title: explants injected with ICD, rep2

city: San Diego

first: Chris

last: Kintner

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute

hyb_protocol: 10ug of cRNA was hybridized to Xenopus laevis Affymetrix chips for 16hrs at 45C, then washed and stained using the Affymetrix Fluidics Station.

scan_protocol: GeneChip Scanner 3000 7G from Affymetrix

data_processing: Data was processed using Microarray Suite 5.0 software using Affymetrix default settings.  Statistical analysis was later performed using Bullfrog software

organism: Xenopus laevis

source_name: explants from embryos injected with ICD

label_protocol: Biotinylated cRNA was prepared according to standard Affymetrix Protocols.

growth_protocol: Xenopus embryos grown in 0.1X MMR until stage 9/10.

extract_protocol: Total RNA was extracted using the Proteinase K method.

treatment_protocol: Animal caps were cut, explanted and cultured in Danilchik's + 0.1% BSA from stage 9/10 until harvest at approximately stage 14.

tag: tissue origin

value: 2-cell stage embryos

value: epithelial explants

tag: injected agent

value: synthetic mRNA encoding ICD

tag: injected timepoint

value: 2-cell stage

tag: explant timepoint

value: stage 9/10

tag: harvest timepoint

value: equivalent of stage 14


title: G-Low-SCS-T5Sa-5046

status: Public on Mar 01 2012

type: RNA

city: CASTANET TOLOSAN CEDEX

first: Cécile

last: Bonnefont

address: Auzeville B.P. 52627

country: France

institute: INRA

description: Mammary epithelial cells (MEC) were stimulated in vitro either by live Staphylococcus aureus (Sa9A strain; Sa) or by its supernatant -soluble factors- (Sp).

hyb_protocol: Three ovine 019921 slides (Agilent Technologies), with eight microarrays each containing 15,008 probes were used. The chips were hybridised with labelled RNA at 65°C during 17h and then washed according to the manufacturer's protocol.

scan_protocol: Intensity values were collected with a 4000B Axon scanner. Two channel images were imported into the Agilent's Feature Extraction software for feature (spot) finding and alignment. Features were flagged as present/absent, saturated/unsaturated, uniform/non-uniform and pixel intensities for feature and background were recorded.

data_processing: Output Feature Extraction results (.txt) files were transferred into R, package LIMMA. The raw data were imported, and they were normalised by a loess function to correct the dye biais and by a T-quantile procedure to decrease the differences across arrays. Then probe data were filtered on the value and the distribution of their intensity. A total of 4225 probes out of the 15008 probes were retained for further analysis.

molecule: total RNA

organism: Ovis aries

source_name: Mammary epithelial cells (MEC)

label_protocol: They were labelled with Cy3 and Cy5 for hybridisation in a two-colour dye-swap experimental design on 60 arrays.

extract_protocol: Total RNA was extracted from mammary epithelial cells using double extraction method with Trizol and RNeasy. Quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using Agilent bioanalyzer 2100 slide.  RNA Integrity Number (RIN) index above 9 was measured for all samples.Two hundred ng of RNA were converted to double-stranded cDNA and amplified with the  QSuick amp Labelling kit, two colors  (Ref : 5190-0424, Agilent's technologies).

tag: cell type

value: Mammary epithelial cells (MEC)

tag: line

value: Low-SCS

tag: time and stimulation

tag: phenotype

value: Low susceptability

tag: time

tag: treatment

value: supernatant


title: ESC_PNS

city: Kobe

first: Kenji

last: Yoshida

address: 2-2-2, Minatojima Minamimachim Chuo-ku

department: Regenerative & Cellular Medicine

country: Japan

institute: Sumitomo Dainippon Pharma Co.,Ltd.

description:
Gene expression data
Sample name: Mouse-009

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450-0001.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: Data analysis was carried out by Expression Console 1.1 (Affymetrix). Detection and signal were obtained by MAS5 algorithm with default settings. Global normalization was performed to make average signal intensity of all probesets equal to 100.

label: biotin

organism: Mus musculus

source_name: Mouse ES cells derived primary neurosphere

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

growth_protocol: Neurospheres were cultured in MHM. iPSC and ESC were cultured in standard conditions.

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

treatment_protocol: Neurospheres were cultured in various conditions.

value: neurosphere, primary, ES-derived


title: EB3_ESC

description:
Gene expression data
Sample name: Mouse-008

source_name: Mouse ES cells

value: ES cells


title: LC cells exposed to hypoxic stress

city: Dublin

first: Ruaidhri

middle: Patrick

last: Kirwan

state: Leinster

address: Belfield

department: Conway Institute of Biomolecular and Biomedical Research & School of Medicine and Medical Science

country: Ireland

institute: University College Dublin

description: Gene expression data from GFAP-negative LC cells maintained in 24 hours of hypoxia

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized to Affymetrix HG-U133A microarrays as per the Affymetrix protocol. Microarrays were washed and stained in using the Affymetrix GeneChip fluidics station protocol EukGE-WS2.

scan_protocol: Following washing and staining, the probe arrays were scanned twice at 532 nm with a filter of 570 nm and 3um resolution using the Affymetrix GeneChip System confocal scanning laser

data_processing: Raw image *.cel files (cell intensity files) were obtained through Affymetrix GeneChip software (MAS 5.0) using the default settings. Raw microarrray output data from MAS 5.0 was background adjusted and normalised using the method of Robust Multichip Average (RMA) using RMA Express Software

organism: Homo sapiens

source_name: GFAP-negative lamina cribrosa (LC) cell from optic nerve head tissue

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

growth_protocol: Dulbecco’s modified eagle medium (DMEM) (Gibco, Paisely, UK) supplemented with 10% fetal calf serum (FCS), penicillin (100U/ml) and streptomycin (100(g/ml) (complete medium). Culture medium was changed every third day

treatment_protocol: Serum free for 24 hours at 37 degrees Celsius in a humidified atmosphere of 1% O2 (hypoxia) with a balance of 95% N2 / 5% CO2 at 37OC. At the end of the 24 hour period, the cells were harvested.

value: GFAP-negative lamina cribrosa (LC)

tag: tissue

value: optic nerve head


title: explants injected with ICD and MCI-HGR, rep1

state: CA

country: USA

source_name: explants from embryos injected with ICD and MCI-HGR

value: synthetic mRNA encoding ICD along with MCI-HGR.


title: explants injected with ICD and MCI-HGR, rep2


title: A549 Vehicle 24hr rep2

city: Watertown

first: Mary

last: Simcox

state: MA

address: 500 Arsenal St

institute: Forma Therapeutics

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: Hybridization Mix contained, in addition to cRNA, reagents from the Hybridization Control Kit and Control Oligo B2. Staining and washing steps were performed as suggested by the manufacturer (Affymetrix, Santa Clara, CA).

scan_protocol: Each hybridized Affymetrix GeneChip array was scanned with a GeneChip Scanner 3000 7G (Agilent/Affymetrix).

data_processing: an in-house implementation of the RMA algorithm (17) was used to perform the background correction, normalization, and signal summarization.

source_name: A549 lung cancer cells treated with Vehicle for 24 hours

label_protocol: RNA was converted into cDNA and cRNA according to the manufacturer’s recommendation and using manufacturer’s kits (Affymetrix, Santa Clara, CA). 15 ug of total RNA was converted to cDNA with the One-cycle cDNA Synthesis Kit with the addition of reagents from the Poly-A RNA Control Kit. cRNA was produced with the IVT Labeling Kit

growth_protocol: cell were grown as recommended by ATCC

extract_protocol: Total RNA was extracted from cells using the Qiagen RNeasy Mini Kit

treatment_protocol: Cells were plated at 35% confluency and allowed to rest overnight.  Vehicle or RO4929097 was added and cell were incubated at 37C for either 6 or 24 hours prior to removal of supernatant and lysing with Buffer RLT.

tag: cell line

value: Vehicle

value: 24 hours


title: G-High-SCS-T5Sp-5012

value: High-SCS

value: High susceptability

value: live Staphylococcus aureus


title: Insig1 flox/flox /Insig2 -/- InsigKO_C2

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: The cRNA was then hybridized to the murine genome MOE430 (consists of ≈ 45000 gene entries) chips (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.

scan_protocol: Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings.

data_processing: MAS 5.0

source_name: Insig1 flox/flox /Insig2 -/-

label_protocol: based on Affymetrix protocols

extract_protocol: Total RNA was isolated from tyII cells by RNeasy Mini Kit according to the manufacturers protocol (Cat. 74104, Qiagen, Valencia, CA).

tag: source tissue

value: lung

tag: strain

value: Insig1 flox/flox /Insig2 -/- ( AT2 cells obtained from 2 months old SpC-rTTA / Otet-CRE / Insig1 flox/flox / Insig2-/- mice treated with doxycycline from E6.5 to E12.5. Control animals lacked either SpC-rtTA or Otet-CRE)

value: Alveolar Type II


title: G-Low-SCS-T1Sp-5046

value: Mammary epithelial cells (MEC)


title: G-High-SCS-Tref-5189

value: Tref

value: reference

value: untreated


title: G-High-SCS-Tref-5182


title: iPSC_PNS

description:
Gene expression data
Sample name: Mouse-004

source_name: Mouse iPS cells-derived primary neurosphere

value: neurosphere, primary, iPS-derived


title: explants injected with DBM, replicate 1

hyb_protocol: 10ug of cRNA was hybridized to Xenopus laevis Affymetrix chips for 16hrs at 45C, then washed and stained using the Affymetrix Fluidics Station

source_name: explants from embryos injected with DBM RNA

label_protocol: Biotynylated cRNA was prepared according to standard Affymetrix Protocols

growth_protocol: Xenopus embryos grown in 0.1X MMR until stage 9/10

extract_protocol: Total RNA was extracted using the Proteinase K method

treatment_protocol: Animal caps were cut, explanted and cultured in Danilchik's + 0.1% BSA from stage 9/10 until harvest at stage 12

tag: injection timepoint

value: 2-cell stage

value: DBM

value: stage 9/10

value: equivalent of stage 12


title: G-High-SCS-T5Sa-5217

value: supernatant


title: A549 RO4929097 6hr rep3

source_name: A549 lung cancer cells treated with gamma secretase inhibitor for 6 hrs

value: gamma secretase inhibitor RO4929097

value: 6 hours


title: A549 RO4929097 6hr rep2


title: G-Low-SCS-T1Sa-5093

value: Low-SCS

value: Low susceptability


title: iPSC_SNS

description:
Gene expression data
Sample name: Mouse-005

source_name: Mouse iPS cells-derived secondary neurosphere

value: neurosphere, secondary, iPS-derived


title: A549 RO4929097 6hr rep4


title: 38C2_iPSC

description:
Gene expression data
Sample name: Mouse-003

source_name: Mouse iPS cells

value: iPS cells


title: explants injected with ICD, replicate 2

source_name: explants from embryos injected with ICD RNA

value: ICD


title: G-Low-SCS-T1Sa-5046

value: Mammary epithelial cells (MEC)


title: G-Low-SCS-T5Sp-5051

value: live Staphylococcus aureus


title: G-High-SCS-T1Sp-5182

value: High-SCS

value: High susceptability


title: explants injected with ICD, rep1

value: 2-cell stage embryos

value: epithelial explants

value: synthetic mRNA encoding ICD

value: equivalent of stage 14


title: A549 Vehicle 6hr rep4

source_name: A549 lung cancer cells treated with Vehicle for 6 hours

value: Vehicle


title: Mouse_adult_fibroblast

description:
Gene expression data
Sample name: Mouse-002

source_name: Adult skin fibroblast

value: fibroblast


title: A549 Vehicle 6hr rep3


title: explants injected with ICD, replicate1

value: 2-cell stage

value: stage 9/10

value: equivalent of stage 12


title: E14_Neurosphere

description:
Gene expression data
Sample name: Mouse-001

source_name: Mouse embryonic GE-derived neurosphere

value: neurosphere, embryonic ganglionic eminence (GE)-derived


title: G-High-SCS-T5Sa-5189

value: supernatant


title: explants injected with HMM, replicate 1

source_name: explants from embryos injected with HMM RNA

value: HMM


title: A549 RO4929097 6hr rep1

value: gamma secretase inhibitor RO4929097

value: 6 hours


title: G-Low-SCS-T5Sa-5130

source_name: Mammary epithelial cells (MEC)

value: Mammary epithelial cells (MEC)

value: Low-SCS

value: Low susceptability


title: G-High-SCS-Tref-5178

value: High-SCS

value: Tref

value: High susceptability

value: reference

value: untreated


title: N2_4 with array type Medicago from Affymetrix

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

description:
N2_4
In compatible interaction between plants and biotrophic microorganisms, neoformation of organs occurs to ensure an efficient relationship between both partners. During the interaction between Medicago truncatula and Sinorhizobium meliloti, bacteria induce the development of root nodule with a permanent meristem, and chronically infect plant cells from zone II before differentiating into atmospheric nitrogen fixing bacteroids. M. truncatula is also plant host for root-knot nematodes, such as Meloidogyne incognita. During this compatible pathogenic interaction, root-knot nematodes induce redifferenciation of root cells from the vascular cylinder into specialized feeding cells called “giant cells”. Hyperplasia and hypertrophy of the surrounding cells lead to the formation of typical root galls. This phenomenon invokes host pathways in common with those necessary for nitrogen-nodule formation suggesting that nematode and rhizobia exploit a relative common strategy of plant cell infection at the cellular and molecular level. In order to highlight key genes involved in gall and nodule developments, parallel laser microdissection of giant cells from galls and cells from zone II of nodules followed by transcriptomic analysis is performed.

hyb_protocol: Standard protocol. Labelled extract quantity: 5ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Medicago truncatula

source_name: N2, S. meliloti

label_protocol: Labelling Biotin indirect, amplification=yes, total RNA.

growth_protocol: root - modified Fahreus medium - 23°C / 16°C - 200 μmol.m-2.s-1 - 16h photoperiod

extract_protocol: Standard protocol. 12.35ng.

treatment_protocol: Name: inoculated with Sinorhizobium meliloti - pathogen - pathogen infection,sinorhizobium meliloti:time 3week. Three days old seedlings were inoculated with 200µl of S. meliloti bacterial culture adjusted to 0.1 OD600. Nodules were harvested 3 weeks post infection for analysis.

tag: cultivar

value: jemalong

value: root nodule infection zone (zone II)

tag: pathogen

value: Sinorhizobium meliloti

tag: harvest date


title: Ct_3 with array type Medicago from Affymetrix

description:
Ct_3
In compatible interaction between plants and biotrophic microorganisms, neoformation of organs occurs to ensure an efficient relationship between both partners. During the interaction between Medicago truncatula and Sinorhizobium meliloti, bacteria induce the development of root nodule with a permanent meristem, and chronically infect plant cells from zone II before differentiating into atmospheric nitrogen fixing bacteroids. M. truncatula is also plant host for root-knot nematodes, such as Meloidogyne incognita. During this compatible pathogenic interaction, root-knot nematodes induce redifferenciation of root cells from the vascular cylinder into specialized feeding cells called “giant cells”. Hyperplasia and hypertrophy of the surrounding cells lead to the formation of typical root galls. This phenomenon invokes host pathways in common with those necessary for nitrogen-nodule formation suggesting that nematode and rhizobia exploit a relative common strategy of plant cell infection at the cellular and molecular level. In order to highlight key genes involved in gall and nodule developments, parallel laser microdissection of giant cells from galls and cells from zone II of nodules followed by transcriptomic analysis is performed.

source_name: Ct, S. meliloti

extract_protocol: Standard protocol. 7.6ng.

value: infected root

tag: sample type

value: control


title: H9 derived NSC_rep3

city: sacramento

first: jing

last: liu

address: 2921 Stockton Blvd

department: Stem Cell Program

institute: UC Davis

description: H9-NSC (3)_raw.txt

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: cell line

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3/Cy5 dye staining.

growth_protocol: H9-NSC was derived from human embryonic stem cell line H9 through a multistep embryonic body-based differentiation protocol and maintained in neurobasal medium plus N2 and bFGF. H9-NSC was then further differentiated into H9-DA in the neurobasal medium plus GDNF/BDNF/AA/CAMP.

extract_protocol: miRNeasy

value: stem cell, brain


title: H9 derived NSC_rep1

description: H9-NSC (1)_raw.txt


title: G-Low-SCS-Tref-5127


title: GC_2 with array type Medicago from Affymetrix

description:
GC_2
In compatible interaction between plants and biotrophic microorganisms, neoformation of organs occurs to ensure an efficient relationship between both partners. During the interaction between Medicago truncatula and Sinorhizobium meliloti, bacteria induce the development of root nodule with a permanent meristem, and chronically infect plant cells from zone II before differentiating into atmospheric nitrogen fixing bacteroids. M. truncatula is also plant host for root-knot nematodes, such as Meloidogyne incognita. During this compatible pathogenic interaction, root-knot nematodes induce redifferenciation of root cells from the vascular cylinder into specialized feeding cells called “giant cells”. Hyperplasia and hypertrophy of the surrounding cells lead to the formation of typical root galls. This phenomenon invokes host pathways in common with those necessary for nitrogen-nodule formation suggesting that nematode and rhizobia exploit a relative common strategy of plant cell infection at the cellular and molecular level. In order to highlight key genes involved in gall and nodule developments, parallel laser microdissection of giant cells from galls and cells from zone II of nodules followed by transcriptomic analysis is performed.

source_name: GC, M. incognita

extract_protocol: Standard protocol. 8.07ng.

treatment_protocol: Name: inoculated with Meloidogyne incognita - pathogen - pathogen infection, meloidogyne incognita:time 1week. Three days old seedlings were inoculated with 100 M. incognita J2 nematodes per apex. Galls were harvested 7 days post infection for analysis.

value: root galls, giant cells

value: Meloidogyne incognita


title: Pediatric_GBM_9

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 580

department: Pediatric Neuro Oncology

country: Germany

institute: German Cancer Research Center

description: Gene expression data from a primary pediatric glioblastoma

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Normalization according to MAS5.0 algorithm. Only probesets called present in at least one sample were included

source_name: Primary brain tumor tissue

label_protocol: Affymetrix protocol

extract_protocol: Trizol

tag: disease state

value: paediatric glioblastoma

tag: age

tag: gender

value: F


title: A549 Vehicle 6hr rep2

value: Vehicle

value: 6 hours


title: H9 derived neurons_rep3

tag: cell type

value: brain


title: H9 derived NSC_rep2

description: H9-NSC (2)_raw.txt


title: Pediatric_GBM_6

value: M


title: Pediatric_GBM_8


title: Pediatric_GBM_46

value: wt


title: N2_3 with array type Medicago from Affymetrix

description:
N2_3
In compatible interaction between plants and biotrophic microorganisms, neoformation of organs occurs to ensure an efficient relationship between both partners. During the interaction between Medicago truncatula and Sinorhizobium meliloti, bacteria induce the development of root nodule with a permanent meristem, and chronically infect plant cells from zone II before differentiating into atmospheric nitrogen fixing bacteroids. M. truncatula is also plant host for root-knot nematodes, such as Meloidogyne incognita. During this compatible pathogenic interaction, root-knot nematodes induce redifferenciation of root cells from the vascular cylinder into specialized feeding cells called “giant cells”. Hyperplasia and hypertrophy of the surrounding cells lead to the formation of typical root galls. This phenomenon invokes host pathways in common with those necessary for nitrogen-nodule formation suggesting that nematode and rhizobia exploit a relative common strategy of plant cell infection at the cellular and molecular level. In order to highlight key genes involved in gall and nodule developments, parallel laser microdissection of giant cells from galls and cells from zone II of nodules followed by transcriptomic analysis is performed.

extract_protocol: Standard protocol. 24.28ng.


title: Ct_1 with array type Medicago from Affymetrix

description:
Ct_1
In compatible interaction between plants and biotrophic microorganisms, neoformation of organs occurs to ensure an efficient relationship between both partners. During the interaction between Medicago truncatula and Sinorhizobium meliloti, bacteria induce the development of root nodule with a permanent meristem, and chronically infect plant cells from zone II before differentiating into atmospheric nitrogen fixing bacteroids. M. truncatula is also plant host for root-knot nematodes, such as Meloidogyne incognita. During this compatible pathogenic interaction, root-knot nematodes induce redifferenciation of root cells from the vascular cylinder into specialized feeding cells called “giant cells”. Hyperplasia and hypertrophy of the surrounding cells lead to the formation of typical root galls. This phenomenon invokes host pathways in common with those necessary for nitrogen-nodule formation suggesting that nematode and rhizobia exploit a relative common strategy of plant cell infection at the cellular and molecular level. In order to highlight key genes involved in gall and nodule developments, parallel laser microdissection of giant cells from galls and cells from zone II of nodules followed by transcriptomic analysis is performed.

extract_protocol: Standard protocol. 7.84ng.


title: Ct_4 with array type Medicago from Affymetrix

description:
Ct_4
In compatible interaction between plants and biotrophic microorganisms, neoformation of organs occurs to ensure an efficient relationship between both partners. During the interaction between Medicago truncatula and Sinorhizobium meliloti, bacteria induce the development of root nodule with a permanent meristem, and chronically infect plant cells from zone II before differentiating into atmospheric nitrogen fixing bacteroids. M. truncatula is also plant host for root-knot nematodes, such as Meloidogyne incognita. During this compatible pathogenic interaction, root-knot nematodes induce redifferenciation of root cells from the vascular cylinder into specialized feeding cells called “giant cells”. Hyperplasia and hypertrophy of the surrounding cells lead to the formation of typical root galls. This phenomenon invokes host pathways in common with those necessary for nitrogen-nodule formation suggesting that nematode and rhizobia exploit a relative common strategy of plant cell infection at the cellular and molecular level. In order to highlight key genes involved in gall and nodule developments, parallel laser microdissection of giant cells from galls and cells from zone II of nodules followed by transcriptomic analysis is performed.

extract_protocol: Standard protocol. 11.21ng.


title: G-Low-SCS-Tref-5093

description: Mammary epithelial cells (MEC) were stimulated in vitro either by live Staphylococcus aureus (Sa9A strain; Sa) or by its supernatant -soluble factors- (Sp).

value: Mammary epithelial cells (MEC)

tag: line

value: Low-SCS

tag: time and stimulation

value: Tref

value: Low susceptability

value: reference


title: CC_1 with array type Medicago from Affymetrix

description:
CC_1
In compatible interaction between plants and biotrophic microorganisms, neoformation of organs occurs to ensure an efficient relationship between both partners. During the interaction between Medicago truncatula and Sinorhizobium meliloti, bacteria induce the development of root nodule with a permanent meristem, and chronically infect plant cells from zone II before differentiating into atmospheric nitrogen fixing bacteroids. M. truncatula is also plant host for root-knot nematodes, such as Meloidogyne incognita. During this compatible pathogenic interaction, root-knot nematodes induce redifferenciation of root cells from the vascular cylinder into specialized feeding cells called “giant cells”. Hyperplasia and hypertrophy of the surrounding cells lead to the formation of typical root galls. This phenomenon invokes host pathways in common with those necessary for nitrogen-nodule formation suggesting that nematode and rhizobia exploit a relative common strategy of plant cell infection at the cellular and molecular level. In order to highlight key genes involved in gall and nodule developments, parallel laser microdissection of giant cells from galls and cells from zone II of nodules followed by transcriptomic analysis is performed.

source_name: CC, M. incognita

extract_protocol: Standard protocol. 9.95ng.

value: jemalong

value: root galls, surrounding cells


title: A549 Vehicle 6hr rep1

tag: time


title: Pediatric_GBM_49


title: Pediatric_GBM_45


title: G-Low-SCS-T1Sp-5129

tag: phenotype

tag: treatment

value: live Staphylococcus aureus


title: G-High-SCS-T1Sa-5217

value: High-SCS

value: High susceptability

value: supernatant


title: Pediatric_GBM_43

value: paediatric glioblastoma

value: F


title: Pediatric_GBM_47


title: GC_3 with array type Medicago from Affymetrix

description:
GC_3
In compatible interaction between plants and biotrophic microorganisms, neoformation of organs occurs to ensure an efficient relationship between both partners. During the interaction between Medicago truncatula and Sinorhizobium meliloti, bacteria induce the development of root nodule with a permanent meristem, and chronically infect plant cells from zone II before differentiating into atmospheric nitrogen fixing bacteroids. M. truncatula is also plant host for root-knot nematodes, such as Meloidogyne incognita. During this compatible pathogenic interaction, root-knot nematodes induce redifferenciation of root cells from the vascular cylinder into specialized feeding cells called “giant cells”. Hyperplasia and hypertrophy of the surrounding cells lead to the formation of typical root galls. This phenomenon invokes host pathways in common with those necessary for nitrogen-nodule formation suggesting that nematode and rhizobia exploit a relative common strategy of plant cell infection at the cellular and molecular level. In order to highlight key genes involved in gall and nodule developments, parallel laser microdissection of giant cells from galls and cells from zone II of nodules followed by transcriptomic analysis is performed.

extract_protocol: Standard protocol. 8.3ng.

tag: tissue

value: root galls, giant cells

value: Meloidogyne incognita


title: GC_1 with array type Medicago from Affymetrix

description:
GC_1
In compatible interaction between plants and biotrophic microorganisms, neoformation of organs occurs to ensure an efficient relationship between both partners. During the interaction between Medicago truncatula and Sinorhizobium meliloti, bacteria induce the development of root nodule with a permanent meristem, and chronically infect plant cells from zone II before differentiating into atmospheric nitrogen fixing bacteroids. M. truncatula is also plant host for root-knot nematodes, such as Meloidogyne incognita. During this compatible pathogenic interaction, root-knot nematodes induce redifferenciation of root cells from the vascular cylinder into specialized feeding cells called “giant cells”. Hyperplasia and hypertrophy of the surrounding cells lead to the formation of typical root galls. This phenomenon invokes host pathways in common with those necessary for nitrogen-nodule formation suggesting that nematode and rhizobia exploit a relative common strategy of plant cell infection at the cellular and molecular level. In order to highlight key genes involved in gall and nodule developments, parallel laser microdissection of giant cells from galls and cells from zone II of nodules followed by transcriptomic analysis is performed.

extract_protocol: Standard protocol. 8.8ng.


title: CC_2 with array type Medicago from Affymetrix

description:
CC_2
In compatible interaction between plants and biotrophic microorganisms, neoformation of organs occurs to ensure an efficient relationship between both partners. During the interaction between Medicago truncatula and Sinorhizobium meliloti, bacteria induce the development of root nodule with a permanent meristem, and chronically infect plant cells from zone II before differentiating into atmospheric nitrogen fixing bacteroids. M. truncatula is also plant host for root-knot nematodes, such as Meloidogyne incognita. During this compatible pathogenic interaction, root-knot nematodes induce redifferenciation of root cells from the vascular cylinder into specialized feeding cells called “giant cells”. Hyperplasia and hypertrophy of the surrounding cells lead to the formation of typical root galls. This phenomenon invokes host pathways in common with those necessary for nitrogen-nodule formation suggesting that nematode and rhizobia exploit a relative common strategy of plant cell infection at the cellular and molecular level. In order to highlight key genes involved in gall and nodule developments, parallel laser microdissection of giant cells from galls and cells from zone II of nodules followed by transcriptomic analysis is performed.

extract_protocol: Standard protocol. 15.62ng.


title: H9 derived neurons_rep2

value: brain


title: H9 derived neurons_rep1


title: G-High-SCS-T1Sp-5178

extract_protocol: Total RNA was extracted from mammary epithelial cells using double extraction method with Trizol and RNeasy. Quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using Agilent bioanalyzer 2100 slide.  RNA Integrity Number (RIN) index above 9 was measured for all samples.Two hundred ng of RNA were converted to double-stranded cDNA and amplified with the  QSuick amp Labelling kit, two colors  (Ref : 5190-0424, Agilent's technologies).


title: G-Low-SCS-T5Sp-5129


title: G-High-SCS-T5Sa-5012


title: 0707_122_20 wt vs. rps9bDi

city: San Francisco

first: Alex

last: Plocik

institute: UCSF

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps9bDi Cy5 rep3
0707_122_20.gpr

hyb_protocol: Competitive hybridization at 65oC for 12h

scan_protocol: Images were acquired using an Axon Instruments GenePix 4000B scanner, reading at wavelengths of 635nm and 532nm (Axon Instruments, http://www.axon.com). Image analysis was performed using Axon Instruments GenePix Pro version 4.0.

data_processing: Spot ratio data were log2 transformed and normalized within each array using global loess regression implemented in the Bioconductor marray package

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae wt strain

label_protocol: aa-dUTP incorporation during cDNA synthesis

growth_protocol: YEPD at 30oC to OD 0.5-0.6

extract_protocol: Acid phenol

value: wt

source_name: Saccharomyces cerevisiae rps9bDi strain


title: G-High-SCS-T5Sp-5182

value: Mammary epithelial cells (MEC)


title: 0707_015_20 wt vs. rps9bDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps9bDi Cy5 rep2
0707_015_20.gpr


title: G-High-SCS-Tref-5071

value: untreated


title: CC_3 with array type Medicago from Affymetrix

description:
CC_3
In compatible interaction between plants and biotrophic microorganisms, neoformation of organs occurs to ensure an efficient relationship between both partners. During the interaction between Medicago truncatula and Sinorhizobium meliloti, bacteria induce the development of root nodule with a permanent meristem, and chronically infect plant cells from zone II before differentiating into atmospheric nitrogen fixing bacteroids. M. truncatula is also plant host for root-knot nematodes, such as Meloidogyne incognita. During this compatible pathogenic interaction, root-knot nematodes induce redifferenciation of root cells from the vascular cylinder into specialized feeding cells called “giant cells”. Hyperplasia and hypertrophy of the surrounding cells lead to the formation of typical root galls. This phenomenon invokes host pathways in common with those necessary for nitrogen-nodule formation suggesting that nematode and rhizobia exploit a relative common strategy of plant cell infection at the cellular and molecular level. In order to highlight key genes involved in gall and nodule developments, parallel laser microdissection of giant cells from galls and cells from zone II of nodules followed by transcriptomic analysis is performed.

extract_protocol: Standard protocol. 9.8ng.


title: Pediatric_GBM_40


title: G-Low-SCS-T5Sa-5051

value: Low-SCS


title: 0422_057_20 wt vs. rps9bDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps9bDi Cy5 rep1
0422_057_20.gpr


title: 0422_057_10 rps9bDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps9bDi Cy3 rep1
0422_057_10.gpr


title: 0707_122_10 rps9bDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps9bDi Cy3 rep3
0707_122_10.gpr


title: Pediatric_GBM_4

value: M


title: 0707_015_10 rps9bDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps9bDi Cy3 rep2
0707_015_10.gpr


title: G-Low-SCS-T1Sp-5127

value: Low susceptability


title: G-High-SCS-T1Sa-5189


title: Pediatric_GBM_39


title: G-Low-SCS-Tref-5051

value: Tref

value: reference


title: Pediatric_GBM_42


title: Pediatric_GBM_41


title: Pediatric_GBM_37


title: N2_1 with array type Medicago from Affymetrix

description:
N2_1
In compatible interaction between plants and biotrophic microorganisms, neoformation of organs occurs to ensure an efficient relationship between both partners. During the interaction between Medicago truncatula and Sinorhizobium meliloti, bacteria induce the development of root nodule with a permanent meristem, and chronically infect plant cells from zone II before differentiating into atmospheric nitrogen fixing bacteroids. M. truncatula is also plant host for root-knot nematodes, such as Meloidogyne incognita. During this compatible pathogenic interaction, root-knot nematodes induce redifferenciation of root cells from the vascular cylinder into specialized feeding cells called “giant cells”. Hyperplasia and hypertrophy of the surrounding cells lead to the formation of typical root galls. This phenomenon invokes host pathways in common with those necessary for nitrogen-nodule formation suggesting that nematode and rhizobia exploit a relative common strategy of plant cell infection at the cellular and molecular level. In order to highlight key genes involved in gall and nodule developments, parallel laser microdissection of giant cells from galls and cells from zone II of nodules followed by transcriptomic analysis is performed.

extract_protocol: Standard protocol. 108.8ng.

value: jemalong

value: root nodule infection zone (zone II)

value: Sinorhizobium meliloti


title: AtBBX32_Event4_3PM_Rep2

city: Saint Louis

first: Jim

last: Morrell

state: Missouri

address: 800 North Lindbergh Blvd

department: Biotechnology

institute: Monsanto Co.

hyb_protocol: Affymetrix GeneChips, custom made for Monsanto Company, were allowed to equilibrate to RT and 1X hybridization buffer (0.10M MES, 0.96M NaCl, 0.02M EDTA and 0.01% Tween) was brought to 45C. Chips were loaded with 1X hybridization buffer and incubated at 45C for 10min with rotation of 60rpm in a Hybridization Oven 640 (Affymetrix). During this time samples were prepared as follows: 20X eukaryotic hybridization controls (Affymetrix) were heated at 65C for 5min. 7.5ug labeled DNA was brought to 100ul with molecular biology grade water and the following were added: 4.0ul of control oligo B2 (Affymetrix), 12ul 20X eukaryotic hybridization controls, 2.4ul 10mg/ml salmon sperm DNA (Invitrogen), 2.4ul 50mg/ml acetylated BSA (Invitrogen) and 120ul 2X hybridization buffer. Samples were then heated at 99C for 5min, followed by 45C for 5min. Samples were centrifuged at 14,000g for 5min at RT to pellet any particulate matter. During this centrifugation, chips were removed from the hybridization oven and drained of the 1X hybridization buffer; replacing it with the hybridization cocktail after centrifugation. Chips were then placed into the hybridization oven and incubated for 16h at 45C with a rotation of 60rpm.

scan_protocol: Hybridized GeneChips were washed, stained and scanned according to the manufacturer’s instructions using the GeneChip Fluidics Station 450 (Affymetrix), an Affymetrix GeneChip Scanner 3000 and the GeneChip Operating Software (GCOS) (Affymetrix).

data_processing: Data from Affymetrix GCOS system were normalized by RMA algorithm and then scaled to 75th percentile of 500 over all chips

organism: Glycine max

source_name: AtBBX32 Event4 sampled at 3PM

label_protocol: For labeling, 500ng of purified total RNA was used as input. TargetAmp™ 1-Round Biotin-aRNA Amplification Kit 105 kit from Epicentre (TAB1R80524) was used in amplification and labeling process following the kit protocol. In the end, Biotin-labelind-aRNA probe was generated and QCed by OD reading (yield) and Agilent bioanalyzer (quality).

growth_protocol: Plants were grown under standard agronomic field practices.  Pre-season fertilizer application was applied at standard rates and all water was supplied through rainfall throughout the season.

extract_protocol: Plant tissues are grounded using pestle and mortar with liquid nitrogen. 150mg-250mg grounded tissues were aliquoted to each Lysing Matix E tube (Qbiogen).  RNA extraction was done using modified CTAB (0.5% CTAB, 0.05M Tris-HCl, 0.8M Nacl, 10mM EDTA/PH8.0) method using Qbiogen Fast Prep instrument. 750 ul of CTAB solution and 400ul of Phenol (PH4, from Amersco) were added to ground tissue. Fasta Prep beat was performed for 45 sec at setting 6. Later contents were centrifuged at 10,000g/10min.Supernatant was extracted twice with Phenol:Chloroform:Isoamyl alcohol (24:24:1) mixture. RNA in the upper phase was precipitated with ethanol. Precipitated RNA pellet was suspended in RNase free water (85ul) and treated with 5ul DNase I (2u/ul, Ambion) for 30min at 37C. DNase treated RNA was purified using RNeasy pink column (Qiagen). Quality of the purified RNA was determined by using Beckman DU640 spectrophotometer and Agilent Bio-analyzer 2100. The A260/A280 O.D. ratio of RNA samples measured using Beckman DU640 spectrophotometer was between 1.8 and 2.3. The 28s/18s ratio determined by using Agilent Bioanalyzer was above 0.8.

treatment_protocol: No treatments were applied to the biological material. Leaf tissue was harvested from plants into liquid nitrogen and stored at -80C until extract

value: Trifoliate Leaf

tag: developmental stage

tag: event

value: AtBBX32 Event4


title: 0707_157_20 wt vs. rps9aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps9aDi Cy5 rep2
0707_157_20.gpr

tag: strain

source_name: Saccharomyces cerevisiae rps9aDi strain


title: Pediatric_GBM_35

description: Gene expression data from a primary pediatric glioblastoma

value: paediatric glioblastoma


title: G-Low-SCS-T1Sp-5093

value: live Staphylococcus aureus


title: Pediatric_GBM_30


title: G-Low-SCS-T5Sp-5127


title: G-High-SCS-T1Sp-5071

value: High-SCS

value: High susceptability


title: AtBBX32_Event4_3PM_Rep3


title: AtBBX32_Event4_3PM_Rep1


title: Pediatric_GBM_29

value: wt


title: Pediatric_GBM_27

value: F


title: G-Low-SCS-T1Sa-5130

value: Mammary epithelial cells (MEC)

value: supernatant


title: 0824_29_20 wt vs. rps8aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps8aDi Cy5 rep3
0824_29_20.gpr

source_name: Saccharomyces cerevisiae rps8aDi strain


title: AtBBX32_Event4_12PM_Rep3

source_name: AtBBX32 Event4 sampled at 12PM


title: 0707_151_10 rps9aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps9aDi Cy3 rep1
0707_151_10.gpr


title: Pediatric_GBM_26

value: M


title: AtBBX32_Event4_12PM_Rep2


title: Pediatric_GBM_22


title: 0707_157_10 rps9aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps9aDi Cy3 rep2
0707_157_10.gpr


title: Pediatric_GBM_2


title: 0422_052_20 wt vs. rps8aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps8aDi Cy5 rep1
0422_052_20.gpr


title: 0824_16_20 wt vs. rps8aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps8aDi Cy5 rep2
0824_16_20.gpr


title: scraified skin, biological rep3

city: Midlothian

first: Neil

middle: A.

last: Mabbott

address: Easter Bush

department: The Roslin Institute & Royal (Dick) School of Veterinary Sciences

country: United Kingdom

institute: University of Edinburgh

description: Gene expression data from mouse ear skin.

hyb_protocol: Following fragmentation, 7.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HT MG-430 PM Array plate. GeneChips were hybridised, washed and stained in the Affymetrix GeneTitan MC instrument.

scan_protocol: GeneChips were scanned using the scanner in the Affymetrix GeneTitan MC instrument.

data_processing: The data were analyzed by Robust Multichip Analysis using RMA Express [http://rmaexpress.bmbolstad.com]

source_name: ear skin, control

label_protocol: Biotinylated cRNA were prepared using the Genechip 3’ IVT Express Labelling Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions.

extract_protocol: Ear skin was collected into RNAlater (Ambion, location) and stored at -80 °C prior to analysis.  Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: ear skin


title: AtBBX32_Event4_12PM_Rep1


title: AtBBX32_Event4_9AM_Rep3

source_name: AtBBX32 Event4 sampled at 9AM


title: 0707_151_20 wt vs. rps9aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps9aDi Cy5 rep1
0707_151_20.gpr


title: scraified skin, biological rep2


title: Pediatric_GBM_17


title: G-High-SCS-Tref-5012

description: Mammary epithelial cells (MEC) were stimulated in vitro either by live Staphylococcus aureus (Sa9A strain; Sa) or by its supernatant -soluble factors- (Sp).

value: Tref

value: untreated


title: 0824_29_10 rps8aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps8aDi Cy3 rep3
0824_29_10.gpr


title: Pediatric_GBM_24


title: 0824_16_10 rps8aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps8aDi Cy3 rep2
0824_16_10.gpr


title: AtBBX32_Event4_9AM_Rep1


title: AtBBX32_Event4_6AM_Rep3

source_name: AtBBX32 Event4 sampled at 6AM


title: Pediatric_GBM_16


title: Pediatric_GBM_14


title: 0707_023_20 wt vs. rps23aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps23aDi Cy5 rep1
0707_023_20.gpr

source_name: Saccharomyces cerevisiae rps23aDi strain


title: 0422_052_10 rps8aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps8aDi Cy3 rep1
0422_052_10.gpr


title: Pediatric_GBM_11


title: 0707_023_10 rps23aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps23aDi Cy3 rep1
0707_023_10.gpr


title: scraified skin, biological rep1


title: AtBBX32_Event4_6AM_Rep2


title: AtBBX32_Event4_9AM_Rep2


title: Pediatric_GBM_15


title: control skin, biological rep2


title: M1726 - O.D. 0.4 - rep 3

city: Hanover

first: Lee

middle: R

last: Lynd

state: NH

address: 8000 Cummings Hall

department: Thayer School of Engineering

institute: Dartmouth College

hyb_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

data_processing: XYS  files were loaded into the R / Bioconductor environment using the packages “pdInfoBuilder” and “oligo”. The obtained probe pair expression levels were preprocessed using the Robust Multichip Average (RMA) method to obtain RMA-normalized signal values for all arrays.

organism: Acetivibrio thermocellus DSM 1313

source_name: Strain M1726 (hpt spo0A), taken at Optical Density point: 0.4

growth_protocol: 5 ml frozen inoculum was added to a 500 mL Qplus fermentor vessel with MTC-medium, and incubated at 200 rpm stirrer speed, pH = 7.2 (controlled: 1M H2SO4 and 4M KOH), with Optical Density measured by Dasgip Probe. 5 mL samples were taken using a syringe, centrifuged to collect cell pellet (5 min, 5,000 x g) and snap-frozen in liquid N2.

extract_protocol: RNA was isolated essentially described previously (Yang et al. 2010. PNAS. 107:10395–10400). Briefly, samples were harvested by centrifugation and the TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).

tag: fermentation run


title: M1726 - O.D. 0.4 - rep 2

scan_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: M1725 - O.D. max - rep 3

source_name: Strain M1725 (ldh+pta), taken at Optical Density point: max

label_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: AtBBX32_Event4_3AM_Rep3

source_name: AtBBX32 Event4 sampled at 3AM


title: M1630 - O.D. 0.4 - rep 3

source_name: Strain M1630 (pta), taken at Optical Density point: 0.4


title: CCALD patient fibroblast, biological rep5

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

description: Gene expression data of CCALD patient dermal fibroblast

hyb_protocol: followed affymetrix protocol

scan_protocol: followed affymetrix protocol

data_processing: WebArray software was used to generate log2-transformed gene expression values using the RMA algorithm

source_name: dermal fibroblast from CCALD patient

label_protocol: followed affymetrix protocol

growth_protocol: Fibroblasts are cultured in DMEM medium supplemented with 10% FBS at 37°C, 5% CO2 until confluence

extract_protocol: as recommended by affymetrix

treatment_protocol: Fibroblasts are dissociated with 0.05% trypsin at 37°C, 5% CO2 for 5minutes and collected by centrifugation

value: dermal fibroblast

tag: genotype

value: CCALD patient


title: 0707_024_10 rps21bDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps21bDi Cy3 rep2
0707_024_10.gpr

source_name: Saccharomyces cerevisiae rps21bDi strain


title: 0707_024_20 wt vs. rps21bDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps21bDi Cy5 rep2
0707_024_20.gpr


title: 0707_018_20 wt vs. rps21bDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps21bDi Cy5 rep1
0707_018_20.gpr


title: AtBBX32_Event4_3AM_Rep2


title: AtBBX32_Event4_6AM_Rep1


title: 0707_018_10 rps21bDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps21bDi Cy3 rep1
0707_018_10.gpr


title: AtBBX32_Event4_3AM_Rep1


title: CCALD patient fibroblast, biological rep3


title: control skin, biological rep1


title: AtBBX32_Event2_3PM_Rep3

source_name: AtBBX32 Event2 sampled at 3PM

value: AtBBX32 Event2


title: M1725 - O.D. 0.4 - rep 3

source_name: Strain M1725 (ldh+pta), taken at Optical Density point: 0.4


title: CCALD patient fibroblast, biological rep2


title: AtBBX32_Event2_3PM_Rep1

value: Trifoliate Leaf


title: AtBBX32_Event2_3PM_Rep2


title: M1726 - O.D. max - rep 3

source_name: Strain M1726 (hpt spo0A), taken at Optical Density point: max


title: CCALD patient fibroblast, biological rep4


title: M1629 - O.D. 0.4 - rep 3

source_name: Strain M1629 (ldh), taken at Optical Density point: 0.4


title: 0824_14_20 wt vs. rps14bDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps14bDi Cy5 rep2
0824_14_20.gpr

source_name: Saccharomyces cerevisiae wt strain

source_name: Saccharomyces cerevisiae rps14bDi strain


title: M1629 - O.D. max - rep 3

source_name: Strain M1629 (ldh), taken at Optical Density point: max


title: 0824_14_10 rps14bDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps14bDi Cy3 rep2
0824_14_10.gpr


title: 0824_27_10 rps14bDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps14bDi Cy3 rep3
0824_27_10.gpr


title: M1630 - O.D. 0.4 - rep 2


title: M1630 - O.D. max - rep 3

source_name: Strain M1630 (pta), taken at Optical Density point: max


title: M1725 - O.D. 0.4 - rep 2


title: 011308_141_20 wt vs. rps14bDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps14bDi Cy5 rep1
011308_141_20.gpr


title: AtBBX32_Event2_12PM_Rep3

source_name: AtBBX32 Event2 sampled at 12PM


title: healthy control fibroblast, biological rep3

description: Gene expression data of healthy control human dermal fibroblast

source_name: dermal fibroblast from healthy control

value: healthy control


title: healthy control fibroblast, biological rep4


title: healthy control fibroblast, biological rep2


title: 011308_141_10 rps14bDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps14bDi Cy3 rep1
011308_141_10.gpr


title: CCALD patient fibroblast, biological rep1


title: healthy control fibroblast, biological rep5


title: AtBBX32_Event2_9AM_Rep3

source_name: AtBBX32 Event2 sampled at 9AM


title: AtBBX32_Event2_12PM_Rep1


title: 0824_26_20 wt vs. rps14aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps14aDi Cy5 rep3
0824_26_20.gpr

source_name: Saccharomyces cerevisiae rps14aDi strain


title: M1629 - O.D. max - rep 2


title: AtBBX32_Event2_12PM_Rep2


title: healthy control fibroblast, biological rep1


title: AtBBX32_Event2_9AM_Rep2


title: M1629 - O.D. max - rep 1


title: AtBBX32_Event2_9AM_Rep1


title: Normal CBD. SOD2.male.benign

city: London

first: michael

last: chapman

address: Rowland Hill St

department: HPB Cancer Group

institute: Univeristy College London

description: Endoscopic bile duct brushings

hyb_protocol: Affy Human 133 plus 2.0 Genechips

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Normal CBD. SOD.male.benign

label_protocol: cDNA labelling for hybridisation to the microarray chips was performed using the FL-Ovation cDNA Biotin Module v2 (Nugen, USA) as per the manufacturers instructions

extract_protocol: Snap frozen in liquid nitrogen, RNA isolated using TRI Reagent and RNEasy minelute spin column plus DNA digestion purification. RNA amplication (starting quantity 75ng total RNA) using WTOvation FFPE kit

treatment_protocol: Samples of biliary epithelium taken using 'through the scope' endoscopic biliary brushesof bile duct strictures from patients undergoing ERCP procedures

value: male

tag: tissue-type

value: benign bile duct


title: AtBBX32_Event2_6AM_Rep3

source_name: AtBBX32 Event2 sampled at 6AM


title: M1630 - O.D. max - rep 2


title: 011308_140_20 wt vs. rps14aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps14aDi Cy5 rep1
011308_140_20.gpr


title: 0824_13_20 wt vs. rps14aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps14aDi Cy5 rep2
0824_13_20.gpr


title: 0824_26_10 rps14aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps14aDi Cy3 rep3
0824_26_10.gpr


title: 0824_13_10 rps14aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps14aDi Cy3 rep2
0824_13_10.gpr


title: M1725 - O.D. max - rep 2

source_name: Strain M1725 (ldh+pta), taken at Optical Density point: max


title: M1629 - O.D. 0.4 - rep 2


title: 011308_140_10 rps14aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps14aDi Cy3 rep1
011308_140_10.gpr


title: 0824_25_20 wt vs. rpl40bDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl40bDi Cy5 rep3
0824_25_20.gpr

source_name: Saccharomyces cerevisiae rpl40bDi strain


title: AtBBX32_Event2_6AM_Rep2


title: M1726 - O.D. 0.4 - rep 1

source_name: Strain M1726 (hpt spo0A), taken at Optical Density point: 0.4


title: M1725 - O.D. 0.4 - rep 1


title: M1726 - O.D. max - rep 2


title: Hilar.CC2.male

description: Endoscopic bile duct brushings

value: Cholangiocarcinoma


title: AtBBX32_Event2_3AM_Rep3

source_name: AtBBX32 Event2 sampled at 3AM


title: AtBBX32_Event2_6AM_Rep1


title: AtBBX32_Event2_3AM_Rep2


title: Hilar.CC1.male

description: Endoscopic bile duct brushings


title: Chronic panc.Distal CBD stricture.female.benign

description: Endoscopic bile duct brushings

value: female


title: Hilar.CC3.female

description: Endoscopic bile duct brushings


title: AtBBX32_Event1_3PM_Rep3

source_name: AtBBX32 Event1 sampled at 3PM

value: AtBBX32 Event1


title: Chronic panc.Distal CBD stricture.male.benign

description: Endoscopic bile duct brushings


title: 0824_12_20 wt vs. rpl40bDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl40bDi Cy5 rep2
0824_12_20.gpr

value: wt


title: Hilar.CC.male

description: Endoscopic bile duct brushings


title: Normal CBD. SOD1.female.benign

description: Endoscopic bile duct brushings

source_name: Normal CBD. SOD.female.benign


title: M1630 - O.D. max - rep 1


title: AtBBX32_Event2_3AM_Rep1


title: 0824_25_10 rpl40bDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl40bDi Cy3 rep3
0824_25_10.gpr


title: 0422_042_20 wt vs. rpl40bDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl40bDi Cy5 rep1
0422_042_20.gpr


title: M1725 - O.D. max - rep 1


title: CBD.CC.2.male

description: Endoscopic bile duct brushings


title: 0824_12_10 rpl40bDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl40bDi Cy3 rep2
0824_12_10.gpr


title: M1629 - O.D. 0.4 - rep 1

source_name: Strain M1629 (ldh), taken at Optical Density point: 0.4


title: AtBBX32_Event1_3PM_Rep2


title: AtBBX32_Event1_3PM_Rep1


title: CBD.CC.1.male

description: Endoscopic bile duct brushings


title: M1726 - O.D. max - rep 1

source_name: Strain M1726 (hpt spo0A), taken at Optical Density point: max


title: S21.0

city: Stanford

first: Sean

last: McGhee

address: 269 Campus Drive, CCSR Rm 2115

department: Pediatrics

institute: Stanford University

hyb_protocol: 3' IVT express kit

scan_protocol: 3' IVT express kit

data_processing: Analysis done using R 2.9, bioconductor using affy, gcrma, and dependent packages.

source_name: Monocytes exposed to saline

label_protocol: 3' IVT express kit

growth_protocol: Human monocytes were extracted from whole blood using ficoll and attached to plastic culture plates.

extract_protocol: Trizol

treatment_protocol: DEP or saline was added to culture media as described.

value: cultured monocytes


title: S21.DEP

source_name: Monocytes exposed to DEP


title: AtBBX32_Event1_12PM_Rep2

source_name: AtBBX32 Event1 sampled at 12PM


title: 0824_06_20 wt vs. rpl35aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl35aDi Cy5 rep2
0824_06_20.gpr

source_name: Saccharomyces cerevisiae wt strain

source_name: Saccharomyces cerevisiae rpl35aDi strain


title: 0422_042_10 rpl40bDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl40bDi Cy3 rep1
0422_042_10.gpr


title: M1630 - O.D. 0.4 - rep 1

source_name: Strain M1630 (pta), taken at Optical Density point: 0.4


title: S22.0


title: AtBBX32_Event1_12PM_Rep3


title: PSy1 - CCR2+

city: Baltimore

first: Lucio

last: Gama

state: MD - EUA

address: 733 N Broadway St - BRB 831

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins School of Medicine

description:
20110112_LGam011011_5_05
Nano-Mono-11
Phenotype for classical monocytes: CD3- CD20- CD14+ CD16-

hyb_protocol: Samples were incubated for 16 hours according to Nanostring's protocols

scan_protocol: Samples were read by an nCounter scanner according to Nanostring's instructions

data_processing:
Data were sent to us in a excel spreadsheet format. Results for each gene were normalized by the geometric mean of 4 housekeeping genes (all corrected for 5,000 counts). Numbers below the higher negative control value for each sample was considered below the level of detection
Additional details: The positive values were not included in the sample table since they are irrelevant the results of the study.  Housekeeping genes: calculated their geometric mean for each of the samples (geomean).  For normalization, each sample geomean divided by 5,000 (/5000), which is the closest rounded number to the higher geomean value (4,995 - sample #8). Any number could have used in this case, but using lower values could lead to counts smaller than 1, which are more cumbersome to plot.

label: Alexa 488, Alexa 594, Alexa 647, Cy3

organism: Macaca nemestrina

source_name: Monocytes

label_protocol:
Codesets for inflammatory genes were designed form macaque RNA. Probes were mixed with samples according to Nanostring's protocols.
Color-coded probe pairs (representing capture and reporter probes; reporter probe carries the fluorescent tags) are mixed together with total RNA in a single hybridization reaction that proceeds in solution.

growth_protocol: PBMCs were isolated from fresh blood by Percoll gradient and frozen in liquid nitrogen.

extract_protocol: AllPrep (Qiagen) for DNA and RNA extraction from FFPe samples, according to manufactor's guidelines. RNA was resuspended in 60 µl of Rnase-free water, then concentrated (ethanol precipitation) to 6 µl.

treatment_protocol: On experiment day, cells were thawed in cold RPMI 25%FBS, washed one in same media, and stained for cytometry (CD3/CD20-FITC; CD14-PerCP; CD16-PE; CCR2-APC). Cells were fixed in 4% formaldehyde and sorted using a BD Aria cytometer.

value: Male

tag: infection status

value: SIV-infected 14 days p.i.

value: Monocytes

tag: cell number

tag: monocyte ccr2 status


title: PNy1 - CCR2-

description:
20110112_LGam011011_4_04
Nano-Mono-10
Phenotype for classical monocytes: CD3- CD20- CD14+ CD16-

tag: gender


title: PSy1 - CCR2-

description:
20110112_LGam011011_6_06
Nano-Mono-12
Phenotype for classical monocytes: CD3- CD20- CD14+ CD16-

tag: cell type


title: AtBBX32_Event1_9AM_Rep2

source_name: AtBBX32 Event1 sampled at 9AM


title: AtBBX32_Event1_12PM_Rep1


title: 0824_19_20 wt vs. rpl35aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl35aDi Cy5 rep3
0824_19_20.gpr


title: PNy1 - CCR2+

description:
20110112_LGam011011_3_03
Nano-Mono-09
Phenotype for classical monocytes: CD3- CD20- CD14+ CD16-


title: 0824_06_10 rpl35aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl35aDi Cy3 rep2
0824_06_10.gpr


title: S22.DEP


title: 0824_27_20 wt vs. rps14bDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rps14bDi Cy5 rep3
0824_27_20.gpr

source_name: Saccharomyces cerevisiae rps14bDi strain


title: PFv1 - CCR2+

description:
20110112_LGam011011_1_01
Nano-Mono-07
Phenotype for classical monocytes: CD3- CD20- CD14+ CD16-


title: S20.DEP


title: PFv1 - CCR2-

description:
20110112_LGam011011_2_02
Nano-Mono-08
Phenotype for classical monocytes: CD3- CD20- CD14+ CD16-


title: 0422_056_10 rpl35aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl35aDi Cy3 rep1
0422_056_10.gpr


title: AtBBX32_Event1_9AM_Rep3


title: AtBBX32_Event1_6AM_Rep3

source_name: AtBBX32 Event1 sampled at 6AM


title: 0422_056_20 wt vs. rpl35aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl35aDi Cy5 rep1
0422_056_20.gpr


title: AtBBX32_Event1_9AM_Rep1


title: S19.DEP


title: AtBBX32_Event1_6AM_Rep1


title: 0824_11_20 wt vs. rpl34aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl34aDi Cy5 rep2
0824_11_20.gpr

source_name: Saccharomyces cerevisiae rpl34aDi strain


title: PSt1 - CCR2-

description:
20110107_LGam010411_10_10
Nano-Mono-06
Phenotype for classical monocytes: CD3- CD20- CD14+ CD16-


title: 0824_24_20 wt vs. rpl34aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl34aDi Cy5 rep3
0824_24_20.gpr


title: S19.0


title: S18.DEP


title: PSt1 - CCR2+

description:
20110107_LGam010411_9_09
Nano-Mono-05
Phenotype for classical monocytes: CD3- CD20- CD14+ CD16-


title: AtBBX32_Event1_6AM_Rep2


title: AtBBX32_Event1_3AM_Rep3

source_name: AtBBX32 Event1 sampled at 3AM


title: S20.0


title: PLy1 - CCR2-

description:
20110107_LGam010411_6_06
Nano-Mono-04
Phenotype for classical monocytes: CD3- CD20- CD14+ CD16-


title: S18.0


title: 0422_051_20 wt vs. rpl34aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl34aDi Cy5 rep1
0422_051_20.gpr


title: PLy1 - CCR2+

description:
20110107_LGam010411_5_05
Nano-Mono-03
Phenotype for classical monocytes: CD3- CD20- CD14+ CD16-


title: 0422_051_10 rpl34aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl34aDi Cy3 rep1
0422_051_10.gpr


title: 0824_11_10 rpl34aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl34aDi Cy3 rep2
0824_11_10.gpr


title: S17.DEP


title: 0824_24_10 rpl34aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl34aDi Cy3 rep3
0824_24_10.gpr


title: S17.0


title: PIv1 - CCR2-

description:
20110107_LGam010411_4_04
Nano-Mono-02
Phenotype for classical monocytes: CD3- CD20- CD14+ CD16-


title: AtBBX32_Event1_3AM_Rep2


title: AtBBX32_Event1_3AM_Rep1


title: SB.0


title: ControlEvent_3PM_Rep2

source_name: non-Transgenic A3244 sampled at 3PM

value: Non-Transgenic


title: 0422_044_20 wt vs. rpl31aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl31aDi Cy5 rep1
0422_044_20.gpr

source_name: Saccharomyces cerevisiae rpl31aDi strain


title: 0824_23_20 wt vs. rpl2bDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl2bDi Cy5 rep3
0824_23_20.gpr

source_name: Saccharomyces cerevisiae rpl2bDi strain


title: SA.0


title: SB.DEP


title: MDA-MB-231 T8 tumor, rep2

city: ANN ARBOR

first: Shaomeng

last: Wang

address: 1150 E Med. Ctr. Dr.

institute: University of Michigan

description:
MDA-MB-231_010
Gene expression data from MDA-MB-231 xenograft tumor cells

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment version 2.7.0. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: MDA-MB-231 xenograft tumor cells sensitive to Smac mimetic SM-164

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

growth_protocol: MDA-MB-231 parental cells were cultured  under standard conditions.

extract_protocol: Total RNA was isolated by RNA miniprep kit (Sigma) according to the manufacturer's instruction.

treatment_protocol: SCID mice with MDA-MB-231 xenograft tumors were treated with 5 mg/kg of SM-164 intravenously for 5 days/week for 2 weeks. Regrown tumors were harvested and tumor cells were isolated.

tag: background cell line

value: breat cancer cells


title: SA.DEP


title: ControlEvent_3PM_Rep1


title: PIv1 - CCR2+

description:
20110107_LGam010411_3_03
Nano-Mono-01
Phenotype for classical monocytes: CD3- CD20- CD14+ CD16-


title: ControlEvent_12PM_Rep3

source_name: non-Transgenic A3244 sampled at 12PM


title: 0824_10_20 wt vs. rpl2bDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl2bDi Cy5 rep2
0824_10_20.gpr


title: 0422_044_10 rpl31aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl31aDi Cy3 rep1
0422_044_10.gpr


title: 0824_23_10 rpl2bDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl2bDi Cy3 rep3
0824_23_10.gpr


title: 0422_047_10 wt vs. rpl2bDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl2bDi Cy5 rep1
0422_047_10.gpr


title: cell line MCF7 24 hour hypoxia timepoint

city: Toronto

first: Maud

middle: HW

last: Starmans

state: Ontario

address: 661 University Avenue

department: Informatics and Biocomputing Program

country: Canada

institute: Ontario Institute for Cancer Research (OICR)

description: This is identical to GPL570 but a custom CDF environment was used to extract data [Brainarray Version 14.0.0, HGU133Plus2_Hs_ENTREZG]. CDF and other files can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.0.0/

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: All analyses were performed in R (v2.12.2). Data processing was performed for each cell line separately using RMA (affy package, v1.28.0) for pre-processing [13] and updated Entrez GeneID annotation (hgu133plus2hsentrezgcdf package, v14.0.0) [14].

source_name: cancer cell line (DU145)

label_protocol: Twenty ng pooled RNA was processed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA) for 2-cycle amplification and samples were hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips.

growth_protocol: Exponentially growing prostate (DU145), colon (HT29) and breast (MCF7) carcinoma cells were seeded on glass dishes in McCoy, DMEM or RPMI media, respectively with 10% FCS.

extract_protocol: Total RNA was isolated for each time-point using RNeasy (Qiagen, Hilden, Germany) following manufacturer’s specifications. RNA quantity/quality was determined using an ND-1000 spectrometer (NanoDrop Technologies, Wilmington, DE) and RNA Nano LabChip kit on the 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: The cells were then transferred to a hypoxic chamber (MACS VA500, Don Whitley Scientific, West-Yorkshire, UK) with atmosphere composition of 5% H2, 5% CO2, 0.0% O2 and residual N2. Cells were exposed to normoxia (time-point 0 hours) and different times of severe hypoxia (1, 2, 4, 8, 12, 16 and 24 hours, respectively).

value: hypoxia


title: cell line MCF7 16 hour hypoxia timepoint


title: cell line MCF7 4 hour hypoxia timepoint


title: cell line MCF7 12 hour hypoxia timepoint


title: MDA-MB-231 T8 tumor, rep1

description:
MDA-MB-231_009
Gene expression data from MDA-MB-231 xenograft tumor cells


title: ControlEvent_3PM_Rep3


title: cell line MCF7 8 hour hypoxia timepoint


title: MDA-MB-231 T6 tumor, rep1

description:
MDA-MB-231_007
Gene expression data from MDA-MB-231 xenograft tumor cells


title: MDA-MB-231 T3 tumor, rep2

description:
MDA-MB-231_006
Gene expression data from MDA-MB-231 xenograft tumor cells

source_name: MDA-MB-231 xenograft tumor cells resistant to Smac mimetic SM-164


title: ControlEvent_9AM_Rep3

source_name: non-Transgenic A3244 sampled at 9AM


title: ControlEvent_9AM_Rep2


title: 0824_10_10 rpl2bDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl2bDi Cy3 rep2
0824_10_10.gpr

source_name: Saccharomyces cerevisiae wt strain


title: ControlEvent_12PM_Rep1


title: MDA-MB-231 T6 tumor, rep2

description:
MDA-MB-231_008
Gene expression data from MDA-MB-231 xenograft tumor cells


title: ControlEvent_9AM_Rep1


title: cell line MCF7 2 hour hypoxia timepoint


title: cell line MCF7 1 hour hypoxia timepoint


title: 0422_047_20 rpl2bDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl2bDi Cy3 rep1
0422_047_20.gpr


title: 0824_09_20 wt vs. rpl2aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl2aDi Cy5 rep2
0824_09_20.gpr

source_name: Saccharomyces cerevisiae rpl2aDi strain


title: 0824_22_20 wt vs. rpl2aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl2aDi Cy5 rep1
0824_22_20.gpr


title: cell line MCF7 normoxia control,0 hour timepoint


title: MDA-MB-231 T3 tumor, rep1

description:
MDA-MB-231_005
Gene expression data from MDA-MB-231 xenograft tumor cells


title: 0824_09_10 rpl2aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl2aDi Cy3 rep2
0824_09_10.gpr


title: MDA-MB-231 T2 tumor, rep1

description:
MDA-MB-231_003
Gene expression data from MDA-MB-231 xenograft tumor cells


title: ControlEvent_6AM_Rep3

source_name: non-Transgenic A3244 sampled at 6AM


title: MDA-MB-231 parental, rep2

description:
MDA-MB-231_002
Gene expression data from MDA-MB-231 parental cells

source_name: MDA-MB-231 parental cells (sensitive to Smac mimetic SM-164)


title: MDA-MB-231 parental, rep1

description:
MDA-MB-231_001
Gene expression data from MDA-MB-231 parental cells


title: 0422_072_20 wt vs. rpl29Di

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl29Di Cy5 rep1
0422_072_20.gpr

source_name: Saccharomyces cerevisiae rpl29Di strain


title: 0707_004_20 rpl2aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl2aDi Cy3 rep1
0707_004_20.gpr


title: MDA-MB-231 T2 tumor, rep2

description:
MDA-MB-231_004
Gene expression data from MDA-MB-231 xenograft tumor cells


title: cell line HT29 16 hour hypoxia timepoint

description: This is identical to GPL570 but a custom CDF environment was used to extract data [Brainarray Version 14.0.0, HGU133Plus2_Hs_ENTREZG]. CDF and other files can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.0.0/


title: cell line HT29 24 hour hypoxia timepoint


title: 0422_072_10 rpl29Di vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl29Di Cy3 rep1
0422_072_10.gpr


title: ControlEvent_6AM_Rep1


title: cell line HT29 12 hour hypoxia timepoint


title: ControlEvent_3AM_Rep3

source_name: non-Transgenic A3244 sampled at 3AM


title: 0824_19_10 rpl35aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl35aDi Cy3 rep3
0824_19_10.gpr

source_name: Saccharomyces cerevisiae rpl35aDi strain


title: cell line HT29 4 hour hypoxia timepoint


title: ControlEvent_6AM_Rep2


title: cell line HT29 8 hour hypoxia timepoint


title: SSEA3-Pos-Rep3

first: James

middle: A

last: Byrne

address: 610 Charles E. Young Drive East

department: Department of Molecular and Medical Pharmacology

institute: University of California, Los Angeles

description: Gene expression data from embryos in slow phase of cellularisation.

hyb_protocol: Following fragmentation, 3.75ug of single strain cDNA were hybridized for 16 hr at 45C onAffymetrix Human Genome U133 Plus 2.0 Array in Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed in the Affymetrix Fluidics Station 450.

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

data_processing: Each CEL file was uploaded to GeneSifter (VisX Labs, Seattle, WA) using the Advanced Upload Method and normalized using the Affymetrix Microarray Analysis Suite (MAS) 5.0 algorithm.

source_name: Primary adult human skin cells

label_protocol: 100ng of total RNA was amplyfied using NuGEN Ovation RNA amplification System V2. Biotinylated cDNA were prepared according to NuGEN FL-Ovation cDNA Biotin Module V2 kit from 3.75 ug single stain cDNA

growth_protocol: The human fibroblast cell lines (HUF-1) used in this study were cultured in Dulbecco's Modified Eagle Medium Nutrient Mixture F-12 (DMEM/F12) supplemented with 10% fetal bovine serum (FBS, Invitrogen) and 100 IU/ml penicillin-streptomycin (Invitrogen) and maintained at 37°C in a 5% CO2 incubator. The culture media was changed every two days.  Cells were allowed to expand up to 80–90% confluence before being passaged through brief exposure to 0.05% trypsin-EDTA (Invitrogen) and seeded at a 1:3 ratio into new dishes with fresh culture media.

extract_protocol: Total RNA was purified from three biological replicates of the SSEA3HIGH and SSEA3NEGATIVE FACS-purified populations (24 hours after sorting) using the RNeasy Mini Kit (Qiagen, Valencia, CA, http://www1.qiagen.com) according to the manufacturer's instructions.  This total RNA was used for U133 plus 2.0 microarray-based analysis using standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001).

treatment_protocol: Up to 30 million HUF1 cells per experiment were trypsinized through a 5 min exposure to 0.05% trypsin-EDTA (Invitrogen), exposed to culture media to inactivate the trypsin and then washed twice with ice cold PBS + 2% goat serum (PBS-G). After the first wash the cells were passed through a 40 micrometer filter to remove cellular clumps. For each wash the cells were centrifuged for 5 min at 80 g, the supernatant was removed and the cells were gently resuspended in ice-cold PBS-G. After the washes the cells were resuspended in a 1.5 ml Eppendorf tube in 1 ml of ice-cold PBS-G containing 1:200 SSEA3 antibody (Millipore, mab4303) and incubated for 45 minutes in the dark at 4°C with gentle rocking. After primary antibody binding the cells were washed three times with ice-cold PBS-G and then resuspended in a 1.5 ml Eppendorf tube in 1 ml of ice-cold PBS-G containing 1:200 Alexa 488-conjugated goat anti-rat IgM (Invitrogen, A21212) and incubated for 45 minutes in the dark at 4°C with gentle rocking. After secondary antibody binding the cells were washed three times with ice-cold PBS-G and then resuspended in 2 ml of ice-cold PBS-G, passed again through a 40 micrometer filter and then immediately analyzed and sorted on a FACSAria cell sorter (BD Biosciences, San Jose, CA, USA, http://www.bdbiosciences.com).  DAPI (Invitrogen, D1306) was used at a 1:100 ratio for the detection and removal of dead cells.  Data was analyzed, doublet-exclusion gating was performed and the relevant populations were sorted using BD FACSDiva Software (BD Biosciences).  A previously established bank of HUF1 cells was used establish consistent SSEA3-NEGATIVE (bottom 10%) and SSEA3-HIGH (top 10%) gating parameters.  Sorted subpopulations were allowed to adhere for 24 hours before total RNA purification and microarrary analysis.

tag: cell line

tag: ssea3 expression

value: High


title: ControlEvent_3AM_Rep1

tag: time


title: SSEA3-Pos-Rep2


title: 0707_017_20 wt vs. rpl24aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl24aDi Cy5 rep1
0707_017_20.gpr

source_name: Saccharomyces cerevisiae rpl24aDi strain


title: cell line HT29 2 hour hypoxia timepoint

tag: treatment


title: SSEA3-Pos-Rep1


title: 0707_017_10 rpl24aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl24aDi Cy3 rep1
0707_017_10.gpr


title: ControlEvent_3AM_Rep2

tag: tissue


title: 0824_15_20 wt vs. rpl23aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl23aDi Cy5 rep3
0824_15_20.gpr

source_name: Saccharomyces cerevisiae rpl23aDi strain


title: cell line HT29 1 hour hypoxia timepoint


title: SSEA3-Neg-Rep2

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

value: Negative


title: SSEA3-Neg-Rep1


title: cell line HT29 normoxia control,0 hour timepoint


title: 0824_07_20 wt vs. rpl23aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl23aDi Cy5 rep2
0824_07_20.gpr


title: 0422_053_20 wt vs. rpl23aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl23aDi Cy5 rep1
0422_053_20.gpr


title: cell line DU145 24 hour hypoxia timepoint


title: cell line DU145 16 hour hypoxia timepoint


title: serous ovarian cancer 526 (affy)

city: Niigata

first: Kosuke

last: Yoshihara

address: 1-757 Asahimachi-dori

department: Obstetrics and Gynecology

institute: Niigata University

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

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

data_processing: The CEL file was normaized and summarized using the robust miltiple average (RMA) in GeneSpring GX11.5

source_name: high-grade serous ovarian cancer

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3'IVT Express Kit（Affymetrix) from 250 ng total RNA according to the manufacturer's instructions.  Biotinylated cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from tissue samples using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's recommendations. RNA was examined with a 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA, USA) using an RNA 6000 Nano LabChip (Agilent Technologies)

value: high-grade serous ovarian cancer tumor


title: SSEA3-Neg-Rep3


title: cell line DU145 12 hour hypoxia timepoint


title: serous ovarian cancer 527 (affy)


title: cell line DU145 8 hour hypoxia timepoint


title: 0824_15_10 rpl23aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl23aDi Cy3 rep3
0824_15_10.gpr


title: 0422_053_10 rpl23aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl23aDi Cy3 rep1
0422_053_10.gpr


title: cell line DU145 2 hour hypoxia timepoint


title: 0824_05_10 rpl16aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl16aDi Cy3 rep2
0824_05_10.gpr

source_name: Saccharomyces cerevisiae rpl16aDi strain


title: 0824_05_20 wt vs. rpl16aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl16aDi Cy5 rep2
0824_05_20.gpr


title: serous ovarian cancer 522 (affy)


title: 0824_07_10 rpl23aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl23aDi Cy3 rep2
0824_07_10.gpr


title: serous ovarian cancer 525 (affy)


title: serous ovarian cancer 523 (affy)


title: cell line DU145 normoxia control,0 hour timepoint


title: serous ovarian cancer 520 (affy)


title: ControlEvent_12PM_Rep2

value: Trifoliate Leaf

tag: developmental stage


title: cell line DU145 1 hour hypoxia timepoint


title: 0707_021_10 rpl16aDi vs. wt

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl16aDi Cy3 rep1
0707_021_10.gpr


title: 0707_021_20 wt vs. rpl16aDi

description:
Saccharomyces cerevisiae intron deletion strain vs. wild-type
rpl16aDi Cy5 rep1
0707_021_20.gpr


title: serous ovarian cancer 519 (affy)


title: cell line DU145 4 hour hypoxia timepoint

description: This is identical to GPL570 but a custom CDF environment was used to extract data [Brainarray Version 14.0.0, HGU133Plus2_Hs_ENTREZG]. CDF and other files can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.0.0/


title: serous ovarian cancer 518 (affy)


title: serous ovarian cancer 521 (affy)


title: serous ovarian cancer 516 (affy)


title: plac_unt_3

status: Public on Feb 27 2012

city: Auckland

first: Priyadarshini

last: Pantham

address: 85 Park Road

department: Obstetrics & Gynaecology

country: New Zealand

institute: The University of Auckland

hyb_protocol: Following fragmentation, 5ug of cRNA was hybridized onto Affymetrix Human Genome  U133 Plus 2 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: RMA (R program).

source_name: First-trimester human placenta, untreated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1µg total RNA (One-cycle cDNA synthesis).

growth_protocol: Placental explants were cultured in Advanced DMEM/F12 media containing 2% FBS and 1%PS for 16h, at 37°C and 5%CO2.

extract_protocol: RNA was extracted using Trizol and the Invitrogen PureLink mini kit according to manufacturer's instructions.

treatment_protocol: Antiphospholipid antibody (25µg/mL) treatment for 16h. Untreated controls were given media only.

value: placenta

tag: gestation

value: 8.5 weeks


title: plac_unt_2

value: 8.1 weeks


title: plac_unt_1

value: 8 weeks


title: NimbleGen: Rhesus macaque cerebral cortex M3

type: genomic

first: Jinkai

address: 650 Charles E. Young Drive South, CHS 33-228

description: Rhesus macaque cerebral cortex DNA methylation

hyb_protocol: Follow standard NimbleGen protocols

scan_protocol: The Scanning was performed with the Axon GenePix 4000B microarray scanner

data_processing: Between array normalization was conducted using Limma package implemented in R, and the probes that were not unique in the respective genomes were removed from the analyses.

molecule: genomic DNA

organism: Macaca mulatta

source_name: MeDIP DNA from rhesus macaque cerebral cortex

label_protocol: Follow standard NimbleGen protocols

extract_protocol: Genomic DNA from cerebral cortex tissues was extracted using DNeasy Blood & Tissue Kit (Qiagen) and fragmented by ultrasonic wave according to the manufacturer’s instructions

treatment_protocol: Post-mortem brain samples from cerebral cortex were collected

tag: age (year)

source_name: Input DNA from rhesus macaque cerebral cortex

tag: age(year)


title: plac_apl_2

source_name: First-trimester human placenta, antiphospholipid antibody treated (25ug/mL)

value: antiphospholipid antibody


title: MCF-7 SN38 resistant vs. sensitive

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: IC50 values of MCF-7 and MCF-7/SNR cells were 0.35 +/- 0.01 ng/mL, and 54.5 +/- 5.7 ng/mL, respectively. In contrast, these cells demonstrated similar resistance to vincristine. IC50 values of MCF-7 and MCF-7/SNR cells were 1.32 +/- 0.07 ng/mL and 1.47 +/- 0.08 ng/mL, respectively.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 7% fetal bovine serum (FBS) at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Extraction of total RNA was performed using an RNeasy Mini kit (QIAGEN) according to the manufacturer’s instruction. Integrity of extracted total RNA was checked by electrophoresis.

value: SN38-sensitive MCF-7 cells

value: SN38-resistant MCF-7 cells

value: derived from MCF-7


title: plac_apl_3


title: NimbleGen: Rhesus macaque cerebral cortex M2

value: Male


title: plac_apl_1


title: Tumor ID 78

status: Public on Feb 16 2012

city: New York

first: FANG

last: FANG

state: NY

address: 1275 York Avenue

department: The Human Oncology and Pathogenesis Program

institute: Memorial Sloan-Kettering Cancer Center

description: mskcc bank number s76

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: data was normalized and analyzed using partek software and R packages. Specifically centered logit transformation was used for data normalization.

source_name: glioma

label_protocol: Standard Illumina protocol for Human Methylation27 DNA Analysis bead chip

extract_protocol: The genomic DNA was extracted from snap-frozen sections from the breast cancer patients by using a DNeasy Tissue kit (Qiagen)

tag: tissue type

value: frozen tissue for primary tumor

value: glioma

tag: status

value: CIMP+


title: Tumor ID 80

description: mskcc bank number s78

value: CIMP-


title: Tumor ID 77

description: mskcc bank number s79


title: Tumor ID 71

description: mskcc bank number s66


title: Tumor ID 75

description: mskcc bank number s71


title: Tumor ID 20

description: mskcc bank number s81


title: Tumor ID 25

description: mskcc bank number s77


title: Tumor ID 79

description: mskcc bank number s75


title: NimbleGen: Rhesus macaque cerebral cortex M1


title: Tumor ID 68

description: mskcc bank number s61


title: Tumor ID 70

description: mskcc bank number s65


title: Tumor ID 74

description: mskcc bank number s73


title: Tumor ID 38

description: mskcc bank number s70


title: Tumor ID 69

description: mskcc bank number s63


title: Tumor ID 54

description: mskcc bank number s64


title: Tumor ID 63

description: mskcc bank number s54


title: Tumor ID 14

description: mskcc bank number s59


title: Tumor ID 66

description: mskcc bank number s60


title: Tumor ID 76

description: mskcc bank number s74


title: Tumor ID 62

description: mskcc bank number s69


title: Tumor ID 55

description: mskcc bank number s72


title: Tumor ID 61

description: mskcc bank number s53


title: Tumor ID 81

description: mskcc bank number s80


title: Tumor ID 64

description: mskcc bank number s58


title: Tumor ID 73

description: mskcc bank number s68


title: Tumor ID 65

description: mskcc bank number s57


title: Tumor ID 59

description: mskcc bank number s55


title: Tumor ID 26

description: mskcc bank number s56


title: Tumor ID 72

description: mskcc bank number s67


title: Tumor ID 67

description: mskcc bank number s62


title: Tumor ID 15

description: mskcc bank number s51


title: Tumor ID 54

description: mskcc bank number s64

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: GeneChips were scanned using  Affymetrix GeneArray scanner 7G.

data_processing: data was normalized and analyzed using partek software and R packages. Specifically log2 transformation was used for data normalization.

label_protocol: 200 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

extract_protocol: The RNA  was extracted using Agencourt RNAdvance Tissue Kit according to the manufacturer's instructions.


title: Tumor ID 70

description: mskcc bank number s65


title: Tumor ID 79

description: mskcc bank number s75


title: Tumor ID 56

description: mskcc bank number s46


title: Tumor ID 71

description: mskcc bank number s66


title: Tumor ID 67

description: mskcc bank number s62


title: Tumor ID 69

description: mskcc bank number s63


title: Tumor ID 24

description: mskcc bank number s49


title: Tumor ID 68

description: mskcc bank number s61


title: Tumor ID 66

description: mskcc bank number s60


title: Tumor ID 60

description: mskcc bank number s52


title: Tumor ID 57

description: mskcc bank number s50


title: Tumor ID 27

description: mskcc bank number s34


title: Tumor ID 45

description: mskcc bank number s37


title: Tumor ID 50

description: mskcc bank number s41


title: Tumor ID 44

description: mskcc bank number s35


title: Tumor ID 53

description: mskcc bank number s44


title: Tumor ID 41

description: mskcc bank number s31


title: Tumor ID 52

description: mskcc bank number s45


title: Tumor ID 47

description: mskcc bank number s38


title: Tumor ID 39

description: mskcc bank number s47


title: Tumor ID 58

description: mskcc bank number s48


title: Tumor ID 49

description: mskcc bank number s39


title: Tumor ID 48

description: mskcc bank number s40


title: Tumor ID 46

description: mskcc bank number s43


title: Tumor ID 42

description: mskcc bank number s32


title: Tumor ID 51

description: mskcc bank number s42


title: Tumor ID 36

description: mskcc bank number s30


title: Tumor ID 34

description: mskcc bank number s29


title: Tumor ID 64

description: mskcc bank number s58


title: Tumor ID 14

description: mskcc bank number s59


title: Tumor ID 16

description: mskcc bank number s24


title: Tumor ID 43

description: mskcc bank number s33


title: Tumor ID 24

description: mskcc bank number s49


title: Tumor ID 33

description: mskcc bank number s26


title: Tumor ID 57

description: mskcc bank number s50


title: Tumor ID 58

description: mskcc bank number s48


title: Tumor ID 40

description: mskcc bank number s36


title: Tumor ID 15

description: mskcc bank number s51


title: Tumor ID 61

description: mskcc bank number s53


title: Tumor ID 59

description: mskcc bank number s55


title: Tumor ID 52

description: mskcc bank number s45


title: Tumor ID 63

description: mskcc bank number s54


title: Tumor ID 39

description: mskcc bank number s47


title: Tumor ID 60

description: mskcc bank number s52


title: Tumor ID 46

description: mskcc bank number s43


title: Tumor ID 50

description: mskcc bank number s41


title: Tumor ID 32

description: mskcc bank number s25


title: Tumor ID 49

description: mskcc bank number s39


title: Tumor ID 35

description: mskcc bank number s28


title: Tumor ID 53

description: mskcc bank number s44


title: Tumor ID 51

description: mskcc bank number s42


title: Tumor ID 37

description: mskcc bank number s27


title: Tumor ID 47

description: mskcc bank number s38


title: Tumor ID 30

description: mskcc bank number s23


title: Tumor ID 27

description: mskcc bank number s34


title: Tumor ID 45

description: mskcc bank number s37


title: Tumor ID 28

description: mskcc bank number s17


title: Tumor ID 43

description: mskcc bank number s33


title: Tumor ID 31

description: mskcc bank number s22


title: Tumor ID 9

description: mskcc bank number s19


title: Tumor ID 36

description: mskcc bank number s30


title: Tumor ID 42

description: mskcc bank number s32


title: Tumor ID 35

description: mskcc bank number s28


title: Tumor ID 37

description: mskcc bank number s27


title: Tumor ID 34

description: mskcc bank number s29


title: Tumor ID 16

description: mskcc bank number s24


title: Tumor ID 33

description: mskcc bank number s26


title: Tumor ID 8

description: mskcc bank number s16


title: Tumor ID 10

description: mskcc bank number s14


title: Tumor ID 7

description: mskcc bank number s13


title: Tumor ID 30

description: mskcc bank number s23


title: Tumor ID 29

description: mskcc bank number s21


title: Tumor ID 12

description: mskcc bank number s18


title: Tumor ID 29

description: mskcc bank number s21


title: Tumor ID 9

description: mskcc bank number s19


title: Tumor ID 31

description: mskcc bank number s22


title: Tumor ID 3

description: mskcc bank number s12


title: Tumor ID 12

description: mskcc bank number s18


title: Tumor ID 8

description: mskcc bank number s16


title: Tumor ID 11

description: mskcc bank number s15


title: Tumor ID 11

description: mskcc bank number s15


title: Tumor ID 4

description: mskcc bank number s10


title: Tumor ID 28

description: mskcc bank number s17


title: Tumor ID 13

description: mskcc bank number s20


title: Tumor ID 2

description: mskcc bank number s8


title: Tumor ID 1

description: mskcc bank number s7


title: Tumor ID 5

description: mskcc bank number s9


title: Tumor ID 17

description: mskcc bank number s5


title: Tumor ID 19

description: mskcc bank number s6


title: Tumor ID 4

description: mskcc bank number s10


title: Tumor ID 22

description: mskcc bank number s2


title: Tumor ID 2

description: mskcc bank number s8


title: Tumor ID 5

description: mskcc bank number s9


title: Tumor ID 18

description: mskcc bank number s4


title: Tumor ID 3

description: mskcc bank number s12


title: 10-day seedling of sahh1 mutant (rep2)

status: Public on Feb 14 2012

city: Saskatoon

first: Ed

last: Tsang

address: 110 Gymnasium Place

department: Plant Bioinformatics Institute

institute: National Research Council of Canada

hyb_protocol: According to standard NimbleGen protocols (www.nimblegen.com)

scan_protocol: scanned at 5 μm resolution using a GenePix 4000B microarray scanner

data_processing: Quantile normalization was performed in all replicate arrays, and RMA (Robust Multichip Average) analysis was performed to generate gene expression values

organism: Arabidopsis thaliana

source_name: seedling

extract_protocol: Total RNA was isolated using RNeasy Plant Mini Kit (Qiagen, Mississauga, ON, Canada) according to the manufacturer’s instructions.

tag: age

value: 10 day

value: seedling

tag: cultivar

value: sahh1 mutant


title: Tumor ID 18

description: mskcc bank number s4


title: Tumor ID 21

description: mskcc bank number s1