title: BT4CTL_(17)

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

institute: university Paris Sud11

description: SAMPLE 7

hyb_protocol: Arrays has been hybridized with the labeled-target hybridization cocktail by rotation at 60 rpm in the Affymetrix Gene Chip hybridization oven at 45 °C for 16 h and washed in the Affymetrix GeneChip Fluidics station FS 450

scan_protocol: Arrays have been scanned by Affymetrix Gene Chip scanner 3000 7G system, to produce image files (.CEL)

data_processing: All expression values for the genes in the GCOS absolute analyses were determined using the global scaling option. The gene expression values were determined by MAS 5 algorithm in GCOS 1.2 (Affymetrix, Inc.).

source_name: Primary hepatocytes transgenic core BT untreated

label_protocol: The Affymetrix GeneChip® Whole Transcript Sense Target Labelling Assay has been used to amplify and reverse-transcribed total RNA (300 ng), and to biotinylate sense-strand DNA targets.

growth_protocol: Primary hepatocytes were isolated from 2 months old mice transgenic for HCV core protein.

extract_protocol: RNA has been extracted by Trizol (Invitrogen, Carlsbad, USA), purified from genomic DNA contamination through a DNase I (Qiagen, Valencia,CA, USA) digestion step and further enriched by Qiagen RNeasy columns for gene expression profiling (Qiagen)

treatment_protocol: Hepatocytes were cultured for 24h and treated with 1ng/ml TGF-beta for 2 h.

tag: background strain

value: 2 months

value: transgenic mice expressing Core variant T (tumoral)

value: primary hepatocytes


title: BT1CTL_(16)

status: Public on Mar 03 2012

type: RNA

country: France

description: SAMPLE 5

label: biotin

molecule: total RNA

organism: Mus musculus

tag: age

tag: genotype/variation

tag: tissue


title: CD4-126-D

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

hyb_protocol: cRNA was hybridized to the Illumina Whole Genome 6 (version 3) BeadChip (Illumina, San Diego, non-RA inflammatory arthritisA), following the manufacturer’s protocol.

scan_protocol: Each BeadChip measured the expression of 48,804 genes (annotation file at http://www.illumina.com/support/annotation_files.ilmn) and was imaged using the Illumina BeadArray Reader.

data_processing:
Phases 1 and 2 of the study were independently normalized in 2 steps: each probe measurement was first divided by the 50th percentile of all measurements in its array, before being centred around its own median expression measurement accross all samples in the phase. The within-phase batch-effect related to RNA labelling was corrected in the R statistical computing environment (http://www.r-project.org/) using the empirical Bayes method of Johnston et al. (2007) before phases were combined.  Phases were then combined and residual between-phase batch effect corrected by the same method.

Non-normalized data is available in 'GSE20098_non-normalized.txt', which is linked to the Series GSE20098 record as a supplementary file.

organism: Homo sapiens

source_name: ex-vivo peripheral blood CD4 T-cells, non-RA/non-inflammatory arthritis

label_protocol: 250ng RNA was reverse transcribed into cRNA, and biotin-UTP labeled, using the Illumina TotalPrep RNA Amplification Kit (Ambion, Texas).

extract_protocol: Monocytes were first depleted by immunorosetting (Rosettesep Human Monocyte depletion cocktail, Stemcell Technologies Inc., Vancouver, non-RA inflammatory arthritisanada), and remaining cells underwent positive selection using Easisep whole blood CD4+ positive selection kit reagents in conjunction with the Robosep automated cell separator (Stemcell). CD4+ T-cell purity was determined using standard flow cytometry techniques; FITC-conjugated anti-CD4 and PE-conjugated anti-CD14 antibodies were used (Beckton Dickinson, New Jersey, USA). RNA was immediately extracted from CD4+ T-cell isolates using RNeasy MINI kits (Qiagen GmbH, Germany), incorporating an “on-column” DNA digestion step.

treatment_protocol: Between 1300hrs and 1630hrs during the clinic appointment, 15ml peripheral whole blood was drawn into EDTA tubes (Greiner Bio-One, ACPA- RAustria) and stored at room temperature for a maximum of 4 hours before processing.

value: peripheral blood

tag: cell type

value: CD4+ T-cells

tag: outcome

value: D

tag: classification

value: UA

tag: phase batch

tag: labelling batch


title: WT2TGF_(25)

description: SAMPLE 12

source_name: Primary hepatocytes wild type treated with TGF-beta

value: control littermate wild type

tag: treated with

value: 1ng/ml TGF-beta for 2 h.


title: WT1TGF_(24)

description: SAMPLE 10


title: WT1CTL_(18)

description: SAMPLE 9

source_name: Primary hepatocytes wild type untreated


title: CD4-137-C

source_name: ex-vivo peripheral blood CD4 T-cells, non-RA inflammatory arthritis

value: C

value: training


title: BT1TGF_(26)

description: SAMPLE 6

source_name: Primary hepatocytes transgenic core BT treated with TGF-beta


title: WT2CTL_(19)

description: SAMPLE 11


title: CD4-118-C


title: BT4TGF_(23)

description: SAMPLE 8


title: BNT5CTL_(20)

description: SAMPLE 3

source_name: Primary hepatocytes transgenic core BNT untreated

value: transgenic mice expressing Core variant NT (non-tumoral)


title: BNT5TGF_(21)

description: SAMPLE 4

source_name: Primary hepatocytes transgenic core BNT treated with TGF-beta


title: BNT2CTL_(15)

description: SAMPLE 1


title: Wild type liver RNA2

city: Columbus

first: kalpana

last: ghoshal

state: OH

address: 420 W. 12th Avenue

department: Molecular and Cellular Biochemistry

country: USA

institute: The Ohio State University

description: 5 week old male mice

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), BioArray Eukaryotic Hybridization Controls (Enzo Life Sciences), heated at 65oC for 5 minutes, 99oC for 5 minutes, 45oC for 5 minutes centrifuged at maximum speed for 5 minutes, hybridized for 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G using AGCC version 3.2

data_processing: Data were processed using Affymetrix Expression Console software. Robust Multichip Average (RMA) method was used to do background correction, quantile normalization, and expression level summarization.

source_name: 5 week old male

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: 5 week old male mice

extract_protocol: total RNA was isolated from livers using miRVana kit from Applied Biosystems

tag: genotype

value: control (miR-122loxP/loxP)

tag: genetic background

value: liver


title: Wild type liver RNA1

description: 5 week old male mice


title: BNT2TGF_(22)

description: SAMPLE 2


title: MDAH2774 rhSTIP1 1

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with MAS5 by Affymetrix Expression Console Ver 1.1

label: Biotin

source_name: MDAH2774 cell treated with rhSTIP1

label_protocol: Standard Affymetrix protocol

extract_protocol: Cellular RNA Extraction with TRIZOL

tag: cell line

tag: treatment

value: 0.4 uM recombinant STIP1


title: miR-122KO liver RNA1

description: 5 week old male mice


title: CD4-442-C


title: AS_F1_LC56

city: Groningen

first: Maarten

last: van den Berge

address: Hanzeplein 1

department: Pulmonary Diseases

country: Netherlands

institute: University Medical Center Groningen

hyb_protocol: The labeled fragmented DNA was hybridized to the Gene Arrays 1.0 ST for 16-18 hours in GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using Affymetrix fluidics station 450. The first stain with streptavidin-R-phycoerythrin (SAPE) was followed by signal amplification using a biotinilated goat anti-streptavidin antibody and another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix, Santa Clara, CA).

scan_protocol: Microarrays were immediately scanned using Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow. Microarray data quality of 230 arrays was assessed using relative log expression (RLE) plots, normalized unscaled standard error (NUSE) plots, and principle component analysis (PCA) of all genes across all samples. Nine arrays were excluded due to a too low quality of the microarray data. Microarray data from 9 biopsies of 9 patients were excluded. All of 221 remaining samples from 90 COPD patients were of sufficient quality for subsequent analysis.

source_name: bronchial biopsy

label_protocol: All procedures were performed at Boston University Microarray Resource Facility as described in GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix, Santa Clara, CA, current version available at www.affymetrix.com). The Qiagen miRNeasy Mini Kit and RNeasy MinElute Cleanup Kit were used to isolate small fractions of RNA. 200 ng of large RNA fraction was reverse transcribed using Whole Transcript cDNA Synthesis kit (Affymetrix, Santa Clara, CA). The obtained cDNA was used as a template for in vitro transcription using Whole Transcript cDNA Amplification Kit (Affymetrix, Santa Clara, CA). The obtained antisense cRNA was purified using GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA), and used as a template for reverse transcription (Whole Transcript cDNA Synthesis kit, Affymetrix, Santa Clara, CA) to produce single-stranded DNA in the sense orientation. During this step dUTP was incorporated. The DNA was then fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) and labeled with DNA Labeling Reagent that is covalently linked to biotin using terminal deoxynucleotidyl transferase (TdT, Whole Transcript Terminal Labeling kit, Affymetrix, Santa Clara, CA). IVT and cDNA fragmentation quality controls were carried out by running an mRNA Nano assay in the Agilent 2100 Bioanalyzer.

extract_protocol: Endobronchial biopsies were immediately snap-frozen and stored at -80 oC. RNA was extracted from bronchial biopsies and fractioned into low molecular weight (< 200 nt) and high molecular weight (> 200 nt) fractions, by using the miRNeasy mini kit (QIAGEN) according to manufacturer’s protocol. Integrity of the RNA and purity of the RNA size fractionation were confirmed by using a 10% Tns-Borate Urea Polyacrylamide Gel Electrophoresis gel.

tag: time-point (0=baseline, 6 = after 6 months of treatment, 30 = after 30 months of treatment)

tag: patient glucold study id

tag: age (years)

tag: treatment (0=placebo 30 months, 1=fluticasone 30 months, 2=fluticasone/salmeterol 30 months, 3 = fluticasone 6 months and then placebo for the remaining 24 months of the study

tag: gender (0=female, 1 = male)


title: AS_F5_LC60


title: AS_F4_LC59


title: CD4-393-B

source_name: ex-vivo peripheral blood CD4 T-cells, ACPA+ RA

value: B


title: AS_E12_LC55


title: AS_E11_LC54


title: AS_F3_LC58


title: AS_E10_LC53


title: AS_E5_LC48


title: CD4-382-B


title: miR-122KO liver RNA2

description: 5 week old male mice


title: AS_E9_LC52


title: AS_E8_LC51


title: AS_E7_LC50


title: CD4-374-B


title: CD4-367-D


title: AS_F2_LC57


title: AS_E6_LC49


title: AS_E2_LC45


title: AS_E4_LC47


title: AS_D12_LC43


title: AS_E1_LC44


title: AS_D11_LC42


title: AS_E3_LC46


title: AS_D7_LC38


title: AS_D8_LC39


title: AS_D2_LC33


title: AS_D6_LC37


title: AS_D9_LC40


title: CD4-337-C


title: AS_D5_LC36


title: AS_D3_LC34


title: AS_D10_LC41


title: AS_D1_LC32


title: AS_D4_LC35


title: CD4-344-A

source_name: ex-vivo peripheral blood CD4 T-cells, ACPA- RA

value: A


title: CD4-323-D


title: AS_C10_LC29


title: AS_C12_LC31


title: AS_C7_LC26


title: AS_C6_LC25


title: CD4-333-B


title: AS_C8_LC27


title: AS_C1_LC20


title: AS_C2_LC21


title: CD4-349-B


title: AS_C9_LC28


title: AS_C3_LC22


title: AS_C5_LC24


title: AS_B12_LC19


title: AS_B10_LC17


title: CD4-301-B


title: CD4-299-A


title: CD4-303-C


title: AS_B9_LC16


title: AS_B8_LC15


title: CD4-310-D


title: CD4-297-C


title: CD4-309-D


title: AS_B1_LC8


title: AS_B5_LC12


title: CD4-293-C


title: CD4-300-D


title: AS_C4_LC23


title: AS_B3_LC10


title: CD4-288-B


title: AS_B11_LC18


title: AS_A9_LC4


title: AS_A11_LC6


title: AS_A10_LC5


title: AS_A12_LC7


title: AS_B6_LC13


title: AS_B2_LC9


title: AS_A8_LC3_.HuGene.1_0.st.v1.


title: CD4-291-D


title: AS_B7_LC14


title: Glucold_P3_lg91_.HuGene.1_0.st.v1.


title: AS_A7_LC2


title: Glucold_P4_lg92_.HuGene.1_0.st.v1.


title: Glucold_P2_lg90_.HuGene.1_0.st.v1.


title: CD4-287-B


title: Glucold_P5_lg94_.HuGene.1_0.st.v1.


title: AS_G3_LC1


title: CD4-285-D


title: CD4-284-C


title: Glucold_P1_lg89_.HuGene.1_0.st.v1.


title: Glucold_O7_lg82_.HuGene.1_0.st.v1.


title: Glucold_O6_lg81_.HuGene.1_0.st.v1.


title: Glucold_O4_lg78_.HuGene.1_0.st.v1.


title: Glucold_O5_lg79_.HuGene.1_0.st.v1.


title: CD4-268-B


title: CD4-276-A


title: CD4-282-C


title: CD4-269-B


title: CD4-277-D


title: Glucold_N7_lg69_.HuGene.1_0.st.v1.


title: Glucold_O3_lg77_.HuGene.1_0.st.v1.


title: CD4-262-D


title: CD4-270-D


title: Glucold_N6_lg67_.HuGene.1_0.st.v1.


title: CD4-259-D


title: Glucold_O1_lg71_.HuGene.1_0.st.v1.


title: Glucold_O8_lg83_.HuGene.1_0.st.v1.


title: CD4-255-D


title: Glucold_O2_lg76_.HuGene.1_0.st.v1.


title: Glucold_N5_lg66_.HuGene.1_0.st.v1.


title: Glucold_N3_lg64_.HuGene.1_0.st.v1.


title: Glucold_N8_lg70_.HuGene.1_0.st.v1.


title: Glucold_N1_lg62_.HuGene.1_0.st.v1.


title: Glucold_N4_lg65_.HuGene.1_0.st.v1.


title: CD4-248-D


title: CD4-256-B


title: CD4-292-D


title: CD4-258-D


title: CD4-249-B


title: Glucold_M6_lg56_.HuGene.1_0.st.v1.


title: CD4-242-C


title: Glucold_M7_lg57_.HuGene.1_0.st.v1.


title: CD4-251-B


title: Glucold_N2_lg63_.HuGene.1_0.st.v1.


title: CD4-246-B


title: CD4-243-C


title: CD4-250-C


title: CD4-244-A


title: Glucold_M4_lg53_.HuGene.1_0.st.v1.


title: Glucold_L8_lg45_.HuGene.1_0.st.v1.


title: Glucold_M2_lg51_.HuGene.1_0.st.v1.


title: Glucold_M5_lg54_.HuGene.1_0.st.v1.


title: Glucold_L7_lg44_.HuGene.1_0.st.v1.


title: CD4-241-A


title: Glucold_M1_lg50_.HuGene.1_0.st.v1.


title: AS_B4_LC11


title: CD4-240-C


title: Glucold_L6_lg43_.HuGene.1_0.st.v1.


title: CD4-237-C


title: CD4-238-C


title: Glucold_L5_lg39_.HuGene.1_0.st.v1.


title: Glucold_K8_lg27_.HuGene.1_0.st.v1.


title: Glucold_M3_lg52_.HuGene.1_0.st.v1.


title: Glucold_K7_lg24_.HuGene.1_0.st.v1.


title: CD4-236-B


title: CD4-230-D


title: CD4-231-C


title: Glucold_L2_lg35_.HuGene.1_0.st.v1.


title: Glucold_K6_lg23_.HuGene.1_0.st.v1.


title: Glucold_K2_lg12_.HuGene.1_0.st.v1.


title: Glucold_K5_lg22_.HuGene.1_0.st.v1.


title: Glucold_L4_lg38_.HuGene.1_0.st.v1.


title: Glucold_L1_lg34_.HuGene.1_0.st.v1.


title: CD4-227-D


title: CD4-222-B


title: CD4-216-D


title: Glucold_K1_lg11_.HuGene.1_0.st.v1.


title: Glucold_K3_lg18_.HuGene.1_0.st.v1.


title: Glucold_K4_lg19_.HuGene.1_0.st.v1.


title: Glucold_J6_lg103_.HuGene.1_0.st.v1.


title: Glucold_J5_lg102_.HuGene.1_0.st.v1.


title: CD4-223-C


title: Glucold_J3_lg100_.HuGene.1_0.st.v1.


title: CD4-213-C


title: Glucold_J4_lg101_.HuGene.1_0.st.v1.


title: Glucold_I7_lg93_.HuGene.1_0.st.v1.


title: Glucold_J1_lg98_.HuGene.1_0.st.v1.


title: CD4-212-D


title: Glucold_I8_lg97_.HuGene.1_0.st.v1.


title: Glucold_I4_lg86_.HuGene.1_0.st.v1.


title: CD4-211-B


title: Glucold_I6_lg88_.HuGene.1_0.st.v1.


title: Glucold_J2_lg99_.HuGene.1_0.st.v1.


title: Glucold_I5_lg87_.HuGene.1_0.st.v1.


title: CD4-209-A


title: CD4-207-D


title: Glucold_I1_lg80_.HuGene.1_0.st.v1.


title: CD4-205-B


title: CD4-197-B


title: Glucold_H8_lg75_.HuGene.1_0.st.v1.


title: Glucold_I2_lg84_.HuGene.1_0.st.v1.


title: Glucold_H7_lg74_.HuGene.1_0.st.v1.


title: CD4-198-D


title: CD4-200-C


title: CD4-192-D


title: CD4-195-B


title: Glucold_H2_lg59_.HuGene.1_0.st.v1.


title: Glucold_H4_lg68_.HuGene.1_0.st.v1.


title: Glucold_I3_lg85_.HuGene.1_0.st.v1.


title: Glucold_H3_lg61_.HuGene.1_0.st.v1.


title: Glucold_H6_lg73_.HuGene.1_0.st.v1.


title: CD4-193-C


title: CD4-181-C


title: CD4-174-A


title: Glucold_G5_lg47_.HuGene.1_0.st.v1.


title: Glucold_G3_lg42_.HuGene.1_0.st.v1.


title: CD4-176-A


title: Glucold_G2_lg41_.HuGene.1_0.st.v1.


title: Glucold_H1_lg58_.HuGene.1_0.st.v1.


title: Glucold_F8_lg36_.HuGene.1_0.st.v1.


title: Glucold_F6_lg32_.HuGene.1_0.st.v1.


title: Glucold_G7_lg49_.HuGene.1_0.st.v1.


title: Glucold_G8_lg55_.HuGene.1_0.st.v1.


title: CD4-183-B


title: CD4-191-C


title: Glucold_G4_lg46_.HuGene.1_0.st.v1.


title: CD4-182-B


title: CD4-177-D


title: CD4-214-B


title: Glucold_G6_lg48_.HuGene.1_0.st.v1.


title: Glucold_F7_lg33_.HuGene.1_0.st.v1.


title: CD4-172-B


title: Glucold_F5_lg31_.HuGene.1_0.st.v1.


title: Glucold_G1_lg40_.HuGene.1_0.st.v1.


title: CD4-173-C


title: CD4-165-D


title: CD4-159-D


title: CD4-163-B


title: Glucold_F4_lg30_.HuGene.1_0.st.v1.


title: CD4-161-D


title: miR-122KO liver RNA5

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G using GCOS version 1.4.0.036

data_processing: Data were processed using Affymetrix Expression Console software. Robust Multichip Average (RMA) method was used to do background correction, quantile normalization, and expression level summarization

source_name: 8 week  old male

growth_protocol: 8 week old male mice

value: mIR-122 KO


title: Glucold_E4_lg16_.HuGene.1_0.st.v1.


title: Glucold_E2_lg14_.HuGene.1_0.st.v1.


title: CD4-170-C


title: CD4-157-D


title: Glucold_F2_lg28_.HuGene.1_0.st.v1.


title: miR-122KO liver RNA4


title: CD4-154-C


title: Glucold_E6_lg20_.HuGene.1_0.st.v1.


title: Glucold_E8_lg25_.HuGene.1_0.st.v1.


title: Glucold_E3_lg15_.HuGene.1_0.st.v1.


title: Glucold_E1_lg13_.HuGene.1_0.st.v1.


title: miR-122KO liver RNA2


title: Glucold_F3_lg29_.HuGene.1_0.st.v1.


title: miR-122KO liver RNA3


title: CD4-153-C


title: Glucold_E5_lg17_.HuGene.1_0.st.v1.


title: CD4-155-D


title: Glucold_D07_2102.11_.HuGene.1_0.st.v1.


title: Glucold_E7_lg21_.HuGene.1_0.st.v1.


title: Glucold_F1_lg26_.HuGene.1_0.st.v1.


title: CD4-156-D


title: CD4-151-C


title: Wild type liver  RNA5

value: wild type


title: Wild type liver  RNA4


title: Wild type liver  RNA2


title: Wild type liver  RNA1


title: miR-122KO liver RNA1


title: Glucold_D06_2102.03_.HuGene.1_0.st.v1.


title: Glucold_D02_2101.01_.HuGene.1_0.st.v1.


title: Glucold_D05_2102.01_.HuGene.1_0.st.v1.


title: Glucold_C08_2097.01_.HuGene.1_0.st.v1.


title: Glucold_D04_2101.11_.HuGene.1_0.st.v1.


title: Wild type liver  RNA3


title: Glucold_C07_2085.11_.HuGene.1_0.st.v1.


title: Glucold_C09_2097.03_.HuGene.1_0.st.v1.


title: Glucold_D03_2101.03_.HuGene.1_0.st.v1.


title: Glucold_C10_2097.11_.HuGene.1_0.st.v1.


title: Glucold_C12_2100.03_.HuGene.1_0.st.v1.


title: Glucold_C05_2085.01_.HuGene.1_0.st.v1.


title: Glucold_C11_2100.01_.HuGene.1_0.st.v1.


title: Glucold_C06_2085.03_.HuGene.1_0.st.v1.


title: Glucold_D01_2100.11_.HuGene.1_0.st.v1.


title: Glucold_C03_2052.03_.HuGene.1_0.st.v1.


title: Glucold_C02_2052.01_.HuGene.1_0.st.v1.


title: Glucold_C01_2047.11_.HuGene.1_0.st.v1.


title: Glucold_B08_2037.01_.HuGene.1_0.st.v1.


title: Glucold_B09_2037.03_.HuGene.1_0.st.v1.


title: Glucold_B12_2047.03_.HuGene.1_0.st.v1.


title: Glucold_C04_2052.11_.HuGene.1_0.st.v1.


title: Glucold_B07_2034.03_.HuGene.1_0.st.v1.


title: CD4-175-D


title: Glucold_B11_2047.01_.HuGene.1_0.st.v1.


title: Glucold_B10_2037.11_.HuGene.1_0.st.v1.


title: Glucold_B06_2034.01_.HuGene.1_0.st.v1.


title: Glucold_B05_2026.11_.HuGene.1_0.st.v1.


title: Glucold_B04_2026.03_.HuGene.1_0.st.v1.


title: H661

type: genomic

city: South San Francisco

first: David

middle: S

last: Shames

state: CA

address: 1 DNA Way

department: Oncology Biomarker Development

institute: Genentech Inc

description: Non-small cell lung cancer cell line H661

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Preprocessed by Bioconductor lumi (v 2.5.3) package and sliding window smoothed with 250bp half-window-size.

molecule: genomic DNA

source_name: cell line

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

value: NSCLC

value: M

tag: response

value: intermediate


title: HOP18

description: Non-small cell lung cancer cell line HOP18

value: E


title: Glucold_B02_2025.11_.HuGene.1_0.st.v1.


title: H1792

description: Non-small cell lung cancer cell line H1792


title: Glucold_B01_2025.03_.HuGene.1_0.st.v1.


title: H2405

description: Non-small cell lung cancer cell line H2405


title: EKVX

description: Non-small cell lung cancer cell line EKVX

value: sensitive


title: Glucold_B03_2026.01_.HuGene.1_0.st.v1.


title: Glucold_A12_2025.01_.HuGene.1_0.st.v1.


title: Glucold_A11_2011.11_.HuGene.1_0.st.v1.


title: RERF-LC-Ad1

description: Non-small cell lung cancer cell line RERF-LC-Ad1


title: SW1573

description: Non-small cell lung cancer cell line SW1573


title: H1373

description: Non-small cell lung cancer cell line H1373


title: SK-MES-1

description: Non-small cell lung cancer cell line SK-MES-1


title: HOP92

description: Non-small cell lung cancer cell line HOP92

value: resistant


title: H1437

description: Non-small cell lung cancer cell line H1437


title: Glucold_A10_2011.03_.HuGene.1_0.st.v1.


title: H1793

description: Non-small cell lung cancer cell line H1793


title: Glucold_A08_1096.11_.HuGene.1_0.st.v1.


title: HOP62

description: Non-small cell lung cancer cell line HOP62


title: Glucold_A07_1096.03_.HuGene.1_0.st.v1.


title: Glucold_A06_1096.01_.HuGene.1_0.st.v1.


title: Calu-6

description: Non-small cell lung cancer cell line Calu-6


title: H2110.1

description: Non-small cell lung cancer cell line H2110.1


title: Glucold_A05_1095.03_.HuGene.1_0.st.v1.


title: HCC4017

description: Non-small cell lung cancer cell line HCC4017


title: Glucold_A09_2011.01_.HuGene.1_0.st.v1.


title: HCC15

description: Non-small cell lung cancer cell line HCC15


title: Glucold_A03_1080.11_.HuGene.1_0.st.v1.


title: H2030

description: Non-small cell lung cancer cell line H2030


title: Glucold_A01_1080.01_.HuGene.1_0.st.v1.


title: Glucold_A02_1080.03_.HuGene.1_0.st.v1.


title: H647

description: Non-small cell lung cancer cell line H647


title: HCC515

description: Non-small cell lung cancer cell line HCC515


title: H2170

description: Non-small cell lung cancer cell line H2170


title: AS_Glucold_D3_2078.01_.HuGene.1_0.st.v1.


title: H727

description: Non-small cell lung cancer cell line H727


title: AS_Glucold_D4_2098.01_.HuGene.1_0.st.v1.


title: HCC1171

description: Non-small cell lung cancer cell line HCC1171


title: H2126

description: Non-small cell lung cancer cell line H2126


title: AS_Glucold_D2_1102.01_.HuGene.1_0.st.v1.


title: AS_Glucold_D1_1041.01_.HuGene.1_0.st.v1.


title: AS_Glucold_C7_2108.01_.HuGene.1_0.st.v1.


title: H2347

description: Non-small cell lung cancer cell line H2347


title: AS_Glucold_C4_2069.11_.HuGene.1_0.st.v1.


title: AS_Glucold_C8_2108.11_.HuGene.1_0.st.v1.


title: H1838

description: Non-small cell lung cancer cell line H1838


title: AS_Glucold_C3_2069.01_.HuGene.1_0.st.v1.


title: AS_Glucold_C6_2083.11_.HuGene.1_0.st.v1.


title: AS_Glucold_C2_2062.11_.HuGene.1_0.st.v1.


title: H1666

description: Non-small cell lung cancer cell line H1666


title: Glucold_A04_1095.01_.HuGene.1_0.st.v1.


title: H1650

description: Non-small cell lung cancer cell line H1650


title: AS_Glucold_C1_2062.01_.HuGene.1_0.st.v1.


title: AS_Glucold_B8_2060.11_.HuGene.1_0.st.v1.


title: H2228

description: Non-small cell lung cancer cell line H2228


title: H1568

description: Non-small cell lung cancer cell line H1568


title: H2444

description: Non-small cell lung cancer cell line H2444


title: AS_Glucold_B7_2060.01_.HuGene.1_0.st.v1.


title: AS_Glucold_B6_2023.11_.HuGene.1_0.st.v1.


title: H1435

description: Non-small cell lung cancer cell line H1435


title: AS_Glucold_B5_2023.01_.HuGene.1_0.st.v1.


title: EBC-1

description: Non-small cell lung cancer cell line EBC-1


title: CHA-GO-K-1

description: Non-small cell lung cancer cell line CHA-GO-K-1


title: AS_Glucold_B2_1106.11_.HuGene.1_0.st.v1.


title: H1651

description: Non-small cell lung cancer cell line H1651


title: AS_Glucold_A8_1101.11_.HuGene.1_0.st.v1.


title: ABC-1

description: Non-small cell lung cancer cell line ABC-1


title: H1755

description: Non-small cell lung cancer cell line H1755


title: AS_Glucold_A7_1101.01_.HuGene.1_0.st.v1.


title: AS_Glucold_A6_1100.11_.HuGene.1_0.st.v1.


title: H2172

description: Non-small cell lung cancer cell line H2172


title: Calu-3

description: Non-small cell lung cancer cell line Calu-3


title: AS_Glucold_A4_1079.11_.HuGene.1_0.st.v1.


title: AS_Glucold_A3_1079.01_.HuGene.1_0.st.v1.


title: A427

description: Non-small cell lung cancer cell line A427


title: H2110

description: Non-small cell lung cancer cell line H2110


title: RERF-LC-MS

description: Non-small cell lung cancer cell line RERF-LC-MS


title: RERF-LC-KJ

description: Non-small cell lung cancer cell line RERF-LC-KJ


title: AS_Glucold_A2_1030.11_.HuGene.1_0.st.v1.


title: AS_Glucold_B4_2018.11_.HuGene.1_0.st.v1.


title: AS_Glucold_8_2088.11_.HuGene.1_0.st.v1.


title: H2087

description: Non-small cell lung cancer cell line H2087


title: AS_Glucold_6_2017.11_.HuGene.1_0.st.v1.


title: AS_Glucold_7_2088.01_.HuGene.1_0.st.v1.


title: H1975

description: Non-small cell lung cancer cell line H1975


title: H2073

description: Non-small cell lung cancer cell line H2073


title: AS_Glucold_5_2017.01_.HuGene.1_0.st.v1.


title: AS_Glucold_4_1092.11_.HuGene.1_0.st.v1.


title: HCC827

description: Non-small cell lung cancer cell line HCC827


title: AS_Glucold_3_1092.01_.HuGene.1_0.st.v1.


title: H1355

description: Non-small cell lung cancer cell line H1355


title: HCC2935

description: Non-small cell lung cancer cell line HCC2935


title: H1703

description: Non-small cell lung cancer cell line H1703


title: HCC4006

description: Non-small cell lung cancer cell line HCC4006


title: H820

description: Non-small cell lung cancer cell line H820


title: AS_Glucold_1_1076.01_.HuGene.1_0.st.v1.


title: H1993

description: Non-small cell lung cancer cell line H1993


title: Ewing positive sample EW1003T

city: Paris

first: Franck

last: Tirode

address: 26 Rue d'Ulm

department: Inserm U830

institute: Institut Curie

description: Gene expression data from Ewing positive sample

hyb_protocol: As according to the manufacturer's instructions.

scan_protocol: GCOS 1.4

data_processing: All data were normalized using the gcrma package version 2.22.0 in R 2.12.0 environment (R Development Core Team, 2005) with quantile normalisation

source_name: Samples from case n°1003

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol using 2µg total RNA

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

treatment_protocol: Frozen tumor biopsy

tag: fusion

tag: pathology

value: Ewing sarcoma

value: frozen tumor biopsy

tag: age

tag: gender

value: Male


title: Ewing positive sample EW1001T

source_name: Samples from case n°1001

tag: cell type

value: Female


title: Ewing positive sample EW999T

source_name: Samples from case n°999


title: Ewing negative sample EWN330T

description: Gene expression data from Ewing negative sample

source_name: Samples from case n°330

value: Poorly differentiated small round cell sarcoma


title: H226

description: Non-small cell lung cancer cell line H226


title: H23

description: Non-small cell lung cancer cell line H23


title: Ewing negative sample EWN997T

source_name: Samples from case n°997


title: Ewing negative sample EWN995T

source_name: Samples from case n°995


title: Ewing positive sample EW1000T

source_name: Samples from case n°1000


title: H322T

description: Non-small cell lung cancer cell line H322T


title: Ewing negative sample EWN994T

source_name: Samples from case n°994


title: H650

description: Non-small cell lung cancer cell line H650


title: Ewing negative sample EWN996T

source_name: Samples from case n°996

value: Fusiform cell sarcoma


title: Ewing negative sample EWN993T

source_name: Samples from case n°993

value: Undifferenciated small round cell malignant tumour


title: H1155

description: Non-small cell lung cancer cell line H1155


title: H2122

description: Non-small cell lung cancer cell line H2122


title: Ewing negative sample EWN991T

source_name: Samples from case n°991


title: H358

description: Non-small cell lung cancer cell line H358


title: Af293 vs Af293+Mast cells 3hrs Replicate 2

status: Public on Mar 02 2012

city: Rockville

first: Natalie

last: Fedorova

state: MD

address: 9704 Medical Center Dr

department: Infectious Disease

institute: JCVI

description: Analysis of the response of A. fumigatus to mast cells

hyb_protocol: Hybridizations were performed as per JCVI PFGRC SOP m008 (http://pfgrc.jcvi.org/index.php/microarray/protocols.html) Briefly:  Hybridizations were incubated for 18 h at 42C.  Post hybridization washes included (twice each) 55C in 2x ssc, 0.1% SDS, RT in 0.1x SSC, 0.1% SDS and RT 0.1x SSC.

scan_protocol: After washing, slides were scanned with a GenePix 4000b scanner using  GenePix Pro 3.0 software.   PMT gains were changed in order to generate images with red:green ratios of as close to 1:1 as possible.  Images were saved as .TIF files and TIGR Spotfinder (Saeed et al, 2003) was used to quantitate fluorescent intensities.  Poor quality spots were identified manually and flagged. After Spotfinder analysis, resulst were exported as TIGR software compatible MEV files following local background subtraction.

data_processing: MEV files were loaded into the JCVI MIDAS array normalization program where they were first normalized by block locally-weighted scatter plot smoothing (LOWESS).   After LOWESS, the flip-dye pairs were combined a consistency check was applied to remove any spots that do not fall within a specified deviation of the array-wide average log2  ratio of the fluorescence values for spot on both slides.   After the flip-dye consistency check the values underwent inter-slide standard deviation regularisation by averaging the values of the replicate spots for each gene.

organism: Aspergillus fumigatus

source_name: Af293 grown in RPMI-1640 with phenol red for 24h and then co-incubated with RPMI-1640 without phenol red for 3hrs

label_protocol: cDNA synthesis and labeling were performed as per JCVI PFGRC SOP m007 (http://pfgrc.jcvi.org/index.php/microarray/protocols.html)  Briefly:  cDNA were generated using Invitrogen Superscript II, incorporating aminoallyl-dUTP.  cDNA Samples were labeled with Cy3 or Cy5 during a 2 hour room temperature incubation followed by purification with a Qiagen PCR purification column to remove unbound dye.

growth_protocol: Conidia were seeded at 1 x 106 conidia/ml in RPMI-1640 without phenol red in cell culture dish and incubated for 24h at 37°C with 5% CO2.

extract_protocol: Total RNA extraction was performed using the filamentous fungi protocol of the Rneasy mini Kit (Qiagen).

treatment_protocol: Mast cells resuspended at 2 x 106 cells/ml or RPMI-1640 without phenol red were added to 24h-grown mature hyphae. Then, hyphae were co-incubated with cells or medium for either 1.5h or 3h at 37°C with 5% CO2.

tag: strain

value: culture medium

tag: time

value: 3 h

source_name: Af293 grown in RPMI-1640 with phenol red for 24h and then co-incubated with RBL-2H3 mast cells for 3hrs

value: co-incubation with .RBL-2H3 mast cells


title: Af293 vs Af293+Mast cells 3hrs Replicate 3


title: H2009

description: Non-small cell lung cancer cell line H2009


title: H292

description: Non-small cell lung cancer cell line H292


title: AS_Glucold_2_1076.11_.HuGene.1_0.st.v1.

source_name: bronchial biopsy


title: Ewing negative sample EWN986T

source_name: Samples from case n°986


title: Calu-1

description: Non-small cell lung cancer cell line Calu-1


title: H441

description: Non-small cell lung cancer cell line H441


title: H1299

description: Non-small cell lung cancer cell line H1299


title: H460

description: Non-small cell lung cancer cell line H460


title: Af293 vs Af293+Mast cells 1.5hr Replicate 1

source_name: Af293 grown in RPMI-1640 with phenol red for 24h and then co-incubated with RPMI-1640 without phenol red for 1.5hr

source_name: Af293 grown in RPMI-1640 with phenol red for 24h and then co-incubated with RBL-2H3 mast cells for 1.5hr


title: Af293 vs Af293+Mast cells 1.5hr Replicate 3


title: Af293 vs Af293+Mast cells 1.5hr Replicate 2


title: DC ko 4h pIC Rep1

city: New York

first: Terry

last: Fang

state: NY

address: 1230 York Ave

institute: Rockefeller University

description: G9a -/- DC stimulated with polyI:C for 4h

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using percentile normalisation with GeneSpringGX 10

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

growth_protocol: To induce expansion of splenic DCs, C57Bl/6, G9afl/fl mice and G9afl/fl;Vav-Cre mice were subcutaneously injected with 5 x 106 B16-Flt3L cells. Two weeks later splenic DCs were enriched for the CD11c+ population using CD11c MACS beads (Miltenyi).

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

treatment_protocol: DCs were directly stimulated with 10 μg/ml polyI:C in RPMI supplemented with 10% FBS, L-Glutamine, Penicillin-Streptomycin, Sodium Pyruvate, HEPES and 2-mercaptoethanol.

tag: genotype

value: G9a -/-, Vav-cre

value: ex vivo isolated splenic DCs


title: LXFL529

description: Non-small cell lung cancer cell line LXFL529

source_name: cell line

value: NSCLC

value: M


title: A549

description: Non-small cell lung cancer cell line A549

value: intermediate


title: DC fl 4h pIC Rep2

description: G9a f/f DC stimulated with polyI:C for 4h

value: G9a f/f, Vav-cre


title: Af293 vs Af293+Mast cells 3hrs Replicate 1


title: Ewing negative sample EWN987T

description: Gene expression data from Ewing negative sample

source_name: Samples from case n°987


title: DC ko 4h pIC Rep2

source_name: G9a -/- DC stimulated with polyI:C for 4h


title: DC fl 0h unstim Rep2

description: G9a f/f DC

source_name: G9a f/f DC


title: DC fl 4h pIC Rep1

source_name: G9a f/f DC stimulated with polyI:C for 4h


title: DC ko 1h pIC Rep2

description: G9a -/- DC stimulated with polyI:C for 1h


title: DC ko 0h unstim Rep2

description: G9a -/- DC

source_name: G9a -/- DC


title: DC ko 1h pIC Rep1

source_name: G9a -/- DC stimulated with polyI:C for 1h


title: Ewing negative sample EWN985T

source_name: Samples from case n°985


title: DC fl 1h pIC  Rep1

description: G9a f/f DC stimulated with polyI:C for 1h


title: DC ko 0h unstim Rep1

description: G9a -/- DC


title: gSAC1_UI

description: normal lung cell line gSAC1_UI

value: Normal


title: H838

description: Non-small cell lung cancer cell line H838

value: sensitive


title: G9a f/f 6h pIC Rep3

description: G9a f/f MEF transfected with polyIC for 6h

source_name: MEF

growth_protocol: MEFs were grown in 10 cm plates with DMEM medium containing 15% FBS, Pen/Strep, Glutamine, NEAA and 2-mercaptoethanol. After immortalization with SV40-LTA, MEFs were grown in 15 cm plates with the same medium except FBS was 10%.

treatment_protocol: Primary MEFs were immortalized at passage 2. At passage 5,  MEFs were treated witheither EtOH as a vehicle control or Tamoxifen to induce deletion of G9a. MEFs were transfected with polyIC using Lipofectamine 2000.

value: G9a -/-, ERT2-Cre

tag: passages

value: Passaged 12-15 times

value: transfected with polyIC for 6h


title: G9a -/- 12h pIC Rep3

description: G9a -/- MEF transfected with polyIC for 12h

value: transfected with polyIC for 12h


title: G9a -/- 6h pIC Rep3

description: G9a -/- MEF transfected with polyIC for 6h


title: gBEC

description: normal lung cell line gBEC


title: G9a f/f 12h pIC Rep3

description: G9a f/f MEF transfected with polyIC for 12h


title: G9a -/- 0h pIC Rep4

description: G9a -/- MEF treated with only transfection reagent

value: treated with only transfection reagent


title: G9a f/f 2h pIC Rep3

description: G9a f/f MEF transfected with polyIC for 2h

value: transfected with polyIC for 2h


title: gSAC1

description: normal lung cell line gSAC1


title: G9a -/- 12h pIC Rep2

value: G9a f/f, ERT2-Cre


title: G9a -/- 2h pIC Rep2

description: G9a -/- MEF transfected with polyIC for 2h


title: G9a -/- 0h pIC Rep3


title: G9a -/- 2h pIC Rep1


title: gBEC1

description: normal lung cell line gBEC1


title: G9a f/f 6h pIC Rep2


title: G9a f/f 12h pIC Rep2


title: G9a -/- 6h pIC Rep1


title: G9a -/- 0h pIC Rep2


title: G9a -/- 6h pIC Rep2


title: G9a -/- 12h pIC Rep1


title: G9a -/- 2h pIC Rep3


title: gBEC1_UI

description: normal lung cell line gBEC1_UI


title: G9a f/f 0h pIC Rep3

description: G9a f/f MEF treated with only transfection reagent


title: DC fl 1h pIC Rep2

source_name: G9a f/f DC stimulated with polyI:C for 1h


title: G9a f/f 12h pIC Rep1


title: G9a f/f 0h pIC Rep4


title: G9a f/f 6h pIC Rep1


title: G9a -/- 0h pIC Rep1


title: G9a f/f 2h pIC Rep1


title: G9a f/f 0h pIC Rep1


title: gSAC

description: normal lung cell line gSAC


title: snf1_KOH_10min vs snf1_KCl_10min_Exp_3

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

description: Spots with either a diameter smaller than 120 microm, or fluorescence intensity for Cy3 and Cy5 lower than 100 units, were not considered for further analysis.

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42ºC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 microl of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five microg of salmon sperm DNA was added to the mix before denaturation for 3 min at 95ºC. DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42ºC.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 microm. The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices).

data_processing: The GEPAS server (http://gepas3.bioinfo.cipf.es/) was used to preprocess the data (merge replicates). The normalization method we used to generate the data reported in the VALUE columns was the log(2) of the medians of ratios for the non-flagged genes.

organism: Saccharomyces cerevisiae

source_name: snf1 mutant strain in log phase culture

label_protocol: Fluorescent labeled cDNA was prepared from 8 microg of purified total RNA by the indirect dUTP-labeling method using the CyScribe post-labeling kit (GE Healthcare) and oligo(dT) as a primer.

growth_protocol: Grown at 28ºC in 50 ml of YPD rich medium (aprox. pH 5.5) until A660=0.5-0.8. Culture medium was alkalized until pH 8.0 by adding KOH (final concentration 16 mM, from 1 M stock solution). Cells were incubated at 28ºC for 10 min, harvested by rapid filtration, washed with cold water, snap frozen and the dried cells were kept at -80ºC until RNA purification.

extract_protocol: Total RNA purification using the Ambion RiboPure™-Yeast Total RNA Isolation Kit.

treatment_protocol: 16 mM KOH (aprox. pH 8.0) from 10 minutes.

growth_protocol: Grown at 28ºC in 50 ml of YPD rich medium (aprox. pH 5.5) until A660=0.5-0.8. KCl was added to the medium (16 mM, form 1 M stock solution), and cells Were incubated at 28ºC for 10 min, harvested by rapid filtration, washed with cold water, snap frozen and the dried cells were kept at -80ºC until RNA purification.

treatment_protocol: 16 mM KCl from 10 minutes.


title: Translatome  NIH3T3 cells+3h thapsigargin treatment

city: Madrid

first: Ivan

last: Ventoso

state: Madrid

address: Nicolas cabrera 1. Universidad Autonoma de Madrid

department: Virology and Microbiology

institute: Centro de Biología Molecular Severo Ochoa

description: biological  replicate 1 of 1. Translatome of NIH3T3 cells treated with thapsigargin for 3 h.

hyb_protocol: Equal volumes of  labeled cRNA product were co-hybridized with  Mouse Gene Expression Microarray (Agilent p/n G2519F-014868).

scan_protocol: Scanned on Agilent Technologies Scanner G2505B US45102947

data_processing:
Data extracted using Agilent Feature Extraction Software 10.7.1 using the grid template  014868_D_F_20100123 following the Agilent protocol GE2_107_Sep09 and the QC Metric Set GE2_QCMT_Sep09. Half background substration was carried in Babelomics 4.0 suite. Probe replicates were averaged. For processed data, only coding mRNAs are shown.
Translation efficiencies are in log2 ratio (Cy5/Cy3) for rawdata, and log2 ratio (Cy3/Cy5) for processed data.

source_name: NIH3T3 cells + 10microM thapsigargin

label_protocol: For labeling, we used equal volumes of FM and P fractions so that the total amount of RNA  for each sample was adjusted to 300 ng. Polysome bound RNA was labeled with Cy3 and  RNA of  FM fraction was labeled with Cy5 using  the low imput Quick Amp Labelling Kit, Two-Color (Agilent p/n 5190-2306) according to the manufacturer’s instructions.

growth_protocol: Four subconfluent p100 plates of NIH3T3 cells were grown in DMEM +10% bovine serum (#16170-078, Gibco).

extract_protocol: The cells were lysed and polysome bound RNA  was separated by centrifugation in a 10-40% sucrose gradient. Fractions were extracted with phenol, ethanol precipitated and  pooled in two fractions: free+monosome (FM) fraction, and polysome bound (P) fraction.

treatment_protocol: Where indicated, the cells were treated with 10microM thapsigargin (# T9033, Sigma) for 3h.

tag: cell line

value: NIH3T3 cells

tag: rna fraction

value: polysomal RNA (P)

value: non-polysomal RNA (FM)


title: Translatome  NIH3T3 cells control

description: biological replicate 1 of 1. Translatome of control NIH3T3 cells

source_name: NIH3T3 cells


title: G9a f/f 2h pIC Rep2

tag: treatment


title: snf1_KOH_10min vs snf1_KCl_10min_Exp_2


title: P_S_abiotic_stress_rep2

city: Yongin

first: Su-Hyun

last: Park

address: 38-2 Nam-dong

country: South Korea

institute: Myongji University

description: This sample is polysomal RNAs of salt-treated leaves.

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Oryza sativa

source_name: Polysomal RNAs of Salt-treated_abiotic stress_study_wild-type_rep2

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

growth_protocol: Non-transgenic rice (Oryza sativa L. cv. Nakdong) plants were grown under the conditions specified. Sterilized seeds were germinated in Murashige-Skoog (MS) solid medium in a growth chamber in the dark at 28°C for three days followed by in the light at 28°C for one day, transplanted into soil, and grown in a glasshouse (16 h light/8 h dark cycle) at 28-30°C. Each plant was grown in a pot (4x4x5 cm3; six plants per pot) filled with rice nursery soil (Bio-media, Kyeongju, Korea) for 14 days after germination. Stress treatment was performed as previously described (Oh et al., 2009; Jeong et al., 2010; Redillas et al., 2011). For drought stress, 14 d seedlings were air-dried in the greenhouse under continuous light of approximately 900-1,000 μmol m-2s-1. For salt stress treatment, 14 d seedlings were transferred to a 400 mM NaCl solution in the greenhouse under identical light conditions. For cold stress treatment, 14 d seedlings were exposed to 4°C in a cold chamber under continuous light of 150 μmol m-2s-1. Non-treated (NT) control seedlings were grown in the greenhouse and a growth chamber under the identical light conditions and harvested at time zero. Following each experimental procedure, leaf tissue was rapidly harvested into liquid nitrogen and stored at -80°C until use.

extract_protocol: Total and polysomal RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

value: Wild-type

tag: phenotype

value: normal

tag: cultivar

value: L. cv. Nakdong


title: snf1 mutant_0.05% Glucose vs snf1 mutant_2% Glucose _Exp_2

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 microm. The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices)

growth_protocol: Grown at 28ºC in 50 ml of YPD rich medium until A660=0.6. Cells were sedimented by centrifugation, washed with water and resuspended in the same volume of fresh YP medium containing 0.05% glucose. Cells were incubated at 28ºC for 15 min. Then cells were harvested by rapid filtration, washed with cold water, snap frozen and the dried cells were kept at -80ºC until RNA purification.

treatment_protocol: 0.05% Glucose for 15 min.

value: snf1 mutant

growth_protocol: Grown at 28ºC in 50 ml of YPD rich medium until A660=0.6. Cells were sedimented by centrifugation, washed with water and resuspended in the same volume of fresh YP medium containing 2% glucose. Cells were incubated at 28ºC for 15 min. Then cells were harvested by rapid filtration, washed with cold water, snap frozen and the dried cells were kept at -80ºC until RNA purification.

treatment_protocol: 2% Glucose for 15 min.


title: DC fl 0h unstim Rep1

description: G9a f/f DC

value: G9a f/f, Vav-cre

value: ex vivo isolated splenic DCs


title: snf1_KOH_10min vs snf1_KCl_10min_Exp_4


title: P_C_abiotic_stress_rep3

description: This sample is polysomal RNAs of cold-treated leaves.

source_name: Polysomal RNAs of Cold-treated_abiotic stress_study_wild-type_rep3


title: P_S_abiotic_stress_rep1

source_name: Polysomal RNAs of Salt-treated_abiotic stress_study_wild-type_rep1


title: P_S_abiotic_stress_rep3

source_name: Polysomal RNAs of Salt-treated_abiotic stress_study_wild-type_rep3


title: Wild type_0.05% Glucose_15 min vs wild type_2% Glucose_15 min_Exp_2

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42ºC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 microl of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five ug of salmon sperm DNA was added to the mix before denaturation for 3 min at 95ºC. DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42ºC.

source_name: WT strain in log phase culture_0.05% Glucose

value: wild type

source_name: WT strain in log phase culture_2% Glucose


title: snf1 mutant_0.05% Glucose vs snf1 mutant_2% Glucose _Exp_1


title: P_C_abiotic_stress_rep2

source_name: Polysomal RNAs of Cold-treated_abiotic stress_study_wild-type_rep2


title: WT_KOH_10min vs WT_KCl_10min_Exp_1

source_name: WT strain in log phase culture


title: WT_KOH_10min vs WT_KCl_10min_Exp_2

source_name: WT strain in log phase culture.


title: P_D_abiotic_stress_rep3

description: This sample is polysomal RNAs of drought-treated leaves.

source_name: Polysomal RNAs of Drought-treated_abiotic stress_study_wild-type_rep3


title: WT_KOH_10min vs WT_KCl_10min_Exp_3


title: WT_KOH_10min vs WT_KCl_10min_Exp_4


title: snf1_KOH_10min vs snf1_KCl_10min_Exp_1


title: Translatome Jurkat cells+ 1h thapsigargin treatment

description: biological replicate 1 of 1. Translatome of Jurkat cells treated with thapsigargin for 1 h.

hyb_protocol: Equal volumes of labeled cRNA product were co-hybridized with human Gene Expression Microarray (Agilent p/n G2519F-014850).

data_processing:
Data extracted using Agilent Feature Extraction Software 10.7.1 using the grid template 014850_D_F_20100115 following the Agilent protocol GE2_107_Sep09 and the QC Metric Set GE2_QCMT_Sep09. Normexp background correction was carried in Babelomics 4.0 suite. Probe replicates were averaged. For processed data, only coding mRNAs are shown.
Translation efficiencies are in log2 ratio (Cy5/Cy3) for rawdata, and log2 ratio (Cy3/Cy5) for processed data.

source_name: Jurkat cells + 10microM thapsigargin 1h

label_protocol: For labeling, we used equal volumes of FM and P fractions so that the total amount of RNA for each sample was adjusted to 300 ng. Polysome bound RNA was labeled with Cy3 and RNA from FM fraction was labeled with Cy5 using the low imput Quick Amp Labeling Kit, Two-Color (Agilent p/n 5190-2306) according to the manufacturer’s instructions.

growth_protocol: About 108 Jurkat cells were grown in RPMI +10% fetal serum (#10270-106, Gibco).

extract_protocol: The cells were lysed and polysome bound RNA was separated by centrifugation in a 10-40% sucrose gradient. Fractions were extracted with phenol, ethanol precipitated and pooled in two fractions: free+monosome (FM) fraction, and polysome bound (P) fraction.

treatment_protocol: Where indicated, the cells were treated with 10microM thapsigargin (#T9033, Sigma) for 1h or 3h.

value: T cell leukemia

value: Jurkat cells


title: Translatome Jurkat cells+ 3h thapsigargin treatment

description: biological replicate 1 of 1. Translatome of Jurkat cells treated with thapsigargin for 3 h.

source_name: Jurkat cells + 10microM thapsigargin 3h


title: G9a f/f 0h pIC Rep2

source_name: MEF

value: Passaged 12-15 times


title: Wild type_0.05% Glucose_15 min vs wild type_2% Glucose_15 min_Exp_1


title: P_C_abiotic_stress_rep1

source_name: Polysomal RNAs of Cold-treated_abiotic stress_study_wild-type_rep1


title: Translatome Jurkat cells control

description: biological replicate 1 of 1. Translatome of control Jurkat cells

source_name: Jurkat cells control


title: P_NC_abiotic_stress_rep3

description: This sample is polysomal RNAs of Negative control

source_name: Polysomal RNAs of Negative control (NC)_abiotic stress_study_wild-type_rep3


title: P_D_abiotic_stress_rep1

source_name: Polysomal RNAs of Drought-treated_abiotic stress_study_wild-type_rep1


title: P_D_abiotic_stress_rep2

source_name: Polysomal RNAs of Drought-treated_abiotic stress_study_wild-type_rep2


title: T_C_abiotic_stress_rep3

description: This sample is total RNAs of cold-treated leaves.

source_name: Total RNAs of Cold-treated_abiotic stress_study_wild-type_rep3


title: T_C_abiotic_stress_rep2

source_name: Total RNAs of Cold-treated_abiotic stress_study_wild-type_rep2


title: MSC-TSA (300nm for 18hrs) vs. MSC

city: BALTIMORE

first: hari

last: easwaran

address: 1650 Orleans Street, CRB1, Room 530

department: Oncology

institute: Johns Hopkins University

description:
Cultured cells.
MSC-TSA:MSC

hyb_protocol: 0.75 microgram of samples labeled with Cy3 or Cy5 were mixed with control targets (Agilent Technologies), assembled on Oligo Microarray, hybridized, and processed according to the Agilent microarray protocol.

scan_protocol: Scanning was performed with the Agilent Technologies Scanner G2505B US2250258 under the default settings recommended by Agilent Technologies.

data_processing: Raw data was processed in Bioconductor running on R (2.12.1) and LOWESS normalized (package Limma version 3.6.9) without background correction.

source_name: MSC

label_protocol: Sample amplification and labeling procedures were carried out using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according to the manufacturer's instructions. The labeled cRNA was purified using the RNeasy mini kit (Qiagen).

growth_protocol: U2OS cells were cultured in McCoys 5A media (Invitrogen) containing 10% FBS. MSCs were isolated from adult bone marrow and differentiated to osteoblasts as described by Jaiswal et al. (J Cell Biochem 64, 295-312; 1997).

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

value: mesenchymal stem cells

source_name: MSC-TSA

treatment_protocol: Cells were treated with 5 uM 5-Azadeoxycytidine (5-Aza-CdR) or 300 nM  Trischostatin-A (TSA) for 96 hours or 18 hours, respectively.

value: trischostatin A (TSA)


title: U2OS-AZA (5 um 96hrs) vs. U2OS

description:
Cultured cells.
U2OS-AZA:U2OS

value: osteosarcoma

value: 5-azadeoxycytidine (5-Aza-CdR)


title: Osteo-TSA (300nm for 18hrs) vs. Osteo

description:
Cultured cells.
Osteo-TSA:Osteo

source_name: Osteo

value: osteoblasts

source_name: Osteo-TSA


title: Osteo-AZA (5um 96hrs) vs. Osteo

description:
Cultured cells.
Osteo-AZA:Osteo

source_name: Osteo-AZA


title: U2OS-TSA (300nm for 18hrs) vs. U2OS

description:
Cultured cells.
U2OS-TSA:U2OS


title: MSC-AZA (5um 96hrs) vs. MSC

description:
Cultured cells.
MSC-AZA:MSC

source_name: MSC-AZA


title: P_NC_abiotic_stress_rep1

source_name: Polysomal RNAs of Negative control (NC)_abiotic stress_study_wild-type_rep1


title: podocyte from normal FVB mouse 3

city: Louisville

first: Jianxiang

last: Xu

state: KY

address: 570 S. Preston ST Suite 304

department: Pediatrics

institute: University of Louisville

description: gene expression data for FVB podocyte

hyb_protocol: Hybridization: 45 °C for 18 hours, Wash Protocol FS450_0004 on FS450.

scan_protocol: Affymetrix, GeneChip Scanner 30007G, GCOS 1.4

data_processing: Partek Genomics Suite, RMA Summarization and Normalization, 1-Way ANOVA: Diabetic vs Normal

source_name: podocyte from mouse kidney

label_protocol: NuGen FL-Ovation and Biotin Labeling Kit (Nugen Inc., San Carlos, CA)

growth_protocol: Mouse kidney was perfused by magnetic bead and kidney was digested by 1mg/ml collagenase solution. Glomeruli were isolated and purified by various magnetic platforms.

extract_protocol: total RNA was extracted by PicoPure RNA isolation kti from Arcturus according to manufacture's protocol.

treatment_protocol: Glomeruli were digested by 0.25% trypsin solution in 37oC, 5%CO2  incubator. Dispersed cell cluster by 1ml pipette until all fluorescence podocyte into singal cell. Washed cell and filtered by 35um cell strain then applied to FACS cell sorting machine.

tag: genotype/variation

tag: background strain

value: FVB

value: 3-4 months

tag: disease state


title: T_S_abiotic_stress_rep3

description: This sample is total RNAs of salt-treated leaves.

source_name: Total RNAs of Salt-treated_abiotic stress_study_wild-type_rep3

value: Wild-type


title: P_NC_abiotic_stress_rep2

source_name: Polysomal RNAs of Negative control (NC)_abiotic stress_study_wild-type_rep2

value: normal


title: podocyte from normal FVB mouse 4

description: gene expression data for FVB podocyte


title: Osteo vs. MSC

description:
Cultured cells.
Osteo:MSC


title: podocyte from OVE26 diabetic mouse 5

description: gene expression data for OVE26 podocyte

value: OVE-GFP

value: diabetic


title: seedling 24h light, (-Lin), rep4

city: East Lansing

first: Michael

middle: E

last: Ruckle

state: MI

address: S-208 Plant Biology, Michigan State University

department: Plant Research Labs

institute: Michigan State University

description: Gene expression data from 7 day old seedlings not treated with the chloroplast biogenesis inhibitor lincomycin (-Lin) 24h after a fluence rate shift from 0.5 to 60 µmol m-2 s-4

hyb_protocol: For each sample, 15μg of labeled target cRNA was purified, fragmented, and hybridized to the GeneChip® Arabidopsis ATH1 Genome Array (Affymetrix) as recommended by the manufacturer. The GeneChip arrays were then washed and stained using a GeneChip Fluidics Station 450 (Affymetrix)

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

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. In the manuscript, the data were normalized using GCRMA in R/Bioconductor (data provided as supplementary file: GSE24517.txt.gz).  Posterior probabilities were calculated using an empirical Bayes analysis on a per gene, per time point, and per treatment basis.  Samples Light_0h_(-LIN)_1 through Light_0h_(-LIN)_4 were used as the reference samples for -Lin at 0.5 h and 1 h.  Samples Light_0h_(+LIN)_1 through Light_0h_(+LIN)_4 were used as the reference samples for +Lin at 0.5 h and 1 h.  Samples Light_0h_(-LIN)_5 through Light_0h_(-LIN)_8 were used as the reference samples for -Lin at 4 h and 24 h.  Samples Light_0h_(+LIN)_5 through Light_0h_(+LIN)_8 were used as the reference samples for +Lin at 4 h and 24 h.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings, not treated with lincomycin, 24 h after the fluence shift

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 µg total RNA for each sample using the GeneChip One-Cycle Target Labeling (Affymetrix, Santa Clara CA).

growth_protocol: Col-0 seeds were surface-sterilized with ethanol, and plated on Linsmaier and Skoog medium containing 2% sucrose and 0.5% Phytoblend (Caisson Laboratories).  0.5mM lincomycin was included to the growth medium to block chloroplast biogenesis.  Seeds were stratified for 4 d at 4°C, irradiated with 125µmol m-2 s-1 red light for 1h at 21°C, incubated in the dark for 23h at 21°C, and incubated for 6 d in 0.5 µmol m-2 s-1 blue plus red (BR) light at 21°C.

extract_protocol: RNA was extracted with Qiagen Rneasy Plant Mini Kit (Qiagen, Valencia, CA) performed according to the manufacturer's instructions.

treatment_protocol: After 6 days of growth in 0.5 µmol m-2 s-1 blue plus red (BR) light, seedlings grown in the presence (+Lin) or absence (-Lin) of lincomycin were transferred to 60 µmol m-2 s-1 BR light.   50-100 seedlings were collected, frozen, and stored at -80°C before (0 h) and 0.5 h, 1 h, 4 h, and 24 h after the 0.5 to 60 µmol m-2 s-1 BR-fluence-rate shift.

tag: tissue

value: seedlings

value: 7 days old


title: T_C_abiotic_stress_rep1

source_name: Total RNAs of Cold-treated_abiotic stress_study_wild-type_rep1

value: L. cv. Nakdong


title: T_S_abiotic_stress_rep1

source_name: Total RNAs of Salt-treated_abiotic stress_study_wild-type_rep1


title: podocyte from OVE26 diabetic mouse 3

description: gene expression data for OVE26 podocyte


title: podocyte from normal FVB mouse 2

description: gene expression data for FVB podocyte

value: wild type


title: podocyte from OVE26 diabetic mouse 4

description: gene expression data for OVE26 podocyte


title: U2OS vs. MSC

description:
Cultured cells.
U2OS:MSC


title: podocyte from normal FVB mouse 1

description: gene expression data for FVB podocyte


title: mock.3

city: Baltimore

first: Claudia

middle: Roxana

last: Ruiz

address: 725 N. Wolfe St

department: Neuroscience

institute: The Johns Hopkins School of Medicine

description: control

data_processing:
Data were compiled in SDS RQ Manager 1.2.1 and analyzed in Data Assist 2.0 (Applied Biosystems); RQ was calculated as 2-ΔCtBDNF / 2-ΔCtmock where ΔCt = (cycle threshold for miRNA of interest) – (cycle threshold for reference control) (Schmittgen and Livak, 2008). Thresholds and cycle threshold (Ct) values were determined using default settings and the maximum allowable Ct value was set at 35.0 inclusive. Data were normalized by arithmetic mean using MammU6 (4395470) and snoRNA202 (4380914) reference RNAs as controls.
Maximum allowable CT value: 40.0 Reference group: mock

label: FRET

source_name: Murine hippocampal cultures

label_protocol: preincubation at 4oC for 5 min; 16 oC for 2 min, 42 oC for 1 min, 50 oC for 1 sec, 40 cycles; 85 oC for 5 min. The entire cDNA RT product (7.5 µl) was subjected to RT-qPCR on an Applied Biosystems 7900HT Fast Real-Time PCR system using Taqman Rodent MicroRNA Array A.

growth_protocol: Dissociated hippocampal cultures were prepared from postnatal day 0 (P0) mice as previously described(Meffert et al., 2003) and were maintained in Neurobasal A medium (Gibco, 10888) with B27 Supplement (Gibco 17504-44).

extract_protocol: 1 µg of total RNA for each sample was reverse-transcribed with stem-looped Megaplex RT Primers (Applied Biosystems) in a final volume of 7.5 µL according to manufacturer’s instructions

treatment_protocol: Murine hippocampal cultures were preincubated for 10-20 minutes with 0.5 µg / ml Actinomycin D and either mock- or BDNF- (100 ng / ml) stimulated for 30 minutes before harvesting.

value: Murine hippocampal cultures

tag: developmental stage

value: DIV 14

value: control


title: podocyte from OVE26 diabetic mouse 1

description: gene expression data for OVE26 podocyte

tag: age


title: mock.1

description: control


title: mock.2

description: control


title: T_D_abiotic_stress_rep3

description: This sample is total RNAs of drought-treated leaves.

source_name: Total RNAs of Drought-treated_abiotic stress_study_wild-type_rep3


title: BDNF.2

description: 30 minutes BDNF treatment

value: 30 minutes BDNF treatment


title: podocyte from OVE26 diabetic mouse 2

description: gene expression data for OVE26 podocyte


title: BDNF.1

description: 30 minutes BDNF treatment


title: T_NC_abiotic_stress_rep3

description: This sample is total RNAs of Negative control

source_name: Total RNAs of Negative control (NC)_abiotic stress_study_wild-type_rep3


title: T_S_abiotic_stress_rep2

source_name: Total RNAs of Salt-treated_abiotic stress_study_wild-type_rep2


title: T_D_abiotic_stress_rep1

source_name: Total RNAs of Drought-treated_abiotic stress_study_wild-type_rep1


title: BDNF.3

description: 30 minutes BDNF treatment


title: T_NC_abiotic_stress_rep1

source_name: Total RNAs of Negative control (NC)_abiotic stress_study_wild-type_rep1


title: T_D_abiotic_stress_rep2

source_name: Total RNAs of Drought-treated_abiotic stress_study_wild-type_rep2


title: [CD4+ T-Cells Peripheral Blood]_[TGFb]_[2]

city: West Lafayette

first: Chang

last: Kim

state: IN

address: 725 Harrison St

department: Comparative Pathobiology

institute: Purdue

description: Human CD4 T cells were cultured in vitro to obtain RNA for the assay

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized with a GeneChip Hybridization Oven 640 for 16 hr at 45C on GeneChip Human HG_U133_Plus_2 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 400 with fludics protocol EukGE_WS2v5 and user prepared solutions, as per protocols provided by Affymetrix in the GeneChip Expression Analysis Technical Manual, 2004. This included Enzo Life Sciences' BioArray Eukaryotic Hybridization Controls.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G enabled for High-Resolution Scanning. The instruments were controlled using GCOS version 1.4 software.

data_processing: The data were processed with MAS 5.0 using the GeneChip Operation Software.

source_name: Human Peripheral Blood

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA according to the Single Round RNA Amplification and Biotin Labeling System (Enzo Life Sciences Intl. Plymouth Meeting, PA)

extract_protocol:
Trizol
Qiagen Total RNA isolation kit

tag: tissue type

value: Peripheral Blood

value: CD4+ T cells

value: presence of TGFb1 + IL-2


title: [CD4+ T-Cells Peripheral Blood]_[Progesterone]_[2]

description: Human CD4 T cells were cultured in vitro to obtain RNA for the assay.

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA according to the Single Round RNA Amplification and Biotin Labeling System  (Enzo Life Sciences Intl.  Plymouth Meeting, PA)

tag: cell type

value: presence of progesterone + IL-2


title: T_NC_abiotic_stress_rep2

source_name: Total RNAs of Negative control (NC)_abiotic stress_study_wild-type_rep2


title: [CD4+ T-Cells Peripheral Blood]_[Control]_[2]

value: absence of progesterone  + IL-2


title: Patient ID 4279 DNA from relapse

city: Newcastle Upon Tyne

first: Vikki

last: Rand

state: Tyne and Wear

address: Paul O'Gorman Building, Newcastle University

department: Northern Institute for Cancer Research

hyb_protocol: as per Agilent protocol

scan_protocol: as per Agilent protocol

data_processing: Agilent Feature Extraction Software (v 9.5) was used for background subtraction and liner and LOWESS normalisation.

source_name: DNA from bone marrow taken at 1st relapse

label_protocol: as per Agilent protocol

extract_protocol: N/A, Patient DNA received from regional cytogenetic laboratories.

tag: gender

value: Male

tag: age (years)

source_name: reference DNA

extract_protocol: N/A, Reference DNA received from regional cytogenetic laboratories.

tag: reference

value: reference DNA


title: [CD4+ T-Cells Peripheral Blood]_[TGFb]_[1]

extract_protocol:
Trizol
Qiagen Total RNA Isolation Kit


title: Patient ID 7583 DNA

data_processing:
Agilent Feature Extraction Software (v 9.5) was used for background subtraction and liner and LOWESS normalisation.
Normalised logRatio values exported from Agilent Feature Extraction Software (v 9.5)

source_name: DNA from bone marrow


title: [CD4+ T-Cells Peripheral Blood]_[Progesterone+TGFb]_[1]

value: presence of progesterone + TGFb1 + IL-2


title: [CD4+ T-Cells Peripheral Blood]_[Progesterone]_[1]


title: [CD4+ T-Cells Cord Blood]_[Progesterone]_[1]

source_name: Human Cord Blood

value: Cord Blood


title: [CD4+ T-Cells Peripheral Blood]_[Progesterone+TGFb_[2]


title: Patient ID 6996 DNA

value: Female


title: Patient ID 6783 DNA


title: Patient ID 7093 DNA


title: Patient ID 7619 DNA


title: Patient ID 9864 DNA


title: [CD4+ T-Cells Peripheral Blood]_[Control]_[1]


title: Patient ID 8743 DNA


title: Patient ID 9028 DNA


title: Memory vs. non-memory Replicate 3

city: Boston

first: Pamela

last: Silver

state: MA

address: 200 Longwood Avenue WAB 536

department: Systems Biology

institute: Harvard Medical School

hyb_protocol: Samples were hybridized to 6.4Kv6 double-spotted yeast ORF microarrays (University Health Networks, Toronto). Microarrays were washed in 1x SSC to remove coverslips, washed 3x at 50 ˚C for 10 min in 1x SSC/0.1 % SDS before a final wash in 1x SSC and drying. Slides were kept overnight in the dark, at room temperature, and scanned the next day.

scan_protocol: Microarrays were scanned and fluorescence intensities quantified using the Axon Genepix 4000B scanner and software (BioPolymer Facility, Harvard Medical School).

data_processing: Individual arrays underwent background subtraction and log transformation. Arrays were global median normalized and intensities across all three arrays at each spot were then averaged, and coefficients of variation (CV) and fold-induction (FI) were calculated. Only genes with CV ≤ 1.5 and FI ≥ 1.5 were considered differentially expressed and analyzed for gene ontology (GO) enrichment via GoStat (http://gostat.wehi.edu.au/). GO enrichment was performed with Benjamini correction to correct for multiple hypothesis testing; enrichment was considered significant with P ≤ 0.001.

source_name: Memory

label_protocol: cDNA was extracted with phenol/chloroform and used as template for random priming with BioPrime DNA labelling kits (Invitrogen) and 3 uL of 1nM Cy5-dUTP or Cy3-dUTP (PerkinElmer). In two biological replicates, memory cells were labelled with Cy3-dUTP and non-memory cells with Cy5-dUTP; in one biological replicate, reverse fluorophore orientation accounted for dye bias.

growth_protocol: Cells were grown in 2% raffinose-SC media at 30˚ on a rotator

treatment_protocol: Log-phase cells were exposed to 0.3% ethyl methanesulfonate (EMS) and recovered for 36 h, sorted based on YFP expression, and grown another 12 h before RNA extraction.

value: Memory cells of HUG1 DNA damage memory strain after 24 h exposure to 0.3% EMS and 48 h recovery from damage

tag: genetic background

value: DBY

tag: strain

source_name: Non-memory

value: Non-memory cells of HUG1 DNA damage memory strain after 24 h exposure to 0.3% EMS and 48 h recovery from damage


title: Patient ID 8983 DNA

institute: Newcastle University


title: [CD4+ T-Cells Cord Blood]_[Progesterone+TGFb]_[1]


title: Patient ID 7255 DNA


title: [CD4+ T-Cells Cord Blood]_[Control]_[1]


title: Patient ID 7828 DNA


title: [CD4+ T-Cells Cord Blood]_[TGFb]_[1]


title: Patient ID 7045 DNA


title: Patient ID 7732 DNA


title: Patient ID 6111 DNA


title: Patient ID 11706 DNA


title: Memory vs. non-memory Replicate 2

extract_protocol: cDNA was extracted with phenol/chloroform

value: after 24 h exposure to 0.3% EMS and 48 h recovery from damage


title: Memory vs. non-memory Replicate 1


title: SW480_SiKRASV12_2

status: Public on Mar 01 2012

first: Manish

last: Gala

state: MASSACHUSETTS

address: 55 Fruit Street, GRJ 825

institute: Massachusetts General Hospital

hyb_protocol: Array hybridization were performed per recommended specifications (Asuragen, Austin, TX).

scan_protocol: Scanning were performed per recommended specifications (Asuragen, Austin, TX).

data_processing: Genechip PrimeView Human Arrays were utilized (Affymetrix, Santa Clara, CA). CEL files were analyzed utilizing R/Bioconductor package, oneChannelGUI. Briefly, normalization of expression values was performed utilizing the “Expresso” option, selecting “RMA” as the background correction, “quantiles” as normalization, “pmonly” as the PM correction, and “MAS” as the expression. Probes were filtered with IQR settings of 0.25. P values were calculated using a two-tailed Student’s t-test.

source_name: SW480 siRNA KRASV12 Biological Replicate #2

label_protocol: Per Affymetrix Protocol

extract_protocol: RNA was isolated from SW480sicontrol  and SW480siKrasV12 cells utilizing the RNeasy Mini Prep Kit per manufacturer’s instructions (Qiagen, Valencia, CA).

tag: cell line

value: siRNA against mutant KRASV12

tag: biological replicate


title: Patient ID 5898 DNA


title: SW480_SiControl_2

source_name: SW480 Control siRNA Biological Replicate #2

tag: treatment

value: scrambled siRNA control


title: SW480_SiKRASV12_1

source_name: SW480 siRNA KRASV12 Biological Replicate #1


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide95_18°C_6h)

city: Tiburon

first: Jonathon

middle: H

last: Stillman

address: 3152 Paradise Drive

department: Romberg Tiburon Center

institute: San Francisco State University

description: Raw data file: Slide95.gpr (linked as supplementary file on Series record).

hyb_protocol: For microarray hybridizations we used n=25 slides in an incomplete loop design where each sample was hybridized n=5 times, 2-3 times labelled with each Cy dye (Fig. S1).  Because we used pooled RNA samples to make aRNA, all of our replication assessed technical variation in estimating the means of the n=5 individuals in each group.    Custom microarrays were printed on poly-L-lysine coated glass slides (Erie Scientific) at the UCSF Center for Advanced Technology using 24,748 PCR amplified cDNAs each representing a unique consensus sequence from a library of 124K cloned cDNAs (Stillman et al., 2006; Tagmount et al., 2010).  Before use, spots were rehydrated by incubating slides in humidified air, snap dried at 100°C, and cross-linked by 200mJ UV exposure in a cross linker (Spectronics Co.).  Slides were shaken in 0.2% SDS, washed in copious amounts of ddH2O, and incubated at 42°C for 30-45 min in pre-warmed blocking solution (0.1% SDS, 5X SSC, and 1% BSA) to block free poly-L-lysine molecules.  Slides were washed in 5-6 changes of ultrapure water, denatured by washing in 95°C ddH2O for 2 min, and centrifuged to dry at 1000rpm for 3 min.  Dried cDNA + polyA RNAs were resuspended in 40µl hybridization buffer (50% deoinized formamide, 5XSSC, 0.1% SDS), heated 2 min at 94°C, chilled on ice, and pipetted underneath an Erie LifterSlip placed on the microarray slide and hybridized for 12-16h at 42°C.  Following hybridization, coverslips were removed and slides were washed for 5min with gentle shaking at 42°C two times in 2X SSC and 0.1% SDS, two times in 1X SSC, and two times in 0.1X SSC.  Slides were dried during gentle centrifugation (500 × g) for 5 min.

scan_protocol: Hybridized slides were scanned at 10µm resolution (Axon Instruments, GenePix 4000B; Axon GenePix Pro v.6.0) while adjusting PMT voltage to balance signal intensity in the red and green channels.  Features that were not usable were flagged, and flagged features were excluded from the results.

data_processing: Differentially expressed features were identified using MAANOVA (version 1.8.1, (Wu et al., 2002) (http://www.jax.org/staff/churchill/labsite/software/Rmaanova/) in Version 2.6.2 of the ‘R’ statistical environment (http://www.r-project.org/).  A full set of R-commands used for each analysis are provided in the supplementary material. Median fluorescence values for each feature were log transformed (Draghici et al., 2003), and a weighted linear least squares regression Lowess normalization was conducted on log2 transformed data using the joint Lowess function (Wu et al., 2002).  Microarray images and sequence data are also available at the Porcelain Crab Array Database (PCAD, http://array.sfsu.edu).  A fixed ANOVA model with array, dye, and sample (= treatment group) terms was fit using restricted maximum likelihood (REML), and a permutated F-test (n=500 permutations) to identify features that significantly differed (tabulated p≤0.05) among items in the sample term using the Fs statistic at a=0.01.  The Fs statistic uses overall gene expression variation to calculate a gene-specific variance (Cui et al., 2005; Wu et al., 2002) and has a much higher stringency than other F or t statistics.   To control for false positives, we employed the q-value false discovery rate correction (Storey, 2002; Storey, 2003; Storey et al., 2004; Storey and Tibshirani, 2003).  For those features selected as significant by the Fs test, we exported log2 expression fold change data for filtering and K-means clustering using Cluster v. 3.0, and visualization as heat maps using Treeview software version 1.60 (http://rana.lbl.gov/EisenSoftware.htm).  Data were filtered to remove flagged features. Mean expression values and standard deviations for each cluster were calculated in Microsoft Excel and data were plotted using DeltaGraph v5.7.5.

organism: Petrolisthes cinctipes

label_protocol: Reverse transcription of aRNA was performed by incubating 3.25 µg aRNA, 1µg random hexamer primers and water to a total volume of 15µl for 5 min at 65°C, then adding 10µl of aa-dNTP cocktail (1X first strand buffer, 1mM DTT, 1.25mM amino allyl dNTP mix (10 mM dATP, dGTP, dCTP, 3.33mM dTTP, 6.66mM amino allyl dUTP), 200U MMLV reverse transcriptase, 5% v/v RNase inhibitor) and incubated at 42°C for 70 min.  aRNA was hydrolyzed by adding 10µl of 1M NaOH (0.22M final conc.) and 10µl 0.5M EDTA, pH 8.0 (0.11M final conc.) at 65°C for 15 min, then neutralized by addition of 25µl HEPES, pH 7.4.  Amino-allyl cDNAs were purified (Qiagen QIAquick PCR purification kit) and cDNA was eluted from the column in 2X 30µl elution steps using pH 8.0 adjusted ddH2O, and dried. Cy3 or Cy5 fluorescent dyes (Amersham Biosciences#PA23001, PA25001) were coupled to cDNAs resuspended in 9µl 0.1M NaHCO3 buffer, pH 9.0.  5 µl dye dissolved in DMSO (final concentration 1.14 mM) were added and incubated at room temperature in the dark for 1h.  Dye coupling was quenched by addition of 4.5µl of 4M hydroxylamine (final concentration 0.97M).  Samples to be hybridized together on a microarray (Fig S1, see below) were combined and diluted to a total volume of 100µl with water.  cDNA was purified (Qiagen QIAquick PCR purification) and eluted in 2X  50µl ddH20.  30µg polyA RNA was added to each tube, and tubes were speed vacuum dried.

growth_protocol: acclimation in seawater aquaria held at different temperatures

extract_protocol: Cardiac tissues from n=8 specimens per group were shaken in guanidinium thiocyanate-phenol-chloroform extraction buffer (38% phenol in saturated buffer pH 6.6, 0.8 M guanidinium thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate pH 5.0, and 5% glycerol (Chomczynski and Sacchi, 1987)) in a Retsch MixerMill MM300 at 30Hz for 10min.  Total RNA was extracted by standard chloroform and isopropanol precipitation methods, and then purified using Qiagen RNeasy columns and quantitated on a NanoDrop spectrophotometer.  In some cases individual cardiac tissues did not yield adequate total RNA to continue, and in one group only n=5 specimens yielded adequate total RNA.  A pooled total RNA sample was prepared for each group by mixing equal quantities of total RNA from n=5 individuals in each group in order to have the same amount of biological diversity within each pooled RNA sample.   Linear amplification of RNA by in vitro transcription (Van Gelder et al., 1990) was performed as follows.  First strand cDNA was synthesized by heating 3μg of pooled total RNA with 500ng of OligodT-T7 primer (5'- GCATTAGCGGCCGCGAAATTAATACGACTCACTATAGGGAGATTTTTTTTTTTTTTTT TTTTTV-3') (Baugh et al., 2001) in a volume of 15μl for 5 min at 70°C and then 5μl 5X first strand buffer (Promega, cat # M531A; final concentration: 50mM Tris-HCl pH 8.3 @ 25°C, 75mM KCl, 3mM MgCl2, 10mM dithiothreitol (DTT)), 1.25μl 10mM dNTPs, 200U MMLV reverse transcriptase (Promega, cat # M1705), 15U RNase inhibitor (Fisher Scientific, cat# BP3225-1), and 2.25μl ddH2O were added and tubes were incubated at 42°C for 60-90 min followed by a heat inactivation at 70°C for 10 min.  Double stranded cDNA was produced by adding 75 μl of the following (1X E.coli DNA polymerase buffer (NEB buffer #2), 0.25 mM dNTPs, 3U E.coli RNaseH (Takara Mirus Bio, #TAK 2150A), 40U E.coli DNA polymerase (New England Biolabs, cat# M0209L). Following 2h incubation at 16°C, 1U E.coli DNA ligase (New England Biolabs, M0205L) and 11μl 10X DNA ligase buffer were added and incubated at room temperature for 15 min. Finally, 6U T4 DNA polymerase (New England Biolabs, cat# M0203L) were added followed by incubation for 15 min at room temperature.  Double stranded cDNAs were purified using the Qiagen QIAquick PCR purification kit following the manufacturers protocol except that cDNA was eluted from the column in 2X 50μl elution steps using RNase free water.  Purified double stranded cDNA was dried by vacuum centrifugation in a Speed Vacuum and stored at -20°C.  For RNA amplification, 40 μl of in vitro transcription cocktail (120mM HEPES, pH 7.5, 28mM MgCl2, 6mM rNTPs (New England Biolabs, cat#N0466L), 1mM spermidine (MP Biomedicals, Inc, cat#19485201), 0.1mM acetylated BSA (Promega, cat# R3961), 40mM dithiothreitol (Sigma, cat#9779), 0.2U pyrophosphatase (Fermentas, cat#EF0221), 200U T7 RNA polymerase (Fermentas, Hanover, MD, cat#EP0113), and 15U RNase inhibitor (Fisher Scientific, cat# BP3225-1)) were added and incubated at 37°C for 14h.  Amplified RNA was purified (Qiagen RNeasy), eluted 2X with 50μl RNase free water, concentrated by speed-vacuum, and quantified from absorbance at 260 nm.  For the seasonal comparison, a second round of amplification was performed except that: (1) random hexamer primers were used in the first strand synthesis and (2) 500 ng of oligodT-T7 primer were added to the second strand reaction.

treatment_protocol: acclimation to 8, 13 or 18°C

value: adult

value: cardiac

tag: collection site

value: specimens collected at Fort Ross, California

tag: acclimation group

tag: time


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide97_18°C_6h)

description: Raw data file: Slide97.gpr (linked as supplementary file on Series record).


title: SW480_SiControl_1

source_name: SW480 Control siRNA Biological Replicate #1


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide94_18°C_12h)

description: Raw data file: Slide94.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide92_18°C_12h)

description: Raw data file: Slide92.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide89_18°C_18h)

description: Raw data file: Slide89.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide93_18°C_12h)

description: Raw data file: Slide93.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide90_18°C_18h)

description: Raw data file: Slide90.gpr (linked as supplementary file on Series record).


title: Patient ID 4414 DNA


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide87_18°C_24h)

description: Raw data file: Slide87.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide85_8°C_24h)

description: Raw data file: Slide85.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide88_18°C_24h)

description: Raw data file: Slide88.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide91_18°C_18h)

description: Raw data file: Slide91.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide84_8°C_24h)

description: Raw data file: Slide84.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide96_18°C_6h)

description: Raw data file: Slide96.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide86_18°C_24h)

description: Raw data file: Slide86.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide83_8°C_18h)

description: Raw data file: Slide83.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide80_8°C_12h)

description: Raw data file: Slide80.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide77_8°C_6h)

description: Raw data file: Slide77.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide81_8°C_18h)

description: Raw data file: Slide81.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide82_8°C_6h)

description: Raw data file: Slide82.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide78_8°C_18h)

description: Raw data file: Slide78.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide76_13°C_24h)

description: Raw data file: Slide76.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide79_8°C_12h)

description: Raw data file: Slide79.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide74_13°C_0h)

description: Raw data file: Slide74.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide75_13°C_24h)

description: Raw data file: Slide75.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide73_13°C_0h)

description: Raw data file: Slide73.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide95_13°C_0h)

description: Raw data file: Slide95.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide94_8°C_12h)

description: Raw data file: Slide94.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide97_18°C_18h)

description: Raw data file: Slide97.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide96_18°C_12h)


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide88_8°C_24h)

description: Raw data file: Slide88.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide92_18°C_24h)

description: Raw data file: Slide92.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide76_8°C_12h)


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide80_8°C_18h)


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide93_13°C_24h)

description: Raw data file: Slide93.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide85_8°C_12h)

description: Raw data file: Slide85.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide89_18°C_24h)

description: Raw data file: Slide89.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide90_18°C_12h)

description: Raw data file: Slide90.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide77_8°C_18h)

description: Raw data file: Slide77.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide87_13°C_24h)

description: Raw data file: Slide87.gpr (linked as supplementary file on Series record).


title: Pr-16

city: Davis

first: Takao

last: Kasuga

address: 382 Huchison Hall

institute: USDA-ARS

hyb_protocol: NimbleGen labeling protocol version 3.1: hybridized at 42C for 12 to 16 hours on MAUI Hybridization system.  NimbleGen Hybridization and Wash Buffer kits were used.

scan_protocol: Axon GenePix 4000B, 500 to 650 PMT, single color scan (532 nm).

organism: Phytophthora ramorum

label_protocol: NimbleGen labeling protocol version 3.1: Cy3-labeled random 9-mers were used to label double stranded cDNA.

growth_protocol: 7 days on solid CV8 medium, constant light, 21C

extract_protocol: Liquid nitrogen frozen samples were disrupted by FastPrep-24 homogenizer with Lysing Matrix A, followed by the Trizol Reagent protocol

tag: host

value: coast live oak

tag: colony morphology

value: nwt

tag: early senescence

value: never

tag: clone/isolate


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide91_8°C_6h)

description: Raw data file: Slide91.gpr (linked as supplementary file on Series record).

tag: developmental stage

tag: tissue


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide81_18°C_6h)

description: Raw data file: Slide81.gpr (linked as supplementary file on Series record).


title: MK649b

value: California bay laurel

value: wt


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide73_8°C_6h)


title: Pr-35

value: has shown


title: HC67-22


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide83_8°C_24h)

description: Raw data file: Slide83.gpr (linked as supplementary file on Series record).


title: Pr-102


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide79_8°C_6h)

description: Raw data file: Slide79.gpr (linked as supplementary file on Series record).


title: HC73-5


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide84_13°C_0h)

description: Raw data file: Slide84.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide74_13°C_24h)

description: Raw data file: Slide74.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide82_18°C_6h)

description: Raw data file: Slide82.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide78_18°C_18h)

description: Raw data file: Slide78.gpr (linked as supplementary file on Series record).


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide75_8°C_24h)

description: Raw data file: Slide75.gpr (linked as supplementary file on Series record).


title: MK649a


title: cardiac muscle acclimated to 8, 13, or 18°C for 0, 6, 12, 18 or 24hours  (slide86_13°C_0h)

description: Raw data file: Slide86.gpr (linked as supplementary file on Series record).


title: MK516d


title: MK548


title: MK558


title: MK106


title: MK79j


title: MK516a


title: BMDM_HSA & M avium (1:1000)_18hr_rep2

city: South Bend

first: Manuel

last: Galvan

address: 1234 Notre Dame Ave

department: Microbiology and Immunology

institute: Indiana University School of Medicine-South Bend

description: This sample is of wildtype Bone Marrow Derived Macrophages

hyb_protocol: Hybridization was performed using  hybridization buffer containing alignment oligos and unique sample tracking controls (Roche NimbleGen Systems Inc, Madison, WI USA) following their standard operating protocol See wwwnimblegencom

scan_protocol: Scanning was performed using a NimbleGen MS 200 Microarray Scanner following their standard operating protocol See wwwnimblegencom

data_processing: The raw data (pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al Biostatistics 4(2):249), quantile normalization (Bolstad et al Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 25 (Roche NimbleGen, Inc)

source_name: C57Bl/6 Bone Marrow Derived Macrophages wildtype

label_protocol: Labeling was performed using  NimbleGen One-color (Cy3) DNA labeling kit (Roche NimbleGen Systems Inc, Madison, WI USA) following their standard operating protocol See wwwnimblegencom

growth_protocol: Bone marrow derived macrophages obtained from C57Bl/6 mice were cultured in serum free HL-1 media  37°C at 5% C02 for 4 or 18 hrs in the presence or absence of M avium or apoptotic Jurkat cells

extract_protocol: Total RNA was extracted using the Trizol method (Sigma, St Louis, MO, USA)  and DNA was removed by DNase digestion with the RNase-Free DNase (Qiagen) RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the University of Notre Dame Genomics Core Facility (University of Notre Dame, Notre Dame, USA)

tag: genotype

value: Wildtype

tag: cell type

value: Bone Marrow Derived Macrophages (BMDM)

value: HSA (control protein) & M avium (1:1000)


title: BMDM_C1q & M avium (1:500)_18hr_rep4


title: BMDM_C1q & M avium (1:500)_18hr_rep1


title: BMDM_C1q & M avium (1:500)_18hr_rep3


title: BMDM_HSA & M avium (1:1000)_18hr_rep3


title: BMDM_C1q & M avium (1:500)_18hr_rep2


title: BMDM_HSA & M avium (1:1000)_18hr_rep5


title: BMDM_HSA & M avium (1:1000)_18hr_rep1


title: BMDM_C1q & M avium (1:500)_18hr_rep5


title: BMDM_HSA & M avium (1:500)_18hr_rep5

value: HSA (control protein) & M avium (1:500)


title: UK1_rep3

city: Pullman

first: Devendra

last: Shah

state: WA

address: 100 Dairy Rd

department: Veterinary Microbiology and Pathology

institute: Washington State University

description: The raw data file (slide_4056_CGH_500PMT_07212011.gpr available as a Series Supplementary file) contains 3 arrays, all of which are for UK1 (rep 1, 2, and 3 corresponds to Block1, Block2, and Block3 portion of the raw data in the file).

hyb_protocol: Labeled DNA was resuspended in 135 μl of hybridization buffer consisting of 4× SSC (60 mM NaCl, 0.6 mM Na-citrate; pH 7.0) and 5× Denhardt’s solution (0.1% Ficoll, 0.1% polyvinylpyrrolidone, 0.1% bovine serum albumin), and heat denatured before being added to the slide for overnight hybridizations at 50°C. Each array on the slide was preblocked at 50°C for 30 min with 1% BSA in 5X SSC and 0.1% SDS. Slides were washed three times with TNT buffer (100 mM Tris-HCl [pH 7.5], 150 mM NaCl, 0.05% Tween 20), and the remaining steps were performed according to the manufacturer’s instructions for the TSA kit (Perkin Elmer). Finally, biotinyl tyramide was washed from the slide, and 2 μg streptavidin/ml conjugated to Alexa Fluor 555 (Invitrogen) was added in 1× SSC and 5× Denhardt’s solution and incubated for 1 h. The slides were then washed with TNT 3X for 1 min each and dried by spinning on a slide microfuge for 15 seconds.

scan_protocol: Slides were scanned using a Genepix400B scanner (Axon Instruments) and the images were quantified using Genepix Pro software

data_processing: Each spot was corrected by subtracting local background values and each “corrected” spot intensity was used to calculate a median signal intensity for each array. Inferior spot intensities (empty spots or those where signal intensity was less than 2 times the background) were reset to an arbitrary number (50) and were not used in the median calculation. The array median intensity was then used for within array normalization. The data was log2 transformed followed by quantile normalization between arrays

organism: Salmonella enterica subsp. enterica serovar Enteritidis

source_name: Strain UK1

label_protocol: 1 μg of genomic DNA was nick translated in the presence of biotin-dATP using the BioNick labeling system (Invitrogen) according to manufacturer’s instructions.

growth_protocol: Frozen stocks of cultures were grown on Luria-Bertani (LB) agar incubated at 37°C for overnight. For all the experiments, a single colony from the overnight culture was inoculated into LB broth and grown at 37°C for 16 h with shaking at 200 rpm.

extract_protocol: Genomic DNA was extracted using the Qiagen DNeasy kit as per manufacturers instructions.

treatment_protocol: There is no treatment.

tag: phage type

tag: pathogenicity/invasiveness

value: High

tag: mlva type


title: BMDM_HSA & M avium (1:1000)_18hr_rep4

tag: strain


title: BMDM_HSA & M avium (1:500)_18hr_rep3


title: BMDM_HSA & M avium (1:500)_18hr_rep1


title: BMDM_C1q_18hr_rep5


title: UK1_rep2


title: UK1_rep1


title: BMDM_C1q_18hr_rep4


title: G45_rep2

description: The raw data file (slide_4067_CGH_400PMT_07212011.gpr available as a Series Supplementary file) contains 3 arrays, all of which are for G45 (rep 1, 2, and 3 corresponds to Block1, Block2, and Block3 portion of the raw data in the file).

source_name: Strain G45

value: Low


title: BMDM_HSA & M avium (1:500)_18hr_rep4


title: BMDM_C1q_18hr_rep2


title: BMDM_C1q_18hr_rep1


title: G45_rep3


title: emf2-RNA-3

type: mixed

city: Berkeley

first: Toshiro

last: Nishimura

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

hyb_protocol: The hybridization and data extraction were performed at the Fred Hutchinson Cancer Research Center DNA array facility according to standard NimbleGen protocols (www.nimblegen.com).

scan_protocol: Standard NimbleGen protocol.

data_processing: Standard NimbleGen protocol.

source_name: emf2 - total RNA

label_protocol: ChIP-chip was performed according to the NimbleGen protocol (Roche, www.nimblegen.com). IP and Input DNA were amplified using the Sigma Whole Genome Amplification kit and labeled with CY5 and CY3, respectively according to the NimbleGen protocol (www.nimblegen.com). Combined samples, which include 10ug of CY5-labeled IP and 10ug of CY3-labeled Input DNA, were hybridized with NimbleGen HD2 arrays.

growth_protocol: Short day growth conditions for 14 days

extract_protocol: ChIP experiment was performed on WT, emf1, emf2, transgenic FIE, and transgenic plants harboring the EMF1-3FLAG construct grown in short day growth conditions for 14 days. Plants were vacuum infiltrated in 1% formaldehyde solution for half an hour to cross-link the chromatin. Tissues were ground in liquid nitrogen, nuclei isolated, and chromatin extracted. Chromatin was sheared by sonication to 0.5-2 kb fragments. For immunoprecipitated chromatin (IP), monoclonal anti-FLAG mouse antibody (Sigma F1804) and polyclonal anti-H3K27me3 antibody (Upstate, rabbit IgG, 07-449) were added to fragmented chromatin to precipitate EMF1-bound and H3K27me3 modified chromatin, respectively. Cross-linking was reversed with 5M NaCl and DNA precipitated by 100% EtOH. For global gene expression studies, total RNA was extracted from 14-day-old WT and mutants using trizol and converted into cDNA. Genomic DNA from WT and cDNA from mutants and WT were labeled with CY3, and CY5, respectively, and combined to hybridize.

tag: ecotype

value: Columbia

tag: chip antibody

source_name: Input DNA (control genomic DNA)

tag: genotype/variation

value: WT

tag: sample type

value: input DNA (control)


title: BMDM_C1q_18hr_rep3

tag: treatment

tag: time