title: DRGexplant_22d_myelination_mouse2_rep2

city: Oulu

first: Salla

middle: Maria

last: Kangas

address: PL 5000 (Aapistie 7A)

department: Institute of Biomedicine

country: Finland

institute: University of Oulu

description:
gene expression at 22 days after switching to myelination medium
T3_M2R2

hyb_protocol: 600 ng of Cy-3 labeled sample was hybridized onto Agilent’s SurePrint G3 Mouse GE 8x60K arrays (Design ID 028005) at 65C overnight using Agilent’s GE Hybridization Kit. Washes were done with Agilent’s Gene Expression Wash Pack with 0.005% Triton X-102 and using Agilent’s “Stabilization and Drying” –solution.

scan_protocol: Arrays were scanned with Agilent Technologies Scanner, model G2565CA. Scan Profile: AgilentG3_GX_1Color.

data_processing:
Numerical results were extracted with Feature Extraction version 10.7.1. Grid: 028005_D_F_20110614, Protocol: GE1_107_Sep09
This data set has been normalized applying the quantile normalization.

source_name: DRG explant, 22 days of myelination

label_protocol: 100 ng total RNA was amplified / Cy3-labeled with Agilent’s Low Input Quick Amp Labeling kit, one-color. Samples were processed together with Agilent’s RNA Spike in kit, single-color. Both before and after amplifications the RNA(starting material) and cRNA (labeled / amplified) concentrations (and also specific activity for cRNA) were checked with Nanodrop ND-2000 and RNA/cRNA quality was controlled by Agilent 2100 bioanalyzer RNA 6000 Nano kit.

growth_protocol: Dorsal root ganglion explant cultures isolated from E13.5 C57BL/6J mouse embryos were cultured on matrigel for 12 days in DRG growth medium prior to starting the experiment.

extract_protocol: RNA was extracted using the RNeasy mini-kit (Qiagen) according to the manufacturer`s instructions. Homogenization of the samples was done by passing them through a 20-gauge needle several times. DNAse treatment was performed with the RNase-Free DNase Set (Qiagen) according to the manufacturer`s instructions. The RNA was eluted in 30 µl of RNase-free water and stored at -70ºC until analysis. RNA was quantified using a NanoDrop ND-1000.

treatment_protocol: To analyze the RNA expression at different stages of myelination, the the total RNA was extracted at three time points: immediately before the addition of the myelination medium (0 days), after 10 days in myelination medium (early myelination), and after 22 days in myelination medium, when abundant mature myelin sheaths are visible in phase-contrast microscopy.

tag: strain

tag: developmental stage

value: Dorsal root ganglion explant culture

tag: treatment

value: myelination medium

tag: time

value: day 22


title: Discovery_CKD_23

status: Public on Aug 16 2015

type: RNA

city: Fukuoka

first: Satohiro

last: Masuda

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Pharmacy

country: Japan

institute: Kyushu University Hospital

description: #23; Renal biopsy specimens #23 in discovery set

hyb_protocol: 1.0 ug of cRNA was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
The signals were normalized with each median.

molecule: total RNA

organism: Homo sapiens

source_name: discovery set_renal biopsy specimen

label_protocol: Cyanine-3-labeled complementary (c) RNA was generated with Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification.  Dye incorporation and cRNA yield were checked with the Spectrophotometer.

extract_protocol: Total RNA was isolated from biopsy specimens using an RNeasy micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA was quantified using a spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: study set

value: discovery set

tag: sample type

value: Renal biopsy specimens

tag: specimen id

tag: tissue

value: kidney

tag: disease status

value: chronic kidney disease (CKD)


title: DRGexplant_22d_myelination_mouse3_rep1

description:
gene expression at 22 days after switching to myelination medium
T3_M3R1

organism: Mus musculus

tag: cell type


title: DRGexplant_22d_myelination_mouse3_rep2

description:
gene expression at 22 days after switching to myelination medium
T3_M3R2


title: Discovery_CKD_14

description: #14; Renal biopsy specimens #14 in discovery set


title: Discovery_CKD_13

description: #13; Renal biopsy specimens #13 in discovery set


title: Discovery_CKD_07

description: #07; Renal biopsy specimens #07 in discovery set


title: Discovery_CKD_09

description: #09; Renal biopsy specimens #09 in discovery set


title: DRGexplant_10d_myelination_mouse1_rep1

description:
gene expression at 10 days after switching to myelination medium
T2_M1R1

source_name: DRG explant, 10 days of myelination

value: day 10


title: DRGexplant_22d_myelination_mouse1_rep1

description:
gene expression at 22 days after switching to myelination medium
T3_M1R1


title: DRGexplant_22d_myelination_mouse1_rep2

description:
gene expression at 22 days after switching to myelination medium
T3_M1R2


title: DRGexplant_10d_myelination_mouse3_rep2

description:
gene expression at 10 days after switching to myelination medium
T2_M3R2


title: Discovery_CKD_10

description: #10; Renal biopsy specimens #10 in discovery set


title: Discovery_CKD_16

description: #16; Renal biopsy specimens #16 in discovery set


title: DRGexplant_10d_myelination_mouse2_rep1

description:
gene expression at 10 days after switching to myelination medium
T2_M2R1


title: Discovery_CKD_12

description: #12; Renal biopsy specimens #12 in discovery set


title: DRGexplant_10d_myelination_mouse3_rep1

description:
gene expression at 10 days after switching to myelination medium
T2_M3R1


title: Discovery_CKD_08

description: #08; Renal biopsy specimens #08 in discovery set


title: DRGexplant_22d_myelination_mouse2_rep1

description:
gene expression at 22 days after switching to myelination medium
T3_M2R1


title: DRGexplant_10d_myelination_mouse1_rep2

description:
gene expression at 10 days after switching to myelination medium
T2_M1R2


title: Discovery_CKD_15

description: #15; Renal biopsy specimens #15 in discovery set


title: Discovery_CKD_06

description: #06; Renal biopsy specimens #06 in discovery set


title: Discovery_CKD_05

description: #05; Renal biopsy specimens #05 in discovery set


title: DRGexplant_0d_myelination_mouse3_rep2

description:
gene expression at day 0, prior to adding myelination medium
T1_M3R2

source_name: DRG explant, prior to myelination

value: control

value: day 0


title: Discovery_CKD_04

description: #04; Renal biopsy specimens #04 in discovery set


title: DRGexplant_10d_myelination_mouse2_rep2

description:
gene expression at 10 days after switching to myelination medium
T2_M2R2


title: DRGexplant_0d_myelination_mouse2_rep2

description:
gene expression at day 0, prior to adding myelination medium
T1_M2R2


title: DRGexplant_0d_myelination_mouse3_rep1

description:
gene expression at day 0, prior to adding myelination medium
T1_M3R1


title: Discovery_CKD_11

description: #11; Renal biopsy specimens #11 in discovery set


title: mot3 mit1-1 sin4 #2 raffinose

status: Public on Aug 15 2015

city: Boston

first: Fred

last: Winston

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

country: USA

institute: Harvard Medical School

hyb_protocol: Hybridization was done for 17 hours at 65C on a rotisserie at 20 rpm.

scan_protocol: Scans were done using Agilent Feature Extractor Software version 9.5. The raw signal intensity values were floored to a value of 350 (values less than 350 were set to 350).

data_processing: Each microarray has the wild type sample (always the wild-type strain grown on raffinose) in fluorescence channel 1 and the mutant sample in fluorescence channel 2. The channels of each array were normalized separately to the total fluorescence intensity for all genes is the same in the two channels. Values were floored to a low intensity value of 350 to prevent the spurious assessment of large fold changes due to low value fluctuations. Then the log2 ratio of Cy5/Cy3 signal (mutant/wt sample 1 on raffinose) was extracted. For duplicate microarrays, the average log2 values are shown.

organism: Saccharomyces cerevisiae

source_name: wild-type reference strain

label_protocol: Standard labeling protocols were used.  Reference RNA from strain FY3054  was labeled with Cy3 and experimental RNA from each mutant was labeled with Cy5.

growth_protocol: Cells were grown at 30C in Ypraffinose to an OD600 of 0.4.  One sample was saved for RNA preps. Two samples were shifted to either YPD or YPgalactose for one hour at which time RNA preps were done.

extract_protocol: A standard yeast method was used for RNA extraction.

source_name: sin4 mot3 mit1 - sample 2


title: mot3 mit1-1 sin4 #1 raffinose

source_name: sin4 mot3 mit1 - sample 1


title: mot3 grr1-1 sin4 #2 raffinose

source_name: sin4 mot3 grr1 - sample 2


title: mot3 grr1-1 sin4 #1 raffinose

source_name: sin4 mot3 grr1 - sample 1


title: mutant 2.3b-2 raffinose

source_name: mutant 2.3b 0 sample 2


title: mutant 2.3b-1 raffinose

source_name: mutant 2.3b - sample 1


title: mutant 2.3a raffinose

source_name: mutant 2.3a - sample 1


title: wild type 2 raffinose

source_name: wild type reference strain


title: Discovery_CKD_03

description: #03; Renal biopsy specimens #03 in discovery set


title: Discovery_CKD_01

description: #01; Renal biopsy specimens #01 in discovery set


title: Discovery_CKD_02

description: #02; Renal biopsy specimens #02 in discovery set


title: wild type 1 raffinose


title: DRGexplant_0d_myelination_mouse1_rep1

description:
gene expression at day 0, prior to adding myelination medium
T1_M1R1


title: mot3 mit1-1 sin4 #1 galactose


title: Skin Keratinocytes_biological rep1

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

description: Human skin was treated with dispase to allow the sepation of dermis and epidermis. The epidermis was cultured for 3 days in medium containing FCS to allow migration of langerhans cells from the epidermis. After 3 days, the epidermis was treated with dispase and DNase to obtain a single cell suspension of keratinocytes. Total RNA was extracted using the Qiagen RNeasy Mini kit and used to probe the GLYCOv4 oligonucleotide array.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the v2 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA Express using the default settings (Background Adjust - Yes, Normalization - Quantile, Summarization Method - Median Polish, Store Residuals - unchecked).

label: Biotin

source_name: Human skin-derived keratinocytes

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

growth_protocol: See for each sample in the column 'Description'. As for LCs, this is the detailed protocol: Primary human LCs and dermal APCs were isolated from human skin explants obtained within 24 h after cosmetic surgery from healthy donors and with informed consent (Bergman Clinics, Bilthoven, The Netherlands). Shortly, 5-mm thick slices of skin, containing the epidermis and dermis, were cut using a dermatome. The slices were incubated in Dispase II (1 mg/ml, Roche Diagnostics) in IMDM supplemented with 10% FCS (BioWhittaker), 50 U/ml penicillin (Lonza), 50 μg/ml streptomycin (Lonza) and 10 μg/ml gentamycin (Lonza) overnight at 4°C followed by the mechanical separation of dermis and epidermis using tweezers. The epidermis was washed in PBS, cut into small pieces and incubated in PBS containing DNase I (200 U/ml, Roche Diagnostics) and trypsin (0.05%, Invitrogen) for 30 min at 37°C. After incubation, a single cell suspension was generated using 100 μm nylon cell strainers (BD Falcon) and cells were layered on a lymphoprep gradient (1.077 g/ml; Alere Technologies AS.). An average of 1x104 LCs per cm2 of tissue with a purity higher than 90% were obtained and characterized as CD1a+ langerin+ cells by flow cytometry as described below. After separation from the epidermis, the dermis was cut in small pieces and incubated in PBS containing collagenase (6 mg/ml, Roche) and dispase II (1 mg/ml) for 2 h at 37°C. A single cell population was generated using 100 μm nylon cell strainers. After obtaining single cells populations, LC and dDC cell suspensions were cultured in IMDM supplemented with 10% FCS, 50 U/ml penicillin, 50 μg/ml streptomycin and 10 μg/ml gentamycin.

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini kit according to manufacturer's instructions.

treatment_protocol: See for each sample in the column 'Description'. Immature refers to as untreated or resting cells, whereas maturing refers to cells treated with the TLR ligand polyIC.

value: epidermis


title: MUTZ DC_2

description: Cell line MUTZ, differentiated to DCs

source_name: MUTZ DC human cell line

tag: cell line

value: MUTZ


title: MUTZ DC_1_biological rep2

description: Cell line MUTZ, differentiated to DCs


title: DRGexplant_0d_myelination_mouse1_rep2

description:
gene expression at day 0, prior to adding myelination medium
T1_M1R2


title: DRGexplant_0d_myelination_mouse2_rep1

description:
gene expression at day 0, prior to adding myelination medium
T1_M2R1


title: mot3 grr1-1 sin4 #2 galactose


title: Skin Keratinocytes_biological rep2


title: MUTZ DC_1_biological rep1

description: Cell line MUTZ, differentiated to DCs


title: Dcone_mature DC_1_biological rep1

description: Cell line DCone, maturing conditions

source_name: Mature Dcone cell line

value: DCone


title: Dcone_mature DC_1_biological rep2

description: Cell line DCone, maturing conditions


title: Dcone_immature DC_2_biological rep2

description: Cell line DCone, resting conditions

source_name: Immature Dcone cell line


title: Dcone_immature DC_2_biological rep1

description: Cell line DCone, resting conditions


title: Dcone_mature DC_2

description: Cell line DCone, maturing conditions


title: mutant 1.2 raffinose

source_name: mutant 1.2 - sample 2


title: mutant 2.3b-2 galactose


title: mutant 2.3b-1 galactose


title: MUTZ LC_2_biological rep2

description: Cell line MUTZ, differentiated to LCs

source_name: MUTZ LC human cell line


title: mot3 mit1-1 sin4 #2 galactose


title: MUTZ LC_1

description: Cell line MUTZ, differentiated to LCs


title: mutant 2.3a galactose


title: Dcone_immature DC_1

description: Cell line DCone, resting conditions


title: wild type 2 galactose


title: mutant 1.2 galactose


title: wild type 1 galactose


title: LCs donor 2_biological rep2

description: Human skin was treated with dispase to allow the sepation of dermis and epidermis. The epidermis was cultured for 3 days in medium containing FCS to allow migration of langerhans cells from the epidermis. After 3 days, migratory LCs were harvasted and LCs were enriched using CD1a+ MACS beads. Total RNA was extracted using the Qiagen RNeasy Mini kit and used to probe the GLYCOv4 oligonucleotide array.

source_name: Human migratory LCs


title: LCs donor 2_biological rep1


title: Dermal APCS donor 2_biological rep2

description: Human skin was treated with dispase to allow the sepation of dermis and epidermis. The dermis was cultured for 3 days in medium containing FCS to allow migration of dermal APCs from the skin. After 3 days, migratory dermal APCs were harvasted and HLA-DR+ APCs were enriched using MACS beads. CD19+ cells were excluded using MACS beads. Total RNA was extracted using the Qiagen RNeasy Mini kit and used to probe the GLYCOv4 oligonucleotide array.

source_name: Human migratory dermal APCs

value: dermis


title: mot3 grr1-1 sin4 #1 galactose

source_name: wild-type reference strain


title: mot3 mit1-1 sin4 #1 glucose


title: mot3 mit1-1 sin4 #2 glucose

source_name: sin4 mot3 mit1 - sample 2


title: Dermal APCS donor 2_biological rep1


title: LCs donor 1


title: mot3 grr1-1 sin4 #2 glucose


title: mutant 2.3b-1 glucose


title: Dermal APCs donor 1


title: mutant 1.2 glucose


title: wild type 2 glucose


title: mutant 2.3a glucose


title: mutant 2.3b-2 glucose


title: mot3 grr1-1 sin4 #1 glucose


title: wild type 1 glucose


title: A549-shRNA-control-sample

city: Shanghai

first: Dan

last: Xiong

address: 227 South Chongqing Road

country: China

institute: Shanghai Jiaotong University School of Medicine

description:
XD_001
Control of cultured cells.

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-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) following the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent Technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Feature Extraction software 10.7 (Agilent Technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US).

source_name: A549, shRNA-control

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent Technologies, Santa Clara, CA, US) following the manufacturer's instructions. Labeled cRNA were purified by RNeasy Mini Kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Human NSCLC cells A549 obtained from the American Type Culture Collection (ATCC, Rockville, MD) and cultured in DMEM containing 10% fetal bovine serum (FBS) in a humidified 5% CO2 incubator at 37°C. (Invitrogen Corp, Carlsbad, CA).

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy Mini Kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The plasmid with shBmi-1 was introduced into A549 cells, and the sequence of short-hairpin RNAs (shRNAs) were as follows: GACCAGACCACUACUGAAU. PRS plasmid was used as control. Retroviruses were produced by transient transfection according to the manipulate method (Invitrogen Corp, Carlsbad, CA). All retrovirally infected cells were maintained under 1.0ug/ml Puromycin selection and used as stable cells.

value: non-small cell lung cancer cell (NSCLC) line

tag: shRNA


title: A549-shRNA-Bmi-1-sample

description:
XD_002
Gene expression of cultured cells.

source_name: A549, shRNA-Bmi-1


title: BC016_10_1

type: mixed

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Washington Road

department: Geosciences

institute: Princeton University

description:
4_cDNA_750_Tf_1
OA2_4Tf750C

hyb_protocol: Samples were hybridized to duplicate arrays by overnight incubation at 64°C and washed.

scan_protocol: The arrays were scanned with a laser scanner (Molecular Devices 4200) Images were analyzed with Gene Pix Pro 6.0 software (Molecular Devices)

data_processing: Quality control was employed to remove noise by eliminating features 1) in which the Cy3 signal was not at least twice the value of the control probes, and 2) in which the Cy3/Cy5 could not pass a Z test to find out the outlier values. The Z test was performed by calculating Zi = ri/(s/square root of 3), i = 1, 2, or 3, where ri represents Cy3/Cy5, s the standard deviation of the triplicate Cy3/Cy5 values. A feature is considered as an outlier if the Z is greater than 1.9 (CI = 80%).

molecule: other

organism: synthetic construct

source_name: Universal Internal Standard (20-mer) + 70-mer

label_protocol: PCR amplification using the primers of Francis et al (2005).  The PCR fragments were labeled with amino-allyl-dUTP (Ambion) during linear amplification using random octamers and a Klenow polymerase (Applied Biosystems). The reaction contained 3.96 mM d(AGC)TP, 0.44 mM dTTP, and 4.84 mM dUaa and was amplified for 3 h at 37°C. The Klenow product was purified and conjugated with Cy3. The Cy3-labelled target (1000 ng) was combined with 2x hybridization buffer (1x final concentration; Agilent) and 0.25 pmol of a Cy5-labelled complementary 20-mer standard oligonucleotide and incubated at 95°C for 5 min before being cooled to room temperature.

extract_protocol: DNA was extracted from the filters using the PureGene DNA kit (Gentra, Minneapolis, MN) or the AllPrep DNA/RNA Mini Kit (Qiagen Sciences, Maryland, USA) with slight modifications (as in Ward 2008).

tag: material

value: synthetic construct

molecule: genomic DNA

organism: seawater metagenome

source_name: PCR fragment,  amoA gene from ammonia oxidizing archaea amplified from DNA extracted from seawater

tag: location

value: Ocean acidification experiment, Southern Ocean, 2013


title: BC016_10_3

description:
4_cDNA_1000_Tf_1
OA2_4Tf1000C


title: BC016_9_4

description:
4_cDNA_Ambient_Tf_2
OA2_4TfAmbC


title: BC016_10_4

description:
4_cDNA_1000_Tf_2
OA2_4Tf1000C


title: BC016_9_3

description:
4_cDNA_Ambient_Tf_1
OA2_4TfAmbC


title: BC016_9_2

description:
4_cDNA_Ambient_To_2
OA2_4ToAmbC


title: BC016_10_2

description:
4_cDNA_750_Tf_2
OA2_4Tf750C


title: BC016_9_1

description:
4_cDNA_Ambient_To_1
OA2_4ToAmbC


title: BC016_8_4

description:
3_cDNA_1000_Tf_2
OA2_3Tf1000C


title: nevirapine_galactosamine_nevirapine_3hr_rat61

city: Research Triangle Park

first: Neal

middle: F

last: Cariello

state: NC

address: 5 Moore Drive, Bldg 9, Rom 2011

department: Safety Assessment

institute: GlaxoSmithKline

description: Gene expression data from snap frozen livers after designated treatments

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affy Rat 230_2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: CEL files were processed using RMA and scaled to a target intensity of 150 using ArrayStudio. These normalized values were then processed using limma in ArrayStudio to give fold-change, q values and p values.

label: biotin

organism: Rattus norvegicus

source_name: 7 days nev treated liver with single ip gal dose on day 7, 3 hrs after ip gal and 5 hrs after 8th oral nev. dose

label_protocol: The RNA was then used in the Affymetrix 3' IVT Express protocol to produce the labeled target cRNA. Biotinylated cRNA were prepared according to the Affymetrix protocol from 6 ug total RNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Lysate was then mixed with ethanol and passed through Qiagen RNeasy Mini columns according to protocol.

treatment_protocol: Female Brown Norway rats were treated for 7 days with an initial oral high dose of nevirapine (150mg/kg) for 1day, 100mg/kg for 2 days and then after a 1 day drug holiday 75mg/kg for three more days. A single ip galactosamine dose of 750mg/kg was given on day 7 and the nevirapine 75mg/kg treatment was continued for 8 more days. The time of galactose administration on day 7 was used as a starting point for time course sampling, with3 rats/timepoint being euthanized at 3hrs, 1 day, 2days and 8 days after galactosamine. At this point rats were euthanized and snap frozen livers were taken for gene expression analysis, MALDI and histopathology.Matching samples were taken for comparison from galactosamine only treated rats and nevirapine only treated rats and from sham dosed controls.

value: Brown Norway

tag: gender

value: female

value: Liver

tag: genotype

value: Bn/Crl strain 091 MHC haplotype RT1n

tag: age

value: 9-11 wks of age


title: nevirapine_galactosamine_nevirapine_48hr_rat72

source_name: 9 days nev treated liver with single ip gal dose on day 7, 48 hrs after ip gal and 2 hrs after 10th oral nev. Dose

tag: strain


title: nevirapine_galactosamine_nevirapine_3hr_rat62


title: nevirapine_galactosamine_nevirapine_3hr_rat63


title: nevirapine_galactosamine_nevirapine_48hr_rat71


title: BC016_8_3

description:
3_cDNA_1000_Tf_1
OA2_3Tf1000C


title: frozen tissue samples from cancer-free women [4974911005_H]

type: genomic

city: London

first: Shahzia

last: Anjum

address: Gower Street

country: United Kingdom

institute: University College London

hyb_protocol: Hybridised to the Illumina Infinium Human Methylation27 BeadChip (Illumina Inc USA, WG-311-1201)

scan_protocol: Preliminary QC performed in Genome Studio v.3.2.3 Illumina Inc. and scanned using the Illumina iScan

data_processing: Genome Studio 3.2.3

label: Cy5 and Cy3

source_name: Normal Endometrium

label_protocol: DNA is amplified, fragmented and hybridised to the Illumina BeadChip arrays and then a single base extension is then performed using labelled DNP- and biotin labelled dNTPs

extract_protocol: DNA was isolated using the Qiagen DNeasy Blood and Tissue Kit (Qiagen Ltd, UK, 69506)


title: frozen tissue samples from cancer-free women [4974911006_F]


title: nevirapine_galactosamine_nevirapine_24hr_rat79

source_name: 8 days nev treated liver with single ip gal dose on day 7, 24 hrs after ip gal and 2 hrs after 9th oral nev. Dose


title: nevirapine_galactosamine_nevirapine_48hr_rat70


title: frozen tissue samples from cancer-free women [4974911006_A]


title: frozen tissue samples from cancer-free women [4974911002_D]


title: frozen tissue samples from cancer-free women [4974911006_G]


title: nevirapine_galactosamine_nevirapine_24hr_rat67


title: BC016_8_2

description:
3_cDNA_750_Tf_2
OA2_3Tf750C


title: frozen tissue samples from cancer-free women [4974911005_J]


title: frozen tissue samples from cancer-free women [4974911004_I]


title: frozen tissue samples from cancer-free women [4974911001_B]


title: BC016_8_1

description:
3_cDNA_750_Tf_1
OA2_3Tf750C


title: BC016_7_4

description:
3_cDNA_Ambient_Tf_2
OA2_3TfAmbC


title: nevirapine_galactosamine_nevirapine_24hr_rat69


title: frozen tissue samples from cancer-free women [4974911005_C]


title: patients with primary spontaneous pneumothorax 3

city: Beijing

first: Huaping

last: Dai

address: No. 8 Gongren Tiyuchang South Road

institute: Beijing Chao-Yang Hospital-Beijing Institute of Respiratory Medicine, Capital Medical University

description: Gene expression data from primary spontaneous pneumothorax patitent

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45 ℃ on GeneChip Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned by using Affymetrix GeneChip Command Console (AGCC)  that installed in GeneChip Scanner 3000 7G.

data_processing: Data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings. Values presented are log2 RMA signal intensity.

source_name: lung tissues

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Eight lung tissues in this study were obtained from surgical lung biopsy.

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

treatment_protocol: Fresh lung tissues were preserved in -80 ℃

tag: disease

value: primary spontaneous pneumothorax)

value: lung


title: frozen tissue samples from cancer-free women [4871081132_I]


title: nevirapine_48hr_rat42

source_name: Nevirapine treated liver 48 hours after first oral dose and sham ip dose, 2hrs after third dose


title: patients with primary spontaneous pneumothorax 2


title: frozen tissue samples from cancer-free women [4871081131_I]


title: nevirapine_48hr_rat40


title: IPF patient 5

description: Gene expression data from IPF patient

value: Idiopathic pulmonary fibrosis


title: frozen tissue samples from cancer-free women [4871081132_C]


title: nevirapine_48hr_rat41


title: BC016_7_2

description:
3_cDNA_Ambient_To_2
OA2_3ToAmbC


title: BC016_7_3

description:
3_cDNA_Ambient_Tf_1
OA2_3TfAmbC


title: nevirapine_3hr_rat32

source_name: Nevirapine treated liver 3 hours after first oral dosing and 1 hr after sham ip dose


title: frozen tissue samples from cancer-free women [4871081132_A]


title: nevirapine_3hr_rat31


title: nevirapine_3hr_rat33


title: frozen tissue samples from cancer-free women [4974911001_C]


title: frozen tissue samples from cancer-free women [4871081131_A]


title: frozen tissue samples from cancer-free women [4871081100_J]


title: patients with primary spontaneous pneumothorax 1


title: IPF patient 4

description: Gene expression data from IPF patient


title: frozen tissue samples from cancer-free women [4871081131_E]


title: BC016_4_4

description:
4_DNA_1000_Tf_2
OA2_4Tf1000D


title: BC016_7_1

description:
3_cDNA_Ambient_To_1
OA2_3ToAmbC


title: IPF patient 3

description: Gene expression data from IPF patient


title: frozen tissue samples from cancer-free women [4871081100_H]


title: IPF patient 2

description: Gene expression data from IPF patient


title: BC016_4_1

description:
4_DNA_750_Tf_1
OA2_4Tf750D


title: BC016_4_2

description:
4_DNA_750_Tf_2
OA2_4Tf750D


title: MUTZ LC_2_biological rep1

description: Cell line MUTZ, differentiated to LCs


title: BC016_3_4

description:
4_DNA_Ambient_Tf_2
OA2_4TfAmbD


title: BC016_4_3

description:
4_DNA_1000_Tf_1
OA2_4Tf1000D


title: BC016_3_3

description:
4_DNA_Ambient_Tf_1
OA2_4TfAmbD


title: nevirapine_24hr_rat39

source_name: Nevirapine treated liver 24 hours after first oral dose and sham ip dose, 2hrs after second dose


title: BC016_6_3

description:
4_DNA_Ambient_To_1
OA2_4ToAmbD


title: nevirapine_15day_after_8day_galactosamine_rat87

source_name: Nevirapine treated liver for 15d, single ip galactosamine treatment on day 7, 2hrs after sixteenth nev dose and 8 days after ip galactosamine dose


title: IPF patient 1

description: Gene expression data from IPF patient


title: frozen tissue samples from cancer-free women [4871081100_A]


title: frozen tissue samples from cancer-free women [4871081079_E]


title: frozen tissue from endometrial cancer samples [4974911003_B]

source_name: Primary tumour


title: nevirapine_15day_after_8day_galactosamine_rat84


title: nevirapine_15day_after_8day_galactosamine_rat73


title: frozen tissue from endometrial cancer samples [4974911003_K]


title: nevirapine_15day_rat45

source_name: Nevirapine treated liver 15d after first oral dose and 8 days after sham ip dose, 2hrs after sixteenth dose


title: nevirapine_24hr_rat38


title: nevirapine_15day_rat43


title: nevirapine_15day_rat44


title: frozen tissue samples from cancer-free women [4871081079_K]


title: frozen tissue from endometrial cancer samples [4974911004_A]


title: BT-A6sh2-1 biological replica 4

city: Nashville

first: Amos

middle: M

last: Sakwe

state: TN

address: 1005 Dr. DB Todd Jr Blvd

department: Biochemistry and Cancer Biology/SOGSR

institute: Meharry Medical Colle

description: Gene expression data from cells transfected with shRNA-2 against annexin A6

hyb_protocol: Labeled cDNA Microarray hybridizations were performed on HG-ST 2.0 arrays (Affymetrix) and gene expression data was analyzed using Bioconductor 2.2 running on R2.7.1.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Normalized probe set expression measures were calculated using the ‘Affy’ package's Robust Multichip Average (RMA) default method. Differential gene expression was assessed between replicate groups (n=4) using an empirical Bayes t-test as implemented in the ‘limma’ package. The resultant p-values were adjusted for multiple testing using the False Discovery Rate (FDR) Benjamini and Hochberg method. Thus, any probe sets that exhibited an adjusted p-value FDR q<0.05 were called differentially expressed. Two-dimensional hierarchical clustering of expression data using differentially expressed genes was performed using a Pearson correlation distance matrix and average linkage clustering. All data have been deposited in a public database. Affymetrix data was also analyzed with Ingenuity Pathways Analysis software (Ingenuity® Systems.

source_name: Breast cancer cell line

label_protocol: RNA from AnxA6-depleted or control cells was amplified using the WT (whole transcriptome)-Ovation Pico RNA Amplification system with a 1-cycle amplification following the manufacturer's instructions (NuGEN), and cDNA was fragmented and labeled using the FL-Ovation cDNA Biotin Module V2 kit.

growth_protocol: Cells were grown in DMEM/F12 supplemented with 10% fetal boven serum and  PEN/STREP until they were 70-80% confluent

extract_protocol: Total RNA was extracted using the Qiagen RNAesy kit

treatment_protocol: Cells were harvested by trypsinization, washed twice with cold DPBS

tag: tissue type

value: breast cancer

tag: transfectant

value: shRNA-2 against annexin A6


title: nevirapine_24hr_rat37


title: frozen tissue samples from cancer-free women [4871081100_F]


title: BT-A6sh2-1 biological replica 3


title: frozen tissue from endometrial cancer samples [4871081079_F]


title: BC016_6_4

description:
4_DNA_Ambient_To_2
OA2_4ToAmbD


title: BC016_6_2

description:
3_DNA_1000_Tf_2
OA2_3Tf1000D


title: BC016_6_1

description:
3_DNA_1000_Tf_1
OA2_3Tf1000D


title: BC016_5_3

description:
3_DNA_750_Tf_1
OA2_3Tf750D


title: BC016_5_2

description:
3_DNA_Ambient_Tf_2
OA2_3TfAmbD


title: BC016_5_1

description:
3_DNA_Ambient_Tf_1
OA2_3TfAmbD


title: galactosamine_8day_rat104

source_name: Galactosamine treated liver 8d after ip dose (and 2 hrs after sham oral dose)


title: BC016_5_4

description:
3_DNA_750_Tf_2
OA2_3Tf750D


title: BT-A6sh5-1 biological replica 4

description: Gene expression data from cells transfected with shRNA-5 against annexin A6

value: shRNA-5 against annexin A6


title: BC016_3_1

description:
3_DNA_Ambient_To_1
OA2_3ToAmbD


title: BC016_3_2

description:
3_DNA_Ambient_To_2
OA2_3ToAmbD


title: frozen tissue from endometrial cancer samples [4974911002_L]


title: BT-A6sh2-1 biological replica 2


title: BT-A6sh2-1 biological replica 1


title: galactosamine_8day_rat102


title: galactosamine_48hr_rat26

source_name: Galactosamine treated liver 48 hrs after ip dose(and 2 hrs after sham oral dose)


title: galactosamine_48hr_rat27


title: galactosamine_3hrs_rat18

source_name: Galactosamine treated liver 3 hrs after ip dose(and 5 hours after sham oral dose)


title: frozen tissue from endometrial cancer samples [4974911002_I]


title: frozen tissue from endometrial cancer samples [4871081100_B]


title: frozen tissue from endometrial cancer samples [4871081132_B]


title: galactosamine_8day_rat103


title: BT-A6sh5-1 biological replica 1


title: BT-A6sh5-1 biological replica 3


title: frozen tissue from endometrial cancer samples [4974911002_J]


title: BT-A6sh5-1 biological replica 2


title: frozen tissue from endometrial cancer samples [4871081079_J]


title: frozen tissue from endometrial cancer samples [4871081132_H]


title: galactosamine_3hrs_rat16


title: frozen tissue from endometrial cancer samples [4871081132_J]


title: galactosamine_3hrs_rat17


title: BC016_22_3

description:
5_cDNA_1000_Tf_1
OA1_5Tf1000C

source_name: Universal Internal Standard (20-mer) + 70-mer

value: Ocean acidification experiment, Arctic Ocean, 2012


title: BC016_20_2

description:
4_cDNA_1000_Tf_2
OA1_4Tf1000C

source_name: PCR fragment,  amoA gene from ammonia oxidizing archaea amplified from DNA extracted from seawater


title: BC016_19_4

description:
3_cDNA_1000_Tf_2
OA1_3Tf1000C


title: BC016_22_4

description:
5_cDNA_1000_Tf_2
OA1_5Tf1000C


title: BC016_19_3

description:
3_cDNA_1000_Tf_1
OA1_3Tf1000C


title: frozen tissue from endometrial cancer samples [4974911004_C]


title: BC016_21_4

description:
1_cDNA_1000_Tf_1
OA1_1Tf1000C


title: frozen tissue from endometrial cancer samples [4974911001_A]


title: galactosamine_24hr_rat22

source_name: Galactosamine treated liver 24 hrs after ip dose(and 2 hrs after sham oral dose)


title: frozen tissue from endometrial cancer samples [4974911002_H]


title: galactosamine_24hr_rat24


title: control_48hr_rat11

source_name: Vehicle control liver at 48 hrs after sham ip dose and 2 hours after sham oral dose


title: BT-EV-1 biological replica 4

description: Gene expression data from controlshRNA transfected cells

value: control shRNA


title: BT-EV-1 biological replica 1


title: Mouse_WT_growthplate_UT_rep2

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Division of Molecular Biology

institute: Institute for Genome Research

description: Gene expression of mouse growth plate (WT), untreated

hyb_protocol: 600ng of Cy5-labelled cDNA (specific activity >6.0 pmol Cy5/ug cDNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent Fragmentation buffer and 1x Agilent Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17.5 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air-dried immediately.

scan_protocol: Slides were scanned immediately after washing and drying on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%, NoXDR setting).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-5 (Cy5) labeled cDNA was prepared from 150 ng RNA using the Trans Plex Complete Whole Transcriptome Amplification Kit (Sigma) according to the manufacturer's instructions, followed by High Pure PCR Cleanup Micro Kit (Roche). cDNA then was labeled by BioPrime Total for Agilent aCGH and cDNA yield was checked with the NanoDrop Spectrophotometer.

growth_protocol: All the mouse protocols were approved by the Animal Experimentation Committee of the University of Tokushima. The mice were maintained under SPF conditions.

extract_protocol: The hind limb bone of the mice were snap frozen in Liquid nitrogen, and total RNA was extracted using the Viogene DNA/RNA extraction kit and cleaned up using the Rneasy MinElute Cleanup Kit according to manufactuer's instructions (QIAGEN Valencia, CA).

treatment_protocol: Untreated

value: male

value: Growthplate

value: WT

tag: treatment

value: untreated


title: BT-EV-1 biological replica 3


title: BC016_23_2

description:
5_cDNA_Ambient_Tf_2
OA1_5TfAmbC

value: synthetic construct


title: BC016_20_1

description:
4_cDNA_1000_Tf_1
OA1_4Tf1000C


title: control_48hr_rat12

value: Brown Norway

value: female


title: control_3hr_rat3

source_name: Vehicle control liver at 3 hrs after sham ip dose, 5 hours after sham oral dose

value: Liver

value: Bn/Crl strain 091 MHC haplotype RT1n


title: control_48hr_rat10

value: 9-11 wks of age


title: galactosamine_24hr_rat23


title: frozen tissue from endometrial cancer samples [4871081131_L]


title: frozen tissue from endometrial cancer samples [4871081131_B]


title: Mouse_ATF6bKO_growthplate_UT_rep2

description: Gene expression of mouse growth plate (ATF6bKO), untreated


title: BT-EV-1 biological replica 2


title: frozen tissue from endometrial cancer samples [4974911004_G]


title: frozen tissue from endometrial cancer samples [4871081131_C]


title: Mouse_WT_growthplate_UT_rep1


title: Mouse_ATF6bKO_growthplate_UT_rep1


title: BC016_23_1

description:
5_cDNA_Ambient_Tf_1
OA1_5TfAmbC


title: BC016_20_3

description:
4_cDNA_Ambient_Tf_1
OA1_4TfAmbC


title: BC016_20_4

description:
4_cDNA_Ambient_Tf_2
OA1_4TfAmbC


title: BC016_23_4

description:
3_cDNA_Ambient_Tf_2
OA1_3TfAmbC


title: frozen tissue from endometrial cancer samples [4974911006_E]


title: BC016_23_3

description:
3_cDNA_Ambient_Tf_1
OA1_3TfAmbC


title: control_3hr_rat2


title: BC016_22_2

description:
1_cDNA_Ambient_Tf_2
OA1_1TfAmbC


title: Mouse_ATF6aKO_growthplate_UT_rep1

description: Gene expression of mouse growth plate (ATF6aKO), untreated


title: control_3hr_rat1


title: Mouse_ATF6aKO_growthplate_UT_rep2


title: BC016_22_1

description:
1_cDNA_Ambient_Tf_1
OA1_1TfAmbC


title: control_24hr_rat4

source_name: Vehicle control liver at 24 hrs after sham ip dose and 2 hours after sham oral dose


title: Medalist +C (Meda+C 2c)

first: Rohit

middle: N

last: Kulkarni

address: One Joslin Place

institute: Joslin Diabetes Center

description:
Replicate 3
Med+C2c

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Medalist +C patient_fibroblasts

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

growth_protocol: Fibroblasts were grown in high Glucose DMEM media supplemented with 10% FBS, 1% NEA

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

treatment_protocol: No treatment

tag: subject status

value: Medalist +C patient

value: 77.2±5.0 years old

value: Fibroblasts


title: control_24hr_rat6


title: frozen tissue from endometrial cancer samples [4974911005_L]


title: control_24hr_rat5


title: control_15d_rat14

source_name: Vehicle control liver at 15d after sham ip dose and 2 hours after sham oral dose


title: frozen tissue from endometrial cancer samples [4871081132_G]


title: frozen tissue from endometrial cancer samples [4974911002_G]


title: frozen tissue from endometrial cancer samples [4871081132_F]


title: Medalist -C (Meda-C 2c)

description:
Replicate 3
Med-C2c

source_name: Medalist -C patient_fibroblasts

value: Medalist -C patient

value: 74.5±12.9 years old


title: Medalist -C (Meda-C 2d)

description:
Replicate 4
Med-C2d


title: frozen tissue from endometrial cancer samples [4871081079_A]


title: Healthy Controls (Ctrl 2e)

description:
Replicate 4
Ctr2e

source_name: healthy control_fibroblasts

value: healthy control

value: 71.2±11.1 years old


title: control_15d_rat15


title: control_15d_rat13


title: BC016_18_4

description:
5_cDNA_Ambient_To_2
OA1_5ToAmbC

value: Ocean acidification experiment, Arctic Ocean, 2012


title: BC016_18_3

description:
5_cDNA_Ambient_To_1
OA1_5ToAmbC


title: BC016_21_2

description:
3_cDNA_Ambient_To_2
OA1_3ToAmbC


title: BC016_19_2

description:
2_cDNA_Ambient_To_2
OA1_2ToAmbC


title: BC016_21_1

description:
3_cDNA_Ambient_To_1
OA1_3ToAmbC


title: Medalist +C (Meda+C 2e)

description:
Replicate 4
Med+C2e


title: frozen tissue from endometrial cancer samples [4974911001_I]


title: control_8d_rat101

source_name: Vehicle control liver at 8d after sham ip dose and 2 hours after sham oral dose


title: frozen tissue from endometrial cancer samples [4974911001_F]

source_name: Primary tumour


title: frozen tissue from endometrial cancer samples [4974911002_K]


title: frozen tissue from endometrial cancer samples [4974911004_F]


title: control_8d_rat100


title: Medalist +C (Meda+C 1e)

description:
Replicate 4
Med+C1e


title: Medalist -C (Meda-C 1d)

description:
Replicate 3
Med-C1d


title: Medalist -C (Meda-C 1e)

description:
Replicate 4
Med-C1e


title: BC016_19_1

description:
2_cDNA_Ambient_To_1
OA1_2ToAmbC


title: frozen tissue from endometrial cancer samples [4974911006_C]


title: Healthy Controls (Ctrl 2d)

description:
Replicate 3
Ctr2d


title: R2t24

city: New York

first: Zhe

last: Cheng

state: New York

address: 12 Waverly Place, 4th Floor

department: Bilogy Department

institute: New York University

description:
Gene expression after 24hr DTT induced stress in HeLa cells
US93503718_252800415559_S02_GE1_107_Sep09_2_4

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2.5x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), and 10 seconds in acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110819).
The normalized data were further processed using ENSG names instead of probe names (provided in the 'normalized_ENSG_IDs.txt', 'normalized_ENSG_IDs_log_filtered_LOWESSsmoothed.txt' files). The probe IDs were converted to transcript IDs, and  then to Gene ENSG IDs based on ensembl_mart_db from biomaRt by R programming software.

source_name: HeLa_24hr stress

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) Protocol (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HeLa cells were used to conduct the 30 hour-long time course experiment. The cells were collected simultaneously at the end point. By this way, all cells grew for the same time period, and the changes of RNA are only due to the effects of stress. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA extraction was conducted using Trizol (Sigma) followed by the PhaseLock Gel-Heavy manufacturer protocol (5-Prime) and finally the RNA was purified using the RNA MinElute Kit (QIAGEN). Nanodrop ND-1000 was used to quantify RNA and assess quality.

treatment_protocol: DTT was used to stress the cells for different lengths, 0, 0.5, 1, 2, 8, 16, 24, 30hrs. To account for different cellular ages at harvest, the experiment was conducted “backwards”. The cells were stressed at different time points 0, 1, … 30hrs before collection and all the stress-end points were aligned at one time point.

value: HeLa

value: cervical cancer cell line

tag: exposed to

value: 2.5mM DTT for 24hr


title: control_8d_rat99

tag: tissue


title: frozen tissue from endometrial cancer samples [4974911004_J]


title: frozen tissue from endometrial cancer samples [4974911002_E]


title: BC016_18_2

description:
1_cDNA_Ambient_To_2
OA1_1ToAmbC

value: synthetic construct


title: Medalist +C (Meda+C 1d)

description:
Replicate 3
Med+C1d


title: BC016_18_1

description:
1_cDNA_Ambient_To_1
OA1_1ToAmbC


title: Healthy Controls (Ctrl 1d)

description:
Replicate 3
Ctr1d


title: R1t8

description:
Gene expression after 8hr DTT induced stress in HeLa cells
US93503718_252800415559_S02_GE1_107_Sep09_2_2

source_name: HeLa_8hr stress

value: 2.5mM DTT for 8hr


title: BC016_16_4

description:
5_DNA_1000_Tf_2
OA1_5Tf1000D


title: frozen tissue from endometrial cancer samples [4974911001_E]

value: female


title: BC016_16_3

description:
5_DNA_1000_Tf_1
OA1_5Tf1000D


title: Medalist +C (Meda+C 2b)

description:
Replicate 2
Med+C2b


title: R1t2

description:
Gene expression after 2hr DTT induced stress in HeLa cells
US93503718_252800415559_S02_GE1_107_Sep09_2_3

source_name: HeLa_2hr stress

value: 2.5mM DTT for 2hr


title: R2t30

description:
Gene expression after 30hr DTT induced stress in HeLa cells
US93503718_252800415559_S02_GE1_107_Sep09_1_3

source_name: HeLa_30hr stress

value: 2.5mM DTT for 30hr


title: Healthy Controls (Ctrl 1e)

description:
Replicate 4
Ctr1e


title: Medalist +C (Meda+C 2a)

description:
Replicate 1
Med+C2a


title: frozen tissue from endometrial cancer samples [4974911003_A]


title: R2t1

description:
Gene expression after 1hr DTT induced stress in HeLa cells
US93503718_252800415559_S02_GE1_107_Sep09_1_2

source_name: HeLa_1hr stress

value: 2.5mM DTT for 1hr


title: BC016_13_4

description:
4_DNA_1000_Tf_2
OA1_4Tf1000D

source_name: Universal Internal Standard (20-mer) + 70-mer


title: Medalist -C (Meda-C 2b)

description:
Replicate 2
Med-C2b


title: Medalist -C (Meda-C 2a)

description:
Replicate 1
Med-C2a


title: R1t30

description:
Gene expression after 30hr DTT induced stress in HeLa cells
US93503718_252800415559_S02_GE1_107_Sep09_1_1


title: frozen tissue from endometrial cancer samples [4974911001_L]


title: frozen tissue from endometrial cancer samples [4871081131_G]


title: R1t0.5

description:
Gene expression after 0.5hr DTT induced stress in HeLa cells
US93503718_252800415558_S01_GE1_107_Sep09_2_4

source_name: HeLa_0.5hr stress

value: 2.5mM DTT for 0.5hr


title: BC016_13_3

description:
4_DNA_1000_Tf_1
OA1_4Tf1000D

source_name: PCR fragment,  amoA gene from ammonia oxidizing archaea amplified from DNA extracted from seawater


title: R1t16

description:
Gene expression after 16hr DTT induced stress in HeLa cells
US93503718_252800415558_S01_GE1_107_Sep09_2_2

source_name: HeLa_16hr stress

value: 2.5mM DTT for 16hr


title: BC016_13_2

description:
3_DNA_1000_Tf_2
OA1_3Tf1000D


title: frozen tissue from endometrial cancer samples [4974911005_E]


title: BC016_13_1

description:
3_DNA_1000_Tf_1
OA1_3Tf1000D


title: BC016_17_2

description:
2_DNA_1000_Tf_2
OA1_2Tf1000D


title: Healthy Controls (Ctrl 2c)

description:
Replicate 2
Ctr2c

value: Fibroblasts


title: BC016_17_1

description:
2_DNA_1000_Tf_1
OA1_2Tf1000D


title: Medalist +C (Meda+C 1b)

description:
Replicate 2
Med+C1b

value: Medalist +C patient

value: 77.2±5.0 years old


title: frozen tissue from endometrial cancer samples [4871081132_L]


title: R1t24

description:
Gene expression after 24hr DTT induced stress in HeLa cells
US93503718_252800415820_S01_GE1_107_Sep09_2_2


title: frozen tissue from endometrial cancer samples [4974911001_H]


title: frozen tissue from endometrial cancer samples [4974911005_B]


title: frozen tissue from endometrial cancer samples [4871081132_E]


title: BC016_15_4

description:
1_DNA_1000_Tf_2
OA1_1Tf1000D


title: R1t0

description:
Gene expression in control without DTT induced stress in HeLa cells
US93503718_252800415558_S01_GE1_107_Sep09_1_2

source_name: HeLa_0hr stress

value: none (untreated control)


title: R2t8

description:
Gene expression after 8hr DTT induced stress in HeLa cells
US93503718_252800415820_S01_GE1_107_Sep09_1_4


title: BC016_15_3

description:
1_DNA_1000_Tf_1
OA1_1Tf1000D


title: BC016_2_4

description:
5_DNA_Ambient_Tf_2
OA1_5TfAmbD


title: Healthy Controls (Ctrl 2b)

description:
Replicate 1
Ctr2b

value: healthy control

value: 71.2±11.1 years old


title: R2t2

description:
Gene expression after 2hr DTT induced stress in HeLa cells
US93503718_252800415819_S01_GE1_107_Sep09_2_2

value: HeLa


title: frozen tissue from endometrial cancer samples [4974911004_B]


title: R2t16

description:
Gene expression after 16hr DTT induced stress in HeLa cells
US93503718_252800415821_S01_GE1_107_Sep09_1_4

value: cervical cancer cell line


title: frozen tissue from endometrial cancer samples [4974911003_F]


title: R2t0

description:
Gene expression in control without DTT induced stress in HeLa cells
US93503718_252800415820_S01_GE1_107_Sep09_2_1

source_name: HeLa cell line,0hr stress


title: Medalist -C (Meda-C 1c)

description:
Replicate 2
Med-C1c

value: Medalist -C patient

value: 74.5±12.9 years old


title: frozen tissue from endometrial cancer samples [4974911001_K]


title: BC016_2_3

description:
5_DNA_Ambient_Tf_1
OA1_5TfAmbD

value: synthetic construct

value: Ocean acidification experiment, Arctic Ocean, 2012


title: frozen tissue from endometrial cancer samples [4974911005_I]

value: female


title: BC016_14_2

description:
4_DNA_Ambient_Tf_2
OA1_4TfAmbD


title: R1t1

description:
Gene expression after 1hr DTT induced stress in HeLa cells
US93503718_252800415821_S01_GE1_107_Sep09_1_1


title: R2t0.5

description:
Gene expression after 0.5hr DTT induced stress in HeLa cells
US93503718_252800415821_S01_GE1_107_Sep09_1_2


title: Healthy Controls (Ctrl 1c)

description:
Replicate 2
Ctr1c


title: BC016_14_1

description:
4_DNA_Ambient_Tf_1
OA1_4TfAmbD


title: BC016_17_4

description:
3_DNA_Ambient_Tf_2
OA1_3TfAmbD


title: Medalist +C (Meda+C 1a)

description:
Replicate 1
Med+C1a

source_name: Medalist +C patient_fibroblasts


title: mouse myoblast (MB), low MeCP2 protein level, rep. 4

city: Darmstadt

first: M. Cristina

last: Cardoso

address: Schnittspahnstr. 10

department: Biology

country: Germany

institute: Technische Universität

description:
R5_10
undifferentiated state,low ectopic MeCP2-YFP levels (mean fluorescent intensity: 247)

hyb_protocol: The resulting cDNA was hybridized to the Affymetrix mouse 430 2.0 microarray. Five independent experiments were performed for all conditions (myoblast, myotube, low and high ectopic MeCP2)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 and according GCOS software.

data_processing: The data were analyzed with Affymetrix Expression Console. Arrays were normalized for condition project individually by the log scale robust multi-array analysis (RMA). Its estimates are based upon a robust average of log2 (B(PM)), where B(PM) are background corrected perfect match intensities. Compared with the GCOS method the RMA method has better precision, provides more consistent estimates of fold change and provides higher specificity and sensitivity when using fold change analysis to detect differential expression (Irizary et al., 2003).     First a Nalimov test was performed to exclude outliers from the statistical analysis (threshold: p=0.0001). No arrays were excluded by this test. The average and standard deviation of the antilog RMA values were calculated and from there the fold change was obtained. An unpaired student t-test was performed.

source_name: pmi 28 mouse myoblast (MB), undifferentiated, low ectopic MeCP-YFP level

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

growth_protocol: Undifferentiated Pmi 28 mouse myoblasts (MB) were cultured and in vitro differentiated as described previously (Brero et al. 2005) to obtain five independent replicas of myoblasts (MB) and myotubes (MT). In brief, for in vitro differentiation 8x10exp5 myoblasts were seeded in standard p100 cell culture dishes. One day post seeding, growth medium (supplemented with 20% fetal calf serum) was replaced by differentiation medium (supplemented with 5 % horse serum) and cells were cultured without medium replacement until the formation of large polynucleated myotubes (4 to 7 days).

extract_protocol: Cell pellets with 6.5x10exp5 to 1.7x10epx6 cells were used for RNA extraction. Following the Affymetrix GeneChip technical manual, total RNA was extracted using Trizol reagent (Invitrogen, Paisley PA4 9RF, UK) and purified using RNeasy Mini kit (Qiagen, Valencia, CA 91355 USA) according to manufacturer’s advice. Double-stranded cDNA was synthesized from total RNA using two different kits according to RNA concentration. If the total RNA yield was between 1-20 μg/μl, the cDNA Synthesis kit from Roche (Roche, Mannheim, Germany) was used, taking 10 μg total RNA. For yield between 10-100 ng/μl the two-cycle kit from Invitrogen (Invitrogen, Paisley PA4 9RF, UK) was used, taking 50 ng/μl total RNA.

treatment_protocol: For total RNA extraction, cell pellets containing 6.5x10exp5 to 1.7x10exp6 cells of undifferentiated myoblasts (MB) and differentiated myotubes (MT) were generated and frozen until RNA extraction.To generate in addition samples with high (R4) and low (R5)  ectopic MeCP2 protein levels,  Pmi 28 myoblast cultures were transiently transfected with a mammalian expression construct coding for YFP tagged rat MeCP2 (Brero et al. 2005). Before FACSorting, transfected cultures were washed twice with PBS-EDTA, trypsinized and collected in medium. After a gentle centrifugation, cell pellets were resuspended in sterile PBS. Fractions of cells with high (R4; fluorescent intensity mean 322) and low (R5; fluorescent intensity mean 247) ectopic MeCP2-YFP protein levels were collected. Cell pellets containing 6.5x10exp5 to 1.7x10exp6 cells were frozen until total RNA extraction.

value: myoblast

tag: mecp2 status

value: low MeCP2-YFP


title: Medalist -C (Meda-C 1b)

description:
Replicate 1
Med-C1b

source_name: Medalist -C patient_fibroblasts

tag: cell type


title: Healthy Controls (Ctrl 1a)

description:
Replicate 1
Ctr1a

source_name: healthy control_fibroblasts


title: mouse myoblast (MB), low MeCP2 protein level, rep. 3

description:
R5_5
undifferentiated state,low ectopic MeCP2-YFP levels (mean fluorescent intensity: 247)

tag: cell line


title: frozen tissue from endometrial cancer samples [4871081079_L]


title: frozen tissue from endometrial cancer samples [4871081100_C]


title: frozen tissue from endometrial cancer samples [4974911006_H]


title: mouse myoblast (MB), low MeCP2 protein level, rep. 5

description:
R5_1807
undifferentiated state,low ectopic MeCP2-YFP levels (mean fluorescent intensity: 247)


title: BC016_15_1

description:
2_DNA_Ambient_Tf_1
OA1_2TfAmbD


title: frozen tissue from endometrial cancer samples [4974911003_H]


title: BC016_17_3

description:
3_DNA_Ambient_Tf_1
OA1_3TfAmbD


title: BC016_15_2

description:
2_DNA_Ambient_Tf_2
OA1_2TfAmbD


title: mouse myoblast (MB), low MeCP2 protein level, rep. 2

description:
R5_3
undifferentiated state,low ectopic MeCP2-YFP levels (mean fluorescent intensity: 247)


title: BC016_16_2

description:
1_DNA_Ambient_Tf_2
OA1_1TfAmbD


title: mouse myoblast (MB), high MeCP2 protein level, rep. 5

description:
R4_1807
undifferentiated state, high ectopic MeCP2-YFP levels (mean fluorescent intensity: 322)

source_name: pmi 28 mouse myoblast (MB), undifferentiated, high ectopic MeCP-YFP level

value: high MeCP2-YFP


title: frozen tissue from endometrial cancer samples [4974911006_K]

source_name: Primary tumour


title: mouse myoblast (MB), low MeCP2 protein level, rep. 1

description:
R5_1
undifferentiated state,low ectopic MeCP2-YFP levels (mean fluorescent intensity: 247)


title: GR2

city: Walkersville

first: Behnam

middle: A

last: Baghbaderani

state: MD

address: 8830 Biggs Ford Road

institute: Lonza

data_processing: Data were normalized using quantile normalization with Illumina version 1.8.0.

source_name: human ESC line

label_protocol: not provided

growth_protocol: iPSC lines were grown using the L7 system from Lonza

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

value: Male

value: Induced pluripotent stem cells

tag: passage

value: passage 15


title: BC016_16_1

description:
1_DNA_Ambient_Tf_1
OA1_1TfAmbD

tag: material


title: frozen tissue from endometrial cancer samples [4974911005_F]


title: mouse myoblast (MB), high MeCP2 protein level, rep. 4

description:
R4_4
undifferentiated state, high ectopic MeCP2-YFP levels (mean fluorescent intensity: 322)


title: BC016_11_4

description:
5_DNA_Ambient_To_2
OA1_5ToAmbD

tag: location


title: GR1

source_name: human iPSC line

tag: gender

value: passage 16


title: mouse myoblast (MB), high MeCP2 protein level, rep. 3

description:
R4_3
undifferentiated state, high ectopic MeCP2-YFP levels (mean fluorescent intensity: 322)


title: frozen tissue from endometrial cancer samples [4974911002_C]


title: NL9

value: Female

value: passage 11


title: frozen tissue from endometrial cancer samples [4974911004_E]


title: mouse myoblast (MB), high MeCP2 protein level, rep. 2

description:
R4_2
undifferentiated state, high ectopic MeCP2-YFP levels (mean fluorescent intensity: 322)


title: BC016_11_3

description:
5_DNA_Ambient_To_1
OA1_5ToAmbD


title: mouse myoblast (MB), high MeCP2 protein level, rep. 1

description:
R4_1
undifferentiated state, high ectopic MeCP2-YFP levels (mean fluorescent intensity: 322)


title: H7 P33+4

value: passage 37


title: mouse myotubes (MT), rep. 5

description:
MT4
differentiated state, high endogenous MeCP2 protein level

source_name: pmi 28 mouse myotube (MT) culture, differentiated

value: myotubes


title: frozen tissue from endometrial cancer samples [4871081079_G]


title: frozen tissue from endometrial cancer samples [4871081100_D]


title: BC016_12_4

description:
4_DNA_Ambient_To_2
OA1_4ToAmbD


title: BC016_12_3

description:
4_DNA_Ambient_To_1
OA1_4ToAmbD


title: LiPSC-PR2


title: mouse myotubes (MT), rep. 4

description:
MT3
differentiated state, high endogenous MeCP2 protein level


title: BC016_14_4

description:
3_DNA_Ambient_To_2
OA1_3ToAmbD


title: LiPSC-PR3

value: passage 33


title: BC016_14_3

description:
3_DNA_Ambient_To_1
OA1_3ToAmbD


title: frozen tissue from endometrial cancer samples [4871081132_K]


title: LiPSC-PR1

value: passage 12


title: mouse myotubes (MT), rep. 3

description:
MT2
differentiated state, high endogenous MeCP2 protein level


title: mouse myotubes (MT), rep. 2

description:
MT1
differentiated state, high endogenous MeCP2 protein level


title: frozen tissue samples from cancer-free women [4974911006_J]

source_name: Normal Endometrium


title: LiPSC ER3


title: frozen tissue from endometrial cancer samples [4974911004_D]


title: frozen tissue from endometrial cancer samples [4871081131_D]


title: LiPSC ER2

value: passage 13


title: LiPSC ER1

value: passage 17


title: BC016_12_1

description:
2_DNA_Ambient_To_1
OA1_2ToAmbD

value: synthetic construct

value: Ocean acidification experiment, Arctic Ocean, 2012


title: frozen tissue from endometrial cancer samples [4871081100_K]

value: female


title: BC016_12_2

description:
2_DNA_Ambient_To_2
OA1_2ToAmbD


title: mouse myotubes (MT), rep. 1

description:
MT0
differentiated state, high endogenous MeCP2 protein level


title: frozen tissue from endometrial cancer samples [4974911006_B]


title: mouse myoblast (MB), rep. 5

description:
MB6
undifferentiated state, low endogenous MeCP2 protein level

source_name: pmi 28 mouse myoblast (MB) cell line, undifferentiated

value: myoblast


title: LiPSC TR2


title: BC016_11_2

description:
1_DNA_Ambient_To_2
OA1_1ToAmbD

source_name: Universal Internal Standard (20-mer) + 70-mer


title: BC016_11_1

description:
1_DNA_Ambient_To_1
OA1_1ToAmbD


title: frozen tissue from endometrial cancer samples [4974911005_D]


title: frozen tissue from endometrial cancer samples [4974911005_K]


title: mouse myoblast (MB), rep. 3

description:
MB3
undifferentiated state, low endogenous MeCP2 protein level


title: frozen tissue from endometrial cancer samples [4974911003_E]


title: LiPSC TR1

value: passage 19


title: frozen tissue from endometrial cancer samples [4974911001_J]


title: mouse myoblast (MB), rep. 4

description:
MB4
undifferentiated state, low endogenous MeCP2 protein level


title: mouse myoblast (MB), rep. 2

description:
MB2
undifferentiated state, low endogenous MeCP2 protein level


title: mammillary body, WT, biological rep9

status: Public on Aug 14 2015

city: Heidelberg

first: Gonzalo

last: Alvarez-Bolado

address: Im Neuenheimer Feld 307

institute: Institute for Anatomy and Cell Biology

description: gene expression data from E10.5 wild type mammillary neuroepithelium

hyb_protocol: Hybridization was performed for 16 hr at 45°C on GeneChip Mouse Gene 1.1 ST arrays. GeneChips were washed and stained in the Affymetrix Fuidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 (GSC3000) with GCOS 1.4

data_processing: The data was analyzed using Expression Console 1.0 (Affymetrix) and Bioconductor package affy under R 2.7.0. Background correction, normalization and probe summarization was performed with RMA

source_name: mammillary neuroepithelium of E10.5 mouse embryos

label_protocol: RNA was labeled using the Ambion WT Expression kit, combined with Affymetrix GeneChip WT terminal labeling kit

growth_protocol: Mice were crossed to obtain E10.5 wild type and Lhx5 mutant embryos.

extract_protocol: RNA was extracted by using the RNeasy Micro Kit (Qiagen) following the manufacturers instructions for animal tissue.

treatment_protocol: The mammillary neuroepithelium of E10.5 wild type and Lhx5 mutant embryos was dissected and immediately frozen at -80°C. The RNA was preserved with RNAlater ICE (Life Technologies).

value: brain (mammillary neuroepithelium)

tag: genotype

value: WT


title: mammillary body, WT, biological rep12

tag: age


title: mammillary body, WT, biological rep10

tag: strain


title: mammillary body, WT, biological rep7


title: mammillary body, WT, biological rep11


title: mammillary body, WT, biological rep5


title: mammillary body, KO, biological rep13

description: gene expression data from E10.5 Lhx5 mutant mammillary neuroepithelium

value: Lhx5 KO


title: mammillary body, KO, biological rep12


title: mammillary body, WT, biological rep6


title: mammillary body, WT, biological rep1


title: mammillary body, WT, biological rep2


title: mammillary body, WT, biological rep4


title: mammillary body, KO, biological rep9


title: mammillary body, KO, biological rep10


title: mammillary body, KO, biological rep7


title: mammillary body, KO, biological rep8


title: JURKAT_shGFP_dup2

city: Singapore

first: Takaomi

last: Sanda

address: 14 Medical Dr 12-01

country: Singapore

institute: Cancer Science Institute of Singapore, National University of Singapore

hyb_protocol: Standard Affymetrix 3' array hybridyzation protocol.

scan_protocol: Standard Affymetrix confocal laser scanner protocol.

data_processing: The data was normalized and analyzed by dChip software.

source_name: T-ALL cell line_shGFP

label_protocol: Standard Affymetrix biotin label protocol.

growth_protocol: JURKAT cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol: After 72 hours of infection, total RNA was harvested by Trizol followed by a column purification using RNeasy Mini kit (Qiagen) following manufacturer's instruction.

treatment_protocol: JURKAT cells were infected with lentivirus encoding shRNA. The infected cells were selected by puromycin.

value: JURKAT

value: T-cell


title: mammillary body, WT, biological rep3


title: JURKAT_shTRIB2_dup1

source_name: T-ALL cell line_shTRIB2


title: mammillary body, WT, biological rep8


title: mammillary body, KO, biological rep5


title: mammillary body, KO, biological rep6


title: mammillary body, KO, biological rep11


title: JURKAT_shTRIB2_dup2


title: GCT_Sample14_StageA

city: Clayton

first: Maria

last: Alexiadis

state: Victoria

address: 27-31 Wright St

department: Centre for Endocrinology & Metabolism

country: Australia

institute: Hudson Institute Of Medical Research

hyb_protocol: 1.6ug of Cy3 labeled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was fragmented at 60oC for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions.  On completion 55ul of 2x Agilent gene expression hybridisation buffer was added and 100ul of sample hybridised for 17 hours at 65oC in a rotating Agilent hybridisation oven.  After hybridisation, microarrays were washed 1 minute at room temperature with GE wash buffer 1(Agilent) and 1 minute with 37oC GE wash buffer 2(Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent C, DNA microarray scanner using one color scan settings for 4x44k array slides; scan area 61x21.6mm, scan resolution 5um, dye channel is set to Green and 20 bit Tiff.

data_processing: The scanned images were analysed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1-1100_Jul11 and Grid:014850_D_F_20120130) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Granulosa Cell Tumour tissue, sample 14, stage Advanced

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared from 0.2ug total RNA using the One-Color Low input Quick Amp labelling Kit (Agilent, v6.6 September 2012) according to the manufacturer’s instructions, followed by RNeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: menopausal status

value: Pre

value: Granulosa Cell Tumour tissue stage Advanced


title: GCT_Sample15_StageA

source_name: Granulosa Cell Tumour tissue, sample 15, stage Advanced

value: Post


title: VaNAC26-OE_drought_5d_rep2

city: Wuhan

first: Lingye

last: Su

address: Lumo Road, Moshan

institute: Wuhan Botanical Garden, Chinese Academy of Sciences

description: Gene expression data from VaNAC26 transgenic Arabdopsis leaf under 5 day drought

hyb_protocol: 12.5 μg of labelled and fragmented cRNA probes were hybridized to the Arabidopsis arrays with the Hybridization, Wash and Stain Kit (Affymetrix, #900720) according to the manufacturer’s instructions

scan_protocol: The arrays were scanned using a GeneChip® Scanner 3000 (Affymetrix, #3000).

data_processing: The data were analyzed with Microarray Suite version 3.0 (MAS 3.0)

organism: Arabidopsis thaliana

label_protocol: The cRNA was labelled with a biotinylated ribonucleotide  analogue and was fragmented with fragmentation buffer using the MessageAmp™ Premier RNA Amplification Kit (Ambion, #1792).

growth_protocol: Plants were grown on soil in a greenhouse (16-h light/8-h dark) at 22 oC

extract_protocol: Total RNA was extracted from 100 mg samples by using the Column Plant RNAout 2.0 (Tiandz Inc., Beijing, China)

treatment_protocol: For drought treatment, seedlings of transgenic lines and wild-type Arabidopsis were grown in soil in 22 oC for 21 d. After irrigation, the phenotypes of plant were observed during the following 5 d without watering.

value: leaf

tag: genotype/variation

tag: stress

value: under 5 day drought


title: mouse myoblast (MB), rep. 1

description:
MB1
undifferentiated state, low endogenous MeCP2 protein level


title: mammillary body, KO, biological rep4


title: VaNAC26-OE_drought_5d_rep1

source_name: VaNAC26 transgenic Arabdopsis leaf under 5 day drought


title: JURKAT_shGFP_dup1


title: GCT_Sample12_StageA

source_name: Granulosa Cell Tumour tissue, sample 12, stage Advanced


title: GCT_Sample13_StageA

source_name: Granulosa Cell Tumour tissue, sample 13, stage Advanced


title: VaNAC26-OE_control_rep2

description: Gene expression data from VaNAC26 transgenic Arabdopsis leaf under normal condition

value: normal condition


title: GCT_Sample11_StageA

source_name: Granulosa Cell Tumour tissue, sample 11, stage Advanced


title: mammillary body, KO, biological rep3


title: mammillary body, KO, biological rep1


title: GCT_Sample10_StageA

source_name: Granulosa Cell Tumour tissue, sample 10, stage Advanced


title: VaNAC26-OE_control_rep1

source_name: VaNAC26 transgenic Arabdopsis leaf under normal condition


title: wild type_drought_5d_rep2

description: Gene expression data from wild type Arabdopsis leaf under 5 day drought

value: wild type


title: mammillary body, KO, biological rep2


title: E. coli Type_III genotype strain, under 45ºC, rep 3

city: Tsukuba

first: Bei-Wen

last: Ying

state: Ibaraki

address: 1-1-1 Tennoudai

institute: University of Tsukuba

hyb_protocol: Following fragmentation, 3 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Microarray data were processed using custom scripts written in R based on the finite hybridisation (FH) model (Ono et al, 2008) and the thermodynamic model of non-specific binding (NSB) on short nucleotide microarrays (Furusawa et al, 2009).

organism: Escherichia coli

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

growth_protocol: Cells were grown in the minimal media, M63. The final cell concentrations were controlled ~ 10^8 cells/mL within the exponential growth phase.

extract_protocol: Total RNAs were extracted using an RNeasy mini kit (Qiagen) in accordance with the manufacturer’s instructions.

treatment_protocol: The cell culture was put into cold phenol-ethanol solution (1 g of phenol in 10 mL of ethanol) prepared in advance. The cells were collected by centrifugation at 7,000 × g for 3 min at 4°C, and the pelleted cells were stored at –80°C prior to use.

tag: condition


title: Patient 8 epileptogenic zone

city: Hualien

first: Ingrid

last: Liu

address: E411, 701, Section 3 Chung Yang Road

department: Molecular Biology and Human Genetics

country: Taiwan

institute: Tzu Chi University

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,097 experimental controls)

hyb_protocol: Phalanx HOA v4 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on HOA in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 33 PMT 600~630 ; 532nm power10, PMT460/ power 100, PMT330) and quantify the fluoresence intensity.

data_processing: The intensity difference between F635median and B635 median was calculated and normalized by median shift normalization method using R software.

source_name: Patient 8 epileptogenic zone

label_protocol: 2.5 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

extract_protocol: RNA extraction by TRIzol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧8).

treatment_protocol: After clinical evaluatng by EEG, SPEC, MRI, and v-EEG, patients were performed with surgical removal of epileptogenic zone and irritative zone. Removed surgical samples were obtained snap-frozen on dry ice for total RNA extraction.

value: human brain

value: Male

tag: causing

value: idiopathic

tag: age-onset

value: 6 years old

tag: surgery age

value: 26 years old

tag: pre-surgery epileptic frequency

value: 3-5 times a month

tag: surgery brain hemisphere

value: left

tag: surgery brain region

value: temporal lobe

tag: post-surgery epileptic frequency

value: < once a month


title: GCT_Sample5_Stage1

source_name: Granulosa Cell Tumour tissue, sample 5, stage 1

tag: cell type

value: Granulosa Cell Tumour tissue stage 1


title: Patient 10 epileptogenic zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,101 experimental controls)

source_name: Patient 10 epileptogenic zone

tag: tissue

value: 8 years old

value: 28 years old

value: right


title: GCT_Sample6_Stage1a

source_name: Granulosa Cell Tumour tissue, sample 6, stage 1a

value: Pre

value: Granulosa Cell Tumour tissue stage 1a


title: Patient 9 irritative zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,098 experimental controls)

source_name: Patient 9 irritative zone

tag: gender

value: 2 years old

value: 27 years old

value: >30 times a month

value: forntal lobe


title: GCT_Sample3_Stage1c

source_name: Granulosa Cell Tumour tissue, sample 3, stage 1c

value: Post

value: Granulosa Cell Tumour tissue stage 1c


title: GCT_Sample4_Stage1

source_name: Granulosa Cell Tumour tissue, sample 4, stage 1


title: Patient 10 irritative zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,100 experimental controls)

source_name: Patient 10 irritative zone

value: human brain

value: Female

value: idiopathic


title: wild type_control_rep2

description: Gene expression data from wild type Arabdopsis leaf under normal condition

value: leaf

value: wild type

value: normal condition


title: P-treated HESCs, rep3

city: Columbus

first: S.

middle: Joseph

last: Huang

state: Ohio

department: Ob/Gyn

institute: The Ohio State University

description:
Sample name: P-3
n=3

hyb_protocol: Amplified RNA was hybridized to HumanHT-12 v4 Expression BeadChip using Illumina's Whole-Genome Gene Expression Direct Hybridization Assay Guide. Hybridized samples were washed using same Hybridization Assay Guide and stained with Amersham Cy3-Streptavidin (GE Healthcare PA43001).

scan_protocol: BeadChips were scanned using the Illumina HiScan System.

data_processing: The data were normalised 75th percentile shift and transforming the baseline to the median of all samples with GX 12.6.1 software.

source_name: HESCs, P

label_protocol: Total RNA samples were normalized to 500ng using Thermo Scientific NanoDrop concentration readings. Samples were then amplified using Ambion's Illumina TotalPrep RNA Amplification Kit (P/N AMIL1791) following Ambion's protocol. Amplified RNA samples were measured for their concentration using the Thermoscientific NanoDrop and normalized to 750ng.

growth_protocol: HESCs were cultured in medium 231 (M231; Life Technologies) with smooth muscle growth supplement which includes 5% FBS; 2 ng/ml human basic fibroblast growth factor, 0.5 ng/ml human epidermal growth factor, 5 ng/ml heparin, 0.2 µg/ml insulin and 5 µg/ml BSA (Life Technologies) with 100U/ml penicillin, 100 ug/ml streptomycin, 0.25 ug/ml fungizone.

extract_protocol: Total RNA was isolated using Qiagen miRNeasy Mini Kit (Qiagen, Valencia, CA) and RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: HESCs were treated with or without ETO, M or P for 6 hours.

value: endometrium

value: cultured human endometrial stromal cells (HESCs)

value: female

tag: developmental stage

value: pre-menopausal

tag: treatment

value: P

tag: treatment duration


title: Patient 8 irritative zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,096 experimental controls)

source_name: Patient 8 irritative zone

value: Male

value: 6 years old

value: 26 years old

value: 3-5 times a month

value: left

value: temporal lobe

value: < once a month


title: Patient 9 epileptogenic zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,099 experimental controls)

source_name: Patient 9 epileptogenic zone

value: human brain

value: 2 years old

value: 27 years old

value: >30 times a month

value: right

value: forntal lobe


title: Patient 7 epileptogenic zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,095 experimental controls)

source_name: Patient 7 epileptogenic zone

value: idiopathic

value: 9 years old

value: 17 years old

value: Twice a month


title: Patient 6 epileptogenic zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,093 experimental controls)

source_name: Patient 6 epileptogenic zone

value: Male

value: 16 years old

value: >20 times a month

value: forntal lobe and temporal lobe


title: wild type_control_rep1

source_name: wild type Arabdopsis leaf under normal condition

value: leaf

value: wild type

value: normal condition


title: P-treated HESCs, rep2

description:
Sample name: P-2
n=3

value: endometrium

value: cultured human endometrial stromal cells (HESCs)

value: female

value: pre-menopausal

value: P


title: E. coli Type_III genotype strain, under 45ºC, rep 2

tag: strain


title: wild type_drought_5d_rep1

source_name: wild type Arabdopsis leaf under 5 day drought

tag: genotype/variation

value: under 5 day drought


title: E. coli Type_III genotype strain, under 45ºC, rep 1


title: M-treated HESCs, rep3

description:
Sample name: M-3
n=3

source_name: HESCs, M

value: M


title: Patient 7 irritative zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,094 experimental controls)

source_name: Patient 7 irritative zone

value: human brain

value: idiopathic

value: 9 years old

value: >30 times a month

value: right

value: forntal lobe


title: Embryonic (E15.5) vs. postnatal (P2) mouse esophagus

city: Des Moines

first: Chunfa

last: Jie

state: IA

address: 3200 Grand Ave

institute: Des Moines University

description:
E15.5vsP2
Single replicate two-color experiment.
Total RNA isolated from pooled esophagi of embryonic day 15.5 (E15.5) C57BL/6 embryos, and total RNA isolated from pooled esophagi of postnatal day 2 (P2) C57BL/6 pups.

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

scan_protocol: Microarrays were scanned using an Agilent G2505B Scanner controlled by Agilent Scan Control 7.0 software. Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing: The log2 ratio (Cy5/Cy3) was normalized with the loess method of the normalizeWithinArrays function in the R bioconductor package limma_3.17.14.

source_name: embryonic (E15.5) mouse esophagus

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70¡C for 10 min, then reversed transcribed at 42¡C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label.

growth_protocol: Timed-pregnant C57BL/6 female mice were sacrificed and whole embryos harvested at E15.5. The presence of a vaginal plug was designated as E0.5. Whole esophagi were isolated using a dissecting microscope from E15.5 embryos and P2 pups.

extract_protocol: Total esophageal RNA from E15.5 and P2 C57BL/6 mice was isolated with Trizol (Invitrogen) and then further purified using RNeasy (Qiagen). RNA was quantitated with a NanoDrop ND-100, and the quality was determined using an Agilent 2100 Bioanalyzer. Sample amplification and labeling procedures were carried out according to the manufacturer's protocol using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent) and 0.3 _g of total RNA as starting material.

tag: strain/background

tag: develomental stage

value: embryonic day 15.5 (E15.5)

value: esophagus

source_name: postnatal (P2) mouse esophagus

value: postnatal day 2 (P2)


title: E. coli Type_III genotype strain, under 37ºC, rep 3

tag: condition


title: E. coli Type_III genotype strain, under 37ºC, rep 2


title: E. coli Type_III genotype strain, under 37ºC, rep 1


title: GCT_Sample2_Stage1

source_name: Granulosa Cell Tumour tissue, sample 2, stage 1

tag: menopausal status

value: Pre

tag: age

value: Granulosa Cell Tumour tissue stage 1


title: Hccs het KO hearts, biological rep5

city: Gießen

first: Jörg-Detlef

last: Drenckhahn

address: Feulgenstrasse 10-12

department: Department of Pediatric Cardiology

institute: Justus-Liebig-University Gießen

description: Gene expression data from regenerating embryonic hearts

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: RMA normalization was performed using Partek Genomic Suite version 6.3, RMA background correction, quantile normalization and median polish probeset summarization.

source_name: Mouse embryonic hearts at 13.5 dpc, Hccs heterozygous knockout

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: After timed matings heterozygous Hccs knockout and littermate control female embryos where prepared at 13.5 dpc.

extract_protocol: 4-5 hearts of the same genotype were pooled and the tissue was homogenized using a micropestle. Total RNA was purified using the RNeasy Mini Kit from Qiagen according to the manufacturer´s instructions including a DNAse digest on the spin column.

treatment_protocol: Embryos and hearts were dissected in ice cold PBS, whole hearts were snap frozen in liquid nitrogen and stored at -80°C until use.

value: embryonic heart

tag: genotype

value: heart conditional heterozygous Hccs knockout


title: M-treated HESCs, rep2

description:
Sample name: M-2
n=3

value: endometrium

value: cultured human endometrial stromal cells (HESCs)

value: female

value: pre-menopausal


title: GCT_Sample1_Stage1

source_name: Granulosa Cell Tumour tissue, sample 1, stage 1


title: P-treated HESCs, rep1

description:
Sample name: P-1
n=3

value: P


title: E. coli Type_II genotype strain, under 45ºC, rep 1


title: ETO-treated HESCs, rep1

description:
Sample name: ETO-1
n=3

source_name: HESCs, ETO

value: E2+ etonogestrel (ETO)


title: ETO-treated HESCs, rep3

description:
Sample name: ETO-3
n=3


title: E. coli Type_II genotype strain, under 45ºC, rep 2


title: Hccs het KO hearts, biological rep3


title: M-treated HESCs, rep1

description:
Sample name: M-1
n=3

value: M


title: ETO-treated HESCs, rep2

description:
Sample name: ETO-2
n=3


title: Hccs het KO hearts, biological rep2


title: E. coli Type_II genotype strain, under 45ºC, rep 3


title: E. coli Type_II genotype strain, under 37ºC, rep 3


title: Patient 5 irritative zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,090 experimental controls)

source_name: Patient 5 irritative zone

value: human brain

value: Male

tag: causing

value: idiopathic

tag: age-onset

value: 9 years old

tag: surgery age

value: 26 years old

tag: pre-surgery epileptic frequency

value: 2-3 times a month

tag: surgery brain hemisphere

value: left

value: temporal lobe


title: Patient 6 irritative zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,092 experimental controls)

source_name: Patient 6 irritative zone

tag: tissue

tag: gender

value: 16 years old

value: >20 times a month

value: right

tag: surgery brain region

value: forntal lobe and temporal lobe

tag: post-surgery epileptic frequency


title: Hccs het KO hearts, biological rep4

value: embryonic heart

tag: developmental stage

value: female

value: heart conditional heterozygous Hccs knockout


title: E. coli Type_II genotype strain, under 37ºC, rep 2

tag: strain


title: control hearts, biological rep5

description: Gene expression data from normal embryonic hearts

source_name: Mouse embryonic hearts at 13.5 dpc, control

value: control


title: Vehicle-treated HESCs, rep3

description:
Sample name: CON-3
n=3

source_name: HESCs, vehicle control

value: endometrium

tag: cell type

value: cultured human endometrial stromal cells (HESCs)

value: pre-menopausal

tag: treatment

value: vehicle

tag: treatment duration


title: Vehicle-treated HESCs, rep2

description:
Sample name: CON-2
n=3


title: Patient 4 epileptogenic zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,089 experimental controls)

source_name: Patient 4 epileptogenic zone

value: human brain

value: Male

value: idiopathic

value: 2 years old

value: 9 years old

value: 20-30 times a month

value: forntal lobe


title: Patient 3 irritative zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,086 experimental controls)

source_name: Patient 3 irritative zone

value: 2 months old

value: 8 years old

value: > 30 times a day

value: left

value: 3-4 times a day


title: Hccs het KO hearts, biological rep1

value: embryonic heart

value: female

value: heart conditional heterozygous Hccs knockout


title: Vehicle-treated HESCs, rep1

description:
Sample name: CON-1
n=3

value: endometrium

value: cultured human endometrial stromal cells (HESCs)

value: pre-menopausal


title: Patient 4 irritative zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,088 experimental controls)

source_name: Patient 4 irritative zone

value: human brain

value: Male

value: right


title: control hearts, biological rep4

value: control


title: Patient 2 epileptogenic zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,085 experimental controls)

source_name: Patient 2 epileptogenic zone

value: idiopathic

value: 7 years old

value: 21 years old

value: Twice a month

value: temporal lobe


title: E. coli Type_II genotype strain, under 37ºC, rep 1

tag: condition


title: Patient 5 epileptogenic zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,091 experimental controls)

source_name: Patient 5 epileptogenic zone

value: 9 years old

value: 26 years old

value: 2-3 times a month

value: left


title: Patient 2 irritative zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,084 experimental controls)

source_name: Patient 2 irritative zone


title: control hearts, biological rep3

value: embryonic heart

value: female


title: Patient 1 epileptogenic zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,083 experimental controls)

source_name: Patient 1 epileptogenic zone

value: 8 years old

value: 24 years old

value: temporal lobe and parietal lobe

value: <one a month


title: Patient 3 epileptogenic zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 32,050 human genome probes probes (30,968 human genome/1,087 experimental controls)

source_name: Patient 3 epileptogenic zone

value: human brain

value: Male

value: 2 months old

value: > 30 times a day

value: forntal lobe

value: 3-4 times a day


title: control hearts, biological rep1

value: control


title: Donor_5; 0.34uM SAHA

status: Public on Aug 13 2015

city: La Jolla

first: Brian

last: Reardon

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

description:
Sample name: 5590177039_H
Donor_5

hyb_protocol: Standard Illumina hybridization protocol; conducted by Asuragen, Inc

scan_protocol: Standard Illumina scanning protocol; conducted by Asuragen, Inc.

data_processing: Expression data were extracted with GenomeStudio software (Illumina); genes with undetectable expression were excluded from analysis.  The lumi package [12] in bioconductor was used to transform (variance-stabilizing) and normalize (robust spline) the raw expression data.  Genes significantly modulated across SAHA doses were identified using a likelihood ratio test (LRT) in the R package Isogene GX [13].  The family wise error rate was controlled using Bonferroni-adjusted p-values (p < 0.05).

source_name: CD4+ T cells; 0.34uM SAHA

label_protocol: Biotinylated cRNA were prepared by Asuragen, Inc using standard Illumina protocols

growth_protocol: Human peripheral blood was drawn according to institutional review board approved protocols from 9 healthy HIV-seronegative donors by venipuncture and collected into sodium heparin containing tubes.  Peripheral blood mononuclear cells (PBMCs) were collected from fresh whole blood by centrifugation.   Primary CD4+ T cells were isolated from PBMCs with Rosette Sep CD4+ Isolation Kits according to the manufacturers protocol (Stem Cell Technologies, Inc.).  CD4+ T cells were incubated at 37°C, 5% CO2 overnight in fresh media (5% human serum AB in RPMI 1640).  CD4+ T cell purity and activation were assessed with flow cytometry.  All CD4+ T cell samples included in microarray analysis had >95% purity with fewer than 10% activated cells (i.e., <10% expressing HLA-DR).

extract_protocol: RNA was extracted from treated cells using Qiagen RNeasy RNA isolation kits according to manufacturer’s protocols.  RNA integrity numbers (RINs) were determined with the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc).  RNA samples submitted for microarray analysis (N=6) had RINs between 7.9 and 9.0 with an average RIN of 8.5.  cRNA was generated and hybridized to IlluminaHT-12 v3 BeadChips (48,803 probes).

treatment_protocol: CD4+ T cells were counted and aliquoted into 6-well plates; 5 million cells per well at a concentration of 2.5 million cells per mL of media (RPMI 1640 with 5% human serum AB).  Wells containing CD4+ T cells were treated with SAHA (Merck) at 0.34 μM, 1 μM, 3 μM, or 10 μM in 0.1% DMSO, or with only 0.1% DMSO.  Treated cells were incubated at 37°C, 5% CO2 for 24 hours.

tag: individual

value: Donor 5

value: peripheral blood

value: CD4+ T cells

tag: agent

value: SAHA

tag: dose

tag: rin


title: Donor_6; 10uM SAHA

description:
Sample name: 5590177039_L
Donor_6

source_name: CD4+ T cells; 10uM SAHA

value: Donor 6


title: control hearts, biological rep2

value: embryonic heart

value: female

tag: genotype


title: Donor_1; 1uM SAHA

description:
Sample name: 5590177039_G
Donor_1

source_name: CD4+ T cells; 1uM SAHA

value: Donor 1


title: Donor_3; 10uM SAHA

description:
Sample name: 5590177039_K
Donor_3

value: Donor 3


title: Donor_2; 10uM SAHA

description:
Sample name: 5590177039_B
Donor_2

value: Donor 2


title: Donor_2; 1uM SAHA

description:
Sample name: 5590177039_J
Donor_2


title: Donor_6; DMSO

description:
Sample name: 5590177039_D
Donor_6

source_name: CD4+ T cells; DMSO

value: DMSO


title: Donor_1; 3uM SAHA

description:
Sample name: 5590177039_E
Donor_1

source_name: CD4+ T cells; 3uM SAHA


title: Donor_3; DMSO

description:
Sample name: 5590177039_I
Donor_3


title: Donor_3; 3uM SAHA

description:
Sample name: 5590177038_G
Donor_3


title: Patient 1 irritative zone

description: RNA samples were evaluated using Phalanx Human OneArray (TM)  with 30,968 human genome probes.

source_name: Patient 1 irritative zone

value: human brain

value: Male

tag: causing

value: idiopathic

tag: age-onset

value: 8 years old

tag: surgery age

value: 24 years old

tag: pre-surgery epileptic frequency

value: Twice a month

value: left

value: temporal lobe and parietal lobe

value: <once a month


title: Donor_4; 10uM SAHA

description:
Sample name: 5590177038_E
Donor_4

value: Donor 4

tag: tissue

value: peripheral blood

value: CD4+ T cells

value: SAHA


title: Donor_5; DMSO

description:
Sample name: 5590177038_K
Donor_5

value: Donor 5

value: control


title: Donor_4; 3uM SAHA

description:
Sample name: 5590177014_J
Donor_4


title: Donor_1; 0.34uM SAHA

description:
Sample name: 5590177014_L
Donor_1


title: Donor_2; 0.34uM SAHA

description:
Sample name: 5590177014_K
Donor_2

value: Donor 2


title: Donor_2; 3uM SAHA

description:
Sample name: 5590177038_D
Donor_2


title: Donor_6; 1uM SAHA

description:
Sample name: 5590177014_I
Donor_6

value: Donor 6


title: Donor_3; 1uM SAHA

description:
Sample name: 5590177038_B
Donor_3

value: Donor 3