title: 34_Rep1


title: 36


title: 50


title: 46


title: 38


title: 39


title: 27_Rep1


title: 42


title: 41


title: 3_Rep3


title: 2_Rep4


title: 5_Rep4


title: 1_Rep6


title: 30_Rep1


title: 35


title: 17_Rep1


title: 40


title: 37


title: 34


title: 32


title: 33


title: 28


title: 30


title: 24


title: 27


title: 29


title: 26


title: 23


title: 25


title: 31


title: 21


title: Foxo3 Knock Out BMM Stimulated with Poly-IC for 2hrs 2

city: Seattle

first: Ayush

last: Raman

state: WA

address: 401 Terry Avenue North

department: Computational Dept.

institute: Institute for Systems Biology

description: Foxo3 knock-out bone marrow macrophages stimulated with poly-IC for 2 hrs sample 2.

hyb_protocol: Labeled, fragmented cDNA was hybridized for 16 hours at 45 deg C and 60rpm to an Affymetrix GeneChip according to the Affymetrix Whole Transcript Sense Target Labeling protocol. The chips were washed and stained using fluidics protocol FS450_0001.

scan_protocol: Scanning was performed using the Affymetrix GeneChip 3000 Scanner. Images were processed into CEL files with the Affymetrix GCOS software.

data_processing: Raw CEL intensity data were RMA normalized using R/Bioconductor and the MBNI custom CDF Entrez Gene version 11 package.

organism: Mus musculus

source_name: Poly-IC-stimulated Foxo3 knock-out bone marrow macrophages

label_protocol: 200ng of total RNA was labeled according to the Ambion WT Expression kit for Affymetrix GeneChip Whole Transcript Expression Arrays followed by the Affymetrix GeneChip WT Terminal Labeling Kit.

growth_protocol: C57BL/6 mice were obtained from Jackson Laboratories. Foxo3-/- mice in the FVB background were obtained from MMRRC and were backcrossed to C57BL/6 mice at least 5 times to generate congenic mice. C57BL/6 Foxo3+/- heterozygotes were intercrossed to generate Foxo3-/- mice. Bone marrow macrophages (BMMs) were isolated from femurs of WT C57BL/6 and Foxo3-null mice and were plated on non-tissue culture-treated plastic in complete RPMI medium containing 10% (vol/vol) FBS (Hyclone Laboratories), 2 mM L-glutamine, 100 IU/ml of penicillin and 100 g/ml of streptomycin (all from Cellgro, Mediatech) and supplemented with recombinant human macrophage colony-stimulating factor (50 ng/ml; Peprotech).

extract_protocol: Total RNA was extracted using a Trizol solution (Invitrogen, and overall RNA quality was analyzed with an Agilent 2100 Bioanalyzer. Sample mRNA was amplified, labeled and hybridized to GeneChip Mouse Exon 1.0 ST arrays according to the array manufacturer’s instructions (Affymetrix).

treatment_protocol: For PIC stimulation, BMMs were treated for 2 hours with PIC (6μg/ml; Amersham).

tag: background/strain

tag: genotype/variation

value: Foxo3 knock-out

tag: cell type

value: bone marrow macrophages

value: poly-IC (PIC)


title: Foxo3 Knock Out BMM Stimulated with Poly-IC for 2hrs 1

description: Foxo3 knock-out bone marrow macrophages stimulated with poly-IC for 2 hrs sample 1.

tag: treatment


title: Foxo3 Knock Out BMM Unstimulated 2

description: Foxo3 knock-out bone marrow macrophages unstimulated sample 2.

source_name: Foxo3 knock-out unstimulated bone marrow macrophages


title: Foxo3 Knock Out BMM Stimulated with Poly-IC for 2hrs 3

description: Foxo3 knock-out bone marrow macrophages stimulated with poly-IC for 2 hrs sample 3.


title: 20

tag: predicted class

tag: age

tag: Sex


title: 17

tag: class confidence

tag: treated status

tag: follow-up status


title: 16

tag: follow-up years


title: Wildtype BMM Stimulated with PIC for 2 Hrs 1

description: Wildtype bone marrow macrophages stimulated with poly-IC for 2 hrs sample 1.

source_name: Poly-IC-stimulated bone marrow macrophages

value: wildtype


title: Wildtype BMM Stimulated with PIC for 2 Hrs 3

description: Wildtype bone marrow macrophages stimulated with poly-IC for 2 hrs sample 3.


title: 18


title: Foxo3 Knock Out BMM Unstimulated 3

description: Foxo3 knock-out bone marrow macrophages unstimulated sample 3.


title: Wildtype BMM Unstimulated 3

description: Wildtype bone marrow macrophages unstimulated sample 3.

source_name: Unstimulated bone marrow macrophages


title: 19


title: Wildtype BMM Stimulated with PIC for 2 Hrs 2

description: Wildtype bone marrow macrophages stimulated with poly-IC for 2 hrs sample 2.


title: 22


title: Foxo3 Knock Out BMM Unstimulated 1

description: Foxo3 knock-out bone marrow macrophages unstimulated sample 1.


title: 15


title: Wildtype BMM Unstimulated 2

description: Wildtype bone marrow macrophages unstimulated sample 2.


title: 2_Rep3

tag: replicate


title: Wildtype BMM Unstimulated 1

description: Wildtype bone marrow macrophages unstimulated sample 1.


title: 3_Rep2


title: 1_Rep5


title: 1_Rep4


title: 13


title: 11


title: 5_Rep3


title: 12_Rep1


title: 13_Rep1


title: 2_Rep2


title: 14


title: 11_Rep1


title: 5_Rep2


title: 14_Rep1


title: Patient 2, 24 h, in vitro

city: Stanford

first: Jonathan

last: Pollack

state: CA

address: 269 Campus Drive, CCSR3245A

department: Pathology

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65515.gif

hyb_protocol: not provided

scan_protocol: Arrays were then imaged using a GenePix 4000B scanner (Axon).  Fluorescence ratios were extracted using SpotReader software, and the data uploaded into the Stanford Microarray Database (SMD) for storage, retrieval and analysis

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: aCR (Stratagene)

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Stratagene Universal reference (derived from 11 different established human cell lines)

label_protocol: For the cell line experiments and on patient sample experiment (ExpID 65407) 50 ug of total RNA from each untreated cell line and 50 ug of total RNA from each VPA treated cell line were differentially labeled with Cy5 and Cy3, respectively, using oligo-dT and random hexamer primers during a first strand reverse transcription reaction. For the other 14 matched patient samples 50 ug of total RNA from each sample (either collected at diagnosis or following treatment) and 50 ug of universal reference mRNA (derived from 11 different established human cell lines) were differentially labeled with Cy5 and Cy3, respectively, using oligo-dT and random hexamer primers during a first strand reverse transcription reaction

extract_protocol: Freshly frozen Ficoll-enriched mononuclear cells from peripheral blood samples (tumor cell content >85%), isolation of total RNA using Trizol reagent

value: acute myeloid leukemia peripheral blood

tag: time

tag: individual

value: Patient 2


title: 12

tag: tissue

value: diffuse large b-cell lymphoma (DLBCL)


title: 10


title: 10_Rep1


title: 8

value: female

value: Dead


title: 7_Rep1


title: 9_Rep1


title: 9


title: Patient 7, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65510.gif

value: 0 h

value: Patient 7


title: Patient 2, 48 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65513.gif


title: 7

value: GCB


title: 6_Rep1

value: male

value: Alive


title: 5_Rep1

value: ABC


title: Patient 1, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65405.gif

value: Patient 1


title: Patient 16, 48 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65548.gif

value: Patient 16


title: Patient 14, 48 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65554.gif

value: Patient 14


title: Patient 8, 48 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65516.gif

value: Patient 8


title: 6


title: 5


title: 4

value: TypeIII


title: 4_Rep1


title: NB4, 0 h against 48 h 1mM VPA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66402.gif

source_name: untreated

tag: leukemia cell line

source_name: treated


title: Patient 10, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65501.gif

value: Stratagene Universal reference (derived from 11 different established human cell lines)

value: Patient 10


title: 3_Rep1


title: Patient 3, 48 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65527.gif

value: acute myeloid leukemia peripheral blood

value: Patient 3


title: 2

value: diffuse large b-cell lymphoma (DLBCL)

value: female


title: Patient 12, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65488.gif

value: 0 h

value: Patient 12


title: Patient 5, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65503.gif

value: Patient 5


title: Patient 12, 48 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65490.gif


title: Patient 8, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65514.gif


title: Patient 10, 48 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65502.gif


title: K562, 0 h against 48 h 1mM VPA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66404.gif


title: Patient 15, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65542.gif

value: Patient 15


title: Patient 11, 48 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65487.gif

value: Patient 11


title: 1_Rep3

value: ABC

value: Alive


title: 3

value: GCB

value: Dead


title: Patient 13, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65551.gif

value: Patient 13


title: 1_Rep2


title: Patient 17, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65541.gif

value: Patient 17


title: Patient 15, 48 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65544.gif

value: Stratagene Universal reference (derived from 11 different established human cell lines)


title: Patient 18, 48 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65547.gif

value: Patient 18


title: BDL_FSAP-/-.3

city: Bergisch Gladbach

first: Ute

last: Bissels

state: NRW

address: Friedrich-Ebert-Str. 68

department: R&D

country: Germany

institute: Miltenyi Biotec GmbH

hyb_protocol: The hybridization procedure was performed according to the the “One-Color Microarray-Based Gene Expression Analysis protocol (version 5.7, part number G4140-90040) using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65 µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software 9.1 was used to read out and process the microarray image files.

data_processing: FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, Rosetta error model; Lee Weng et al 2006).

source_name: liver

label_protocol: 100 ng of each total RNA samples was used for the amplification and labeling step using the Agilent Quick Amp Labeling Kit (Agilent Technologies). Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: Liver RNA was isolated by guanidine thiocyanate, chloroform and isopropanol precipitation, followed by DNAase digestion. Quantification and quality control of the RNA was checked with Agilent 2100 Bioanalyzer platform (Agilent Technologies, Palo Alto, CA, USA). Only total RNA with an RNA integrity number ≥ 7.2 was used for microarray hybridization (N = 3 mice per group)

treatment_protocol: FSAP-/- mice were backcrossed on to the BalbC background up to the F3 generation. FSAP-/- and littermate FSAP+/+ (WT) mice obtained from crossings between heterozygous mice were used for the experiment between 20 and 30 weeks of age. Surgical ligation of the common bile duct (BDL) was performed under isoflurane anesthesia and sham-operated mice underwent the same procedures except that the bile duct was not ligated. After 2 weeks the mice were sacrificed and the liver was flash frozen and stored at -80°C for further analysis.

tag: background strain

value: BalbC

tag: group

value: bile duct ligation (BDL)

value: FSAP-deficient


title: Sham_FSAP-/-.3

value: sham-operated

tag: genotype/variation


title: Patient 4, 24 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65529.gif

tag: cell type

value: acute myeloid leukemia peripheral blood

value: Patient 4


title: Patient 6, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65505.gif

value: 0 h

value: Patient 6


title: Patient 5, 24 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65504.gif

value: Patient 5


title: Patient 3, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65526.gif

value: Patient 3


title: BDL-WT.3

value: WT


title: BDL_FSAP-/-.1


title: Patient 16, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65546.gif

value: Patient 16


title: 1_Rep1

value: diffuse large b-cell lymphoma (DLBCL)

tag: predicted class

value: ABC

value: female

value: Alive


title: 1

tag: age


title: Sham-FSAP-/-.1


title: Sham_FSAP-/-.2


title: 2_Rep1

value: GCB

tag: Sex

value: Dead


title: BDL_FSAP-/-.2

value: BalbC

value: bile duct ligation (BDL)


title: BDL-WT.1


title: Butanol_Challenge_Step_1-2

type: other

city: College Station

first: James

last: Winkler

state: TX

address: 3122 TAMU

institute: Texas A&M University

description: Sample 15

hyb_protocol: Samples were for hybridization by adding lyophilized 10X Blocking Agent (supplied with Agilent Oligo aCGH Hybridization Kit), following manufacture's protocol.  The samples were hybridazed in a Agilent's E. coli Gene Expression Microarray, 8x15K

scan_protocol: The arrays were scanned using the GenePix 4100A Microarray Scanner

data_processing: The image analysis performed using GenePix Pro 6.0 Software (Molecular Devices), normalized with MIDAS (LOWESS method), with clustering analysis in MeV (CAST)

molecule: other

organism: Escherichia coli

label_protocol: 5 µg of plasmid DNA was digested with 5 U of AluI and 5 U of RsaI at 37°C 2h. 0.5 µg of fragmented plasmid DNA was labeled using Alexa Fluor Oligo CGH 2X reation mixes following manufacture's instructions.

growth_protocol: Genomic Library of E. coli was enriched via serial transfers. The cells were grown in M9 minimal media (5 g/L glucose), and in increasing concentration of n-butanol (0.5, 0.9, 1.3 and 1.7% v/v).

extract_protocol: other extracted using alkalyne lysis preparation. Plasmid DNA was clean and concentrated using Zymo Clean & Concentrated -5 kit

value: bacterial liquid culture

tag: extracted molecule

value: plasmid DNA

source_name: Non-challenged Library


title: Control_Step_2-2

description: Sample 14


title: Butanol_Challenge_Step_2-2

description: Sample 13


title: Sham-WT.3

value: sham-operated


title: Patient 6, 72 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65506.gif

value: Stratagene Universal reference (derived from 11 different established human cell lines)

value: acute myeloid leukemia peripheral blood


title: Sham-WT.1


title: BDL-WT.2


title: Control_Step_1-2

description: Sample 16


title: Sham-WT.2


title: Patient 7, 48 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65512.gif

value: Patient 7


title: HL60, 0 h against 48 h 1mM VPA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66403.gif

value: 0 h


title: Control_Step_3-2

description: Sample 12


title: Butanol_Challenge_Step_3-2

description: Sample 11


title: Control_Step_4-2

description: Sample 10


title: Butanol_Challenge_Step_4-2

description: Sample 9


title: Control_Step_4-1

description: Sample 8


title: Patient 17, 72 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65543.gif

value: Patient 17


title: Butanol_Challenge_Step_4-1

description: Sample 7


title: Patient 13, 48 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65552.gif

value: Patient 13


title: Patient 11, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65486.gif

value: Patient 11


title: Control_Step_3-1

description: Sample 6


title: TB patient 2

city: Shanghai

first: Chanyi

last: Lu

address: 220 Handan Rd

country: China

institute: Fudan University

description: RNA extracted after culture for 4 hours

hyb_protocol: Each Slide was hybridized with 825ng Cy3-labeled cRNA and 825ng Cy-5 labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US)in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US)with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Lowess(locally weighted scatter plot smoothing) algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: PPD-stimulated PBMCs from TB patient

label_protocol: Total RNA were amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX, US), Cy3 NHS ester (Cat#PA13105, GE healthcare Biosciences, Pittsburgh, PA, US) ，Cy5 NHS ester (Cat#PA15100, GE healthcare Biosciences, Pittsburgh, PA, US)followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: PBMCs were cultured with AIM-V (Invitrogen Life Technologies, USA) containing 2 mM L-glutamine, 50 ug/ml streptomycin sulfate, and 10 ug/ml gentamicin.

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

treatment_protocol: 10 ug/ml Mycobacterium tuberculosis purified protein derivative (PPD, Mycos Research LLC, Loveland, CO) treated or untreated for 4 hours before RNA extraction.

value: PBMCs

tag: infection status

value: tuberculosis patient

source_name: unstimulated PBMCs from TB patient


title: TB patient 3

description: RNA extracted after culture for 4 hours


title: Patient 14, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65553.gif

value: Patient 14


title: TB patient 4

description: RNA extracted after culture for 4 hours


title: Butanol_Challenge_Step_3-1

description: Sample 5


title: Control_Step_2-1

description: Sample 4


title: SKBr3 control 2

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

institute: IARC WHO

description: Gene expression data

hyb_protocol: labeled and fragmented cRNA hybridized to HG-U133_Plus_2 Affymetrix GeneChips using standard techniques recommended by the manufacturer.

scan_protocol: Affymetrix 7G GeneArray scanner

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was performed by the RMA algorithm using Agilent Genespring GX11 program. No further adjustments were made to the data in the table.

source_name: SKBr3 cells

label_protocol: Labeled target cRNA population was generated with the Affymetrix 3’-IVT Express kit

growth_protocol: Cell were grown in DMEM, high glucose, containing 10% fetal bovine serum and antibiotics.

extract_protocol: Total RNA was extracted from cells using the RNAqueous-4PCR kit (AM1914, Ambion).

treatment_protocol: For MCF_TET samples, cells were treated with either vehicle (MCF_TET_C) or doxycycline (1ug/ml) (MCF_TET_A) for 72 hours to induce ACSL4 expression.  For MCF_ and SK_ samples, cells were stably transfected with a lentivirus-empty vector (MCF_C and SK_C) or lentivirus-ACSL4 vector (MCF_A and SK_A), and selscted clones from each transfection used as the source of RNA to be analyzed.

tag: cell line

tag: disease state

value: HER2-positive breast cancer

value: breast cancer

tag: treatment

value: control-transfected


title: SKBr3 control 1

description: Gene expression data


title: Patient 9, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65499.gif

tag: reference

value: Patient 9


title: Patient 1, 0 h against 48 h

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65407.gif

tag: time

value: Patient 1


title: Butanol_Challenge_Step_2-1

description: Sample 3

value: bacterial liquid culture

value: plasmid DNA


title: SKBr3 control 3

description: Gene expression data


title: SKBr3 ACSL4 2

description: Gene expression data


title: Patient 9, 48 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65500.gif

value: Stratagene Universal reference (derived from 11 different established human cell lines)

tag: individual


title: SKBr3 ACSL4 1

description: Gene expression data

tag: tissue


title: Control_Step_1-1

description: Sample 2


title: Patient 2, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65511.gif

value: acute myeloid leukemia peripheral blood

value: Patient 2


title: Butanol_Challenge_Step_1-1

description: Sample 1


title: MCF-7 ACSL4 3

description: Gene expression data

source_name: MCF-7 cells

value: Estrogen receptor positive breast cancer


title: Patient 1, 48 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65406.gif


title: Patient 2, 48 h, in vitro

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65517.gif


title: Healthy control 4

description: RNA extracted after culture for 4 hours

source_name: PPD-stimulated PBMCs from healthy control

value: Healthy control

source_name: unstimulated PBMCs from healthy control


title: SKBr3 ACSL4 3

description: Gene expression data


title: HEL, 0 h against 48 h 1mM VPA

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66405.gif

value: 0 h

tag: leukemia cell line

value: HEL


title: MCF-7 ACSL4 1

description: Gene expression data


title: Healthy control 3

description: RNA extracted after culture for 4 hours

value: PBMCs


title: Healthy control 1

description: RNA extracted after culture for 4 hours


title: Healthy control 2

description: RNA extracted after culture for 4 hours


title: MCF-7 control 3

description: Gene expression data


title: MCF-7 ACSL4 2

description: Gene expression data


title: Patient 18, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65545.gif

value: Patient 18


title: MCF-7 control 2

description: Gene expression data


title: Latent TB infectious individual 4

description: RNA extracted after culture for 4 hours

source_name: PPD-stimulated PBMCs from latent TB infectious individual

value: Latent tuberculosis

source_name: unstimulated PBMCs from latent TB infectious individual


title: Latent TB infectious individual 1

description: RNA extracted after culture for 4 hours


title: MCF-7 Tet-On ACSL4 2

description: Gene expression data

source_name: MCF-7 Tet-On cells


title: MCF-7 Tet-On control 1

description: Gene expression data

value: control


title: Patient 4, 0 h, in vivo

description: Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65528.gif

value: Patient 4


title: MCF-7 Tet-On control 3

description: Gene expression data

value: breast cancer


title: MCF-7 Tet-On control 2

description: Gene expression data


title: Latent TB infectious individual 3

description: RNA extracted after culture for 4 hours


title: MCF-7 Tet-On ACSL4 3

description: Gene expression data


title: Latent TB infectious individual 2

description: RNA extracted after culture for 4 hours


title: MCF-7 Tet-On ACSL4 1

description: Gene expression data


title: Raptor Mutant (KO) rep3

first: Amit

last: Sinha

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: Labeled cDNA was hybridized to the Affymetrics 430 2.0 microarray using standard conditions.

scan_protocol: Standard Affymetrix protocol

data_processing: RMA background correction and quantile normalization done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/) which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al Biostatistics (2003).

source_name: Raptor Mutant (KO)

label_protocol: RNA was amplified with the Ovation® Pico WTA System (Nugen, San Carlos, CA), and fragmented and biotinylated with the Encore™ Biotin Module (Nugen)

growth_protocol: In vivo

extract_protocol: RNA was extracted using the Arcturus® PicoPure®  RNA isolation Kit according to the manufacturer’s recommendations (Applied Biosystems, Carlsbad, CA)

treatment_protocol: Mice were treated with 15 micrograms/g body weight polyinosinic-polycytidylic acid (pIpC) three times once daily over 5 days, cells were sorted 5 weeks after the last injection

tag: strain background

value: Sorted HSPC 5 weeks post pIpC

value: Raptor Mutant (KO)


title: HMVEC-D-BMP9treated-Biological Rep2

city: Scarborough

first: Calvin

last: Vary

state: Maine

address: 81 Research Drive

department: Maine Medical Center Research Institute

institute: Maine Medical Center

description:
sm011107_sample-b2
Data providing  endothelial cell expression following BMP9 treatment for 24 hours

hyb_protocol: Slides are prehybridization buffer: 5x SSC, 0.1% SDS and 1% BSA (Sigma #B-4287) and heated to 50°C while stirring. Slides are placed in 2X hybridization buffer: 50% formamide, 10X SSC and 0.2% SDS. Incubate the solution until it reaches 48°C. The Cy3 and Cy5 labeled targets are suspended in 9 µl water, and the mixture is heated to 95°C for 3 min to denature, and centrifuged at maximum angular velocity for 1 min. The slide is placed in a sealed hybridization chamber (Corning, Acton, MA), and 12 µl water is added to the small reservoirs at each end of the chamber. The sealed chamber is placed in a 48°C water bath and incubated for 40-60 hr.

scan_protocol: The finished microarray slide is scanned and gridded using an Axon GenePix 4000 A or B with GenePixPro 5.0 software (Axon Instruments, Sunnyvale, CA).

data_processing: The raw data from the microarray study are statistically analyzed in three steps: (i) the data are normalized [Algorithm: ExpressionStat 5.0], (ii) ANOVA for each gene is determined, and (iii) clustering analysis is carried out. The statistically analyzed datasets are merged into EASE computer programs to determine biological meaning.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Low passage HMVEC-D were grown under standard conditions human dermal microvascular endothelial cells were maintained in EGM-2-MV medium (Lonza) at 37°C and 5% CO2. EGM-2-MV medium consists of EMB-2 with 1% fetal bovine serum and other additives, including growth factors.

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

treatment_protocol: HMVEC-D were grown under standard conditions human dermal microvascular endothelial cells were maintained in EGM-2-MV medium (Lonza) at 37°C and 5% CO2. EGM-2-MV medium consists of EMB-2 with 1% fetal bovine serum and other additives, including growth factors. Following 24 hours of culture, the cells in the BMP9-treated arm of the study were provided BMP9 at 5 ng/ml. Cwells were harvested 24 hours later and polyA+ RNA was prepared.

value: cultured passage-3 human dermal microvascular endothelial cells

tag: media

value: complete EBM2 endothelial cell media

tag: treated with

value: 5 ng/ml human recombinant BMP9 for 24hrs


title: HMVEC-D-untreated-Biological Rep2

description:
sm011107_sample-a2
Data providing basal endothelial cell expression

source_name: HMVEC-D-untreated

tag: cell type

value: none (control)


title: HMVEC-D-untreated-Biological Rep3

description:
sm011107_sample-a3
Data providing basal endothelial cell expression


title: Raptor Mutant (KO) rep2

tag: genotype/variation


title: Raptor Wildtype rep2

source_name: Raptor Wildtype

value: Raptor Wildtype


title: HMVEC-D-untreated-Biological Rep1

description:
sm011107_sample-a1
Data providing basal endothelial cell expression


title: HMVEC-D-BMP9treated-Biological Rep1

description:
sm011107_sample-b1
Data providing  endothelial cell expression following BMP9 treatment for 24 hours


title: Raptor Wildtype rep3


title: mock_10day_leaf_rep3

city: No.12 Zhongguancun South Street, Haidian

first: Jun

last: Liu

state: Beijing

address: 1230 York Avenue

department: Chinese Academy of Agricultural Sciences

institute: Institute of Crop Science

hyb_protocol: Probe synthesis, hybridization and scanning of all arrays were carried out at the Genomics Resource Center in the Rockefeller University following the manufacturer’s manual (Affymetrix).

data_processing: Background correction was performed as described by Irizarry et al. (2003). Quantile normalization was performed as described by Bolstad et al (2003). Finally, probes were summarized into single gene expression (probe-set) values on a per chip basis using the medianpolish algorithm (Tukey, 1977).

organism: Arabidopsis thaliana

source_name: mock 10day leaf replicate3

growth_protocol: Arabidopsis thaliana ecotype Columbia-0 was used as Wild-type.For hydroponic culture, WT seeds  after a 3-day cold treatment at 4°C were sowed on rock wool (Grodan Inc.) pre-soaked  in MGRL media. In short, plants were  grown at 22°C with a 150 μmol m-2 S-1 fluorescence rate and under 12 hour / 12 hour  light dark cycle in MGRL hydroponic medium.

extract_protocol: Each array probe for Arabidopsis Genechip ATH1 was synthesized from 1 μg total RNA extracted by RNA easy extraction kit (Qiagen). Eighteen individual Genechip probes with three biological replicates for CL (Col Leaf), CR (Col Root), OL (Osmotic stressed Leaf), OR (Osmotic stressed Root), RL (Recovery Leaf), and RR (Recovery Root).

treatment_protocol: Thirty-day-old plants were then subjected to high osmotic stress by adding 0.3M mannitol to the basal MGRL medium for 3 hr in the light. Recovery plants were transfer back to the MGRL medium for 1 day after stress treatment and sampled.  to high osmotic stress by adding 0.3M mannitol to the basal MGRL medium for 3 hr in  the light. Recovery plants were transfer back to the MGRL medium for 1 day after stress  treatment and sampled.

tag: ecotype

value: leaves

value: mock

tag: time point


title: Raptor Wildtype rep1


title: Raptor Mutant (KO) rep1


title: mock_10day_root_rep3

scan_protocol: Probe synthesis, hybridization and scanning of all arrays were carried out at the Genomics Resource Center in the Rockefeller University following the manufacturer’s manual (Affymetrix).

source_name: mock 10day root replicate3

value: roots


title: mock_10day_root_rep2

source_name: mock 10day root replicate2

label_protocol: Probe synthesis, hybridization and scanning of all arrays were carried out at the Genomics Resource Center in the Rockefeller University following the manufacturer’s manual (Affymetrix).


title: mock_10day_leaf_rep1

source_name: mock 10day leaf replicate1


title: mock_10day_root_rep1

source_name: mock 10day root replicate1


title: 070321b; MFT121,p53f/f

status: Public on Sep 18 2012

type: genomic

city: Worcester

first: Karl

last: Simin

address: 364 Plantation St.

institute: UMass Medical School

hyb_protocol: The test and reference DNAs together with 100 ug human Cot-1 DNA were hybridized to the BAC arrays for ~48 hrs at 37C. After post-hybridization washes, the arrays were mounted in a solution containing 90% glycerol, 10% PBS and 1 uM DAPI and sealed with a cover slip.

scan_protocol: A custom built CCD camera system was used to acquire 16 bit 1024x1024 pixel DAPI, Cy3 and Cy5 images (Pinkel et al., 1998). Image analysis was carried out using UCSF SPOT software (Jain et al., 2002).

data_processing: The log2ratio of the total integrated Cy3 and Cy5 intensities for each spot after background subtraction was calculated, normalized to the median log2ratio of all the clones on the array and the average of the triplicates calculated using a second custom program, SPROC. Automatic data filtering to reject data points based on low DAPI intensity, low correlation between Cy3 and Cy5 within each segmented spot and low reference/DAPI signal intensity was also carried out using SPROC. Data files were subsequently manually edited by rejecting clones for which only one spot of the triplicate survived after SPROC analysis and for which the standard deviation of the log2ratio of the triplicate was >0.2. For each tumor, the data are plotted as the mean log2ratio of the triplicate spots for each clone normalized to the genome median log2ratio. The clones are ordered by position in the genome (UCSC draft genome sequence, May 2004 freeze) beginning at chromosome 1 and ending with chromosome X.

molecule: genomic DNA

source_name: tumor; MFT121,p53f/f

label_protocol: Tumor genomic DNA and normal individually-matched genomic reference DNA (300 ng each) were labeled by random priming in separate 50 ul reactions to incorporate Cy3-dUTP and Cy5-dUTP, respectively.

extract_protocol: Genomic DNA was isolated using commercial silica columns and standard techniques.

treatment_protocol: Tissues were flash frozen in liquid nitrogen.

value: adenocarcinoma

tag: genotype

tag: sample type

value: tumor

tag: genetic background

value: FVB

source_name: spleen; MFT121,p53f/f

value: reference

value: normal spleen


title: 070313b; MFT121,p53f/f Brca1f/f

source_name: tumor; MFT121,p53f/f Brca1f/f

value: MFT121,p53f/f Brca1f/f

source_name: spleen; MFT121,p53f/f Brca1f/f


title: 070309b; MFT121,p53f/f


title: 070313d; MFT121,p53f/f


title: 070313a; MFT121,p53f/f Brca1f/f


title: H3K27me3 ChIP using anti H3K27me3 antibody (Abcam, ab6002) [S2_Fp2K27]

city: Edinburgh

first: Iain

last: Williamson

address: Crewe Road

department: Chromosomes and Gene Expression

institute: IGMM MRC Human Genetics Unit

description: ChIP-chip immortalized mouse embryonic limb cells

hyb_protocol: Samples were hybridized according to standard protocol (http://www.nimblegen.com/products/lit/NG_ChIP-chip_Guide_v6p2.pdf)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: The median signal intensity of the 4 replicate probes, on each array was taken. Loess normalization was used within arrays to correct for the dye bias. The log enrichment was calculated by subtracting of log2 input intensities from the mean of log2 enriched intensities.

source_name: Input DNA from immortalized E10.5 posterior limb cells

label_protocol: 0.4 to 1.0 µg ChIP DNA or Input DNA was directly labeled by Klenow random priming with Cy3/Cy5 nonamers as per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Immortalized limb cells were used

extract_protocol: For crosslinked ChIP: cells from dissected E10.5 forelimbs were immediately fixed with 1% formaldehyde (25C, 10 min) in PBS, and stopped with 0.125M Glycine. Chromatin immunoprecipitation (ChIP) was performed as described previously(Stock et al 2007). The nuclei were sonicated using a Diagenode Bioruptor (Liege, full power 30s on, 30s off, in an icebath for 50 min) to produce fragments of < 300bp. An arbitrary concentration of 30-50 µg chromatin was incubated with 1 µg IgG (Santa Cruz, sc-2025) or 1 µg Ring1B antibodies and washed and eluted as described in (Stock et al 2007). Reverse cross-linked DNA was purified as described above. For native ChIP: cell lines - nuclei were prepared and resuspended in NB-R as previously described (Gilbert et al. 2003). Nuclei corresponding to 1 - 6 x 108 cells were digested with 40-46 Boehringer units of MNase (Worthington) for 10 minutes at room temperature in the presence of 20mg RNase A to obtain a chromatin ladder enriched in tri-, tetra-, and pentanucleosomes. Chromatin Immunoprecipitation was performed as previously described in (Eskeland et al. 2010). Between 50-150 mg released chromatin were mixed with 10 mg prebound (to Protein A or G magnetic beads, Invitrogen) H3K27me3 antibody or mouse IgG (Santa Cruz, sc-2025) in the presence of 100 mg BSA and incubated for 3 hours at 4°C. Limb tissue - distal anterior and posterior forelimb buds were dissected from 50 – 55 E10.5 embryos. Cells were digested with 8 - 9 Boehringer units of MNase (Worthington) for 10 minutes at room temperature in the presence of 20mg RNase A. Between 10 - 30 mg released chromatin were mixed with 3 - 5 mg prebound (to Protein A or G magnetic beads, Invitrogen) H3K27me3 antibody in the presence of 25 mg BSA and incubated for 3 hours at 4°C. Immunoprecipitated and input DNA were purified with Proteinase K (Genaxxon) and QIAGEN MinElute PCR purification kit.

value: Immortalized E10.5 distal posterior limb cells

source_name: H3K27me3 ChIP DNA from immortalized E10.5 posterior limb cells

tag: antibody

tag: antibody vendor

value: Abcam

tag: antibody catalog#


title: TB patient 1

description: RNA extracted after culture for 4 hours

source_name: PPD-stimulated PBMCs from TB patient

value: PBMCs

tag: infection status

value: tuberculosis patient

source_name: unstimulated PBMCs from TB patient


title: 070313c; MFT121,p53f/f


title: 070306b; MFT121,p53f/f Brca1f/f


title: 070321a; MFT121,p53f/f Brca1f/f


title: H3K27me3 ChIP using anti H3K27me3 antibody (Abcam, ab6002) [S1_Fa1K27]

source_name: Input DNA from immortalized E10.5 anterior limb cells

value: Immortalized E10.5 distal anterior limb cells

source_name: H3K27me3 ChIP DNA from immortalized E10.5 anterior limb cells


title: H3K27me3 ChIP using anti H3K27me3 antibody (Millipore, 07-449) [S3_A2K27]

description: ChIP-chip mouse embryonic limb tissue Ring1B

source_name: Input DNA from E10.5 anterior limb tissue

growth_protocol: Dissected embryonic tissue was used

value: E10.5 distal anterior limb tissue

source_name: H3K27me3 ChIP DNA from E10.5 anterior limb tissue

value: Millipore


title: H3K27me3 ChIP using anti H3K27me3 antibody (Millipore, 07-449) [S3_P2K27]

source_name: Input DNA from E10.5 posterior limb tissue

value: E10.5 distal posterior limb tissue

source_name: H3K27me3 ChIP DNA from E10.5 posterior limb tissue


title: 070316b; MFT121,p53f/f


title: H3K27me3 ChIP using anti H3K27me3 antibody (Millipore, 07-449) [S2_P1K27]


title: 060828h; MFT121,p53f/f Brca1f/f


title: H3K27me3 ChIP using anti H3K27me3 antibody (Millipore, 07-449) [S2_A1K27]


title: H3K27me3 ChIP using anti H3K27me3 antibody (Abcam, ab6002) [S1_Fp1K27]


title: H3K27me3 ChIP using anti H3K27me3 antibody (Millipore, 07-449) [S1_P1K27]


title: H3K27me3 ChIP using anti H3K27me3 antibody (Millipore, 07-449) [S4_P2K27]


title: Ring1B ChIP using anti Ring1B antibody (MBL, D139-3) [S2_A2R1B]

source_name: Ring1B ChIP DNA from E10.5 limb tissue

value: MBL


title: H3K27me3 ChIP using anti H3K27me3 antibody (Millipore, 07-449) [S1_A1K27]


title: H3K27me3 ChIP using anti H3K27me3 antibody (Millipore, 07-449) [S4_A2K27]


title: 060905a; MFT121,p53f/f


title: 060828d; MFT121,p53f/f


title: H3K27me3 ChIP using anti H3K27me3 antibody (Abcam, ab6002) [S2_Fa2K27]


title: Ring1B ChIP using anti Ring1B antibody (MBL, D139-3) [S1_P1R1B]


title: 060828b; MFT121,p53f/f


title: 060823d; MFT121,p53f/f Brca1f/f


title: 060905b; MFT121,p53f/f


title: HMVEC-D-BMP9treated-Biological Rep3

description:
sm011107_sample-b3
Data providing  endothelial cell expression following BMP9 treatment for 24 hours

value: cultured passage-3 human dermal microvascular endothelial cells

value: complete EBM2 endothelial cell media

value: 5 ng/ml human recombinant BMP9 for 24hrs


title: 060823c; MFT121,p53f/f Brca1f/f

value: adenocarcinoma

value: tumor


title: Ring1B ChIP using anti Ring1B antibody (MBL, D139-3) [S2_P2R1B]


title: 060828f; MFT121,p53f/f Brca1f/f

value: FVB

value: reference


title: 060828c; MFT121,p53f/f

value: normal spleen


title: MCF-7 control 1

description: Gene expression data

source_name: MCF-7 cells

tag: cell line

tag: disease state

value: Estrogen receptor positive breast cancer

value: breast cancer

tag: treatment

value: control-transfected


title: Ring1B ChIP using anti Ring1B antibody (MBL, D139-3) [S1_A1R1B]

tag: tissue


title: HeatSet1 6h-rep2

city: Verona

first: Sara

last: Zenoni

address: Le Grazie

department: Biotecnology

country: Italy

institute: University of Verona

description:
Heat-tolerant; 6h; rep2
raw data file: HS6b.txt

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 5x Denhardt's solution, 100 ng/ul Salmon Sperm DNA, 0.05% SDS) for 60 minutes at 45 °C. 5 ug of labeled aRNA were fragmented by incubation with Fragmentation Solution (40mM Tris Acetate pH 8.1, 100 mM KOAc, 30 mM MgOAc) for 20 min at 95 °C.    Hybridization was performed at 45°C for 16 hours in hybridization solution (6X SSPE, 0.05% Tween-20, 20mM EDTA, 25% DiFormamide, 100 ng/ul Salmon Sperm DNA, 0.04% SDS).    Hybridization washings were performed as the following:  - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20).  - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20).  - wash with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20).  - wash with PBST wash solution (2X PBS, 0.1% Tween-20).  - 2 washes with 2X PBS

scan_protocol: After hybridization and washing, the microarray was dipped in imaging solution, covered with LifterSlip™, and then scanned using a Perkin Elmer ScanArray 4000XL and the accompanying acquisition software (ScanArray Express Microarray Analysis System v4.0). Multiple scanning at different PMT was provided for each hybridization.

data_processing: Data extraction was carried out using CombiMatrix Microarray Imager software, and a median normalization of raw medians and log2 transformation were performed. Further statistical processing was performed using the SAM analysis (T-Mev 3.4).  Hybridization signals with a variability coefficient higher than 0.5 were filtered out.

label: Alexa Fluor 647

organism: Solanum lycopersicum

source_name: Meiotic anther of HS1 heat tolerant tomato

label_protocol: Total RNA (1μg) was used as a template to synthesize antisense RNA (aRNA) with the SuperScript™ Indirect RNA Amplification System Kit (Invitrogen) incorporating Alexa Fluor 647 Reactive Dye according to manufacturer's instructions.

growth_protocol: Seeds were germinated in potting compost in trays and transferred after two weeks to a growth chamber under standard temperature (ST) conditions, with a 16-h light (26°C) / 8-h dark (18°C) cycle. Fluorescent and incandescent lighting provided a photosynthetic photon flux density of 450-500 μmol m-2 sec-1.

extract_protocol: Anther cones ranging in size from 2-4mm were isolated, immediately frozen in liquid N2 and pooled for RNA extraction. Tissues were homogenized using glass rods and RNA was extracted using a Plant RNA isolation kit (Plant RNeasy Mini Kit, Qiagen Benelux BV, Venlo the Netherlands) according to the manufacturer’s recommendations.

treatment_protocol: Six-week-old plants were heat stressed by raising the temperature to a regime of MHS (32°C /26°C; day/night).

tag: heat tolerance

value: Heat-tolerant

value: anther

tag: stress

value: heat stress [raising the temperature to a regime of MHS (32°C /26°C; day/night)]

tag: time


title: HeatSet1 6h-rep1

description:
Heat-tolerant; 6h; rep1
raw data file: HS6a.txt

tag: genotype/variation


title: HeatSet1 2h-rep3

description:
Heat-tolerant; 2h; rep3
raw data file: HS2c.txt


title: HeatSet1 2h-rep2

description:
Heat-tolerant; 2h; rep2
raw data file: HS2b.txt


title: H3K9me2 in SIRT1 knockdown IMR90 cells IP vs INPUT slide2

city: Los Angeles

first: Jing-Yu

last: Li

address: 615 Charles E. Young Dr. South BSRB 357

institute: University of California, Los Angeles

description: SIRT1 knockdown

hyb_protocol: Labeled DNA were mixed with human Cot-1 DNA, Agilent aCGH Blocking solution, and Agilent aCGH hybridization buffer. After 5-minute denaturing, and 30-minute incubation at 37 degree, mixed solution was added to array, and hybridized for 40 hours at 65 degree.

scan_protocol: Scanned on Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction 10.5.1.1

data_processing: Agilent ChIP Analytics was used for inter-array median normalization. Background subtraction, common features median normalization, and dye bias normalization were performed by using MATLAB.

source_name: human fetal lung fibroblasts

label_protocol: DNA were labeled with Cy3- or Cy5-dCTP by using Invitrogen BioPrime DNA Labeling kit following manufacturere's instructions.

growth_protocol: H1 hESCs were plated on Matrigel (BD Biosciences)-coated plates, and maintained in mTeSR (StemCell). Before purification, cells were trypsinized to single cells and TRA-1-60 expressing cells were isolated by using MACS cell separation columns (Miltenyi Biotec). Isolated cells were tested by flow cytometry, and samples with >99% purity were used. IMR90 human primary lung embryo fibroblasts (ATCC) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) plus 10% FBS (Hyclone), 100 U/ml penicillin (Gibco), and 100 µg/ml streptomycin (Gibco) at 37°C in 5% CO2. Growing cells with 50~70% confluence were used for further analysis. Human primary hepatocytes (Zen-bio #HP-F) were grown in Hepatocyte Maintenance Medium (Zen-Bio #HM-2), and passage 4 was used. Human ESCs (HSF1) were differentiated to neural progenitor cells (NPCs) in DMEM:F12 (Gibco) plus B27 (Gibco), N2-supplement (Gibco), 20ng/ml bFGF (R and D systems), 1µM Retinoic Acid (Sigma), and 1µM Smoothened Agonist (Calbiochem). NPCs were mechanically isolated from culture based on rosette morphology as described(Elkabetz et al., 2008) and expanded in DMEM:F12 plus B27, N2-supplement, 20ng/ml bFGF, and 50ng/ml EGF (Gibco).  NPCs were further differentiated to neurons and glia by withdrawal of the maintenance factors (bFGF and EGF) for 10 days.  Human keratinocytes were cultured per manufacturer’s protocol in KSFM (Invitrogen).  To induce differentiation, calcium chloride was added to 1.5mM for 48 hours(Lowry et al., 2005).

extract_protocol: Cells were fixed with 1% formaldehyde for 10 minutes at 37 degree followed by incubation with 140 mM glycine for 15 minutes at room temperature. Nuclear extracts were sonicated to get 150 ~ 500 bp genomic DNA fragments, diluted, precleared with 50 µl of Invitrogen Dynabeads Protein A (for Rabbit IgG) or Dynabeads Protein G (for mouse IgG) for 1 hour at 4 degree, and the supernatant was incubated with primary antibody overnight at 4 degree. Appropriate Dynabeads were then added to the solution and incubated for another 3 hours before washing steps. Reverse crosslinking of the precipitated complex was performed at 65 degree overnight followed by RNase A digestion, proteinase K treatement, phenol/chlorform extraction, and ethanol precipitation. DNA pelletes were air dried, and disolved in ddH2O.

tag: cell type

value: human fetal lung fibroblasts

value: H3K9me2 antibody

tag: antibody manufacturer

value: Millipore

tag: antibody catalog #


title: H3K9me2 in H1.5 knockdown IMR90 cells IP vs INPUT slide2

description: H1.5 knockdown


title: HeatSet1 6h-rep3

description:
Heat-tolerant; 6h; rep3
raw data file: HS6c.txt


title: HeatSet1 2h-rep1

description:
Heat-tolerant; 2h; rep1
raw data file: HS2a.txt


title: H1.5 in IMR90 IP vs INPUT rep2 slide2

description: wild-type

value: H1.5 antibody

value: Abcam


title: ULL-L-072

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24799.gif

hyb_protocol: 1. Prepare the reaction for each aRNA sample.   aRNA Rhx Primer(8?ug/?ul) ddH2O Total  Cy5 X ul(3 ug) 1 ul 16-(X+1) 16 ul  Cy3 Y ul(3 ug) 1 ul 16-(Y+1) 16 ul   2. Heat to 70?C for 10 min and cool on ice.   3. Prepare reaction mixture for each Cye dye.   5X First-Strand Buffer 6 ?l   50X dNTPs 0.7 ul   Cye Dyes 3 ul   0.1 M DTT 3 ul   Superscript II 1.7 ul   Total Volume 14.4 ul   4. Add 14.4 ul of reaction mixture to the 16 ul reaction tube, mix well, and incubate at 42?C for 1 hour.   5. Add another 1 ul of SSII to each sample and incubate at 42?C for 1 hour.   6. Add 15 ul of 0.1 N NaOH (with 2mM EDTA) and incubate at 65?C for 8 min.   7. Neutralize by adding 15 ul of 0.1 HCl.   8. Add 450 ?l of TE to a Microcon YM-30 Microcon. Add 15 ul of COT1 (1 mg/ml) DNA.   9. Add Cy5 and Cy3 labeled probe to the same Microcon.   10. Wash 1: Spin column for 7 min at 14,000 x g.   Wash 2. Remove flow through and add 500 ?l TE Spin for 7 min.   Wash 3. Repeat Wash 2 and concentrate probe to less than or equal to 30-35 ul.   11. Invert the Microcon into a clean 1.5 ml tube and spin for 2 min. at 14,000 RPM to recover  the probe.   12. Transfer 26.1 ul of probe to new PCR tube:   Sample 26.1ul   Poly (A) DNA 2 ul (10 ug/ul)   Yeast tRNA 1 ul (10 ug/ul)   20X SSC 5.3 ul   10% SDS 0.6 ul   Total hybridization volume 35 ul   13. Denature probe by heating for 2 min at 92?C and 42?C for 20-30 min.   14. Spin briefly and place 35 ul to on array.   15. Place a coverslip (24 X 60 mm size) on to array and add 20-30 ul of 3X SSC to each corner of the hybridization chamber.   16. Hybridize at 65?C for 14-18 hours.   17. Wash slide once with 2X SSC/ 0.05% SDS, for 2 min.   18. Transfer slide to 1X SSC for 2 min.   19. Wash slide in 50?C 0.2X SSC for 2 min, twice.   20. Spin slide in 600RPM for 5min

scan_protocol: Scanner Model: GenePix 4000B

source_name: Stratagene Reference, ampl. totRNA

tag: reference

value: Stratagene Reference, amplified total RNA

source_name: ULL-L-072, ampl. totRNA

label_protocol: Jeffrey Lab RNA Amplification Protocol   First strand cDNA synthesis   Mix the following contents in 0.2 ml PCR tube and spin briefly:  N microl (3 mg) Total RNA 1 microl (0.5 mg/ml) Eberwine primer* 9-N microl RNase-free H2O   * Eberwine primer = T7-oligo-dT(15) (5?-AAA CGA CGG CCA GTG AAT TGT AAT ACG ACT CAC TAT AGG CGC TTT TTT TTT TTT TTT-3?)   Incubate in PCR machine at 70?C for 3 min, cool on ice for 2 min. Spin briefly.    Add the following contents:   4 microl 5X first strand buffer 2 microl 0.1M DTT 1 microl RNasin 2 microl 10mM dNTP mix 2 microl Superscript?II   Mix contents, spin briefly, and incubate at 42?C for 1.5 hours.   Second strand cDNA synthesis   Add the following contents to the first strand synthesis reaction:   RNase-free H2O 106 microl  10X Advantage? PCR buffer (Clontech) 15 microl  10mM dNTP mix 3 microl  RNase H (2U/microl) 1 microl  Advantage? Polymerase Mix (Clontech) 3 microl   Incubate in PCR machine at 37?C for 5 min, 94?C for 2 min, 65?C for 1 min, 75?C for 30 min. Stop reaction by adding 7.5 microl of 1M NaOH with 2mM EDTA and incubate in PCR machine at 65?C for 10 min.   ds cDNA cleanup   If necessary, transfer to a larger tube. Add 150 microl phenol:chloroform:isoamyl alcohol 25:24:1 and mix by pipetting. Transfer to phase lock gel tube and spin at ~16,000g for 5min. Transfer aqueous layer to new tube. Add 1 microl acrylamide (0.1 mg/ml), 70 microl 7.5M NH4Ac, 1 ml 100% EtOH. Spin at ~16,000g for 20 min at room temperature (not at 4?C). Wash pellet with 500 microl 75% EtOH, spin at ~16,000g for 5 min. Air dry, and suspend the pellet in 16 microl RNase-free H2O.   In vitro transcription (IVT)   Mix at room temperature (the spermidine in the 10X transcription buffer can coprecipitate the template DNA if  the reaction is assembled on ice):   16 microl cDNA  4 microl 10X reaction buffer (room temperature)  16 microl 75mM NTP mix (on ice)  4 microl T7 enzyme mix*   *Ambion T7 MEGAscript? kit  Incubate at 37?C for 5 hours (we have tried incubating for 2-6 hours and achieved the highest correlation between amplified and unamplified samples at 5 hours incubation).   aRNA cleanup (using Qiagen RNeasy? mini kit)   Add 10 microl b-mercaptoethanol to 1ml buffer RLT before use (stable for 1 month).   Transfer IVT reaction into a 1.5 ml new tube, add 60 microl RNase-free H2O, add 350 microl buffer RLT, mix by pipetting. Add 250 microl 100% EtOH, mix by pipetting. Apply sample to RNeasy? column, spin at ~12,000g for 15 sec at room temperature. Transfer column to new collection tube. Add 500 microl buffer RPE, spin at ~12,000g for 15 sec. Discard flow through, add 500 microl buffer RPE, spin at ~12,000g for 2 min. Transfer column to new collection tube, add 30 microl RNase-free H2O to the membrane, spin at ~12,000g for 1 min to elute   Measure aRNA yield at A260;

growth_protocol: A Series of 212 primary breast cancer cases were studied; 80 of these tumors were analyzed using cDNA microarrays, along with one normal breast tissue sample collected from breast reduction surgery. Patient samples were sequentially collected at Ullev?l University Hospital from 1990 to 1994 (IRB approval 350, protocol 75026). The last update of patient information was done in 2006, providing an observation time of 12 to 16 years. Patients were followed until death or emigration, and only 12 patients were lost to follow-up. The average age of the 80 cases analyzed by cDNA microarrays was 65.0 years at time of primary surgery (range 28.2 to 87.7 years), similar to the average age of 64.4 years (range 28.2 to 91.5 years) for the total series. The 80 cases were selected from the total series based only on sufficient amount of fresh frozen tissue for microarray analysis. Consequently, a slightly higher fraction of patients with larger tumor size was observed in this subcohort. A summary of the clinical and histopathological data of the patients is shown in Table 1 (see Additional file 1 for more detailed information). All patients were treated according to Norwegian national guidelines at the time of diagnosis [19]. Patients receiving adjuvant systemic therapy were given nine courses of CMF (cyclophosphamide, methotrexate, 5-fluorouracil) and/or Tamoxifen for two years. Dosage of radiation given as adjuvant treatment was dependent on indication; after breast conserving therapy the mammary gland was given 50 Gy (2 Gy ? 25). The number of samples entered into the survival analyses is smaller than 212 (full dataset) and 80 (subset with gene expression data); excluding patients with missing information or distant metastases at the time of diagnosis and primary surgery, leaves us with a maximum number of 200 (full set) and 77 (subset) patients. <br>  Primary breast carcinoma tissue was snap frozen and stored at -80?C. Frozen sections stained with hematoxylin/eosin were reviewed to confirm tumor content, and specimens in which at least 5% of the cells were carcinoma cells were included in this study. The majority of samples (80%) analyzed using microarrays had at least 40% tumor cell content

extract_protocol: Total RNA was isolated from snap frozen tumor tissue using TRIzol? solution (Invitrogen?, Carlsbad, California, USA). The concentration of total RNA was determined using an HP 8453 spectrophotometer (Hewlett Packard) and the integrity of the RNA was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, California, USA). Performer: Hongjuan,,Zhao

value: primary breast carcinoma

tag: ID


title: RNA polymerase II in H1 hESC IP vs INPUT slide2

description: wild-type

source_name: human H1 embryonic stem cells

tag: antibody

value: human H1 embryonic stem cells

value: RNA polymerase II ChIP


title: ULL-D-027

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27441.gif

hyb_protocol: 1. Prepare the reaction for each aRNA sample.   aRNA Rhx Primer(8?ug/?ul) ddH2O Total  Cy5 X ul(3 ug) 1 ul 16-(X+1) 16 ul  Cy3 Y ul(3 ug) 1 ul 16-(Y+1) 16 ul   2. Heat to 70?C for 10 min and cool on ice.   3. Prepare reaction mixture for each Cye dye.   5X First-Strand Buffer 6 ?l   50X dNTPs 0.7 ul   Cye Dyes 3 ul   0.1 M DTT 3 ul   Superscript II 1.7 ul   Total Volume 14.4 ul   4. Add 14.4 ul of reaction mixture to the 16 ul reaction tube, mix well, and incubate at 42?C for 1 hour.   5. Add another 1 ul of SSII to each sample and incubate at 42?C for 1 hour.   6. Add 15 ul of 0.1 N NaOH (with 2mM EDTA) and incubate at 65?C for 8 min.   7. Neutralize by adding 15 ul of 0.1 HCl.   8. Add 450 ?l of TE to a Microcon YM-30 Microcon. Add 15 ul of COT1 (1 mg/ml) DNA.   9. Add Cy5 and Cy3 labeled probe to the same Microcon.   10. Wash 1: Spin column for 7 min at 14,000 x g.   Wash 2. Remove flow through and add 500 ?l TE Spin for 7 min.   Wash 3. Repeat Wash 2 and concentrate probe to less than or equal to 30-35 ul.   11. Invert the Microcon into a clean 1.5 ml tube and spin for 2 min. at 14,000 RPM to recover  the probe.   12. Transfer 26.1 ul of probe to new PCR tube:   Sample 26.1ul   Poly (A) DNA 2 ul (10 ug/ul)   Yeast tRNA 1 ul (10 ug/ul)   20X SSC 5.3 ul   10% SDS 0.6 ul   Total hybridization volume 35 ul   13. Denature probe by heating for 2 min at 92?C and 42?C for 20-30 min.   14. Spin briefly and place 35 ul to on array.   15. Place a coverslip (24 X 60 mm size) on to array and add 20-30 ul of 3X SSC to each corner of the hybridization chamber.   16. Hybridize at 65?C for 14-18 hours.   17. Wash slide once with 2X SSC/ 0.05% SDS, for 2 min.   18. Transfer slide to 1X SSC for 2 min.   19. Wash slide in 50?C 0.2X SSC for 2 min, twice.   20. Spin slide in 600RPM for 5min.

source_name: ULL-T-027, ampl. totRNA

growth_protocol: A Series of 212 primary breast cancer cases were studied; 80 of these tumors were analyzed using cDNA microarrays, along with one normal breast tissue sample collected from breast reduction surgery. Patient samples were sequentially collected at Ullev?l University Hospital from 1990 to 1994 (IRB approval 350, protocol 75026). The last update of patient information was done in 2006, providing an observation time of 12 to 16 years. Patients were followed until death or emigration, and only 12 patients were lost to follow-up. The average age of the 80 cases analyzed by cDNA microarrays was 65.0 years at time of primary surgery (range 28.2 to 87.7 years), similar to the average age of 64.4 years (range 28.2 to 91.5 years) for the total series. The 80 cases were selected from the total series based only on sufficient amount of fresh frozen tissue for microarray analysis. Consequently, a slightly higher fraction of patients with larger tumor size was observed in this subcohort. A summary of the clinical and histopathological data of the patients is shown in Table 1 (see Additional file 1 for more detailed information). All patients were treated according to Norwegian national guidelines at the time of diagnosis [19]. Patients receiving adjuvant systemic therapy were given nine courses of CMF (cyclophosphamide, methotrexate, 5-fluorouracil) and/or Tamoxifen for two years. Dosage of radiation given as adjuvant treatment was dependent on indication; after breast conserving therapy the mammary gland was given 50 Gy (2 Gy ? 25). The number of samples entered into the survival analyses is smaller than 212 (full dataset) and 80 (subset with gene expression data); excluding patients with missing information or distant metastases at the time of diagnosis and primary surgery, leaves us with a maximum number of 200 (full set) and 77 (subset) patients. <br>  Primary breast carcinoma tissue was snap frozen and stored at -80?C. Frozen sections stained with hematoxylin/eosin were reviewed to confirm tumor content, and specimens in which at least 5% of the cells were carcinoma cells were included in this study. The majority of samples (80%) analyzed using microarrays had at least 40% tumor cell content.

extract_protocol: Total RNA was isolated from snap frozen tumor tissue using TRIzol? solution (Invitrogen?, Carlsbad, California, USA). The concentration of total RNA was determined using an HP 8453 spectrophotometer (Hewlett Packard) and the integrity of the RNA was assessed using a 2100 Bioanalyzer (Agilent, Santa Clara, California, USA).


title: RNA polymerase II in IMR90 cells IP vs INPUT slide2

description: wild-type


title: SIRT1 in knockdown control IMR90 cells IP vs INPUT slide2

description: knockdown control

value: SIRT1 antibody


title: HeatSet1 0h-rep3

description:
Heat-tolerant; 0h; rep3
raw data file: HS0c.txt

value: control


title: SIRT1 in IMR90 cells IP vs INPUT rep2 slide2

description: wild-type


title: H3K9me2 in knockdown control IMR90 cells IP vs INPUT slide2

description: knockdown control


title: H1.5 in knockdown control IMR90 cells IP vs INPUT slide2

description: knockdown control


title: ULL-MU-060

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24786.gif

source_name: ULL-T-060, ampl. totRNA


title: H1.5 in SIRT1 knockdown IMR90 cells IP vs INPUT slide2

description: SIRT1 knockdown


title: SIRT1 in IMR90 cells IP vs INPUT rep1 slide2

description: wild-type


title: H3K9me2 in IMR90 cells IP vs INPUT rep2 slide2

description: wild-type


title: HeatSet1 0h-rep2

description:
Heat-tolerant; 0h; rep2
raw data file: HS0b.txt


title: HeatSet1 0h-rep1

description:
Heat-tolerant; 0h; rep1
raw data file: HS0a.txt


title: SIRT1 in H1.5 knockdown IMR90 cells IP vs INPUT rep1 slide2

description: H1.5 knockdown


title: Falcorosso 6h-rep3

description:
Heat-sensitive; 6h; rep3
raw data file: F6c.txt

source_name: Meiotic anther of FR heat-sensitive tomato

value: Falcorosso

value: Heat-sensitive


title: ULL-D-022

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27435.gif

source_name: ULL-T-022, ampl. totRNA


title: H3K9me2 in IMR90 cells IP vs INPUT rep1 slide2

description: wild-type


title: ULL-D-007

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26064.gif

source_name: ULL-T-007, ampl. totRNA


title: Falcorosso 6h-rep2

description:
Heat-sensitive; 6h; rep2
raw data file: F6b.txt


title: Falcorosso 6h-rep1

description:
Heat-sensitive; 6h; rep1
raw data file: F6a.txt


title: ULL-L-046

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24783.gif

source_name: ULL-L-046, ampl. totRNA


title: SIRT1 in H1.5 knockdown IMR90 cells IP vs INPUT rep2 slide2

description: H1.5 knockdown


title: Falcorosso 2h-rep1

description:
Heat-sensitive; 2h; rep1
raw data file: F2a.txt


title: Falcorosso 2h-rep3

description:
Heat-sensitive; 2h; rep3
raw data file: F2c.txt


title: Falcorosso 0h-rep3

description:
Heat-sensitive; 0h; rep3
raw data file: F0c.txt


title: H1.5 in neural progenitor cells IP vs INPUT slide2

description: in vitro differentiated from HSF1 cells

source_name: neural progenitor cells

value: neural progenitor cells


title: Falcorosso 0h-rep2

description:
Heat-sensitive; 0h; rep2
raw data file: F0b.txt


title: H1.5 in HSF1 hESC IP vs INPUT slide 2

description: wild-type

source_name: human HSF1 embryonic stem cells

value: human HSF1 embryonic stem cells


title: ULL-L-176

description:
Simple annotation: Breast, Primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24811.gif

source_name: ULL-L-176, ampl. totRNA