title: Stripped oocytes collected from female 5 sampled in Ria de Aveiro

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description:
STR5
Clam (Ruditapes decussatus) stripped between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal.
Oocytes RNA of Ruditapes decussatus.

hyb_protocol: Hybridized to the Agilent-043932 array according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Array was scanned with an Agilent scanner G2565BA according to the standard Agilent protocol at a resolution of 2 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%). The scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction v10.7.3.1 used XDR ID to link the pairs of scans together automatically when extracting data.

data_processing: The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal. The fluorescence values were normalized by performing a quantile normalization in R statistical software. Statistical analyses were performed on 31,862 out of 59,951 probes with signal higher than background in at least 5 out of 15 target samples. A log base 2 transformation was applied to all expression values and finally, the parametric Combat algorithm was implemented in R in order to adjust for the known between-experiments batch effect.

organism: Ruditapes decussatus

source_name: stripped oocytes

label_protocol: Amplified and labeled according to the Agilent Low Input One-Color Microarray-Based Gene Expression Analysis protocol.

growth_protocol: Spawning of females was induced by thermal stimulation, consisting of exposure to alternate cycles of 29°C (1 hour) and 5°C (30 minutes). As each female began to spawn, it was removed from the spawning tank and transferred to an individual spawning beaker with filtered seawater at the same temperature. Once spawning was completed, the obtained oocytes were gently washed into a clean glass. The remaining oocytes of each female spawning were mixed with a sperm suspension (from 7 males) by gentle agitation, aiming to obtain around 10 spermatozoids by oocyte in a microscopic view. Moreover, to evaluate the quality of the collected oocytes, the D-larval rate (ratio between the number of free swimming larvae at 48h post fertilization and the number of starting eggs) of each eggs batch was registered. Based on that observation, oocytes were divided into two experimental groups: spawned oocytes with low hatching rate (LHR, 5%-21% of D-larval rate) and spawned oocytes with medium hatching rate (MHR, 40%-47% of D-larval rate). In addition, gonads from five females were dissected and oocytes were collected through a practice known as gamete stripping. As the name indicates, this procedure involves removal of gametes from gonad tissue. Briefly, fully ripe gonads were slashed repeatedly with a scalpel and washed with filtered seawater to harvest the gametes. Finally, sex determination and oocytes appearance were achieved through microscopy examination. About 20,000 oocytes for each spawning/stripping were collected and filtered in a 40 µm sieve. The oocytes were transferred into an Eppendorf tube and, after a short spin, the seawater was removed. To remove salts, the pellet of oocytes was re-suspended with a solution of ammonium formate 3%, which was immediately removed after a short spin. Then the oocytes were included in 1.5 ml of Extract-all solution (Eurobio) and preserved in liquid nitrogen until RNA isolation.

extract_protocol: Total RNA was isolated using the Extract-all (Eurobio) procedure. RNA quality and integrity were controlled on the Agilent Bioanalyzer using RNA nanochips and Agilent RNA 6000 nanoreagents (Agilent Technologies, Waldbronn, Germany). RNA concentrations were measured at 260 nm using a ND-1000 spectrophotometer (Nanodrop Technologies) using the conversion factor 1 OD = 40 mg/mL total RNA. Samples were stored at -80°C until further use.

value: oocytes

tag: type

value: stripped

tag: d-larval rate (%)


title: genomic DNA from whole blood_6055432122_R03C02

status: Public on Nov 05 2014

type: genomic

city: Druham

first: Weiwei

last: Zhang

address: 101 Research Drive

department: Biostatistics and Bioinformatics

country: USA

institute: Duke University

description:
Sample name: X19
normal whole blood sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio softwarewas used to process the raw signal. After the beta values are calculated (Beta value=methylated signal/(methylated signal+unmethylated signal), data quality control was implemented using R (http://www.r-project.org/) (version 2.15.3). We removed 17,764 CpG sites for which probes mapped to multiple loci in the human genome reference sequence. CpG sites that are SNPs, that had missing values, or that had detection p-values >0.01 were excluded. Methylation data from probes mapping to the X and Y chromosomes were excluded. We were left with 394,354 CpG sites from 100 individuals in downstream analyses.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from whole blood samples

tag: 450k chip

tag: order on 450k chip

tag: gender

value: Female

tag: tissue

value: whole blood

tag: disease state

value: normal

tag: date born


title: Blood_P001_H48

type: RNA

city: Lyon

first: Marie-Angélique

last: Cazalis

address: Pl, Arsonval

country: France

institute: LCR HCL-bioMérieux

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

scan_protocol: GeneChips were scanned using the GeneArray Scanner G3000.

data_processing: The data were normalized using RMA methods.

label: biotin

molecule: total RNA

source_name: patient 001, H48

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

extract_protocol: Whole blood Paxgene tubes extraction

tag: age

value: FEMALE

tag: sapsii

value: SAPSII-High

tag: collection time

value: 48 hr


title: genomic DNA from whole blood_6055432120_R04C02

description:
Sample name: X17
normal whole blood sample


title: Stripped oocytes collected from female 4 sampled in Ria de Aveiro

description:
STR4
Clam (Ruditapes decussatus) stripped between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal.
Oocytes RNA of Ruditapes decussatus.


title: genomic DNA from whole blood_6055432109_R02C01

description:
Sample name: X18
normal whole blood sample


title: S0058192

city: Austin

first: Christopher

last: Daige

address: 2150 Woodward street, suite 100

institute: Mirna Therapeutics

description:
Sample name: Empty Liposomes 2-3
control 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard can protocol

data_processing: Data processed by CRO Asuragen Inc who performed arrays

label: Biotin

source_name: tumor

label_protocol: Standard Illumina label protocol

growth_protocol: Nod/Scid mice were surgically implanted with 1 x 106 cultured Hep3B cells and tumors were allowed to grow for ~ 5 weeks

extract_protocol: RNA was isolated from whole tumors using the mirVana PARIS RNA isolation Kit (Lifetech; cat# AM1556, or equivalent)

treatment_protocol: Animals received a single IV injection of test or control articles 24 hours prior to sacrifice

tag: cell line

tag: surgically implanted into

value: livers of Nod/Scid mice

tag: treatment

value: control (Empty Liposomes)

value: Hep3B orthotopic liver tumors


title: S0058191

description:
Sample name: Empty Liposomes 2-2
control 5


title: S0058190

description:
Sample name: Empty Liposomes 2-1
control 4


title: Blood_P001_H00

source_name: patient 001, H0

value: 0 hr


title: S0058189

description:
Sample name: Dilution Buffer 1-3
control 3

value: control (Dilution Buffer)


title: Stripped oocytes collected from female 3 sampled in Ria de Aveiro

description:
STR3
Clam (Ruditapes decussatus) stripped between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal.
Oocytes RNA of Ruditapes decussatus.


title: genomic DNA from whole blood_6042308121_R03C02

description:
Sample name: X21
normal whole blood sample


title: genomic DNA from whole blood_6057825006_R05C02

description:
Sample name: X20
normal whole blood sample


title: genomic DNA from whole blood_6057825005_R01C02

description:
Sample name: X16
normal whole blood sample


title: Stripped oocytes collected from female 2 sampled in Ria de Aveiro

description:
STR2
Clam (Ruditapes decussatus) stripped between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal.
Oocytes RNA of Ruditapes decussatus.


title: S0058188

description:
Sample name: Dilution Buffer 1-2
control 2


title: genomic DNA from whole blood_6042316028_R06C01

description:
Sample name: X14
normal whole blood sample


title: Stripped oocytes collected from female 1 sampled in Ria de Aveiro

description:
STR1
Clam (Ruditapes decussatus) stripped between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal.
Oocytes RNA of Ruditapes decussatus.


title: genomic DNA from whole blood_6055432144_R01C02

description:
Sample name: X13
normal whole blood sample


title: H9-2

city: Taipei City

first: Shau-Ping

last: Lin

state: select a state

address: 4F, No. 81, Chang-Xing St.,

department: Institute of Biotechnology

country: Taiwan

institute: National Taiwan University

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization were carried out using Partek commercial microarray analysis software

source_name: hESC

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

growth_protocol: ReproCELL primate and human ES Cell culture medium on MEF;

extract_protocol: Total RNA from the cells were isolated using TRIzol® reagent (Invitrogen, Calsbad, CA) and purified with RNeasy® mini kits (Qiagen)

tag: esc cell line

tag: genotype/variation

tag: neural differentiation capacity

value: not detected


title: genomic DNA from whole blood_6929726035_R05C02

description:
Sample name: X12
normal whole blood sample


title: Oocyte samples collected from female 59 sampled in Ria de Aveiro (bad quality)

description:
59
Clam (Ruditapes decussatus) spawned between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal.
Oocytes RNA of Ruditapes decussatus.

source_name: spawned oocytes

tag: type

value: spawned

tag: hatching rate

value: bad quality


title: genomic DNA from whole blood_6057825033_R06C01

description:
Sample name: X15
normal whole blood sample

tag: 450k chip


title: NTU1-8

value: worse


title: H9-1


title: Oocyte samples collected from female 37 sampled in Ria de Aveiro (bad quality)

description:
37
Clam (Ruditapes decussatus) spawned between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal.
Oocytes RNA of Ruditapes decussatus.

value: oocytes

tag: d-larval rate (%)


title: genomic DNA from whole blood_6929726055_R05C02

description:
Sample name: X11
normal whole blood sample

tag: order on 450k chip

tag: gender


title: NTU1-9


title: Oocyte samples collected from female 32 sampled in Ria de Aveiro (good quality)

description:
32
Clam (Ruditapes decussatus) spawned between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal.
Oocytes RNA of Ruditapes decussatus.

tag: tissue

value: good quality


title: Oocyte samples collected from female 44 sampled in Ria de Aveiro (bad quality)

description:
44
Clam (Ruditapes decussatus) spawned between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal.
Oocytes RNA of Ruditapes decussatus.


title: NTU1-7


title: NTU1-5


title: NTU1-6


title: Oocyte samples collected from female 27 sampled in Ria de Aveiro (good quality)

description:
27
Clam (Ruditapes decussatus) spawned between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal.
Oocytes RNA of Ruditapes decussatus.


title: genomic DNA from whole blood_6057825019_R05C01

description:
Sample name: X10
normal whole blood sample

value: Female

tag: disease state

tag: date born


title: SGBS_miR192* overexpressing4

city: Helsinki

first: YOU

last: ZHOU

address: Tukholmankatu 8

country: Finland

institute: Minerva Institute for Medical Research

hyb_protocol: For hybridization the Agilent Gene Expression Hybridisation Kit® was used and arrays were incubated in Agilent SureHyb® chambers for 17 hours in a hybridization oven at 65°C while rotating. Washing was performed according to the manufacturer’s instructions.

scan_protocol: Scanning was done with the Agilent G2565CA Microarray Scanner System.

data_processing: The resulting TIFF files were processed with Agilent Feature Extraction software 10.7. Generated raw data were evaluated using ChipInspector software (Genomatix, Munich, Germany). Background noise within arrays was corrected by using normal-exponential convolution model. Data were normalized by quantile method to ensure intensities have the same empirical distribution across arrays. Box plot and density plot of data was used for quality control.

source_name: transduction with shMIMIC miR-192* (VHS5841-101207549, Thermo Scientific, Waltham, MA), sample 4

label_protocol: Total RNA (300 ng) was labeled with Cy3 using the Agilent Quick-Amp® Labeling Kit - 1 color according to the manufacturer´s instructions. cRNA was purified with the RNeasy Mini® Kit (Qiagen). The concentration and labeling efficiency of cRNA was measured with NanoDrop ND-1000 (PeqLab, Erlangen, Germany).

growth_protocol: SGBS preadipocytes were cultured at 37oC in 5% Co2 in Dulbecco’s Modified Eagle Medium (DMEM) F12 (Sigma-Aldrich, St. Louis, MO) supplemented with 33 μM biotin, 17 μM pantothenate, 10% foetal bovine serum, 100 I.U./ml penicillin, and 100 μg/ml streptomycin.

extract_protocol: SGB were lysed in miRNeasy® lysis buffer, and total RNA was isolated and purified by using the miRNeasy Mini® Kit (Qiagen, Valencia, CA). The quality of RNA was verified by 2100 Bioanalyzer (Agilent).

treatment_protocol: Differentiation into adipocytes was carried out under controlled serum-free conditions by employing a previously established 14-day protocol (Fischer-Posovszky P, Newell FS, Wabitsch M, Tornqvist HE: Human SGBS cells - a unique tool for studies of human fat cell biology. Obes Facts 2008;1:184-189).

tag: cell type

value: SGBS human adipocytes


title: Oocyte samples collected from female 14 sampled in Ria de Aveiro (bad quality)

description:
14
Clam (Ruditapes decussatus) spawned between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal.
Oocytes RNA of Ruditapes decussatus.


title: Oocyte samples collected from female 30 sampled in Ria de Aveiro (intermediate quality)

description:
30
Clam (Ruditapes decussatus) spawned between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal.
Oocytes RNA of Ruditapes decussatus.

value: intermediate quality


title: EB

value: EB


title: genomic DNA from whole blood_6055432118_R01C01

description:
Sample name: X8
normal whole blood sample

value: whole blood

value: normal


title: Oocyte samples collected from female 9 sampled in Ria de Aveiro (good quality)

description:
9
Clam (Ruditapes decussatus) spawned between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal.
Oocytes RNA of Ruditapes decussatus.


title: NTU1-4

value: better


title: SGBS_NT control4

source_name: transduction with non-targeting miRNA-encoding (HRM5872, Thermo Scientific) lentiviral particles_sample4


title: genomic DNA from whole blood_6042308108_R02C02

description:
Sample name: X9
normal whole blood sample


title: S0058187

description:
Sample name: Dilution Buffer 1-1
control 1

value: livers of Nod/Scid mice


title: genomic DNA from whole blood_6042308121_R05C02

description:
Sample name: X3
normal whole blood sample

value: Male


title: NTU1-3


title: SGBS_NT control3

source_name: transduction with non-targeting miRNA-encoding (HRM5872, Thermo Scientific) lentiviral particles_sample3


title: NTU1-2


title: genomic DNA from whole blood_6055432118_R02C02

description:
Sample name: X6
normal whole blood sample


title: SGBS_miR192* overexpressing1

source_name: transduction with shMIMIC miR-192* (VHS5841-101207549, Thermo Scientific, Waltham, MA), sample 1


title: Oocyte samples collected from female 5 sampled in Ria de Aveiro (good quality)

description:
5
Clam (Ruditapes decussatus) spawned between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal.
Oocytes RNA of Ruditapes decussatus.


title: genomic DNA from whole blood_6042308154_R03C01

description:
Sample name: X1
normal whole blood sample


title: genomic DNA from whole blood_6057825033_R04C02

description:
Sample name: X2
normal whole blood sample


title: SGBS_miR192* overexpressing2

source_name: transduction with shMIMIC miR-192* (VHS5841-101207549, Thermo Scientific, Waltham, MA), sample 2


title: genomic DNA from whole blood_6042316028_R03C02

description:
Sample name: X4
normal whole blood sample


title: NTU1-1


title: genomic DNA from whole blood_6057825036_R02C01

description:
Sample name: X5
normal whole blood sample


title: SGBS_miR192* overexpressing3

source_name: transduction with shMIMIC miR-192* (VHS5841-101207549, Thermo Scientific, Waltham, MA), sample 3


title: SGBS_NT control1

source_name: transduction with non-targeting miRNA-encoding (HRM5872, Thermo Scientific) lentiviral particles_sample1


title: E2F3 at 250nM

status: Public on Nov 04 2014

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Protein was diluted to 250 nM in a 185-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated rabbit IgG antibody to GST-tag (Life Technologies; A-11131) was diluted to 50 ng/ml in PBS / 2% milk and 180uL was applied to each chamber four-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple Alexa 488 scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the Alexa 488 signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. The adjusted Alexa 488 signals are provided in the raw data files. Next, for each genomic sequence represented on the array, we computed the median intensity over each of the two orientations, forward and reverse (i.e. the median intensity for the three forward replicates with probe names ending in o1_r1, o1_r2 and o1_r3, as well as the median intensity for the three reverse replicates with probe names ending in o2_r1, o2_r2 and o2_r3), and we report the maximum of the two median intensities as the normalized signal for that sequence; these normalized signals are available on the series record in the file Normalized_data.txt.

label: Alexa 488

molecule: protein

source_name: Human E2F3

label_protocol: Proteins were tagged with N-terminal GST by cloning. Protein-bound arrays were incubated with 50ng/uL Alexa-488-conjugated rabbit IgG antibody to GST tag (Life Technologies; A-11131) in 2% milk in PBS, for one hour, in the dark.

growth_protocol: The Life Technologies Gateway cloning system was used to insert full length human E2F1, 3, and 4 genes into the pET-60 destination vector with a c-terminal GST tag. Cells were grown in LB culture to an OD600 of 0.4, then protein expression was induced with 1mM IPTG at 30°C for 2hrs (E2F1 and E2F3), or 20°C overnight (E2F4).

extract_protocol: Cells were lysed in PBS lysis buffer (140mM NaCl, 2.7mM KCl, 10mM Na2HPO4, 1.8mM KH2PO4, 1mM EDTA, 1% (v/v) Triton X-100, 200kU Ready-Lyse Lysozyme, 0.5mM AEBSF, 1.5kU Benzonase, and 1mM DTT, pH 7.3) for two hours at 4°C while gently rocking. The lysate was centrifuged, and the protein was purified by FPLC (AKTAprime plus) using GSTrapTM FF affinity columns (GE Healthcare). Anti-GST Western blots were performed to assess protein quality and concentration.

tag: transcription factor

tag: protein concentration

value: Protein concentration:250nM


title: SGBS_NT control2

source_name: transduction with non-targeting miRNA-encoding (HRM5872, Thermo Scientific) lentiviral particles_sample2


title: TMK3

city: Lorenskog

first: Peder

last: Aabel

address: Sykehusvn. 27

department: ENT

country: Norway

institute: Akershus University Hospital

description: Primary cells from surgical patients

hyb_protocol: Fragmented and labeled sense strand DNA was hybridized to the GeneChip Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA). The arrays were washed and stained using FS-450 fluidics station (Affymetrix).

scan_protocol: Fluorescent images were scanned by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA).The scanned images were then analyzed using Affymetrix GeneChip Command Console

data_processing: The CEL files were imported into Partek Genomics Suite software (Partek, Inc., St. Louis, MO). Robust microarray analysis (RMA) was applied for normalization. Exon array data were filtered to include only those probe sets derived from the core meta-probe list.

source_name: Tympanic membrane keratinocyte

label_protocol: Total RNA (150 ng) from each sample was prepared using the Ambion WT Expression Kit (Ambion Inc., Austin, Texas, USA) according to manufacturer’s instructions.

extract_protocol: Total RNA from samples of cultivated TMK and EK cells was extracted using the miRNeasy mini kit from Qiagen

treatment_protocol: No treatment

value: keratinocyte

value: Tympanic membrane


title: EK1

description: Purchased cells from ScienCell, HEK-a

source_name: Epidermal keratinocyte

value: Epidermis


title: Oocyte samples collected from female 3 sampled in Ria de Aveiro (good quality)

description:
3
Clam (Ruditapes decussatus) spawned between April 2013 and June 2013 in the experimental bivalve hatchery in Portugal.
Oocytes RNA of Ruditapes decussatus.

value: spawned


title: E2F1 at 250nM

source_name: Human E2F1


title: EK2

description: Purchased cells from ScienCell, HEK-a


title: E2F4 at 250nM

source_name: Human E2F4


title: TMK2

description: Primary cells from surgical patients


title: EK3

description: Purchased cells from ScienCell, HEK-a


title: SMC ST1 -/- control, rep2

city: Poznań

first: Hans

last: Bluyssen

address: Umultowska 89

department: Department of Human Molecular Genetics

country: Poland

institute: Faculty of Biology, University of Adam Mickiewicz

description:
SAMPLE 14
8911191020_G
Cell line
Replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data were background subtracted and quantile normalised in GenomeStudio (Illumina).

organism: Mus musculus

source_name: VSMCs, Stat1 KO, control

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays (LifeTechnologies).

growth_protocol: VSMCs were cultivated in DMEM medium containing 4,5mg/l Glucose, 2mM L-glu, supplemented with 100U/ml penicillin and 100μg/ml streptomycin and 10% FBS.

extract_protocol: Total RNA was isolated from VSMCs using RNeasy Mini Kit (Qiagen) together with DNase digestion step according to the manufacturer's protocol.

treatment_protocol: VSMCS were treated with 10ng/ml IFNγ for 8h or with 1ug/ml of LPS for 4h or with IFNγ for 4h followed by IFNγ and LPS for additional 4h.

tag: strain/background

value: STAT1 knock-out

value: aortic vascular smooth muscle cells

value: control


title: SMC ST1 -/- IFNg + LPS, rep1

description:
SAMPLE 22
8911191020_D
Cell line
Replicate 1

source_name: VSMCs, Stat1 KO, IFNg + LPS

tag: treatment

value: interferon-gamma + lipopolysaccharide


title: SMC ST1 -/- control, rep3

description:
SAMPLE 15
8911191037_B
Cell line
Replicate 3


title: SMC ST1 -/- LPS, rep3

description:
SAMPLE 21
8911191005_E
Cell line
Replicate 3

source_name: VSMCs, Stat1 KO, LPS

value: lipopolysaccharide


title: SMC ST1 -/- LPS, rep1

description:
SAMPLE 19
8911191020_E
Cell line
Replicate 1


title: SMC WT LPS, rep3

description:
SAMPLE 9
8911191005_F
Cell line
Replicate 3

source_name: VSMCs, wild type, LPS

value: wild type


title: SMC WT IFNg + LPS, rep1

description:
SAMPLE 10
8911191037_A
Cell line
Replicate 1

source_name: VSMCs, wild type, IFNg + LPS


title: SMC ST1 -/- control, rep1

description:
SAMPLE 13
8911191020_G
Cell line
Replicate 1


title: SMC ST1 -/- IFNg + LPS, rep3

description:
SAMPLE 24
8911191037_D
Cell line
Replicate 3


title: SMC ST1 -/- IFNg, rep2

description:
SAMPLE 17
8911191037_C
Cell line
Replicate 2

source_name: VSMCs, Stat1 KO, IFNg

value: interferon-gamma


title: SMC WT IFNg + LPS, rep3

description:
SAMPLE 12
8911191037_E
Cell line
Replicate 3


title: SMC ST1 -/- IFNg + LPS, rep2

description:
SAMPLE 23
8911191020_H
Cell line
Replicate 2


title: SMC ST1 -/- IFNg, rep1

description:
SAMPLE 16
8911191020_C
Cell line
Replicate 1


title: genomic DNA from whole blood_6042316098_R06C01

description:
Sample name: X7
normal whole blood sample

source_name: whole blood

value: Female

value: whole blood


title: SMC ST1 -/- LPS, rep2

description:
SAMPLE 20
8911191020_F
Cell line
Replicate 2


title: TMK1

description: Primary cells from surgical patients


title: SMC WT IFNg + LPS, rep2

description:
SAMPLE 11
8911191020_B
Cell line
Replicate 2


title: SMC ST1 -/- IFNg, rep3

description:
SAMPLE 18
8911191037_H
Cell line
Replicate 3


title: SMC WT control, rep1

description:
SAMPLE 1
8911191037_G
Cell line
Replicate 1

source_name: VSMCs, wild type, control


title: SMC WT LPS, rep2

description:
SAMPLE 8
8911191005_C
Cell line
Replicate 2


title: SMC WT IFNg, rep3

description:
SAMPLE 6
8911191005_G
Cell line
Replicate 3

source_name: VSMCs, wild type, IFNg


title: SMC WT control, rep3

description:
SAMPLE 3
8911191005_B
Cell line
Replicate 3


title: SMC WT LPS, rep1

description:
SAMPLE 7
8911191020_A
Cell line
Replicate 1


title: SMC WT IFNg, rep1

description:
SAMPLE 4
8911191005_A
Cell line
Replicate 1


title: SMC WT IFNg, rep2

description:
SAMPLE 5
8911191005_D
Cell line
Replicate 2


title: SMC WT control, rep2

description:
SAMPLE 2
8911191037_F
Cell line
Replicate 2


title: Surf1 Act-Gal4 KD, biological replicate 3 (IR3)

city: Padova

first: Cristiano

last: De Pitta

address: Via U. Bassi, 58/B

department: Biology

description: Gene expression of Surf1 KD first instar larvae (IR3).

hyb_protocol: 1.65 μg of labeled cRNA were used in each reaction and the hybridization was carried out at 65°C for 17 hours in an hybridization oven rotator (Agilent Technologies, Palo Alto, CA). The arrays were washed by Agilent Gene expression washing buffers and Stabilization and Drying Solution as suggest by the supplier.

scan_protocol: Slides were scanned on an Agilent microarray scanner (model G2565CA) and Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

data_processing: Inter-array normalization of expression levels was performed with quantile method (47) to correct for possible experimental distortions. A normalization function was applied to the expression data of all the experiments and the values of within-arrays replicate spots were then averaged. Feature Extraction Software, which provided spot quality measures, was used to evaluate the quality and reliability of the hybridization. In particular, the flag glsPosAndSignif (set to 1 if the spot had an intensity value significantly different from the local background and to 0 when otherwise) was used to filter out unreliable probes: the flag equal to 0 was noted as null. Probes with a high proportion of null values were removed from the dataset in order to carry out a more solid, unbiased, statistical analysis. Fifty percent of null was used as the threshold in the filtering process, and a total of 24,630 Drosophila transcripts were obtained.

organism: Drosophila melanogaster

source_name: Whole body of first instar larvae

label_protocol: 800 ng of total RNA were labeled with “Agilent One-Color Microarray-Based Gene Expression protocol” according to the manufacturer’s instructions. The synthesized cDNA was transcribed into cRNA and labeled with Cy3-dCTP. Labeled cRNA was purified with RNeasy Mini columns (Qiagen, Valecia, CA). The quality of each cRNA sample was verified by total yield and specificity calculated with NanoDrop ND-1000 spectrophotometer measurements (Nanodrop, Wilmington, DE).

extract_protocol: Total RNA was extracted from approximately 10  larvae for each genotype using Trizol (Life Technologies) according to the manufacter's instructions and further purified with LiCl 8M. All RNA samples were checked for quality by capillary electrophoresis (RNA 6000 Nano LabChip, Agilent Bioanalyzer 2100, Agilent Technologies).

value: Surf1 KD


title: PD1

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

description: PD, frozen biopsy specimen

hyb_protocol: The hybridization and subsequent washing and staining were performed on the Affymetrix GeneChip® Array Station (GCAS) automation platform.

scan_protocol: The arrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332).

data_processing: The data was normalised using Robust Multichip Average (RMA) method that include background adjustment, quantile normalization and final summarization of 11 oligonucleotides per transcript using the median polish algorithm

source_name: peritoneal biopsy

label_protocol: cDNA samples were cleaved and 3'-biotinylated with the Encore Biotin Module (NuGen Technologies, San Carlos, CA).

extract_protocol: Total RNA was isolated from frozen biopsy specimens by homogenizaion in Trizol.

treatment_protocol: biopsy specimens were stored in RNALater12 hrs at room temperature, then stored at -80C until time of total RNA extraction

value: PD, frozen biopsy specimen

value: peritoneal biopsy


title: s9129_3

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

description: Gene expression data from induced sample

hyb_protocol: 15ug of labeled cRNA for three biological replicates (n=3) was hybridized to an Affymetrix Human Genome U133 Plus PM Array for 16 h at 45°C and subsequently washed on a GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan array scanner to generate CEL files with corresponding intensity values.

data_processing: Affymetrix CEL files were normalized by RMA using the BioConductor (release 2.13) package affy

source_name: Zen-Bio, Inc. (Research Triangle Park, NC) - SL0044

label_protocol: 5ug of RNA was used to generate cDNA with the one-cycle cDNA synthesis kit (Affymetrix Corp., Santa Clara, CA). cRNA generated from the cDNA was biotin labeled with the GeneChip IVT labeling kit (Affymetric Corp.).

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum, L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin at 5% CO2 in a 37°C humidified chamber.

extract_protocol: Total RNA was extracted with the Qiagen RNeasy mini kit (Qiagen, Valencia, CA) and quantitated on a NanoDrop spectrophotometer (NanoDrop Tech, Wilmington, DE).

treatment_protocol: ASC were seeded at 28,000 cells/cm2 in 6-well plates and transfected with MYC siRNA for 72 hours to reach confluence. Differentiation was initiated with adipogenic cocktail and maintained for an additional 72 hours.

value: female

tag: mean age

tag: mean bmi

tag: depot

value: abdomen

value: white adipose tissue

tag: ethnicity

value: Caucasian


title: Surf1 Act-Gal4 KD, biological replicate 1 (IR1)

description: Gene expression of Surf1 KD first instar larvae (IR1).

tag: genotype/variation


title: Pooled_1

tag: type


title: s9129_1


title: Non_Target_3


title: Surf1 Act-Gal4 KD, biological replicate 4 (IR4)

description: Gene expression of Surf1 KD first instar larvae (IR4).


title: EPS4

description: EPS, frozen biopsy specimen

value: EPS, frozen biopsy specimen

value: encapsulating peritoneal sclerosis


title: EPS1

description: EPS, frozen biopsy specimen


title: PD2

description: PD, frozen biopsy specimen


title: Pooled_3


title: EPS2

description: EPS, frozen biopsy specimen

source_name: pertoneal biopsy


title: EPS3

description: EPS, frozen biopsy specimen


title: UREMIC2

description: UREMIC control, frozen biopsy specimen

value: UREMIC control, frozen biopsy specimen


title: Surf1 Act-Gal4 KD, biological replicate 2 (IR2)

description: Gene expression of Surf1 KD first instar larvae (IR2).


title: wt1118 control, biological replicate 4 (CTR4)

description: Gene expression of wt1118 first instar larvae (CTR4).

value: wt1118 control


title: s9129_2


title: UREMIC1

description: UREMiC control, frozen biopsy specimen


title: Pooled_2


title: wt1118 control, biological replicate 2 (CTR2)

description: Gene expression of wt1118 first instar larvae (CTR2).


title: Non_Target_2


title: wt1118 control, biological replicate 3 (CTR3)

description: Gene expression of wt1118 first instar larvae (CTR3).


title: Non_Target_1


title: Control_3

description: Gene expression data from non-induced control


title: wt1118 control, biological replicate 1 (CTR1)

description: Gene expression of wt1118 first instar larvae (CTR1).


title: Control_2


title: Control_1


title: R/R pool versus WT pool

city: Madrid

first: Marcos

last: Malumbres

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

description: Sample 4

hyb_protocol: Microarray: Mouse Gene Expression G3 60K (Agilent microarray design ID 028005, P/N G4852A). Microarray sequences and annotations are listed in sheet '028005_mm9_20121126'.  Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 300 ng. Volume: 50 uL. Temperature (C): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent).

data_processing: Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. No background subtraction was performed.

source_name: Pool CDK4/6-KI

label_protocol: Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 of May 2010. Amplification: by RNA polymerases. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores. Labeled samples are purified with silica-based spin columns.

growth_protocol: Cells were grown in RPMI 1640

extract_protocol: Total RNA fraction. RNA Integrity Numbers were in the range 9.8 to 10.0 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.

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

tag: strain background

value: mixed C57BL/6J x CD-1

tag: sample type

value: Pool CDK4/6-KI

value: Cdk4 R24C/R24C; Cdk6 R31C/R31C cells

source_name: Pool WT


title: R/R Clon 3 versus WT pool

description: Sample 3

value: Pool WT

value: wild type

value: Cdk4 R24C/R24C; Cdk6 R31C/R31C cells;

tag: clone id


title: R/R Clon 2 versus WT pool

description: Sample 2


title: R/R Clon 1 versus WT pool

description: Sample 1


title: CTS 3

city: Palo Alto

first: Subarna

last: Sinha

state: CA

address: 450 Serra Mall

department: Computer Science

institute: Stanford University

description: Sample 12

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing: BeadStudio software v3.2

source_name: CTS

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

value: cell line

tag: cell line source tissue

value: peripheral blood

tag: cell line

value: CTS


title: primary AML sample w/ WT1 mutation 3

description: Sample 15

source_name: primary AML sample w/ WT1 mutation

value: primary AML sample

value: WT1 mutation


title: primary AML sample w/ WT1 mutation 1

description: Sample 13


title: THP1 parental 2

description: Sample 2

source_name: THP1 parental

value: Male

tag: cell line background

value: THP1; ATCC TIP-202

value: THP1 parental


title: CTS 1

description: Sample 10


title: primary AML sample w/ WT1 mutation 2

description: Sample 14


title: THP1 expressing mutant IDH2 R172G 2

description: Sample 8

source_name: THP1 expressing mutant IDH2 R172G

value: THP1 expressing mutant IDH2 R172G


title: THP1 expressing mutant WT1 (exon 7 truncation) 2

description: Sample 5


title: THP1 expressing mutant WT1 (exon 7 truncation) 1

description: Sample 4


title: THP1 expressing mutant IDH2 R172G 1

description: Sample 7


title: THP1 parental 3

description: Sample 3


title: CTS 2

description: Sample 11


title: THP1 parental 1

description: Sample 1


title: THP1 expressing mutant WT1 (exon 7 truncation) 3

description: Sample 6


title: muscle_T2_20_rep1

city: Stockholm

first: Francesco

last: Marabita

address: Karolinska University Hospital

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Beachips were scanned using an iScan

data_processing: Raw intesities exported from GenomeStudio were imported into R. Probes on chromosomes X and Y were removed. Probes with a detection P-value > 0.01 exceeding 5% of the samples were also filtered out. Color-bias adjustment and quantile normalization were performed as implemented in lumi. BMIQ correction was applied to correct for probe type bias. Finally, M-values were batch-corrected usign the ComBat function.

label: Cy3 and Cy5

source_name: vastus lateralis muscle, after training, subject 20

extract_protocol: DNA was isolated with the Gentra Puregene Tissue Kit (Qiagen) from 5-10 mg muscle tissue

treatment_protocol: Healthy, sedentary subjects performed supervised one-legged, knee-extension exercise training for three months. Skeletal muscle biopsies from the vastus lateralis were taken at rest, before and after the training period.

tag: tissue

value: vastus lateralis muscle

tag: slide

tag: array

tag: batch

value: B

tag: group

tag: subject

value: female


title: muscle_T1_16_rep1

source_name: vastus lateralis muscle, before training, subject 16


title: muscle_T2_24_rep1

source_name: vastus lateralis muscle, after training, subject 24


title: muscle_T1_20_rep1

source_name: vastus lateralis muscle, before training, subject 20


title: muscle_T2_22_rep1

source_name: vastus lateralis muscle, after training, subject 22


title: muscle_T2_18_rep1

source_name: vastus lateralis muscle, after training, subject 18


title: muscle_T1_22_rep1

source_name: vastus lateralis muscle, before training, subject 22


title: muscle_T1_24_rep1

source_name: vastus lateralis muscle, before training, subject 24


title: muscle_T1_27_rep1

source_name: vastus lateralis muscle, before training, subject 27


title: muscle_T1_23_rep1

source_name: vastus lateralis muscle, before training, subject 23


title: muscle_T1_18_rep1

source_name: vastus lateralis muscle, before training, subject 18


title: muscle_T2_27_rep1

source_name: vastus lateralis muscle, after training, subject 27


title: muscle_T2_23_rep1

source_name: vastus lateralis muscle, after training, subject 23


title: muscle_T2_15_rep1

source_name: vastus lateralis muscle, after training, subject 15


title: liver_Pink1 knockout_24 weeks_replicate_3

city: Tuebingen

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

country: Germany

institute: University of Tuebingen

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 gene chip scanner with GCOS 1.4.

data_processing: The data were analysed using Bioconductor packages 'affy' and 'limma' under R-2.7.0. Background correction, normalization and probe summarization was performed with RMA (function just.rma()).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were housed in Type II L cages (365x207x140 mm, floor area 530 cm2; IVC-based)at an environmental temperature 20-24°C, humidity: 55±10%and under 12/12 h light/dark cycle with food and water ad libitum.

extract_protocol: RNA  was extracted by using RNeasy Midi Kit (Qiagen) following manufacturers instructions for animal tissues.

treatment_protocol: not applicable

tag: age

value: 24 weeks postnatal

value: liver

value: Pink1 knockout


title: muscle_T2_16_rep1

source_name: vastus lateralis muscle, after training, subject 16


title: THP1 expressing mutant IDH2 R172G 3

description: Sample 9


title: liver_wild type_24 weeks_replicate_1

value: Pink1 wild type


title: muscle_T1_15_rep1

source_name: vastus lateralis muscle, before training, subject 15


title: liver_wild type_12 weeks_replicate_1

value: 12 weeks postnatal


title: liver_Pink1 knockout_24 weeks_replicate_1


title: liver_wild type_12 weeks_replicate_2


title: liver_wild type_24 weeks_replicate_2


title: muscle_T2_9_rep1

source_name: vastus lateralis muscle, after training, subject 9


title: liver_wild type_6 weeks_replicate_3

value: 6 weeks postnatal


title: muscle_T1_11_rep1

source_name: vastus lateralis muscle, before training, subject 11


title: muscle_T2_11_rep1

source_name: vastus lateralis muscle, after training, subject 11


title: liver_Pink1 knockout_12 weeks_replicate_1


title: muscle_T1_13_rep2

source_name: vastus lateralis muscle, before training, subject 13

value: male


title: liver_Pink1 knockout_24 weeks_replicate_2


title: liver_wild type_6 weeks_replicate_2


title: liver_wild type_6 weeks_replicate_1


title: liver_Pink1 knockout_6 weeks_replicate_3


title: liver_Pink1 knockout_12 weeks_replicate_2


title: liver_Pink1 knockout_6 weeks_replicate_2


title: muscle_T2_26_rep1

source_name: vastus lateralis muscle, after training, subject 26

value: A


title: striatum_wild type_18 month_replicate 3

value: 18 month postnatal

value: striatum


title: muscle_T2_7_rep1

source_name: vastus lateralis muscle, after training, subject 7


title: muscle_T2_13_rep2

source_name: vastus lateralis muscle, after training, subject 13


title: striatum_wild type_18 month_replicate 1


title: striatum_wild type_18 month_replicate 2


title: midbrain_wild type_18 month_replicate 3

value: midbrain


title: midbrain_Pink1 knockout_18 month_replicate 3


title: striatum_Pink1 knockout_18 month_replicate 2


title: muscle_T2_13_rep1


title: midbrain_wild type_18 month_replicate 2


title: striatum_Pink1 knockout_18 month_replicate 1


title: muscle_T1_7_rep1

source_name: vastus lateralis muscle, before training, subject 7


title: midbrain_wild type_18 month_replicate 1


title: midbrain_Pink1 knockout_18 month_replicate 1


title: striatum_Pink1 knockout_18 month_replicate 3


title: midbrain_Pink1 knockout_18 month_replicate 2


title: muscle_T2_12_rep1

source_name: vastus lateralis muscle, after training, subject 12


title: liver_wild type_24 weeks_replicate_3


title: muscle_T1_26_rep1

source_name: vastus lateralis muscle, before training, subject 26


title: muscle_T1_13_rep1


title: liver_Pink1 knockout_12 weeks_replicate_3


title: liver_Pink1 knockout_6 weeks_replicate_1


title: 0000027054

type: other

city: San Francisco

first: Tara

last: Sigdel

address: 513 parnassus

department: Surgery

institute: University of California San Francisco

description:
IRBP of FSGS recurrence
IgG antobodies

hyb_protocol: Manufacturer's protocol for Protoarrays (Life Technologies) for immune response profiling (IRBP) was followed

data_processing: Data was generated by using GenePix6.0 softeare

label: Alexa Fluor 647

molecule: other

source_name: serum, pretransplantation

extract_protocol: Serum was collected from Red-top tubes by letting it stand upright for 30 minutes.

value: Serum

tag: disease state

value: recurrence of focal segmental glomerulosclerosis


title: muscle_T1_12_rep1

source_name: vastus lateralis muscle, before training, subject 12


title: muscle_T2_5_rep1

source_name: vastus lateralis muscle, after training, subject 5


title: cerebellum_wild type_18 month_replicate 3

value: cerebellum

tag: genotype/variation


title: 0000027025

description:
IRBP of FSGS recurrence
IgG antobodies

scan_protocol: Manufacturer's protocol for Protoarrays (Life Technologies) for immune response profiling (IRBP) was followed


title: muscle_T1_9_rep1

source_name: vastus lateralis muscle, before training, subject 9

value: vastus lateralis muscle


title: 0000027024

description:
IRBP of FSGS recurrence
IgG antobodies

label_protocol: Manufacturer's protocol for Protoarrays (Life Technologies) for immune response profiling (IRBP) was followed


title: muscle_T1_5_rep1

source_name: vastus lateralis muscle, before training, subject 5


title: cerebellum_Pink1 knockout_18 month_replicate 2


title: 0000027019

description:
IRBP of FSGS recurrence
IgG antobodies


title: muscle_T2_4_rep1

source_name: vastus lateralis muscle, after training, subject 4


title: cerebellum_wild type_18 month_replicate 2


title: striatum_wild type_24 weeks_replicate 1


title: striatum_wild type_24 weeks_replicate 2


title: muscle_T1_4_rep1

source_name: vastus lateralis muscle, before training, subject 4


title: muscle_T1_1_rep1

source_name: vastus lateralis muscle, before training, subject 1


title: cerebellum_Pink1 knockout_18 month_replicate 1


title: striatum_Pink1 knockout_24 weeks_replicate 1


title: 0000027018

description:
IRBP of FSGS recurrence
IgG antobodies


title: 0000027059

description:
IRBP of FSGS recurrence
IgG antobodies


title: striatum_Pink1 knockout_24 weeks_replicate 2


title: striatum_Pink1 knockout_24 weeks_replicate 3


title: cerebellum_Pink1 knockout_18 month_replicate 3


title: striatum_wild type_12 weeks_replicate 2


title: cerebellum_wild type_18 month_replicate 1


title: muscle_T2_1_rep1

source_name: vastus lateralis muscle, after training, subject 1


title: 0000027058

description:
IRBP of FSGS recurrence
IgG antobodies


title: 0000027056

description:
IRBP of FSGS recurrence
IgG antobodies


title: 0000027049

description:
IRBP of FSGS recurrence
IgG antobodies

value: no recurrence of focal segmental glomerulosclerosis


title: 0000027050

description:
IRBP of FSGS recurrence
IgG antobodies


title: striatum_wild type_12 weeks_replicate 3


title: 0000027060

description:
IRBP of FSGS recurrence
IgG antobodies


title: striatum_wild type_6 weeks_replicate 3


title: striatum_wild type_6 weeks_replicate 2


title: striatum_wild type_12 weeks_replicate 1


title: striatum_Pink1 knockout_12 weeks_replicate 3


title: striatum_Pink1 knockout_12 weeks_replicate 2


title: striatum_wild type_24 weeks_replicate 3


title: striatum_Pink1 knockout_12 weeks_replicate 1


title: striatum_Pink1 knockout_6 weeks_replicate 3


title: 0000026870

description:
IRBP of FSGS recurrence
IgG antobodies


title: 0000026871

description:
IRBP of FSGS recurrence
IgG antobodies


title: striatum_wild type_6 weeks_replicate 1


title: 0000026865

description:
IRBP of FSGS recurrence
IgG antobodies


title: 0000026867

description:
IRBP of FSGS recurrence
IgG antobodies


title: midbrain_Pink1 knockout_24 weeks_replicate 3


title: striatum_Pink1 knockout_6 weeks_replicate 1


title: midbrain_wild type_24 weeks_replicate 2


title: midbrain_Pink1 knockout_24 weeks_replicate 2


title: midbrain_Pink1 knockout_24 weeks_replicate 1


title: midbrain_wild type_24 weeks_replicate 3


title: striatum_Pink1 knockout_6 weeks_replicate 2


title: midbrain_wild type_12 weeks_replicate 1


title: midbrain_wild type_24 weeks_replicate 1


title: midbrain_wild type_12 weeks_replicate 2


title: 0000027017

description:
IRBP of FSGS recurrence
IgG antobodies


title: 0000027016

description:
IRBP of FSGS recurrence
IgG antobodies


title: midbrain_Pink1 knockout_12 weeks_replicate 1


title: midbrain_Pink1 knockout_12 weeks_replicate 2


title: 0000027013

description:
IRBP of FSGS recurrence
IgG antobodies


title: midbrain_Pink1 knockout_12 weeks_replicate 3


title: midbrain_wild type_6 weeks_replicate 3


title: midbrain_wild type_6 weeks_replicate 1


title: midbrain_wild type_6 weeks_replicate 2


title: cerebellum_wild type_24 weeks_replicate 2


title: midbrain_Pink1 knockout_6 weeks_replicate 3


title: cerebellum_wild type_24 weeks_replicate 3


title: midbrain_Pink1 knockout_6 weeks_replicate 1


title: striatum_WT_6 months_replicate 2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HT MG-430 PM Array Plates. Plates were hybridized, washed and stained in the Affymetrix Gene Titan.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Titan instrument  with AGCC 3.0 software.

data_processing: The data were analysed using Bioconductor package 'affy' (1.28.0) under R-2.12.0. Background correction, normalization and probe summarization was performed with RMA.

source_name: striatum,WT,6 months

label_protocol: Biotinylated cRNA were prepared using the 3'IVT Express Kit (Ambion) from 100ng total RNA according to the manufacturer.

value: WT (129SvEv+FVB/N F1 hybrids)

value: 6 months


title: striatum_WT_6 months_replicate 3


title: cerebellum_Pink1 knockout_24 weeks_replicate 3

value: 24 weeks postnatal


title: midbrain_Pink1 knockout_6 weeks_replicate 2

value: Pink1 knockout


title: striatum_Pink1 -/- || A53T-SNCA_6 months_replicate 3

source_name: striatum,Pink1 -/- || A53T-SNCA,6 months

value: Pink1 -/- || A53T-SNCA


title: Mad1 at 1uM concentration and Max at 100nM concentration

description: Mad

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to 200 or 100 nM in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated rabbit polyclonal antibody to His (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the Alexa 488 signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber.

source_name: Human Mad1 and Max

label_protocol: Proteins were tagged with N-terminal His by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to His (Invitrogen).

growth_protocol: Plasmids were transformed into BL21 (DE3) expression strain of E. coli (New England BioLabs).  Overnight bacterial culture (5 mL) was diluted into 1 L LB (10 g BACTO Tryptone (BD); 5 g BACTO Yeast Extract (BD); 10 g NaCl; pH 7.5) and grown to OD 0.6 (600 nm visible light). Protein expression was then induced with 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) for 3 hours at 37ºC. Cells were pelleted by centrifugation @ 12,000 rpm for 10 min and stored at -20ºC. Each pellet (from 1 L culture) was thawed in 15 ml lysis buffer (150 mM Tris-HCl, pH 8.0; 150 mM NaCl; 2 mM dithiothreitol (DTT); 1 tablet complete Mini, EDTA-free protease inhibitor cocktail (Roche, #11 836 170 001); 50 uM C4H10O6Zn (zinc acetate); 1 mg/ml chicken egg white lysozyme (Sigma, # L6876)) and subjected to two freeze-thaw cycles in dry ice/ethanol. To digest DNA, to each 15 ml lysis solution was added 10 uL recombinant, RNase-free DNAse I (Roche, #04 716 728 001, 10 U/ul), 30 uL 1 M MgCl2, and 2 mL 10% Triton X-100,  and digested at room temperature until solution was runny (~1 hr).  Solutions were centrifuged at 12,000 rpm for 25 min at 4ºC, and supernatant was used for protein purification.

extract_protocol: Full-length open reading frames were cloned into the Gateway pDEST17 (N-terminal His-tag) expression vector by recombinational cloning from previously created pENTR clones. All proteins were produced by over-expression in E. coli BL21 (DE3) cells (New England BioLabs), and purified by FPLC (AKTAprime plus) using HisTrap FF affinity columns (GE Healthcare). Anti-His Western blots were performed to assess protein quality and concentration.

tag: transcription factor

value: Mad1, Max

tag: protein concentration

value: 100nM Max, 1uM Mad1


title: cerebellum_wild type_24 weeks_replicate 1

value: Pink1 wild type


title: cerebellum_Pink1 knockout_24 weeks_replicate 1


title: striatum_Pink1 -/- || A53T-SNCA_6 months_replicate 2


title: cerebellum_wild type_12 weeks_replicate 3

value: 12 weeks postnatal


title: striatum_WT_6 months_replicate 1


title: striatum_Pink1 -/- || A53T-SNCA_6 months_replicate 1


title: cerebellum_wild type_12 weeks_replicate 1


title: c-Myc at 1uM concentration and Max at 100nM concentration

description: Myc

source_name: Human c-Myc and Max

value: c-Myc, Max

value: 100nM Max, 1uM c-Myc


title: midbrain_WT_6 months_replicate 2

source_name: midbrain,WT,6 months

value: midbrain


title: cerebellum_Pink1 knockout_12 weeks_replicate 3


title: midbrain_WT_6 months_replicate 1


title: 0000027014

description:
IRBP of FSGS recurrence
IgG antobodies

tag: sample type

value: Serum


title: cerebellum_wild type_12 weeks_replicate 2


title: cerebellum_wild type_6 weeks_replicate 3

value: 6 weeks postnatal


title: cerebellum_Pink1 knockout_12 weeks_replicate 2

value: cerebellum


title: Max at 100nM concentration

description: Max

source_name: Human Max

value: Max

value: 100nM Max


title: cerebellum_WT_6 months_replicate 2

source_name: cerebellum,WT,6 months

value: WT (129SvEv+FVB/N F1 hybrids)


title: cerebellum_Pink1 knockout_12 weeks_replicate 1


title: cerebellum_wild type_6 weeks_replicate 1


title: midbrain_Pink1 -/- || A53T-SNCA_6 months_replicate 2

source_name: midbrain,Pink1 -/- || A53T-SNCA,6 months

value: 6 months


title: cerebellum_WT_6 months_replicate 3


title: cerebellum_Pink1 -/- || A53T-SNCA_6 months_replicate 3

source_name: cerebellum,Pink1 -/- || A53T-SNCA,6 months


title: midbrain_Pink1 -/- || A53T-SNCA_6 months_replicate 3


title: cerebellum_Pink1 knockout_6 weeks_replicate 1


title: cerebellum_Pink1 knockout_6 weeks_replicate 3


title: cerebellum_wild type_6 weeks_replicate 2


title: cerebellum_WT_6 months_replicate 1


title: striatum_Pink1 -/- || A53T-SNCA_6 weeks_replicate 2

source_name: striatum,Pink1 -/- || A53T-SNCA,6 weeks

value: striatum

value: 6 weeks


title: striatum_Pink1 -/- || A53T-SNCA_6 weeks_replicate 3

value: Pink1 -/- || A53T-SNCA


title: striatum_WT_6 weeks_replicate 1

source_name: striatum,WT,6 weeks


title: striatum_WT_6 weeks_replicate 2


title: midbrain_Pink1 -/- || A53T-SNCA_6 months_replicate 1


title: cerebellum_Pink1 knockout_6 weeks_replicate 2

value: Pink1 knockout


title: midbrain_WT_6 weeks_replicate 3

source_name: midbrain,WT,6 weeks


title: 0000027055

description:
IRBP of FSGS recurrence
IgG antobodies

source_name: serum, pretransplantation

value: recurrence of focal segmental glomerulosclerosis


title: midbrain_WT_6 months_replicate 3


title: midbrain_WT_6 weeks_replicate 2


title: midbrain_WT_6 weeks_replicate 1


title: BCL-3 vector, biological rep2

city: Liege

first: Alain

last: Chariot

state: Liege

address: Avenue de l'hopital

country: Belgium

institute: University of Liege

description: Gene expression data from cells expressing BCL-3

hyb_protocol: The arrays have been hybridized with 15 micrograms of fragmented aRNA as recommended. The Affymetrix GeneChip Hybridization, Wash, and Stain Kit has been used to hybridize and wash the arrays. The fluidics station 450 has been used following manufacturer's recommendations.

scan_protocol: The arrays have been scanned with the Affymetrix GeneChip Scanner 3000 7G with appropriate recommended protocols.

data_processing: We used the BRB ArrayTools software in order to analyse the data. First, the data were normalized with RMA procedure included in the BRB Array tools software then filtered out based on the variance for the gene across the arrays, a feature included in the BRB Array tools software which allows to remove unexpressed or equally expressed transcripts. The variance of the log-ratios for each gene is compared to the median of all the variances. Those genes not significantly more variable than the median gene are filtered out. Specifically, the quantity (n-1) Vari / Varmed is computed for each gene i. Vari is the variance of the log intensity for gene i across the entire set of n arrays and Varmed is the median of these gene-specific variances. This quantity is compared to a percentile of the chi-square distribution with n-1 degrees of freedom. This is an approximate test of the hypothesis that gene i has the same variance as the median variance. In order to identify significant differentially expressed transcripts, we used the Class Comparison Tool (BRB Array Tools software). This tool computes the number of genes that are differentially expressed among the classes at the statistical significance level selected in the t-test menu and creates a gene list containing information about the significant genes. The Class Comparison Between Groups of Arrays Tool computes a t-test separately for each gene using the normalized log-intensities for one color oligonucleotide arrays.  The Class Comparison Tool also provides univariate permutation tests for the significance of individual genes. The univariate permutation tests are computed separately for each gene. The output gene list table is ordered by univariate p value with the most significant genes listed first. The false discovery rate (FDR) associated with a row of the table is an estimate of the proportion of the genes with univariate p values less than or equal to the one in that row that represent false positives. The method of Benjami and Hochberg is used for this FDR estimation. We used the t-test pvalue <0.001 threshold in our analysis.

source_name: HaCat cells infected with a BCL-3-expressing  lentiviral construct. Replicat 2

label_protocol: The Affymetrix GeneChip 3’ IVT Express Kit has been used to label targets from 100 nanograms of total RNA, following manufacturer's recommendations

growth_protocol: HaCat cells are maintained in DMEM supplemented with 10% FCS, glutamine and antibiotics.

extract_protocol: Total RNAs were extracted from the resulting HaCat cells cultured in triplicate, using the RNeasy Mini kit from Qiagen (Valencia, CA). The integrity of the RNAs from those six distinct experimental conditions was checked with the Agilent Bioanalyzer using the RNA 6000 Nano kit (Agilent, Santa Clara, CA).

treatment_protocol: HaCat cells are infected with an empty pLENTI6-EGFP vector or with a  pLENTI6-EGFP vector in which a BCL-3 cDNA was inserted

tag: treatment

value: BCL-3 vector

value: HaCaT

value: Immortalized keratinocytes

tag: cell type

value: Immortalized cell line


title: striatum_Pink1 -/- || A53T-SNCA_6 weeks_replicate 1


title: midbrain_Pink1 -/- || A53T-SNCA_6 weeks_replicate 3

source_name: midbrain,Pink1 -/- || A53T-SNCA,6 weeks

value: midbrain


title: midbrain_Pink1 -/- || A53T-SNCA_6 weeks_replicate 2


title: cerebellum_Pink1 -/- || A53T-SNCA_6 months_replicate 2


title: BCL-3 vector, biological rep1

source_name: HaCat cells infected with a BCL-3-expressing  lentiviral construct. Replicat 1


title: cerebellum_Pink1 -/- || A53T-SNCA_6 months_replicate 1


title: empty vector, biological rep3

description: Gene expression data from cells expressing empty vector

source_name: HaCat cells infected with a control lentiviral construct. Replicat 3

value: empty vector


title: midbrain_Pink1 -/- || A53T-SNCA_6 weeks_replicate 1


title: BCL-3 vector, biological rep3

source_name: HaCat cells infected with a BCL-3-expressing  lentiviral construct. Replicat 3


title: cerebellum_WT_6 weeks_replicate 3

source_name: cerebellum,WT,6 weeks


title: cerebellum_WT_6 weeks_replicate 1


title: cerebellum_ WT_6 weeks_replicate 2


title: cerebellum_Pink1 knockout_24 weeks_replicate 2

value: 24 weeks postnatal


title: empty vector, biological rep2

source_name: HaCat cells infected with a control lentiviral construct. Replicat 2


title: cerebellum_Pink1 -/- || A53T-SNCA_6 weeks_replicate 3

source_name: cerebellum,Pink1 -/- || A53T-SNCA,6 weeks

value: cerebellum


title: NWMN_0641 gene deletion mutant, biological rep2

city: Shanghai

first: Lefu

last: Lan

address: 555 Zu Chong Zhi Road

department: Shanghai Institute of Materia Medica

country: China

institute: Chinese Academy of Sciences

hyb_protocol: 3µg of biotinylated cDNA were hybridized for 16 hr at 50°C on Affymetrix S. aureus Genome Array with constant rotation at the speed of 60 rpm in the Affymetrix® Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix® Fluidics Station 450.

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

data_processing: The data were normalized using Robust Multi-array Average (RMA).

organism: Staphylococcus aureus subsp. aureus str. Newman

source_name: Bacteria growing TSB medium (Difco, 286220)

label_protocol: Following fragmentation, biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10µg total RNA (Cat. AM1792, Ambion).

growth_protocol: Overnight S. aureus cultures were washed and diluted 100-fold in fresh TSB medium (Difco, 286220) in a 20-ml tube with a tube volume-to-medium volume ratio of 5:1. The liquid culture was grown at 37 °C for about 6 h with shaking  (OD600 ≈ 5.0), 250 rpm of aeration.

extract_protocol: Total RNA was extracted by using a Qiagen RNeasy kit following the manufacturer's instructions.

treatment_protocol: Total RNA was immediately stabilized with RNAprotect Bacteria Reagent (Qiagen, Valencia, CA) following the manufacturer's instructions.

value: NWMN_0641 deletion mutant


title: NWMN_0641 gene deletion mutant, biological rep1


title: Wild type S. aureus Newman strain, biological rep1

value: Wild-type


title: cerebellum_Pink1 -/- || A53T-SNCA_6 weeks_replicate 1


title: Wild type S. aureus Newman strain, biological rep3


title: NWMN_0641 gene deletion mutant, biological rep3


title: cerebellum_Pink1 -/- || A53T-SNCA_6 weeks_replicate 2


title: OEA, adipocytes-2

city: Sagamihara

first: Takahiro

last: Yamaguchi

country: Japan

institute: Acel, Inc

hyb_protocol: Fifteen micrograms of the cRNA was hybridized to Affymetrix Human Genome U133 Plus 2.0 Array (Affymetrix). The array was incubated for 16 hr at 45°C, then automatically washed and stained with GeneChip Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: The Probe Array was scanned using a GeneChip Scanner 3000 7G.

data_processing: The resulting data was analyzed with Affymetrix GeneChip Command Console Software and Affymetrix Expression Console.

source_name: OEA-treated adipocytes

label_protocol: Biotinylated cRNA were prepared using the GeneChip 3’ IVT Express Kit (Affymetrix) from 100 ng total RNA.

growth_protocol: Human pre-adipocytes were differentiated into adipocytes for  6 days in the adipocyte differentiation medium (Lonza).

extract_protocol: Total RNA was extracted using the Rneasy plus micro kit according to the manufacturer's instructions.

treatment_protocol: Adipocytes 6 days after differentiation were treated with vehicle- or OEM (0.01mM) - containing medium for 24hr.

value: Human subcutaneous adipocytes


title: OEA, adipocytes-1


title: control, adipocytes-3

source_name: Vehicle-treated adipocytes


title: OEA, adipocytes-3


title: Wild type S. aureus Newman strain, biological rep2


title: empty vector, biological rep1


title: control, adipocytes-2


title: AZ_26 Dominant follicle

city: Belfield

first: Paul

last: McGettigan

state: Co Dublin

address: Veterinary Sciences Centre, UCD

department: School of Agriculture, Food Science and Veterinary Medicine

country: Ireland

institute: University College Dublin

description: Dominant follicle

hyb_protocol: The hybridization was performed according to the miRCURY LNATM microRNA Array Instruction manual using a Tecan HS4800TM hybridization station (Tecan, Austria). After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes.

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNATM microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNATM microRNA Array Analysis Software, Exiqon, Denmark).

data_processing: The image analysis was carried out using the ImaGene® 9 (miRCURY LNATM microRNA Array Analysis Software, Exiqon, Denmark). The quantified signals were background corrected (Normexp with offset value 0, see Ritchie et al. 2007) and normalized using the printtiploess algorithm (normexp default). Sample AZ_11 was excluded from the results in our paper following QC checks.

organism: Bos taurus

source_name: bovine ovarian follicle

label_protocol: 300 ng total RNA from both sample and reference was labeled with Hy3TM and Hy5TM fluorescent label, respectively, using the miRCURY LNATM microRNA Hi-Power Labeling Kit, Hy3TM/Hy5TM (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: six cross-breed beef heifers were subjected to an estrus synchronization program combined with daily ultrasonography of ovaries.

extract_protocol: The two largest follicles were collected from the ovaries of each animal and individual follicle diameter was measured. Theca and granulosa cells were separated as previously described snap frozen and stored at -80 oC prior to RNA extractions. Total RNA, including small RNA was isolated from theca and granulosa samples using miRNeasy® Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions followed by DNase treatment step using Rnase-Free DNase set (Qiagen). Total RNA quantity was determined by NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and quality was assed using the Agilent Bioanalyzer 2100 with RNA 6000 Nano Chip kit (Agilent Technologies, Santa Clara, CA). All RNA samples were shown to have RIN values greater than 7.5.

treatment_protocol: Animals were kept and fed under the same conditions. Heifers were synchronized using an 8 day progesterone-releasing intra-vaginal device (CIDR, Pfizer Animal Health) and a single intramuscular injection (25 mg) of prostaglandin F2 alpha (Dinolityc, Pfizer) on the seventh day. Estrus was observed every 6 hours between 24-48 hours after CIDR withdrawal. Each animal was subjected to daily, individual ovarian ultrasound scans to monitor ovarian follicle development. Animals were slaughtered between Day 2.5 and 3.5 of the synchronized estrus cycle (Day 0 = onset of estrus).

tag: tissue type

value: Theca

value: Dominant

tag: follicle type

value: theca pool of all samples


title: AZ_24 Subordinate follicle

description: Subordinate follicle

value: Subordinate


title: striatum_ WT_6 weeks_replicate 3

value: striatum

value: WT (129SvEv+FVB/N F1 hybrids)

value: 6 weeks


title: AZ_28 Subordinate follicle

description: Subordinate follicle


title: AZ_18 Dominant follicle

description: Dominant follicle


title: AZ_20 Subordinate follicle

description: Subordinate follicle


title: AZ_22 Dominant follicle

description: Dominant follicle


title: Adn-C/EBPα-/-_HFD 1 month_rep1

city: Dallas

first: Qiong

middle: A.

last: Wang

state: TX

address: 5323 Harry Hines Blvd.

department: Internal Medicine

institute: UT Southwestern Medical Center

description: replicate 1

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: Mouse subcutaneous adipose tissue_Adn-C/EBPα-/-_HighFatDiet_1month

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

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.

tag: genotype

value: Adn-C/EBPα-/-

tag: strain

value: 14 weeks

value: subcutaneous adipose tissue


title: Control for Adn-C/EBPα-/-_HFD 1 month_rep1

description: replicate 1

source_name: Mouse subcutaneous adipose tissue_Adn-C/EBPα-/-_control_1month

tag: tissue


title: 5458

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

description: Amyloid-ß (Aß) plaques are pathological hallmarks of Alzheimer disease. However, the precise neuropathological changes that occur in brain in response to amyloid deposition are largely unknown. To study the molecular mechanism(s) responsible for Aß-mediated neuropathology, we performed a gene expression analysis on frontal neocortical brain tissue of APPPS1 mice compared to their littermate controls.

hyb_protocol: For Cy3 14 pmol and for Cy5 14 pmol incorporated dye was fragmented and resuspended in 55ul hybridization buffer HI-RPM (Agilent). The arrays were hybridized in microarray hybridization chambers (Agilent) overnight at 65ºC, rpm=10 for 17 hours.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent) using the `extended dynamic range' and images were processed with the Feature Extraction Software version 9.5 (Agilent).

data_processing: Log-ratios of the Agilent processed signal values (i.e., feature gProcessedSignal for the Cy3 signal and rProcessedSignal for the Cy5 signal from Agilent Feature Extraction v9.5.3.1) were used for the data analysis. In case of multiple probes for the same Agilent ID, log-intensities were averaged.  Control probes were remove  prior to analysis.

label_protocol: ~1µg of sample was spiked with 10 viral polyA transcript controls (Agilent), converted to double stranded cDNA in a reverse transcription reaction, converted to antisense cRNA, amplified and labeled with Cy3 in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

extract_protocol: RiboPure kit (Ambion, Huntingdon, Cambridgeshire, UK) followed by DNase treatment (DNA-free™, Ambion).

tag: model

value: APPPS1 (Radde et al EMBO Rep 2006)

tag: mutations

tag: gender

value: female

value: 3 months

tag: condition

value: transgenic

value: brain neocortex

label_protocol: ~1µg of sample was spiked with 10 viral polyA transcript controls (Agilent), converted to double stranded cDNA in a reverse transcription reaction, converted to antisense cRNA, amplified and labeled with Cy5 in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

value: non-transgenic


title: Adn-C/EBPα-/-_HFD 1 month_rep3

description: replicate 3

tag: age


title: 5289

description: Amyloid-ß (Aß) plaques are pathological hallmarks of Alzheimer disease. However, the precise neuropathological changes that occur in brain in response to amyloid deposition are largely unknown. To study the molecular mechanism(s) responsible for Aß-mediated neuropathology, we performed a gene expression analysis on laser-microdissected brain tissue of Tg2576 mice compared to their littermate controls.

hyb_protocol: For Cy3 28 pmol incorporated dye was fragmented and resuspended in 55ul hybridization buffer HI-RPM (Agilent). The arrays were hybridized in microarray hybridization chambers (Agilent) overnight at 65ºC, rpm=10 for 17 hours.

data_processing: The Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v9.5.3.1) were used for the data analysis. Intensities were base 2 log-transformed and in case of multiple probes for the same Agilent ID, log-intensities were averaged.  Control probes were remove  prior to analysis.

label_protocol: 2-cycle amplification (Baugh et al, Nucl Acids Res, 2001) with labeling (2.4µl dye in stead of 4.8µl) in the second in vitro transcription according to Agilent’s protocol.

extract_protocol: RNeasy micro kit with an on-column DNase-treatment as recommended  (Qiagen, Venlo, The Netherlands)

value: Tg2576 (Hsiao et al, Science, 1995)

tag: mutation

value: 17 months

value: Brain hippocampus


title: SOX11-positive MCL xenograft derived tumor.3

city: Barcelona

first: Virginia

last: Amador

state: Barcelona

address: Rossello 153

department: Pathology

institute: IDIBAPS

hyb_protocol: GeneChips were scanned using the 7G- 3000.

scan_protocol: The data were analyzed with the Expression Console applilcation from Affymetrix. We performed RMA to summarize the data.

data_processing: Signal obtained with RMA

source_name: Z138-shSOX11.3 tumor

label_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on HU133plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

growth_protocol: With the use of a protocol approved by the animal testing Ethical Committee of the University of Barcelona, CB17-severe combined immunodeficient (CB17-SCID) mice (Charles River Laboratory, Wilmington, MA) were subcutaneously inoculated into their lower dorsum with Z138 shSOX11.1, shSOX11.3, shControl in Matrigel basement membrane matrix (Becton Dickinson, San Jose, CA) as previously described (Vegliante et al. 2013).

extract_protocol: Total RNA of xenograft Z138shControl (n=4), shSOX11.1 (n=5) and shSOX11.3 (n=5) was extracted with the TRIzol reagent following the manufacturer’s recommendations (Invitrogen Life Technologies). RNA integrity was examined with the Agilent 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA).

tag: infection

value: shControl

value: MCL xenotransplant derived tumors


title: SOX11-positive MCL xenograft derived tumor.4

value: CB17-severe combined immunodeficient (CB17-SCID) mice


title: 5291


title: AZ_16 Subordinate follicle

description: Subordinate follicle

value: Theca

value: Subordinate

value: theca pool of all samples


title: control, adipocytes-1

value: Human subcutaneous adipocytes


title: AZ_14 Dominant follicle

description: Dominant follicle

value: Dominant


title: Control for Adn-C/EBPα-/-_HFD 1 month_rep2

description: replicate 2

value: Adn-C/EBPα-/-

value: 14 weeks

value: subcutaneous adipose tissue


title: Control for Adn-C/EBPα-/-_HFD 1 month_rep3

description: replicate 3


title: SOX11-positive MCL xenograft derived tumor.2


title: 5290

value: female

value: transgenic


title: Adn-C/EBPα-/-_HFD 3 days_rep2

description: replicate 2

source_name: Mouse subcutaneous adipose tissue_Adn-C/EBPα-/-_HighFatDiet_3d

value: 10 weeks


title: Adn-C/EBPα-/-_HFD 3 days_rep3

description: replicate 3


title: SOX11-positive MCL xenograft derived tumor.1


title: 5288

value: Tg2576 (Hsiao et al, Science, 1995)


title: 5456

value: APPPS1 (Radde et al EMBO Rep 2006)

value: 3 months

value: non-transgenic

value: brain neocortex


title: SOX11-negative shSOX11.3 MCL xenograft derived tumor.4

value: CB17-severe combined immunodeficient (CB17-SCID) mice

value: MCL xenotransplant derived tumors


title: SOX11-negative shSOX11.3 MCL xenograft derived tumor.5


title: 5457


title: 5455


title: Adn-C/EBPα-/-_HFD 1 month_rep2

description: replicate 2


title: Adn-C/EBPα-/-_HFD 3 days_rep1

description: replicate 1


title: AZ_10 Dominant follicle

description: Dominant follicle

value: Theca


title: AZ_12 Subordinate follicle

description: Subordinate follicle

value: Subordinate

value: theca pool of all samples


title: AZ_4 Subordinate follicle

description: Subordinate follicle


title: SOX11-negative shSOX11.3 MCL xenograft derived tumor.3


title: AZ_2  Dominant follicle

description: Dominant follicle

value: Dominant


title: SOX11-negative shSOX11.1 MCL xenograft derived tumor.5

source_name: Z138-shSOX11.1 tumor


title: Control for Adn-C/EBPα-/-_HFD 3 days_rep1

description: replicate 1

source_name: Mouse subcutaneous adipose tissue_Adn-C/EBPα-/-_control_3d

value: Adn-C/EBPα-/-


title: SOX11-negative shSOX11.3 MCL xenograft derived tumor.2


title: Ndst1f/fLysMCre+_2.2

city: La Jolla

first: Philip

middle: Leo Stefan Maria

last: Gordts

department: CMM

institute: UCSD

description:
Ndst1f/fLysMCre+ mouse 2
Replicate 2
6668263036_B

hyb_protocol: standard Illumina

scan_protocol: standard Illumina

data_processing: Illumina GenomeStudio: cubic spline normalization

source_name: BMDM, Ndfst1-deficient, 0 µg/ml agLDL

label_protocol: standard Illumina

growth_protocol: BMDM were grown in DMEM/F12 medium supplemented with 10% fetal calf serum, 100 units/ml penicillin, 100 μg/ml streptomycin and 20 ng/ml recombinant mouse Macrophage Colony Stimulatinf Factor 1

treatment_protocol: BMDM were treated with or without 50 µg/ml of aggregated LDL for 24 hours in DMEM/F12 medium supplemented with 10% lipoprotein-eficient fetal calf serum, 100 units/ml penicillin, 100 μg/ml streptomycin and 20 ng/ml recombinant mouse Macrophage Colony Stimulatinf Factor 1

tag: background strain

value: 12 week old

value: bone marrow derived macrophages

tag: phenotype


title: agLDL WT_2.2

description:
Ndst1f/fLysMCre- mouse 2
Replicate 2
6668263002_F

source_name: BMDM, Ndfst1 wild type, 50 µg/ml agLDL

value: Ndfst1 wild type


title: WT_2.2

description:
Ndst1f/fLysMCre- mouse 2
Replicate 2
6668263002_B

source_name: BMDM, Ndfst1 wild type, 0 µg/ml agLDL


title: SOX11-negative shSOX11.3 MCL xenograft derived tumor.1


title: Control for Adn-C/EBPα-/-_HFD 3 days_rep3

description: replicate 3

value: subcutaneous adipose tissue


title: AZ_25 Dominant follicle

description: Dominant follicle

value: Granulosa

value: granulosa pool of all samples


title: AZ_27 Subordinate follicle

description: Subordinate follicle


title: Adn-PPARγ-/-_chow 3 days_rep3

description: replicate 3

source_name: Mouse subcutaneous adipose tissue_Adn-PPARγ-/-_chow_3d

value: Adn-PPARγ-/-

value: 10 weeks


title: SOX11-negative shSOX11.1 MCL xenograft derived tumor.4

source_name: Z138-shControl tumor


title: SOX11-negative shSOX11.1 MCL xenograft derived tumor.2


title: AZ_21 Dominant follicle

description: Dominant follicle


title: agLDL Ndst1f/fLysMCre+_2.1

description:
Ndst1f/fLysMCre+ mouse 2
Replicate 1
6668263036_E

source_name: BMDM, Ndfst1-deficient, 50 µg/ml agLDL


title: SOX11-negative shSOX11.1 MCL xenograft derived tumor.3


title: WT_2.1

description:
Ndst1f/fLysMCre- mouse 2
Replicate 1
6668263002_A


title: agLDL WT_2.1

description:
Ndst1f/fLysMCre- mouse 2
Replicate 1
6668263002_E


title: Control for Adn-C/EBPα-/-_HFD 3 days_rep2

description: replicate 2


title: AZ_19 Subordinate follicle

description: Subordinate follicle


title: Control for Adn-PPARγ-/-_chow 3 days_rep3

description: replicate 3

source_name: Mouse subcutaneous adipose tissue_Adn-PPARγ-/-_control_3d


title: Adn-PPARγ-/-_chow 3 days_rep1

description: replicate 1


title: Adn-PPARγ-/-_chow 3 days_rep2

description: replicate 2


title: agLDL Ndst1f/fLysMCre+_1.2

description:
Ndst1f/fLysMCre+ mouse 1
Replicate 2
6668263036_H


title: SOX11-negative shSOX11.1 MCL xenograft derived tumor.1


title: AZ_23 Subordinate follicle

description: Subordinate follicle


title: AZ_17 Dominant follicle

description: Dominant follicle


title: AZ_11 Subordinate follicle

description: Subordinate follicle


title: APL2

city: Isehara

first: Hiromichi

last: Matsushita

state: Kanagawa

address: 143 Shimokasuya

institute: Tokai University School of Medcine

hyb_protocol: Chips hybridized according to Manufacturer's protocol

scan_protocol: AGCC

data_processing: MAS 5.0 (Genespring GX)

source_name: Bone marrow specimen from an APL patient

label_protocol: Chips labeled with biotin according to Manufacturer's protocol

growth_protocol: Bone marrow specimen from Tumor cells

extract_protocol: Trizol reagent standard protocol

value: primary AML-M3


title: AZ_13 Dominant follicle

description: Dominant follicle


title: AZ_15 Subordinate follicle

description: Subordinate follicle


title: Control for Adn-PPARγ-/-_chow 3 days_rep1

description: replicate 1


title: Ndst1f/fLysMCre+_2.1

description:
Ndst1f/fLysMCre+ mouse 2
Replicate 1
6668263036_A


title: Ndst1f/fLysMCre+_1.2

description:
Ndst1f/fLysMCre+ mouse 1
Replicate 2
6668263036_D


title: APL1

value: Bone marrow specimen from an APL patient


title: Adn-C/EBPα-/-_chow 3 days_rep3

description: replicate 3

source_name: Mouse subcutaneous adipose tissue_Adn-C/EBPα-/-_chow_3d


title: WT_1.2

description:
Ndst1f/fLysMCre- mouse 1
Replicate 2
6668263002_D


title: agLDL WT_1.2

description:
Ndst1f/fLysMCre- mouse 1
Replicate 2
6668263002_H


title: Control for Adn-PPARγ-/-_chow 3 days_rep2

description: replicate 2


title: induced APL2

source_name: PML-RARA-induced human hematopoietic cells proliferating in an immunodeficient mouse


title: agLDL Ndst1f/fLysMCre+_1.1

description:
Ndst1f/fLysMCre+ mouse 1
Replicate 1
6668263036_G


title: Adn-C/EBPα-/-_chow 3 days_rep2

description: replicate 2


title: Control for Adn-C/EBPα-/-_chow 3 days_rep3

description: replicate 3


title: induced APL3

value: PML-RARA-induced human hematopoietic cells proliferating in an immunodeficient mouse


title: Ndst1f/fLysMCre+_1.1

description:
Ndst1f/fLysMCre+ mouse 1
Replicate 1
6668263036_C


title: AZ_3 Subordinate follicle

description: Subordinate follicle

source_name: bovine ovarian follicle


title: B40

status: Public on Nov 03 2014

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

description: Reference

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing:
The array image was acquired using Affymetrix Command Console Software (version 2.0.1). Processing of the raw signals and raw copy-number calculation were performed using the CRMAv2 procedure of the aroma.affymetrix package (version 2.0.0) for R Statistical platform (version 2.12.1) according to the aroma.affymetrix vignette total copy-number analysis. A combined reference (mean values) was calculated from the Buffy-Coat samples and used as reference for a paired analysis (ALL patients vs reference). Circular Binary Segmentation (Ohlsen et al., 2004) was then applied using DNAcopy package for R Bioconductor to perform the segmentation. Affymetrix  "GenomeWideSNP_6.na30.annot.csv" annotation (Genome Build version hg18) was used.
Primary data description: Smoothed copy-number signal ratios and detected segments and segment mean values. Genome Build version hg18 was used.

source_name: Buffy-coat 40

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: Genomic DNA was isolated from mononuclear cells from peripheral blood or bone marrow of leukemic mice using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: reference

value: Buffy-coat of healthy person


title: Adn-C/EBPα-/-_chow 3 days_rep1

description: replicate 1


title: induced APL1


title: agLDL WT_1.1

description:
Ndst1f/fLysMCre- mouse 1
Replicate 1
6668263002_G


title: B31

description: Reference

source_name: Buffy-coat 31


title: AZ_1 Dominant follicle

description: Dominant follicle


title: B43

description: Reference

source_name: Buffy-coat 43


title: Control for Adn-C/EBPα-/-_chow 3 days_rep2

description: replicate 2


title: WT_1.1

description:
Ndst1f/fLysMCre- mouse 1
Replicate 1
6668263002_C


title: ALL109

description: Primary human ALL sample isolated from transplanted mice

source_name: mouse propagated ALL109

tag: primary all sample


title: ALL113

source_name: mouse propagated ALL113


title: B44

description: Reference

source_name: Buffy-coat 44


title: ALL115

source_name: mouse propagated ALL115


title: AZ_9 Dominant follicle

description: Dominant follicle


title: ALL119

source_name: mouse propagated ALL119


title: B22

description: Reference

source_name: Buffy-coat 22


title: ALL22089

source_name: mouse propagated ALL22089


title: ALL24429

source_name: mouse propagated ALL24429


title: ALL114

source_name: mouse propagated ALL114


title: R48

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

description: mtDNA-depleted, replicate 3

data_processing: The scanner operating software, GenomeStudio, converts the signal on the    array into a TXT file for analysis. The data were then calibrated and quantile normalized using the neqc method of Shi et al. (2010) [PMID:20929874]. This analysis was was carried out in R using the limma package.

source_name: Mcl1 knockout mouse embryonic fibroblast

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

tag: sample type

value: mt-depleted

value: embryonic

tag: cell population

value: fibroblasts

tag: beadchip position


title: MW48

description: Parental control, replicate 3

value: Parental


title: R35

description: mtDNA-depleted, replicate 2


title: tamoxifen-day 28-4

city: Baltimore

first: Andreas

middle: Sebastian

last: Barth

state: MD

address: 720 Rutland Ave.

department: Medicine, Division of Cardiology

institute: Johns Hopkins University

description: Tamoxifen x5 days + 23 days normal diet -4

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization with Solo, a simple standalone tood implementing the quantile-quantile normalization method (Univ. of Strasbourg, France)

source_name: mouse myocardium, left ventricle

growth_protocol: All mice were supplied with the same diet and water ad libitum; Mice were maintained on a 12-hour light/dark cycle in a temperature and humidity controlled environment.

extract_protocol: Total RNA was preparted using TRIzol reagent (Invitrogen) from left ventricular myocardial tissue. Total RNA yield and purity (260nm:280nm) were determined spectrophotometrically. The integrity (RIN>9.0) of the re-suspended total RNA was determined using the RNA Nano Chip Kit on the Bioanalyzer 2100 and the 2100 Expert software (Agilent).

treatment_protocol: For intraperitoneal injection, 10mg tamoxifen free base (T5648, Sigma) was dissolved in 1mL peanut oil (Sigma) and then sonicated. 100microL (1.0 mg tamoxifen) was injected daily (40mg/kg/day, i.p.) for 5 days.

value: male

value: 12-20 weeks

value: myocardium, left ventricle


title: tamoxifen-day 28-3

description: Tamoxifen x5 days + 23 days normal diet -3


title: tamoxifen-day 28-2

description: Tamoxifen x5 days + 23 days normal diet -2


title: LK6

description: Caspase9 Knock-out, replicate 3

data_processing: The scanner operating software, GenomeStudio, converts the signal on the  array into a TXT file for analysis. The data were then calibrated and quantile normalized using the neqc method of Shi et al. (2010) [PMID:20929874]. This analysis was was carried out in R using the limma package.

source_name: Lineage-Kit+CD45.2+ hematopoietic cells

value: Casp9 KO

value: bone marrow

value: HSPC-enriched

value: 12-16 weeks post transplant

tag: experiment number


title: MW35

description: Parental control, replicate 2

tag: strain


title: tamoxifen-day 10-2

description: Tamoxifen x5 days + 5 days normal diet -2

tag: tissue


title: tamoxifen-day 28-1

description: Tamoxifen x5 days + 23 days normal diet -1


title: tamoxifen-day 10-3

description: Tamoxifen x5 days + 5 days normal diet -3


title: MW3

description: Wild-type control, experiment 2, replicate 2


title: MW6

description: Bak/Bax Double Knock-out, replicate 3

value: Bak/Bax DKO


title: tamoxifen-day 3-2

description: Tamoxifen x3 days -2


title: tamoxifen-day 10-1

description: Tamoxifen x5 days + 5 days normal diet -1


title: tamoxifen-day 3-3

description: Tamoxifen x3 days -3


title: MW5

description: Wild-type control, experiment 2, replicate 3


title: MW4

description: Bak/Bax Double Knock-out, replicate 2


title: tamoxifen-day 2-4

description: Tamoxifen x2 days -4


title: MW10

description: Parental control, replicate 1


title: LK4

description: Caspase9 Knock-out, replicate 2


title: MW1

description: Wild-type control, experiment 2, replicate 1


title: tamoxifen-day 2-3

description: Tamoxifen x2 days -3


title: tamoxifen-day 3-1

description: Tamoxifen x3 days -1


title: agLDL Ndst1f/fLysMCre+_2.2

description:
Ndst1f/fLysMCre+ mouse 2
Replicate 2
6668263036_F

source_name: BMDM, Ndfst1-deficient, 50 µg/ml agLDL

value: 12 week old

tag: cell type

value: bone marrow derived macrophages


title: R10

description: mtDNA-depleted, replicate 1


title: MW2

description: Bak/Bax Double Knock-out, replicate 1


title: Control for Adn-C/EBPα-/-_chow 3 days_rep1

description: replicate 1

source_name: Mouse subcutaneous adipose tissue_Adn-C/EBPα-/-_control_3d

tag: genotype

value: Adn-C/EBPα-/-

value: 10 weeks

value: subcutaneous adipose tissue


title: LK3

description: Wild-type control, experiment 1, replicate 2


title: LK2

description: Caspase9 Knock-out, replicate 1


title: tamoxifen-day 2-2

description: Tamoxifen x2 days -2

tag: gender


title: tamoxifen-day 2-1

description: Tamoxifen x2 days -1


title: control 5

description: non-failing control - 5


title: LK5

description: Wild-type control, experiment 1, replicate 3


title: control 4

description: non-failing control - 4


title: LK1

description: Wild-type control, experiment 1, replicate 1


title: control 3

description: non-failing control - 3


title: cyn mutant at 5 days after pollination stage biological rep1

city: Kunming

first: LI

last: JUAN

state: Yunnan

address: Black Dragon Pool

department: Rice Research Institute

institute: Yunnan Agricultural University

description: Gene expression data from panicles of cyn wild lines at 5 days after pollination stage

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip ** Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were analyzed with Expression Console Software using RMA algorithm.

organism: Oryza sativa Japonica Group

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

growth_protocol: All of materials were grown in a greenhouse under natural daylight.

extract_protocol: The samples for microarray analysis were homogenized in 1 ml Trizol (Invitrogen, Carlsbad, CA), and RNA extracted using RNEasy miniprep columns (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

value: panicles

tag: developmental stage

value: 5 days after pollination stage

value: cyn mutant

tag: cultivar

value: japonica


title: cyn mutant at before flowering stage biological rep3

description: Gene expression data from panicles of cyn wild lines at before flowering stage

source_name: cyn mutant at before flowering stage

value: before flowering stage


title: control 1

description: non-failing control - 1

value: male

tag: age

value: 12-20 weeks


title: CYN wild lines at 5 days after pollination stage biological rep2

description: Gene expression data from panicles of CYN wild lines at 5 days after pollination stage

value: wild type


title: NJ15_1

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

description:
Seedlings, sprayed with 10 µM NJ15 and were gravistimulated by turning then 90° relative to the first direction for 8h after grown vertically for 4 days on MS plates, biological rep1
No additional information

hyb_protocol: Following fragmentation, 12.5 µg aRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with the Factor Analysis for Robust Microarray Summarization (FARMS) method, using the statistical language R (R-2.7.2) and Bioconductor 2.2.

organism: Arabidopsis thaliana

label_protocol: biotinylated aRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was purified with an RNA Extraction Kit Mini for plant (RBC Bioscience).

treatment_protocol: For DNA microarray analysis, wild type Col-0 plants, grown vertically as a gravitropic response assay for 4 days on MS plates, were sprayed with mock or with 10 µM NJ15 and were gravistimulated by turning then 90° relative to the first direction. After 8 h, plants were harvested and total RNA was extracted with a Total RNA Extraction Kit Mini for plant (RBC Bioscience), then total RNA was subjected to microarray analysis.

tag: treatment

value: Seedlings

value: 4 days


title: CYN wild lines at before flowering stage biological rep1

description: Gene expression data from panicles of CYN wild lines at before flowering stage


title: cyn mutant at before flowering stage biological rep2