title: Tlr4 KO_right thigh skeletal muscle after ischemia 2h and reperfusion 1d rep3

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description:
Tlr ISC2h/RE 1D*D
pure isolated skeletal muscle based on vascular pedicle

hyb_protocol: The pre-hybridization of MRmiOA v1 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled small RNA was hybridize on MRmiOA v1 in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 560-600 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing:
The data processing was processed by R program (2.12.1). Import (Foreground minus background) value of each miRNA probes in triplicates from GPR files, plus the absolute value of minimum value of array to replace the week signal. Filter out probes that ﬂag <0 in all samples. Porbes that passed the criteria were normalized by 75% media scaling between arrays.
The Matrix value is normalized intensities. Based on the normalized intensities, we calculate average ratios and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

label_protocol: Small RNA population were enriched by (Nanosep100k, Pall Corp.) from 2.5 µg of total RNA. NHS-CyDye (Cy5, Amershan) were direct labeled to Guanine (G) by chemical labeling method using ULS™ microRNA Labeling Kit (EA-038, Kreatech).

extract_protocol: RNA extraction by RNeasy Protect Animal Blood Kit (QIAGEN Cat. no. 73224). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: Isolated skeletal muscle ischemia-reperfusion injury (IRI): Mice were anesthetized with an anesthetic cocktail consisting of 0.1 mg/g ketamine and 0.01 mg/g xylazine, given as an intraperitoneal injection (0.01 ml/g body weight). After the induction of anesthesia, the mice were restrained in a supine position on a heating pad to maintain body temperature at 37°C. The quadriceps muscle perfused based on the femoral artery of the mouse was carefully isolated away from the femoral bone and the underlying adductor muscle group. In the ischemic group, ischemia was induced by placing a microvascular clamp carefully across the proximal site of vascular pedicle for 2 h and then the microvascular clamp was removed. Good vascular inflow and outflow through the pedicle was verified under direct magnified vision. In the sham-operated control group, the muscle was isolated without microvascular clamp being applied. The incision wound was closed with interrupted sutures (4-0 nylon) and the animals were allowed to awaken in the remaining periods of reperfusion.

value: Tlr4–/– (C57BL/6ScNJ)

value: right thigh femoralis muscle


title: h322_shya_2

status: Public on Jan 01 2016

type: RNA

city: MILANO

first: DILETTA

last: DOLFINI

state: MILANO

address: VIA CELORIA 26

department: DIPARTIMENTO DI BIOSCIENZE

country: Italy

institute: UNIVERSITA' DEGLI STUDI DI MILANO

hyb_protocol: Following fragmentation fragmented RNA was hybridized. Intruments used were Affymetrix GeneChip Fluidics Station 450, Affymetrix GeneChip Hybridization Oven 640.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Arrays were RMA normalized (Irizarry et al. 2003), gene expression levels calculated, differential expression determined using the following R packages from the Bioconductor project: affy (Gautier et al. 2004), limma (Smyth 2004).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: H322 cells treated with shNF-YA

label_protocol: RNA were prepared using Affymetrix GeneChip WT Terminal Labeling Kit

growth_protocol: Cells were grown as adherent cells in DMEM (HCT116) or McCoy's media(H322)  supplemented with 10% fetal bovin serum with penn/strep.

extract_protocol: Trizol extraction and Qiagen RNeasy kit purification performed according to the manufacturer's instructions.

treatment_protocol: Cells were transduced with shSCM (control) or shNF-YA viral supernatants and  cells collected after 72 hr of incubation.

tag: cell line

tag: genotype/variation

value: NF-YA knockdown


title: h322_shc_1

source_name: H322 cells treated with shSC

value: control


title: h322_shya_3


title: Tlr4 KO_right thigh skeletal muscle after ischemia 2h and reperfusion 1d rep1

description:
Tlr ISC2h/RE 1D*A
pure isolated skeletal muscle based on vascular pedicle

organism: Mus musculus

tag: strain

tag: tissue


title: Tlr4 KO_right thigh skeletal muscle after ischemia 2h and reperfusion 1d rep2

description:
Tlr ISC2h/RE 1D*B
pure isolated skeletal muscle based on vascular pedicle


title: h322_shc_2


title: Cells after adipogenic differentation with MDI, biological replicate 3

city: Worcester

first: Silvia

last: Corvera

state: MA

address: 373 Platantion Street

department: Molecular Medicine

country: USA

institute: UMASS Medical School

description:
MDI_3
Cells after adipogenic differentation with MDI (methylisobutylxanthine, dexamethasone, insulin), biological replicate 3

hyb_protocol: Affymetrix protocols were followed for the preparation of cRNA, which was hybridized to HTA-v2.0 Chips.

scan_protocol: Raw expression data collected from an Affymetrix HP GeneArrayScanner

data_processing:
The data were analyzed with Affymetrix Expression Console_1_4_0
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0

source_name: adipocytes from human vascular progenitors

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Adipose tissue from three individuals was cultured in matrigel under pro-angiogenic conditions. Capillary networks emerging from the explants were subcultured on plastic, grown to confluence, subjected to adipogenic differentiation and after 12 days treated with vehicle or forskolin for 7 days

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

treatment_protocol: No differentiation, differentation and vehicle, or differentation plus forskolin 50 uM for 7 days

tag: cell type


title: NF-κB KO_right thigh skeletal muscle after ischemia 2h and reperfusion 1d rep1

description:
ISC2h/RE1D NF-KB*1
pure isolated skeletal muscle based on vascular pedicle

value: NF-κB–/– (B6.Cg-Nfkb1tm1Bal/J)


title: h322_shc_3


title: hct_shya_1

source_name: HCT116 cells treated with shNF-YA


title: hct_shc_2

source_name: HCT116 cells treated with shSC


title: hct_shc_1


title: hct_shya_3


title: h322_shya_1


title: C57BL/6_right thigh skeletal muscle after ischemia 2h and reperfusion 7d rep3

description:
isc-2h-re7d-4
pure isolated skeletal muscle based on vascular pedicle


title: Cells after adipogenic differentation with MDI, biological replicate 2

description:
MDI_2
Cells after adipogenic differentation with MDI (methylisobutylxanthine, dexamethasone, insulin), biological replicate 2

value: adipocytes from human vascular progenitors


title: Cells after adipogenic differentation with MDI, treated with forskolin, biological replicate 1

description:
FSK_1
Cells after adipogenic differentation with MDI (methylisobutylxanthine, dexamethasone, insulin), treated with forskolin, biological replicate 1

source_name: adipocytes from human vascular progenitors treated with forskolin

tag: treatment

value: forskolin


title: NF-κB KO_right thigh skeletal muscle after ischemia 2h and reperfusion 1d rep3

description:
ISC2h/RE1D NF-KB*4
pure isolated skeletal muscle based on vascular pedicle


description:
Control_3
Cells without differentation, biological replicate 3

source_name: pre-adipocytes from human vascular progenitors


title: NF-κB KO_right thigh skeletal muscle after ischemia 2h and reperfusion 1d rep2

description:
ISC2h/RE1D NF-KB*3
pure isolated skeletal muscle based on vascular pedicle


title: hct_shc_3


title: drug resistant_Group 2 [A-06]

status: Public on Jan 02 2016

city: Vellore

first: Poonkuzhali

last: Balasubramanian

state: Tamil Nadu

address: Ida Scudder Road

department: Department of Haematology

country: India

institute: Christian Medical College Vellore

description: Gene expression at diagnosis

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Hi-RPM large Hybridization Kit (Part No: 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression Wash Buffers Set (Part No: 5188-5327).  The hybridized, washed microarray slides were then scanned on a G2505C scanner (Agilent Technologies)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.7)

data_processing: Data extraction from Images was done using Feature Extraction software and Percentile shift Normalization of the data was done in GeneSpring GX.

source_name: Bone Marrow MNC at diagnosis

label_protocol: The samples were labeled using Agilent Quick Amp Labeling Kit one color (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using  RNeasy Mini Kit(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

extract_protocol: Bone marrow mononuclear cells (BM MNCs) from each patient at diagnosis were separated using Ficoll-Paque (GE Healthcare) separation. RNA was isolated from BM MNCsusing Tri Reagent (Sigma), following the manufacturer's recommendations.

tag: gender

value: male

tag: age


description:
Control_2
Cells without differentiation, biological replicate 2

value: pre-adipocytes from human vascular progenitors


description:
Control_1
Cells without differentiation, biological replicate 1


title: C57BL/6_right thigh skeletal muscle after ischemia 2h and reperfusion 7d rep2

description:
isc 2h re7d-2
pure isolated skeletal muscle based on vascular pedicle


title: C57BL/6_right thigh skeletal muscle after ischemia 2h and reperfusion 1d rep2

description:
isc2h re1d-5
pure isolated skeletal muscle based on vascular pedicle


title: C57BL/6_right thigh skeletal muscle after ischemia 2h and reperfusion 4h rep1

description:
isc2h re4h-4
pure isolated skeletal muscle based on vascular pedicle


title: C57BL/6_right thigh skeletal muscle after ischemia 2h and reperfusion 1d rep1

description:
isc2h re1d-4
pure isolated skeletal muscle based on vascular pedicle


title: C57BL/6_right thigh skeletal muscle after ischemia 2h and reperfusion 4h rep3

description:
isc-2h-re4h
pure isolated skeletal muscle based on vascular pedicle


title: C57BL/6_right thigh skeletal muscle after ischemia 2h and reperfusion 1d rep3

description:
isc2h re1d-6
pure isolated skeletal muscle based on vascular pedicle


title: C57BL/6_right thigh skeletal muscle after ischemia 2h and reperfusion 4h rep2

description:
isc2h re4h-5
pure isolated skeletal muscle based on vascular pedicle


title: C57BL/6_right thigh skeletal muscle in sham operation rep1

description:
sham CTL-4
pure isolated skeletal muscle based on vascular pedicle


title: C57BL/6_right thigh skeletal muscle after ischemia 2h rep3

description:
isc 2h-3
pure isolated skeletal muscle based on vascular pedicle


title: C57BL/6_right thigh skeletal muscle after ischemia 2h and reperfusion 7d rep1

description:
isc 2h re7d-1
pure isolated skeletal muscle based on vascular pedicle


title: C57BL/6_right thigh skeletal muscle in sham operation rep3

description:
sham CTL-5
pure isolated skeletal muscle based on vascular pedicle


title: C57BL/6_right thigh skeletal muscle after ischemia 2h rep2

description:
isc 2h-2
pure isolated skeletal muscle based on vascular pedicle


title: C57BL/6_right thigh skeletal muscle after ischemia 2h rep1

description:
isc 2h-1
pure isolated skeletal muscle based on vascular pedicle


title: C57BL/6_right thigh skeletal muscle in sham operation rep2

description:
Sham CTL-2
pure isolated skeletal muscle based on vascular pedicle


title: hct_shya_2


title: PEF_rep3

city: Castanet-Tolosan

first: Herve

last: Acloque

address: 24 chemin de Borde Rouge

department: Animal Genetics

country: France

institute: INRA

description:
Gene expression in porcine embryonic fibroblasts
PEF_C

hyb_protocol: Microarray hybridation oven according to manufacturer's instruction

scan_protocol: Image analysis using the Feature Extraction software (Agilent).

data_processing: Data were filtered to keep only spots of sufficient intensity and quality for at least 2 out of 3 technical replicates. Intensity values were log-transformed and normalized by the quantile normalization method. Differential analysis was then performed using the Limma package (Bioconductor). Threshold parameters were defined as follow: maximal adjusted p-value (Benjamini& Hochberg) of 0.01 and minimal log-fold change (lfc) of 2.

organism: Sus scrofa

source_name: Cultured cells

label_protocol: Label, hybridation , scan and data extraction were performed by the GeT-Biopuces platform following manufacturer's intruction. Samples were then marked by Cyanine-3 fluorochrome and converted in cDNA before hybridization on the 60K customized chip from Agilent (Voillet et al., 2014).

growth_protocol: PEF were culture in F medium, all iPS-like cells were culture in piPS medium.  Floating embryoïd bodies were cultured 10 days in in DIFF medium. For medium composition see the Material and Methods section of the associated publication.

extract_protocol: Total RNA from cell pellets of each sample was extracted in triplicate using the Nucleospin RNA kit (Macherey-Nagel). Quantity and quality of RNA was evaluated by NanoDrop dosage and Bioanalyser analysis (Agilent Technologies).

tag: reprogramming technique

value: Non reprogrammed

tag: starting cell type

value: Normal embryonic fibroblast

tag: culture conditions

value: F medium

value: PEF


title: Osteosarcoma cell line - NY (expression)

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

description: Tumor sampls were obtained from the tissues bank at the Laboratory of Oncology Research of the Rizzoli Orthopaedic Institute, Bologna, Italy

hyb_protocol: Hybridization, washing and scanning were performed according to the manufacturer's directions

data_processing: Expression data were normalized by the VST-RSN method using the lumi R package available at Bioconductor

label: Biotin

source_name: Osteosarcoma cell line

label_protocol: Biotinylated cRNA was prepared using Ambion TotalPrep RNA Amplification Kit starting with 200 ng total RNA

growth_protocol: Commercially available osteosarcoma cell lines were grown according to the supplier’s recommendations.

extract_protocol: Total RNA  was extracted using Trizol and chloroform. Purification was performed on RNAeasy columns according to manufacturer’s instructions

tag: Sample type

value: cell line


title: Osteosarcoma cell line - MG-63 (expression)

scan_protocol: Hybridization, washing and scanning were performed according to the manufacturer's directions


title: Osteosarcoma cell line - HUO9N2 (expression)


title: Osteosarcoma cell line - 143B (expression)


title: Osteosarcoma cell line - HUO3N1 (expression)


title: Osteosarcoma tumor - 24424b (expression)

source_name: Osteosarcoma tumor

value: osteosarcoma tumor


title: Osteosarcoma cell line - HOS (expression)


title: Osteosarcoma cell line - CAL72 (expression)


title: Osteosarcoma cell line - G292 (expression)


title: Osteosarcoma tumor - 22753B (expression)


title: Osteosarcoma cell line - HUO9 (expression)


title: 5-mC_CPE-NS Repl 1

type: genomic

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description: Comparision of Stem/progenitor cells and differentiated retinal neuronal cells

hyb_protocol: For the hybridization, Cy3-labeled Input was mixed with Cy5-labeled IP DNA.  Hybridizations were performed with the Hybridization kit of Agilent (Part Number 5188-6420). Hybridization was carried out in Agilent’s Surehyb Chambers at 67º C for 40 hours.

scan_protocol: Agilent Microarray Scanner G2505C

data_processing: Data extraction from Images was done using Feature Extraction software v 10.7 of Agilent.Feature extracted raw data was analyzed using Data analysis was done using Agilent Genomic Workbench Lite Edition 6.5

molecule: genomic DNA

source_name: Input DNA from CPE derived neurospheres

label_protocol: The Input DNA and IP samples were labeled using Agilent Genomic DNA Labeling Kit.  Random primer labeling using Exo-Klenow to label IP and Input DNA samples (Agilent Methylation Protocol )DNA yield and incorporation of labeled nucleotide (specific activity) were measured by NanoDrop estimation

extract_protocol: 2 × 107 cells form the Neurosphere cultures and the Differentiated cultures were colleted and the genomic DNA was isolated and purified using QIAamp DNA mini kit (Qiagen). The purified genomic DNA was sonicated into 200-600bp. 30μg sonicated DNA was incubated with 200μl pan-mouse IgG Dynal magnetic beads (Invitrogen) coupled to 20μg antibody against 5’-methylcytosine (Eurogentec, Seraing, Belgium) overnight at 4°C. The genomic DNA-beads-antibody complex was washed and methylated DNA was eluted using the Dynal Magnetic Particle Concentrator. Eluted DNA and WCE (Whole cell extract) DNA (Reference DNA) were extracted/purified using phenol: chloroform: isoamylalcohol and precipitated with ethanol.

value: Stem/progenitor cells

tag: chip antibody

value: none, input DNA

source_name: 5-mC MeDIP DNA from CPE derived neurospheres


title: Osteosarcoma cell line - U2OS (expression)


title: Osteosarcoma tumor - 24805 (expression)


title: Osteosarcoma tumor - 22900 (expression)


title: Osteosarcoma tumor - 22981 (expression)


title: Osteosarcoma tumor - 24955b (expression)


title: Osteosarcoma tumor - 22164 (expression)


title: Osteosarcoma cell line - SAOS (expression)


title: Osteosarcoma tumor - 24875 (expression)


title: Osteosarcoma tumor - 20122 (expression)


title: Osteosarcoma tumor - 25491 (expression)


title: Osteosarcoma tumor - 24954 (expression)


title: Osteosarcoma tumor - 25350 (expression)


title: iPS-I4-ep_rep1

description:
Gene expression in I-iPS-like cells at early passages
I4ep_A

value: Integrative

value: t(Y;14) fibroblasts

tag: resulting cell type

value: I-iPS-like cells

value: piPS medium

tag: passage

value: early


title: Osteosarcoma tumor - 20174 (expression)


title: Osteosarcoma tumor - 25384 (expression)


title: Osteosarcoma tumor - 25044 (expression)


title: Osteosarcoma tumor - 25712 (expression)


title: Osteosarcoma tumor - 26442 (expression)


title: Osteosarcoma tumor - 18900 (expression)


title: Osteosarcoma tumor - 20772 (expression)


title: Osteosarcoma tumor - 25268 (expression)


title: Osteosarcoma tumor - 26713 (expression)


title: Osteosarcoma cell line - CL (expression)


title: K5 rep2

city: Catania

first: Sebastiano

last: Cavallaro

state: Catania

address: Via Paolo Gaifami 18

institute: CNR-ISN

hyb_protocol: Aliquots (750 ng) of Cy3 labeled cRNA targets were hybridized on Whole Rat Genome Oligo Microarrays (Agilent Technologies, Milano, Italy).

scan_protocol: Microarrays were scanned at 5-μm resolution using a GenePix Personal 4100A microarray scanner and the GenePix Pro 6.0 acquisition and data-extraction software (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
Raw data were processed and analyzed with GeneSpringGX 12.5 (Agilent Technologies, Milano, Italy). To remove unreliable data, all genes from all samples were filtered for quality to include only probe data fulfilling all of the following criteria in all replicates of at least one out of four experimental conditions: the spot had <3% of saturated pixels at 532 nm; the spot was not flagged “bad”, “not found” or “absent”; the spot was detectable well above background (signal-to-noise ratios at 532 nm were >10).
Normalized signal intensity_Threshold: 1.0 . Logbase: 2 . Normalization: Shift to 75 percentile . Baseline Transformation: median of all samples .

organism: Rattus norvegicus

source_name: CGNs_medium aspirated_K5 + 0% FCS

label_protocol: Complementary RNAs (cRNAs) labeled with Cy3-CTP were synthesized from 1 μg of total RNA of each sample using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent  Technologies, Milano, Italy) following the manufacturer’s protocol.

extract_protocol: After six hours of incubation, total RNA was extracted with Trizol (Life Technologies, Monza, Italy) from four biological replicates for each of the experimental conditions (K25, K5, K5 + Gip; K25, K5, K5 + Sp; K25, K5, K5 + Igf1; K25, K5, K5 + Pacap). RNA integrity was confirmed by using a RNA chip and a 2100 Bioanalyzer (Agilent Technologies, Milano, Italy) with the protocol outlined by the manufacturer.

treatment_protocol: After six days “in vitro” (DIV), extracellular KCl of CGNs was shifted from 25 to 5 mM for neuronal apoptotic death induction. After two washes with serum-free BME containing 5 mM KCl, neurons were incubated with the same medium for 6 h (K5), while control neurons were incubated with serum free medium supplemented with 25 mM KCl (K25). K5 neurons were also treated with a maximal effective dose of Gip, Sp, Igf1 and Pacap.  Four biological replicates (derived from the same litter) for each of the experimental conditions (K25, K5, K5 + Gip; K25, K5, K5 + Sp; K25, K5, K5 + Igf1; K25, K5, K5 + Pacap) were analyzed.

value: Wistar

value: 8-day-old (P8)

value: Cerebella

value: Cerebellar Granule Neurons (CGNs) primary culture

tag: div

value: 6 days “in vitro” (DIV)

tag: culture condition

value: 5mM KCl + 0% FCS


title: Osteosarcoma tumor - 22231 (expression)


title: K5 + GIP rep1

source_name: CGNs_medium aspirated_K5 + 0% FCS + GIP 10 nM

value: 5mM KCl + 0% FCS + GIP 10 nM


title: Osteosarcoma tumor - 23622 (expression)


title: Osteosarcoma tumor - 20490 (expression)


title: Osteosarcoma tumor - 26395 (expression)


title: C6-eGFP_MP

city: Tokyo

first: Kouichi

last: Tabu

address: 1-5-45, Yushima, Bunkyo-ku

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression of MP cells just after sorting from the whole C6-eGFP cells

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x GEx Hybridization buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays 4x44k (G4131F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then rinsed with acetonitrile for cleaning up and drying.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 014879_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: C6-eGFP_Hoechst stained_MP

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: C6-eGFP cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS) at 37 ºC in a humidified incubator with 5% CO2. The cells were maintained under 5 μg/ml puromycin selection.

extract_protocol: RNAs were extracted from SP and MP cells using RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instruction. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: C6-eGFP cells were resuspended in 2% FBS-DMEM at the final concentration of 1×106/ml and incubated in dark with 5 μg/ml Hoechst 33342 dye (Molecular Probes) for 90 minutes at 37 °C. Sorting was performed on a BD FACS Aria II (BD Biosciences) equipped with UV laser (355 nm) for SP analysis and Ar laser (488nm) for checking EGFP expression. The fluorescence of Hoechst 33342 dye was excited with UV laser and read through a 405/20 nm band pass filter (Hoechst blue) and a 670 nm long pass filter (Hoechst red).　SP and MP cells were collected from three independent experiments, and mixed three as one sample, respectively.

tag: cell line

value: glioma cell line

value: stably expressing EGFP

tag: selection antibiotic

value: puromycin

tag: cell population

value: Hoechst 33342 dye-retaining main population cells (MP; non-GSCs)


title: K25 rep3

source_name: CGNs_medium aspirated_K25 + 0% FCS

tag: strain

tag: tissue

value: 25mM KCl + 0% FCS


title: C6-eGFP_SP

description: Gene expression of SP cells just after sorting from the whole C6-eGFP cells

source_name: C6-eGFP_Hoechst stained_SP

tag: cell type

tag: genotype/variation

value: Hoechst 33342 dye-effluxing side population cells (SP; glioma stem cells, GSCs)


title: K25 rep4

tag: age


title: K5 rep3


title: K5 rep4


title: K5 + SP rep2

source_name: CGNs_medium aspirated_K5 + 0% FCS + SP 200 ng/ml

value: 5mM KCl + 0% FCS + SP 200 ng/ml


title: K5 + SP rep3


title: K5 + SP rep4


title: K5 + IGF1 rep2

source_name: CGNs_medium aspirated_K5 + 0% FCS + IGF 25 ng/ml

value: 5mM KCl + 0% FCS + IGF 25 ng/ml


title: K5 + IGF1 rep4


title: K5 + SP rep1


title: K5 + IGF1 rep3


title: K5 + IGF1 rep1


title: K25 rep2


title: F4-luc (miRNA)

city: Taipei

first: Mong-Hsun

last: Tsai

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

department: Institute of Biotechnology

institute: National Taiwan University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Standard Illumina data processing procedures

source_name: parental cell line

label_protocol: Standard Illumina label protocol

growth_protocol: Cells were cultured in DME/F12+10% FBS+1%PS media under 1% O2 condition for 24h incubation.

extract_protocol: Total RNA of cells was isolated with Trizol solution and purified with QIAGEN columns.

treatment_protocol: No treatment

value: lung cancer parental


title: F4-luc_bm#7 (miRNA)

source_name: lung cancer brain metastatic cell line clone #7

value: lung cancer brain metastatic cell line


title: F4-luc_bm#2 (miRNA)

source_name: lung cancer brain metastatic cell line clone #2


title: Mock 5 h

city: Taoyuan

first: Wen-Fang

last: Tang

address: No.259, Wenhua 1st Rd., Guishan Dist.

department: Biochemistry and Molecular Biology

institute: Chang Gung University

description: miRNA expression after 5 h mock infection RD cells

hyb_protocol: The labeled RNAs were hybridized to Agilent Unrestricted Human miRNA microarrays V2 chip

scan_protocol: Slides were scanned with an Agilent microarray scanner as recommended by the manufacturer.

data_processing: Agilent Feature Extraction Software (9.5.3.1) was used for data extraction.

source_name: Mock 5 h

label_protocol: 0.1 ug total RNA was used to label with Cy3 and these precedures were performed by Welgene Biotech Corporation (Taioei).

growth_protocol: RD cells were seeded (2*106 cells) in 10 cm dishes and incubated overnight. Total cellular RNA extraction and miRNA microarray analyses were performed  using the Agilent Human MicroRNA Array V2 chip, which contains 723 human and 76 viral miRNAs, each with 16 duplicates. Total gene signals were detected and analyzed using the GeneSpring 7.3.1 software and were normalized to the 75th percentile.

extract_protocol: Total cellular RNA was extracted by Trizol according the manufacturer's recommendations.

treatment_protocol: The cells were infected with EV71 (strain 2231) on ice at an M.O.I. of 10. After adsorption for 1 h, the virus suspension was replaced with DMEM containing 2% FBS, and the cells were harvested at the indicated times.

value: RD

tag: moi

value: Mock

tag: harvest time (p.i.)

value: 5 h


title: EV71 5 h

description: miRNA expression after 5 h EV71 infection RD cells

source_name: EV71 5 h

value: MOI=10 PFU/cell


title: EV71 10 h

description: miRNA expression after 10 h EV71 infection RD cells


title: Mock 10 h

description: miRNA expression after 10 h mock infection RD cells

source_name: Mock 10 h


title: K5 rep1

value: Wistar

value: 8-day-old (P8)

value: Cerebella

value: Cerebellar Granule Neurons (CGNs) primary culture

value: 6 days “in vitro” (DIV)


title: K5 + PACAP rep3

source_name: CGNs_medium aspirated_K5 + 0% FCS + PACAP 100 nM

value: 5mM KCl + 0% FCS + PACAP 100 nM


title: K5 + PACAP rep2


title: K5 + GIP rep3

value: 5mM KCl + 0% FCS + GIP 10 nM


title: K5 + GIP rep4


title: K25 rep1

value: 25mM KCl + 0% FCS


title: K5 + PACAP rep4


title: K5 + GIP rep2


title: ΔPgm vs.ΔPgm ΔluxS rep6

city: Ames

first: Chris

last: Minion

state: IA

address: 1130 Vet Med

department: VMPM

institute: Iowa State University

description: The strain Pgm- is the Y.pestis CO92 pigmentation-negative mutant. The luxS is the Y.pestis CO92 Pgm- luxS::Kan strain.

hyb_protocol: Microarray hybridization and post washes were performed using a Lucidea Slidepro Hybridization Station (GE Healthcare). Corresponding equal amounts (1.5 µg) of Cy3- or Cy5-labelled cDNA targets were mixed and dried using a Thermo Scientific Savant DNA SpeedVac Concentrator (Waltham, MA). Targets were suspended in 225 μl Long Oligo hybridization solution (Corning, Inc., Corning, NY), incubated at 95°C for 5 min, centrifuged (10,000 x g, 4 min), and kept at room temperature until injected into the hybridization station. Hybridization lasted for 16 hours at 42°C and washed in a series of wash buffers (2x saline-sodium citrate (SSC), 0.1% SDS; 1x SSC, and 0.1x SSC) by the hybridization station and dried by centrifugation at 1500 x g for 30 secs.

scan_protocol: Arrays scanned on a ProScanArray HT scanner (Perkin Elmer, Wellesley, MA) three times with varying photomultiplier tube gain and laser power settings.

data_processing: Background correction, compression, normalization and fitting each probe with a mixed model were conducted as previously described (Carruthers MD and Minion C. 2009. Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock. FEMS Microbiol. Lett. 295:96-102 [PMID 19473256]).

organism: Yersinia pestis

source_name: ΔPgm ΔluxS

label_protocol: Target generation and labeling were performed as described (Carruthers MD and Minion C. 2009. Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock. FEMS Microbiol. Lett. 295:96-102 [PMID 19473256]).

growth_protocol: An overnight culture was diluted 1:100 and grown at 30°C in HIB.

extract_protocol: Cells were pelleted and immediately resuspended in 0.5 ml of RNA Protect Reagent (Qiagen, Valencia, CA). RNA was extracted from frozen cell pellets using the RNeasy Mini kit (Qiagen). The RNA was treated with DNase I (Ambion, Austin, TX) at 37°C for 30 min to remove the genomic DNA. The RNA was purified and concentrated by Microcon Ultracel/YM 30(Millipore, Billerica, MA).

treatment_protocol: The overnight cultures of wild type and ΔPgm ΔluxS strains were diluted 1:100 in fresh culture medium and incubated at 30°C until the cell density reached OD600 = 1.0, about 10 hours. The cells from each culture were collected. The wild type was considered as treatment and the ΔPgm ΔluxS was considered as control.

value: ΔPgm ΔluxS

source_name: ΔPgm

value: ΔPgm


title: K5 + PACAP rep1


title: 3 signals add in vs. control rep2

description: The ΔPgm strain R88 is the Y.pestis CO92 pigmentation-negative mutant.

source_name: 3 signals add in

growth_protocol: An overnight culture was diluted 1:100 and grown at 30°C in HI.

treatment_protocol: The overnight wild type cultures were washed twice with PBS buffer to remove the endogenous quorum sensing signals, the cells were diluted 1:100 in fresh culture medium, and then the cells were incubated for 2 hours at 30°C. Purified signals were then added to the cultures at the following concentrations: AI-2 (500 nM final concentration), AHLs (5 μM N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone). The control consisted of cells grown and treated under the same conditions without added signals. After 4 hours of induction, all of the cultures were centrifuged.

tag: sample type

value: 3 signals add in R88

source_name: control

value: control R88


title: 3 signals add in vs. control rep4


title: Seed rep. #2

city: Wuhan

first: yongming

last: zhou

state: Hubei

address: No.1,Shizishan Street, Hongshan District

country: China

institute: Huazhong Agricultural University

description: Untreated seeds and seeds harvested at 24 h after heat stress.

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

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing:
Data were extracted from scanned images using Agilent’s Feature Extraction Software (Agilent Technologies). Data were analyzed using a Perl script called BoaoAnalyzer (CapitalBio Corporation, Beijing, China) with LOWESS normalization.
In order to identify differentially expressed genes in Untreated seeds and silique walls, only the signal intensity of controlled sample Channels (Untreated Samples) are reported in the Sample data table.

organism: Brassica napus

source_name: heat stressed seeds (24hr)

label_protocol: 500 ng of total RNA from each sample was amplified and labeled with a fluorescent dye (Cy3 or Cy5) using the Low RNA Input Linear Amplification Labeling kit (Agilent Technologies, Palo Alto, CA, USA) following the manufacturer’s protocol. The amount and quality of the fluorescently labeled cRNA was assessed using a NanoDrop ND-1000 spectrophotometer and an Agilent Bioanalyzer.

growth_protocol: Zhongshuang 9, a semi-winter Brassica napus variety, was grown in a greenhouse at 23/18°C (day/night) and a relative humidity of 70% under a 13-h illumination time with a light density of 230-300 µEm-2s-1. At the three-leaf stage, seedlings were vernalized at 4°C for 14 d. Seedlings were then transplanted to a larger pot with one seedling per pot, and continued to grow in the greenhouse until the plants were heat-treated.

extract_protocol: Total RNA was extracted using a cetyltrimethylammonium bromide extraction method as discribed by Wang XM et al. (1998)

treatment_protocol: Plants were heat-treated during pod development. To mimic temperature changes in the field, the temperature was increased linearly from 23°C to 35°C over 4 h, and after heat stress for 5 h at 35°C, the temperature was reduced to 23°C at the same rate; siliques at 20 DAF were randomly sampled after a recovery time of 24 h and 48 h.

tag: variety

value: Zhongshuang 9

tag: developmental stage

value: 20 days after flowering

tag: stress

value: heat stress

tag: time

value: 24 hr

value: seeds

source_name: control  seeds (24hr)

value: control


title: ΔPgm vs.ΔPgm ΔluxS rep5


title: 3 signals add in vs. control rep5


title: 3 signals add in vs. control rep3


title: 3 signals add in vs. control rep1


title: Seed rep. #1


title: ΔPgm vs.ΔPgm ΔluxS rep2


title: ΔPgm vs.ΔPgm ΔluxS rep4


title: ΔPgm vs.ΔPgm ΔluxS rep3


title: 3 signals add in vs. control rep6


title: ΔPgm vs.ΔPgm ΔluxS rep1


title: SW rep. #2

description: Untreated silique walls and silique walls harvested at 24 h after heat stress.

source_name: heat stressed silique walls (24hr)

value: silique walls

source_name: control silique walls (24hr)


title: Seed rep. #3

description: Untreated seeds and seeds harvested at 48 h after heat stress.

source_name: heat stressed seeds (48hr)

value: 48 hr

source_name: control  seeds (48hr)


title: SW rep. #1


title: SW rep. #3-2

description: Untreated silique walls and silique walls harvested at 48 h after heat stress.

source_name: control silique walls (48hr)

source_name: heat stressed silique walls (48hr)


title: Pgm- vs. 3XQS rep4

description: Biological replicate 4 of 6. Control: 3XQS. Treatment: Pgm-.

data_processing: Background correction, compression, normalization and fitting each probe with a mixed model were conducted as previously described (Madsen, M. L., D. Nettleton, E. L. Thacker, and F. C. Minion. 2006.Transcriptional profiling of Mycoplasma hyopneumoniae during iron depletion using microarrays. Microbiology 152:937-944) excluding slide region and slide-by-region interaction effects. intensity = mu + trt + dye + slide

label: Cy 3

source_name: Pgm- 4

label_protocol: Target generation and labeling were performed as described (Carruthers, M. D., and C. Minion. 2009. Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock. FEMS Microbiol. Lett. 295:96-102).

growth_protocol: An overnight culture was diluted 1:100 and grown at 30°C in BHI broth until an optical density 600 nm of 1.0 is reached.

treatment_protocol: Two strains, Pgm- as treatment and 3XQS as control.

value: Pgm-

label: Cy 5

source_name: 3XQS mutant 4


title: Pgm- vs. 3XQS rep5

description: Biological replicate 5 of 6. Control: 3XQS. Treatment: Pgm-.

source_name: 3XQS mutant 5

label_protocol:
Target generation and labeling were performed as described (Carruthers, M. D., and C. Minion. 2009. Transcriptome analysis of
Escherichia coli O157:H7 EDL933 during heat shock. FEMS Microbiol. Lett.
295:96-102).

source_name: Pgm- 5


title: Pgm- vs. 3XQS rep6

description: Biological replicate 6 of 6. Control: 3XQS. Treatment: Pgm-.

data_processing:
Background correction, compression, normalization and fitting each probe with a mixed model were conducted as previously described (Madsen, M. L., D. Nettleton, E. L. Thacker, and F. C. Minion. 2006.
Transcriptional profiling of Mycoplasma hyopneumoniae during iron depletion
using microarrays. Microbiology 152:937-944) excluding slide region and slide-by-region interaction effects. intensity = mu + trt + dye + slide

source_name: Pgm- 6

source_name: 3XQS mutant 6


title: Pgm- vs. 3XQS rep3

description: Biological replicate 3 of 6. Control: 3XQS. Treatment: Pgm-.

source_name: 3XQS mutant 3

source_name: Pgm- 3


title: Pgm- vs. 3XQS rep2

description: Biological replicate 2 of 6. Control: 3XQS. Treatment: Pgm-.

source_name: Pgm- 2

label_protocol: Target generation and labeling were performed as described(Carruthers, M. D., and C. Minion. 2009. Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock. FEMS Microbiol. Lett. 295:96-102).

source_name: 3XQS mutant 2


title: CEN.PK 113-7D with BSA, rep3

city: Göteborg

first: Zihe

last: Liu

address: Kemivägen 10

country: Sweden

institute: Chalmers University of Technology

description: Gene expression data from wildtype strain with BSA added to the culture, biological rep3

hyb_protocol: Following fragmentation, 7.5 ug of cRNA were hybridized on the Yeast Genome 2.0 Array (Affymetrix) for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Images were analyzed using R 2.10.1 software and Bioconductor packages. Briefly, data normalization was carried out using the method of Probe Logarithmic Intensity Error (PLIER) with perfect match probe only (PM-only).

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae strain CEN. PK 113-7D at aerobic shake flask fermentations, with BSA

label_protocol: RNA was processed to cRNA using the GeneChip 3' IVT Express Kit (Affymetrix). Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: Strains were cultured at 30 degree, 175 rpm with 50 mL of media in a 250 mL shake flask with baffles and cotton plug.

extract_protocol: RNA was isolated using the RNeasy Minikit (Qiagen).

treatment_protocol: 5 mL samples were taken at 48 h, and centrifuged at 4 degree for 3min, depleted supernatant, and stored in liquid nitrogen for short time and stored at -80 °C until processing.

tag: strain/background

value: CEN. PK 113-7D

value: wildtype

tag: condition

value: BSA


title: Pgm- vs. 3XQS rep1

description: Biological replicate 1 of 6. Control: 3XQS. Treatment: Pgm-.

source_name: 3XQS mutant 1

label_protocol:
Target generation and labeling were performed as described
(Carruthers, M. D., and C. Minion. 2009. Transcriptome analysis of Escherichia coli O157:H7 EDL933 during heat shock. FEMS Microbiol. Lett. 295:96-102).

source_name: Pgm- 1


title: CEN.PK 113-7D wo BSA, rep3

description: Gene expression data from wildtype strain, biological rep3

source_name: Saccharomyces cerevisiae strain CEN. PK 113-7D at aerobic shake flask fermentations, without BSA

value: no BSA


title: CEN.PK 113-7D with BSA, rep1

description: Gene expression data from wildtype strain with BSA added to the culture, biological rep1


title: CEN.PK 113-7D wo BSA, rep2

description: Gene expression data from wildtype strain, biological rep2


title: D456MG GIC 20% O2 12h rep1

city: Durham

first: Xiao-Fan

last: Wang

address: Duke University

institute: Duke University

description: gene expression after GICs cultured in 20% O2 for 12hrs

hyb_protocol: Hybridization, blocking and washing were performed according to Agilent protocol (One-Color Microarray-Based Gene Expression Analysis, Version 6.5).

scan_protocol: Hybridized microarray slides were scanned with an Agilent DNA Microarray Scanner G2505B at 5 micron resolution with the manufacturer’s software (Agilent ScanControl ). The scanned TIFF images were analyzed using the Agilent Feature Extraction Software according to the Agilent standard protocol GE1_107_Sep09.

data_processing: We used Agilent Feature Extraction for quantification, and GeneSpring 12 for data analysis. Normalized value is generated after log transformation and normalization and baseline transformation. Normalization: (Threhold raw signals to 1.0, Normalization algorithm: Pencentile shift, Pencentile target: 75) Baseline to median of all samples.

source_name: D456MG GIC 20% O2 12h rep1

label_protocol: We used Agilent Low Input Quick Amp Labeling Kit, and followed manufacturer's protocol (One-Color Microarray-Based Gene Expression Analysis, Version 6.5).

growth_protocol: CD133+ D456MG GICs were cultured in Neurobasal media (Invitrogen) supplemented with B27 (without vitamin A from Invitrogen), L-glutamine (Invitrogen), sodium pyruvate (Invitrogen), 10 ng/ml bFGF, and 10 ng/ml EGF (Millipore).

extract_protocol: Total RNA was prepared using the mirVanaTM miRNA Isolation Kit (Ambion)

treatment_protocol: CD133+ D456MG GICs were cultured in 1% O2 and 20% O2 for 12 hrs and harvested

value: CD133+ D456MG Glioma-Initiating Cells

tag: tumor stage

value: Glioblastoma Grade IV


title: CEN.PK 113-7D with BSA, rep2

description: Gene expression data from wildtype strain with BSA added to the culture, biological rep2


title: D456MG GIC 1% O2 12h rep3

description: gene expression after GICs cultured in 1% O2 for 12hrs

source_name: D456MG GIC 1% O2 12h rep1


title: D456MG GIC 20% O2 12h rep2


title: CEN.PK 113-7D wo BSA, rep1

description: Gene expression data from wildtype strain, biological rep1


title: D456MG GIC 1% O2 12h rep1


title: D456MG GIC 20% O2 12h rep3


title: SAMP8 - (Cy3) x SAMP8 + (Cy5)

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description:
Sample name: SAMP8 Whale meat extract (WME) diet
Dye-swap (Cy3/Cy5) SAMP8 LSO x SAMP8 WME

hyb_protocol: Hybridization kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing:
Software: Feature Extraction ver 11.0.1.1
Normalization was performed by LOWESS (locally weighted linear regression), which calculates the log ratio of dye-normalized Cy5- and Cy3-signals.

source_name: SAMP8, LSO

label_protocol: Manual: Low Input Quick Amp Labeling Kit, Two-Color (Agilent)

growth_protocol: 6-week-old mice (SAMP8 and SAMR1; CLEA, Tokyo, Japan) were housed at the Animal Institution Facility in Showa University, and maintained in individual cages in a ventilated animal room with controlled temperature and relative humidity under a 12-h light: 12-h dark regime (8:00 AM, lights turned on). Mice were fed chow (CE-2, CLEA Japan) and tap water ad libitum until 24-weeks-old.

extract_protocol: Kit: QIAGEN, RNeasy Mini

treatment_protocol: The 24-week-old SAMs mice were given experimental diet, LSO diet as a control diet and WME-supplemented diet, both in a powder form, for 26 weeks. SAMR1 mice were given LSO diet only until 50-weeks-old. The behavioral tests were performed at the timing of 49-weeks-old for 8 days. At 50 weeks of age following the behavioral analysis and the last day of the feeding, the mice were removed from their cages, decapitated and their brains carefully removed on ice. The whole brains were quickly frozen in liquid nitrogen in a sterile freeze tube and stored at -80ºC till extraction of total RNA followed by DNA microarray analysis.

value: senescence-accelerated mouse prone 8 (SAMP8)

tag: genetic background

value: AKR/J, suspected outbreeding to unknown line

tag: treatment

value: low-safflower oil (LSO) control diet

value: whole brain

value: 50 weeks

source_name: SAMP8, WME

value: whale meat extract (WME)-supplemented diet


title: skin i.d. animal 3 48h

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: skin 48h post intra dermal immunization

hyb_protocol: After precipitation, purification and quantification, 1.25µg labeled samples were  hybridized according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies). The extracted MAGE-ML files were further analyzed with the Rosetta Resolver, Build 7.2.2.0 SP1.31 (Rosetta Biosoftware, Seattle, USA).

source_name: skin

label_protocol: Total RNA labeling was performed with the single color Quick Amp Labeling Kit (Agilent Technologies).

extract_protocol: Animals were euthanized at 2h, 4h, 18h and 48h post-immunization using lethal dose of pentobarbital (5 animals per time and 5 mock animals). Blood (about 50 microliters) was sampled in retro-orbital sinus and immediately mixed to heparin (50 microliters diluted in 400 microliters of phosphate buffered saline [PBS]). Red blood cells were then lyzed twice using Qiagen buffer EL according to supplier's instructions. Total RNA from remaining blood cells (i.e. leucocytes) was then extracted by column-based method using Nucleospin II RNA kit (Macherey-Nagel). Punch biopsies of skin were sampled using Stiefel Biopsy punch 3 mm diameter and frozen in liquid nitrogen. Total RNA from skin was extracted using TRI Reagent® (Ambion) method according to supplier's instructions after homogenization using Ultra Turrax homogenizer.

treatment_protocol: Two days before immunization, female C57BL/6J (6 weeks old [Janvier labs, France]) mice were carefully shaved over their flanks and abdomen with an electric razor. Mice were then immunized with the TLR5 agonist: the flagellin FliC from Salmonella enterica serovar Typhimurium (1 microgram diluted in 50 microliters of PBS) by intradermal administration using 30G x 1/2 hypodermic needle (BD Microlance 0.3 x 13 mm) that was inserted at a shallow angle into the skin to generate a tense, pale raised area about 2-3 millimeters over the needle. The skin area of injection was marked for later sampling the site of flagellin administration.

tag: strain

value: skin

value: 48h post intra dermal immunization


title: D456MG GIC 1% O2 12h rep2


title: skin i.d. animal 2 48h

description: skin 48h post intra dermal immunization

tag: tissue


title: SAMR1 - (Cy5) x SAMP8 - (Cy3)

description:
Sample name: SAMP8 Regular (control, LSO) diet
Dye-swap (Cy3/Cy5) SAMP8 LSO x SAMR1 LSO

source_name: SAMR1, LSO

value: senescence-accelerated mouse resistant 1 (SAMR1)


title: SAMP8 - (Cy5) x SAMP8 + (Cy3)

description:
Sample name: SAMP8 Whale meat extract (WME) diet
Dye-swap (Cy3/Cy5) SAMP8 WME x SAMP8 LSO


title: skin i.d. animal 5 18h

description: skin 18h post intra dermal immunization

value: 18h post intra dermal immunization


title: SAMR1 - (Cy3) x SAMP8 - (Cy5)

description:
Sample name: SAMP8 Regular (control, LSO) diet
Dye-swap (Cy3/Cy5) SAMR1 LSO x SAMP8 LSO


title: skin i.d. animal 5 48h

description: skin 48h post intra dermal immunization


title: skin i.d. animal 1 48h

description: skin 48h post intra dermal immunization


title: skin i.d. animal 4 48h

description: skin 48h post intra dermal immunization


title: SW rep. #3-1

description: Untreated silique walls and silique walls harvested at 48 h after heat stress.

source_name: heat stressed silique walls (48hr)

value: Zhongshuang 9

value: 20 days after flowering

value: heat stress

value: 48 hr

value: silique walls

source_name: control silique walls (48hr)

value: control


title: skin i.d. animal 4 18h

description: skin 18h post intra dermal immunization


title: skin i.d. animal 1 18h

description: skin 18h post intra dermal immunization


title: skin i.d. animal 2 4h

description: skin 4h post intra dermal immunization

value: 4h post intra dermal immunization


title: skin i.d. animal 2 18h

description: skin 18h post intra dermal immunization


title: skin i.d. animal 1 4h

description: skin 4h post intra dermal immunization


title: skin i.d. animal 3 4h

description: skin 4h post intra dermal immunization


title: skin i.d. animal 3 18h

description: skin 18h post intra dermal immunization


title: skin i.d. animal 4 4h

description: skin 4h post intra dermal immunization


title: skin i.d. animal 3 2h

description: skin 2h post intra dermal immunization

value: 2h post intra dermal immunization


title: skin i.d. animal 2 mock-ref

description: skin mock reference

value: mock reference


title: skin i.d. animal 2 2h

description: skin 2h post intra dermal immunization


title: skin i.d. animal 5 2h

description: skin 2h post intra dermal immunization


title: skin i.d. animal 3 mock-ref

description: skin mock reference


title: skin i.d. animal 4 mock-ref

description: skin mock reference


title: skin i.d. animal 5 mock-ref

description: skin mock reference


title: skin i.d. animal 5 4h

description: skin 4h post intra dermal immunization


title: skin i.d. animal 4 2h

description: skin 2h post intra dermal immunization


title: skin i.d. animal 1 mock-ref

description: skin mock reference


title: skin i.d. animal 1 2h

description: skin 2h post intra dermal immunization


title: blood i.d. animal  4 48h

description: blood 48h post intra dermal immunization

source_name: blood

value: blood


title: blood i.d. animal  4 18h

description: blood 18h post intra dermal immunization


title: blood i.d. animal  1 48h


title: blood i.d. animal  5 18h


title: blood i.d. animal  2 48h


title: blood i.d. animal  3 18h


title: blood i.d. animal  3 48h


title: blood i.d. animal  2 4h

description: blood 4h post intra dermal immunization


title: blood i.d. animal  2 18h


title: blood i.d. animal  1 18h


title: blood i.d. animal  5 48h


title: blood i.d. animal  4 4h

description: blood 4h post intra dermal immunization


title: blood i.d. animal  1 4h

description: blood 4h post intra dermal immunization


title: fetal-3

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

description: Human fetal heart sample3

hyb_protocol: Manufature's protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

source_name: fetal heart sample3

label_protocol: Manufature's protocol

growth_protocol: Undifferentiated iPSCs were dissociated, and then suspended in StemPro34 medium supplemented with Y-27632 and BMP4 and allowed to form EBs by being placed into 96-well dish. On day 1, media, which included activin A, BMP4 and bFGF, were added into the wells. On day 3, EBs were collected and dissociated, and then suspended in differentiation media supplemented with VEGF and  IWP-3. Approximately 10000-20000 cells were put in each well to again form aggregates for 4 days. On day 7, the media were changed to StemPro 34 media supplemented with VEGF and bFGF. For the maintenance of iPSC-CMs, the culture media were refed every 2-3 days.

extract_protocol: RNA was prepared using the miRNeasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: After cardiac differentiation, we collected GFP positive cardiomyocytes by FACS sorting on day8, 20, and 30.

tag: cell type

value: Human fetal heart


title: adult-3

description: Human adult heart sample3

source_name: adult heart sample3

value: Human adult heart


title: fetal-1

description: Human fetal heart sample1

source_name: fetal heart sample1


title: blood i.d. animal  2 2h

description: blood 2h post intra dermal immunization


title: blood i.d. animal  4 2h

description: blood 2h post intra dermal immunization


title: blood i.d. animal  3 4h

description: blood 4h post intra dermal immunization


title: adult-2

description: Human adult heart sample2

source_name: adult heart sample2


title: blood i.d. animal  3 2h

description: blood 2h post intra dermal immunization


title: day30-3

description: Differentiated cardiomyocytes 30days after induction from human induced pluripotent stem cells 3

source_name: differentiated CMs day30 sample3

value: Differentiated cells from human induced pluripotent stem cells


title: day30-1

description: Differentiated cardiomyocytes 30days after induction from human induced pluripotent stem cells 1

source_name: differentiated CMs day30 sample1


title: fetal-2

description: Human fetal heart sample2

source_name: fetal heart sample2


title: day30-2

description: Differentiated cardiomyocytes 30days after induction from human induced pluripotent stem cells 2

source_name: differentiated CMs day30 sample2


title: blood i.d. animal 5 mock-ref

description: blood naive reference

value: naive reference


title: blood i.d. animal 4 mock-ref

description: blood naive reference


title: blood i.d. animal  1 2h

description: blood 2h post intra dermal immunization


title: blood i.d. animal  5 2h

description: blood 2h post intra dermal immunization


title: blood i.d. animal 3 mock-ref

description: blood naive reference


title: day20-3

description: Differentiated cardiomyocytes 20days after induction from human induced pluripotent stem cells 3

source_name: differentiated CMs day20 sample3


title: blood i.d. animal 2 mock-ref

description: blood naive reference


title: day20-1

description: Differentiated cardiomyocytes 20days after induction from human induced pluripotent stem cells 1

source_name: differentiated CMs day20 sample1


title: day8-3

description: Differentiated cardiomyocytes 8days after induction from human induced pluripotent stem cells 3

source_name: differentiated CMs day8 sample3


title: day20-2

description: Differentiated cardiomyocytes 20days after induction from human induced pluripotent stem cells 2

source_name: differentiated CMs day20 sample2


title: day8-2

description: Differentiated cardiomyocytes 8days after induction from human induced pluripotent stem cells 2

source_name: differentiated CMs day8 sample2


title: adult-1

description: Human adult heart sample1

source_name: adult heart sample1


title: blood i.d. animal 1 mock-ref

description: blood naive reference


title: CEN.PK113-7D Aerobic batch 2 sampled during expo phase

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description: CEN.PK113-7D Aerobic batch sampled during expo phase

hyb_protocol: Hybridization of labelled fragmented aRNA to the microarrays and staining, washing and scanning of the microarrays was performed according to Affymetrix instructions (EukGE_WS2v5).

data_processing: The 6383 yeast open reading frames were extracted from the 9335 transcript features on the YG-S98 microarrays. To allow comparison, all expression data were normalized to a target value of 240 using the average signal from all gene features. To eliminate variation in genes that are not expressed, genes with expression values below 12 were set to 12 and the gene features for which the maximum expression was below 20 for all 20 arrays were discarded. The average deviation of the mean transcript data of replicate batches was ca. 11%, similar to the reproducibility usually observed in replicate steady state chemostat cultures (Daran-Lapujade et al, J Biol Chem 2004, 279:9125-9138). The expression of housekeeping genes ACT1, PDA1, TFC1, ALG9, TAF10 and UBC6 (Teste et al, BMC Mol Biol 2009, 10:99) remained stable for both conditions and all sample points (average coefficient of variation 17% ± 5%).   To identify genes that were differentially expressed between aerobic and anaerobic stationary phase cultures, a pairwise comparison was performed between aerobic samples taken at time 6 and anaerobic samples taken at time 4 as previously described (Hebly et al, Appl Environ Microbiol 2014, 80:4433-4449). Similarly genes differently expressed during growth on glucose under aerobic or anaerobic conditions were identified through a pairwise comparison of aerobic and anaerobic samples taken at time  1. Differences with adjusted p-values lower than 0.05 and a fold difference of 2 or higher were considered statistically significant. Furthermore genes with average intensity signals over all 20 arrays below 20 were excluded. Time-dependent expression profiles of selected genes were clustered according optimal k-means clustering using positive correlation as distance metric (Expressionist Pro version 3.1, Genedata, Basel, Switzerland) resulting in an optimal number of 9 clusters. For display of time-dependent transcript levels, expression values were normalized per gene by dividing single expression values by the average expression value of both conditions and all time points. Mean values of  these average-normalized values for all genes in each cluster are shown, as well as minimal and maximal average-normalized values.    Gene expression clusters were analysed for overrepresentation of functional annotation categories of the Gene Ontology (GO) database (http://www.geneontology.org/), based on a hypergeometric distribution analysis tool (Knijnenburg et al., BMC Genomics., 8:25).

label: Biotin-Streptavidin

label_protocol: Total RNA extraction, isolation of mRNA, cDNA synthesis, cRNA synthesis, labelling and array hybridization was performed as described previously [Mendes et al, Appl Environ Microbiol 2013, 79:5949-5961].

growth_protocol: Previously described synthetic medium (Verduyn et al, Yeast 1992, 8:501-517) was used with 20 g.L-1 glucose as sole carbon-source and 0.2 g.L-1 antifoam Emulsion C (Sigma, St. Louise, USA). In case of  anaerobic cultivations, the medium was supplemented with anaerobic growth factors ergosterol (10 mg.L-1) and Tween 80 (420 mg.L-1) dissolved in ethanol. Inocula for batch fermentations consisted of 100 mL overnight grown yeast cultures to an OD600 of 4 in synthetic medium with 20 g.L-1 glucose. Aerobic and anaerobic batch fermentations were carried out at 30 °C in 2 L bioreactors (Applikon, Schiedam, The Netherlands), with a working volume of 1.4 L. Cultures were stirred at 800 rpm and sparged at a flow-rate of 700 mL.min-1 with either dried air or nitrogen  gas (<10 ppm oxygen, Linde Gas Benelux, The Netherlands). The bioreactors were equipped with Norprene tubing (Saint-Gobain Performance Plastics, Courbevoie, France) and Viton O-rings  (Eriks, Alkmaar, The Netherlands) to minimize diffusion of oxygen. During aerobic cultivations, dissolved oxygen levels remained above 40% of the initial saturation level as measured by Clark electrodes (Mettler Toledo, Greifensee, Switzerland). The culture pH was maintained at 5.0 by automatic addition of 2 M KOH and 2 M H2SO4.

extract_protocol: Prior to RNA extraction, samples were stored in a mixture of phenol/chloroform and TEA buffer at -80°C. Total RNA extraction, isolation of mRNA, cDNA synthesis, cRNA synthesis, labelling and array hybridization was performed as described previously [Mendes et al, Appl Environ Microbiol 2013, 79:5949-5961], with the following modifications.

treatment_protocol: Independent duplicate aerobic and anaerobic batch cultures were sampled at six and four different time points respectively (see Figure 4A & 4B) for microarray analysis, resulting in a total dataset of 20 microarrays. Sampling from batch cultures for transcriptome analysis was performed using liquid nitrogen for rapid quenching of mRNA turnover (Piper et al., J Biol Chem. 277:37001-8.). Prior to RNA extraction, samples were stored in a mixture of phenol/chloroform and TEA buffer at -80°C. .

value: CEN.PK113-7D (MATa MAL2-8C SUC2 )

tag: genotype/variation

value: MATa MAL2-8C SUC2

tag: c-source

value: glucose


title: CEN.PK113-7D Aerobic batch 2 sampled during early SP

description: CEN.PK113-7D Aerobic batch sampled during early SP

scan_protocol: Hybridization of labelled fragmented aRNA to the microarrays and staining, washing and scanning of the microarrays was performed according to Affymetrix instructions (EukGE_WS2v5).


title: CEN.PK113-7D Aerobic batch 1 sampled during late SP

description: CEN.PK113-7D Aerobic batch sampled during late SP


title: CEN.PK113-7D Aerobic batch 2 sampled during late SP

source_name: CEN.PK113-7D Aerobic batch sampled during late SP


title: CEN.PK113-7D Aerobic batch 2 sampled during diauxic shift

description: CEN.PK113-7D Aerobic batch sampled during diauxic shift


title: CEN.PK113-7D Aerobic batch 2 sampled during late expo phase

description: CEN.PK113-7D Aerobic batch sampled during late expo phase


title: fat body_after 24h exposure to phoxim Replicate3

city: Suzhou

first: Zhi

middle: Ya

last: Gu

address: Renai Road

department: School of Basic Medicine and Biological Sciences

institute: Soochow University

description:
Transcriptional profiling of fat body in the domestic silkworms comparing control untreated fat body with phoxim-treated fat body
Sample 3

hyb_protocol: Cy5-dCTP for test samples and Cy3-dCTP for reference samples labeled double-stranded cDNA dissolved in 80μl hybridization solution containing 3×SSC, 0.2%SDS, 5×Denhart’s, and 25% formamide. The slides were covered with a LifterSlip™ coverslip (Erie Company, Portsmouth, NH, USA) and hybridized in chamber at 42℃ for over night. After hybridization, slides were washed three times in 0.2% SDS, 2x SSC at 42℃ for 5 minutes and three times in 0.2 x SSC at room temperature for 5 minutes before signal scanning.

scan_protocol: Scanned on an confocal LuxScan 10 KA scanner (CapitalBio Corp.).The slides were scanned with a confocal LuxScan 10 KA scanner (CapitalBio Corp.) and the raw data were extracted from imagines using LuxScan™ 3.0 software (CapitalBio Corp.)

data_processing: The Lowess (Locally Weighted Scatterplot Smoothing) method was used to normalize the dual channel data with the total intensity of all genes in each array. Data with a signal intensity of 400 and above were accepted as the standard for gene expression. In a comparison analysis, a one-class, unpaired method from the Significance Analysis of Microarrays (SAM version 3.02, Stanford University, CA) software was used to compare significantly differentially expressed genes in both the control and the phoxim-treated fat body groups. Expression ratios were compared between control and treated samples based on the normalized data. Statistical differences of values were determined with t-test.

organism: Bombyx mori

source_name: Treated fat body of day 3 of the fifth instar larva after 24h of phoxim exposure Replicate3

label_protocol: 5µg of total RNA were primed with 1 µl of 100 µM primer containing T7 RNA polymerase promoter sequence at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U CbcScript (CapitalBio Corp, China), and synthesis of the second strand of cDNA at 16°C for 2 h in the presence of RNaseH and DNA Polymerase. cRNA was synthesized by T7 Enzyme Mix (CapitalBio Corp, China) with the template of cDNA. 2 µl of cRNA were primed with 1 µl random primer at 65°C for 10 min, then reversed transcribed at 25°C for 10 min and 37°C for 1.5h in the presence of CbcScript II (CapitalBio Corp, China). The Cy3- and Cy5-dCTP double-stranded cDNA was labeled using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China). And, Cy5-dCTP or Cy3-dCTP were added at a final concentration of 120µM each dATP, dGTP, and dTTP and 60µM dCTP and 40µM Cy5-dCTP for test samples (or Cy3-dCTP for reference samples), respectively.

growth_protocol: Silkworm larvae (p50 strain) maintained at the National Engineering Laboratory for Modern Silk (Soochow University, China) were reared on mulberry leaves at 25°C-26°C

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

treatment_protocol: Fifty grams of fresh mulberry leaves were dipped in 4 μg/mL phoxim solution for one minute. After dried in the air, the leaves were used to rear the ﬁfth larval instar B. mori on the third day three times a day. Each experiment was performed with 30 larvaes for three times. The control mulberry leaves were treated with water. The fat body of both phoxim-induced and control larvae were collected 24 h later by dissection on ice and snap-frozen immediately in liquid nitrogen.

tag: gender

value: mixed-sex

value: day 3 of the fifth instar larva

value: fat body

source_name: control fat body of day 3 of the fifth instar larva Replicate3


title: day4

description: Differentiated cells 4days after induction from human induced pluripotent stem cells

source_name: differentiated cells day4


title: day8-1

description: Differentiated cardiomyocytes 8days after induction from human induced pluripotent stem cells 1

source_name: differentiated CMs day8 sample1


title: day0

source_name: Human induced pluripotent stem cell line 1 (201B7 MHC-GFP)

value: Undifferentiated human induced pluripotent stem cells


title: fat body_after 24h exposure to phoxim Replicate2

description:
Transcriptional profiling of fat body in the domestic silkworms comparing control untreated fat body with phoxim-treated fat body
Sample 2

source_name: Treated fat body of day 3 of the fifth instar larva after 24h of phoxim exposure Replicate2

source_name: control fat body of day 3 of the fifth instar larva Replicate2


title: CEN.PK113-7D Aerobic batch 1 sampled during post diauxic phase

description: CEN.PK113-7D Aerobic batch sampled during post diauxic phase


title: CEN.PK113-7D Aerobic batch 1 sampled during early SP

source_name: CEN.PK113-7D Aerobic batch sampled during early SP


title: CEN.PK113-7D Aerobic batch 1 sampled during diauxic shift

source_name: CEN.PK113-7D Aerobic batch sampled during diauxic shift


title: CEN.PK113-7D Anaerobic batch 2 sampled during end expo phase

description: CEN.PK113-7D Anaerobic batch sampled during end expo phase


title: CEN.PK113-7D Anaerobic batch 2 sampled during early SP

description: CEN.PK113-7D Anaerobic batch sampled during early SP


title: CEN.PK113-7D Aerobic batch 1 sampled during expo phase

source_name: CEN.PK113-7D Aerobic batch sampled during expo phase


title: CEN.PK113-7D Anaerobic batch 2 sampled during late SP

description: CEN.PK113-7D Anaerobic batch sampled during late SP


title: CEN.PK113-7D Aerobic batch 1 sampled during late expo phase

source_name: CEN.PK113-7D Aerobic batch sampled during late expo phase


title: CEN.PK113-7D Anaerobic batch 2 sampled during expo phase

description: CEN.PK113-7D Anaerobic batch sampled during expo phase


title: microspore_DMSO_8h_rep2

city: Wageningen

first: Kim

last: Boutilier

address: Droevendaalsesteeg 1

institute: Plant Research International

hyb_protocol: standard Affymetrix protocolol, NASC Affymetrix service

data_processing: RMA

source_name: microspore culture, DMSO, 8h

growth_protocol: Isolated Brassica napus microspores cultured in NLN-13 medium  (Custers, J.B.M. (2003). Microspore culture in rapeseed (Brassica napus L.). In Doubled haploid production in crop plants: a manual, M. Maluszynski, K.J. Kasha, B.P. Forster, and I. Szarejko, eds (Dordrecht: Kluwer Academic Publishers), pp. 185-193)

extract_protocol: Microspores are collected by centrifuge at 12000rpm for 10min, then frozen in liquid nitrogen. Total RNA were isolated using InviTrap Spin Plant RNA Mini Kit (Invitek).

treatment_protocol: A: microspores treated for 8 h at 33 oC with 0.5 µM TSA and 10 µM cycloheximide; B: microspores treated for 8h 33 oC with 10 µM cycloheximide; C: microspores treated for 8h 33 oC with 0.5µM TSA; D: microspores treated for 8h 33 oC with DMSO.

value: DMSO

value: microspore culture


title: CEN.PK113-7D Anaerobic batch 1 sampled during expo phase

source_name: CEN.PK113-7D Anaerobic batch sampled during expo phase


title: fat body_after 24h exposure to phoxim Replicate1

description:
Transcriptional profiling of fat body in the domestic silkworms comparing control untreated fat body with phoxim-treated fat body
Sample 1

source_name: Treated fat body of day 3 of the fifth instar larva after 24h of phoxim exposure Replicate1

source_name: control fat body of day 3 of the fifth instar larva Replicate1


title: microspore_DMSO_8h_rep1

scan_protocol: standard Affymetrix protocolol, NASC Affymetrix service


title: A4 Xenograft tumor sorted Euploid  Replicate-3

city: Pune

first: Sharmila

last: Bapat

address: NCCS Complex, Ganeshkhind

institute: National Centre for Cell Science

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Custom Agilent Human Gene Expression Microarray 8x60K designed by Genotypic Technology Private Limited (AMADID No: 27114) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Microarrays slides  8X60K were scanned using the Agilent Microarray Scanner

data_processing:
Images were quantified using Feature Extraction Software (Agilent).
Log transformed and median over entire array normalization method was used using BRB array tool (version 3.8.0), duplicate probes were collapsed into unique probes using GSEA offline software based on median intensity criteria

source_name: Ovarian cancer Xenograft tumor sorted Euploid

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

extract_protocol: Flow cytometer sorted tumor cells were subjected to RNA isolation which was done by using TRIzol method as per the manufacturer’s instructions.

treatment_protocol: A4T cells were injected subcutaneously in NOD/SCID mice, tumors were harvested at day 28 processed  for  single cell suspension. Further cells were subjected to staining with Hoechst (33342) for 45min at 37˚C followed by pyronin Y for  45min at 37˚C and processed for FACS sorting.

tag: host strain

value: NOD/SCID

tag: injected with

value: A4T cells (from a patient with Grade IV serous adenocarcinoma)

tag: time point

value: day 28 (4 weeks)

value: Tumor xenograft sorted fraction

tag: sorted cell genotype

value: Euploid


title: A4 Xenograft tumor sorted Aneuploid Replicate-3

source_name: Ovarian cancer Xenograft tumor sorted Aneuploid

value: Aneuploid


title: CEN.PK113-7D Anaerobic batch 1 sampled during late SP phase

description: CEN.PK113-7D Anaerobic batch sampled during late SP phase


title: CEN.PK113-7D Anaerobic batch 1 sampled during end expo phase

source_name: CEN.PK113-7D Anaerobic batch sampled during end expo phase


title: CEN.PK113-7D Aerobic batch 2 sampled during post diauxic phase

source_name: CEN.PK113-7D Aerobic batch sampled during post diauxic phase


title: A4 Xenograft tumor sorted Aneuploid Replicate-2

description: T1 Aneuploid(9.02)


title: CEN.PK113-7D Anaerobic batch 1 sampled during early SP phase

description: CEN.PK113-7D Anaerobic batch sampled during early SP phase


title: A4 Xenograft tumor sorted Euploid Replicate-2


title: A4 Xenograft tumor sorted Aneuploid Replicate-1


title: 48hpi mensenchyme, biological rep2

first: Xia

last: Gao

state: NC

address: 353 Nanaline Duke Bldg. Research Dr.

description: Gene expression data of 48hpi mouse tracheal mesenchyme replicate 2

hyb_protocol: Targets were hybridized to GeneChip® Mouse Genome 430 2.0 arrays in Affymetrix GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip® Scanner 7G and AGCC software version 1.1

data_processing: Affymetrix Expression Console version 1.1 was used to generate the .cel files. Partek Genomics Suite 6.5 (Partek Inc., St. Louis, MO) was used to perform data analysis. Robust multi-chip analysis (RMA) normalization was done on the entire data set.

source_name: mouse tracheal mesenchyme 48hrs post SO2 injury

label_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA.

growth_protocol: Mouse tracheas were cleaned well, cut into pieces and incubated in Dispase at RT for 23min. Digestion was stopped by addition of DMEM with 5% FBS. Epithelium was peeled off with forcepsThe remaining total mesenchyme was used without further manipulation

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

treatment_protocol: Adult male C57Bl/6 mice were placed in individual compartments within a chamber and exposed to 500 ppm SO2 in air for 4 hr.

value: trachea

value: mesenchyme

value: male


title: microspore_TSA_8h_rep1

source_name: microspore culture, TSA, 8h

label_protocol: standard Affymetrix protocolol, NASC Affymetrix service

value: TSA


title: A4 Xenograft tumor sorted Euploid Replicate-1


title: 48hpi mensenchyme, biological rep3

description: Gene expression data of 48hpi mouse tracheal mesenchyme replicate 3


title: microspore_CHX_8h_rep2

source_name: microspore culture, CHX, 8h

value: CHX


title: microspore_CHX_8h_rep1


title: microspore_TSA_8h_rep2


title: control mensenchyme, biological rep3

description: Gene expression data of normal mouse tracheal mesenchyme replicate 3

source_name: normal mouse tracheal mesenchyme

value: normal control


title: 48hpi epithelium, biological rep3

description: Gene expression data of 48hpi mouse tracheal epithelium replicate 3

source_name: mouse tracheal epithelium 48hrs post SO2 injury

growth_protocol: Mice tracheas were cleaned well, cut into pieces and incubated in Dispase at RT for 23min. Digestion was stopped by addition of DMEM with 5% FBS. Epithelium was peeled off with forceps and incubated in 0.1% trypsin, 1.6mM EDTA 20 min at 37 °C.Mouse CD45 MicroBeads (Miltenyi Biotec) were used to deplete CD45+ leukocytes from mouse tracheal epithelial cells.

treatment_protocol: Adult mice were placed in individual compartments within a chamber and exposed to 500 ppm SO2 in air for 4 hr.

value: epithelium


title: 48hpi epithelium, biological rep2

description: Gene expression data of 48hpi mouse tracheal epithelium replicate 2


title: microspore_TSA+CHX_8h_rep2

source_name: microspore culture, TSA+CHX, 8h

value: TSA + CHX


title: control mensenchyme, biological rep1

description: Gene expression data of normal mouse tracheal mesenchyme replicate 1


title: 48hpi epithelium, biological rep1

description: Gene expression data of 48hpi mouse tracheal epithelium replicate 1


title: A4 Xenograft tumor sorted PKHneg  Replicate-3

description: Set 11_PKH Neg (13-9-11)

data_processing:
Images were quantified using Feature Extraction Software ( Agilent).
Log transformed and median over entire array normalization method was used using BRB array tool (version 3.8.0), duplicate probes were collapsed into unique probes using GSEA offline software based on median intensity criteria

source_name: Ovarian cancer Xenograft tumor sorted PKHneg

treatment_protocol: A4T cells were labeled with PKH26 and injected subcutaneously in NOD/SCID mice, tumors were harvested at day 28 processed  for  single cell suspension. Further cells were subjected to FACS sorting where freshly labeled A4T celline with PKH26 was positive control and unalebeled tumor cells as negative control, accordingly PKHhi, PKHlo and PKHneg tumor fractions were sorted.

tag: cell line source

value: A4T from a patient with Grade IV serous adenocarcinoma

value: A4 PKH26-labeled cells

value: ovarian cancer xenograft

tag: sorted fraction

value: PKHneg


title: control epithelium, biological rep3

description: Gene expression data of normal mouse tracheal epithelium replicate 3

source_name: normal mouse tracheal epithelium


title: 48hpi mensenchyme, biological rep1

description: Gene expression data of 48hpi mouse tracheal mesenchyme replicate 1


title: A4 Xenograft tumor sorted PKHhi   Replicate-3

description: Set 11_PKH Hi (13-9-11)

source_name: Ovarian cancer  Xenograft tumor sorted PKHhi

value: NOD/SCID

value: PKHhi


title: A4 Xenograft tumor sorted  PKHhi  Replicate-1

description: Set 5_PKH_Hi

source_name: Ovarian cancer Xenograft tumor sorted  PKHhi

value: day 28 (4 weeks)


title: control epithelium, biological rep2

description: Gene expression data of normal mouse tracheal epithelium replicate 2


title: A4 Xenograft tumor sorted PKHlo   Replicate-3

description: Set 11_PKH Lo (13-9-11)

source_name: Ovarian cancer  Xenograft tumor sorted PKHlo

value: PKHlow


title: Day 14 MESP1neg derivative replicate 3

city: Leiden

first: Sabine

last: Den Hartogh

state: Zuid-Holland

address: Einthovenweg 20

department: Anatomy and Embryology

institute: LUMC

description: replicate 3

hyb_protocol: Per sample, 750 ng of the obtained biotinylated cRNA samples was hybridized onto the Illumina HumanHT-12 v4  (Illumina, Inc., San Diego, CA, U.S.A.). Hybridization and washing  were performed according to the Illumina Manual “Direct Hybridization Assay Guide”.

scan_protocol: Scanning was performed on the Illumina iScan (Illumina, Inc., San Diego, CA, U.S.A.).

data_processing: Image analysis and extraction of raw expression data was performed with Illumina GenomeStudio v2011.1 Gene Expression software with  default settings (no background subtraction and no normalization).

source_name: human embryonic stem cells

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin,  TX, U.S.A.) according to the manufacturer’s specifications with an input of 200 ng total RNA.

growth_protocol: Total RNA was isolated using Macherey Nagel RNA isolation XS kit, according to company's protocol. The Quality control, RNA labeling, hybridization and data extraction were performed at ServiceXS B.V. (Leiden, The Netherlands).

value: NEG

tag: xav939 treatment

value: POS

value: hESC


title: AFO f/f white fat, biological rep1

first: Chao-Yung

address: 5 Fu-Hsing street

department: Cardiology

institute: Chang Gung Memorial Hospital

description: Gene expression data from Adiponectin cre + FTO flox/flox gonadal white fat, pool 1

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Normalize with RMA by Affymetrix Expression Console Ver 1.4

source_name: Adiponectin cre FTO flox/flox mouse white fat

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix GeneChip 3' IVT Express kit protocol

extract_protocol: Tri Reagent extraction of total RNA was performed according to the Ambion's instruction

treatment_protocol: White fat tissues were harvested under random fed condition.

value: Male

value: Visceral white fat

value: Adiponectin-cre FTO flox/flox

tag: diet

value: Chow diet

tag: age

value: 16 weeks


title: Day 14 MESP1neg derivative replicate 1

description: replicate 1

extract_protocol: Total RNA was isolated using Macherey Nagel RNA isolation XS kit, according to company's protocol.


title: A4 Xenograft tumor sorted PKHlo   Replicate-2

description: Set  10_PKH_LO 5/09/11

source_name: Ovarian cancer Xenograft tumor sorted PKHlo


title: control epithelium, biological rep1

description: Gene expression data of normal mouse tracheal epithelium replicate 1

value: trachea

value: epithelium

value: normal control


title: AFO f/f white fat, biological rep3

description: Gene expression data from Adiponectin cre + FTO flox/flox gonadal white fat, pool 3


title: control mensenchyme, biological rep2

description: Gene expression data of normal mouse tracheal mesenchyme replicate 2

value: mesenchyme

value: male


title: FTO f/f white fat, biological rep3

description: Gene expression data from FTO flox/flox gonadal white fat, pool 3

source_name: FTO flox/flox mouse white fat

value: FTO flox/flox


title: A4 Xenograft tumor sorted PKHlo   Replicate-1

description: Set 5_PKH_Lo

value: A4T from a patient with Grade IV serous adenocarcinoma

value: NOD/SCID

value: A4 PKH26-labeled cells

value: ovarian cancer xenograft


title: FTO f/f white fat, biological rep2

description: Gene expression data from FTO flox/flox gonadal white fat, pool 2


title: AFO f/f white fat, biological rep2

description: Gene expression data from Adiponectin cre + FTO flox/flox gonadal white fat, pool 2


title: A4 Xenograft tumor sorted PKHhi  Replicate-2

description: Set  10_PKH_HI 5/09/11

source_name: Ovarian cancer Xenograft tumor sorted PKHhi

value: day 28 (4 weeks)

value: PKHhi


title: A4 Xenograft tumor sorted PKHneg  Replicate-2

description: Set  10_PKH_Neg 5/09/11

source_name: Ovarian cancer  Xenograft tumor sorted PKHneg

value: PKHneg


title: FTO f/f white fat, biological rep1

description: Gene expression data from FTO flox/flox gonadal white fat, pool 1

value: Male

value: Visceral white fat


title: Day 14 MESP1neg derivative replicate 2

description: replicate 2

value: NEG

value: POS

value: hESC


title: microspore_TSA+CHX_8h_rep1

value: TSA + CHX

value: microspore culture


title: A4 Xenograft tumor sorted PKHneg Replicate-1

description: Set 5_PKH_Neg


title: Control embryos at 24 hpf - Cortisol-treated embryos at 24 hpf

city: Padua

first: Andrea

last: Celeghin

state: Veneto

address: Via Ugo Bassi 58 B

department: Biology

institute: University of Padua

description:
Zebrafish were purchased from a local pet shop.
Danio rerio control embryos treated for two hours (from 0 hpf to 2 hpf) with the vehicle absolute ethanol (2ml in 1L of fish water) compared to embryos treated for the same two hours with the steroid cortisol. All the embryos were fixed at 24 hours post fertilization.

hyb_protocol: The samples were mixed with 25X Fragmentation Buffer and 10X Blocking Agent (Agilent Gene Expression Hybridization Kit) and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on Agilent Technologies Scanner G2505B US22502723. Images were quantified using Agilent Feature Extraction Software.

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

organism: Danio rerio

source_name: Control embryos (24hpf)

label_protocol: 200 ng of total RNA were primed and reversed transcribed using the Agilent Quick-Amp labeling Kit protocol following manufacturer's instructions.

growth_protocol: Treated embryos were raised in fish water at 28.5 C degrees and were fixed at 5hpf, 12hpf, or 24hpf.

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

treatment_protocol: Danio rerio ovulated oocytes were treated for two hours, from 0 hpf to 2 hpf, with 5 mg/L (13.8 µM) of cortisol, by adding the steroid directly to the fish water. Control embryos were treated with 2 ml of absolute ethanol (the vehicle used to dissolve the cortisol) in 1L of fish water from 0 hpf to 2 hpf.

value: wild type

value: 24 hours post fertilization

value: ethanol vehicle

tag: treatment duration

value: 2 hours (0-2hpf)

source_name: Cortisol-treated embryos (24hpf)

value: cortisol


title: Control 1 embryos at 12 hpf - Cortisol-treated 1 embryos at 12 hpf

description:
Zebrafish were purchased from a local pet shop.
Danio rerio control embryos treated for two hours (from 0 hpf to 2 hpf) with the vehicle absolute ethanol (2ml in 1L of fish water) compared to embryos treated for the same two hours with the steroid cortisol. The experiment was carried out in triplicate. All the embryos were fixed at 12 hours post fertilization.

source_name: Control 1 embryos (12hpf)

value: 12 hours post fertilization

tag: treatment

source_name: Cortisol-treated 1 embryos (12hpf)


title: Control embryos at 5 hpf - Cortisol-treated embryos at 5 hpf

description:
Zebrafish were purchased from a local pet shop.
Danio rerio control embryos treated for two hours (from 0 hpf to 2 hpf) with the vehicle absolute ethanol (2ml in 1L of fish water) compared to embryos treated for the same two hours with the steroid cortisol. All the embryos were fixed at 5 hours post fertilization.

source_name: Control 1 embryos (5hpf)

value: 5 hours post fertilization

source_name: Cortisol-treated 1 embryos (5hpf)


title: bcat +/-, masses C57ms-0

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: Gene expression data from mouse tissue

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

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

data_processing: Data were normalized by Robust Multichip Average (RMA) using R with Bioconductor.

source_name: Mouse Tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT Express protocol from 100 ng total RNA.

extract_protocol: Total RNA was extracted by Qiagen RNEasy kit according to the manufacturer's instructions.

value: breast

tag: genotype

value: bcat +/-, masses


title: Day 14 MESP1pos derivative replicate 1

description: replicate 1


title: Day 14 MESP1pos derivative replicate 3

description: replicate 3


title: Quadruple (SB/Tg/K5Cre/Bcat) Q535

description: Gene expression data from mouse tissue

tag: tissue

value: Quadruple (SB/Tg/K5Cre/Bcat)


title: Quadruple (SB/Tg/K5Cre/Bcat) Q545

description: Gene expression data from mouse tissue


title: Day 10 MESP1neg derivative replicate 3

description: replicate 3

tag: cell type


title: Day 14 MESP1pos derivative replicate 2

description: replicate 2


title: Day 10 MESP1pos derivative replicate 2

description: replicate 2


title: bcat +/-, masses C57ms-7

description: Gene expression data from mouse tissue


title: Day 10 MESP1neg derivative replicate 1

description: replicate 1


title: Quadruple (SB/Tg/K5Cre/Bcat) Q651

description: Gene expression data from mouse tissue


title: Normal mammary gland sample from Triple(SB/Tg/k5Cre) MGT635

description: Gene expression data from mouse tissue

value: Normal mammary gland


title: Quadruple (SB/Tg/K5Cre/Bcat) Q2154B

description: Gene expression data from mouse tissue


title: Quadruple (SB/Tg/K5Cre/Bcat) Q409

description: Gene expression data from mouse tissue


title: Normal mammary gland sample from Triple(SB/Tg/k5Cre) MGT627

description: Gene expression data from mouse tissue


title: Quadruple (SB/Tg/K5Cre/Bcat) Q2154A

description: Gene expression data from mouse tissue


title: Normal mammary gland sample from Quadruple(SB/Tg/k5Cre/Bcat)  MGQ440

description: Gene expression data from mouse tissue


title: Normal mammary gland sample from Triple(SB/Tg/Bcat)  MG-Tbc-139

description: Gene expression data from mouse tissue


title: Triple (SB/Tg/Bcat) Tbc-2173

description: Gene expression data from mouse tissue

value: Triple (SB/Tg/Bcat)


title: Triple (SB/Tg/Bcat) Tbc-266A

description: Gene expression data from mouse tissue


title: NCI-HPN-M2C Colon p55 Late Transformed

city: Bethesda

first: Hesed

middle: Maria

last: Padilla-Nash

address: 50 South Drive

department: Genetics Branch

institute: NCI

description: male

hyb_protocol: The arrays were hybridized according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: The arrays were scanned using an Agilent Scanner System with the following settings:   5µm resolution scan, scan area (61 x21.6mm), single pass 5um scanning mode, eXtended Dynamic range, Dye channel Green, and Green PMT XDR Hi 100%, XDR Lo 10% . Images were quantified using Agilent Feature Extraction Software (version 8.1.1).

data_processing: Raw data were log2 transformed and normalized to 75 percentile according to Agilent protocol

source_name: mouse colon epithelial cells

label_protocol: The denatured probe was applied to the Agilent Mouse Gene Expression 4 X44K Microarray Kit along with 2xGE Hybridization Buffer according to the manufacturer's instructions.

extract_protocol: 700ng of total input RNA was used from each of the cell lines and uncultured  was labeled with Cy3 and fragmented before application to the microarray.

treatment_protocol: RNAwas extracted from the murine epithelial cells during the various stages of cellular transformation.   The uncultured colon epithelial cells served as a normal control. The Qiagen RNAeasy Mini Kit was used to extract the RNA according to manufacturer's protocols.

tag: Stage

tag: strain

value: male


title: NCI-HPN-F1K Colon p6 Immortal

description: female

tag: gender

value: female


title: Triple (SB/Tg/Bcat) Tbc-266B

description: Gene expression data from mouse tissue


title: NCI-HPN-F3K Colon p52 Late Transformed

description: female


title: Day 10 MESP1pos derivative replicate 1

description: replicate 1

value: POS

value: hESC


title: Day 7 MESP1neg derivative replicate 3

description: replicate 3

value: NEG


title: Day 10 MESP1neg derivative replicate 2

description: replicate 2


title: Quadruple (SB/Tg/K5Cre/Bcat) Q520

description: Gene expression data from mouse tissue


title: Day 10 MESP1pos derivative replicate 3

description: replicate 3


title: Bcat +/- 3 tumours on the ventral side of mouse C57-1650-T3

description: Gene expression data from mouse tissue

value: 3 tumours on the ventral side of mouse


title: Triple (SB/Tg/k5Cre) T856

description: Gene expression data from mouse tissue

value: Triple (SB/Tg/k5Cre)


title: Day 7 MESP1neg derivative replicate 2

description: replicate 2


title: NCI-HPN-F1K Colon p3 PreImmortal

description: female


title: NCI-HPN-F4K Colon p54 Late Transformed

description: female


title: Bcat +/- 3 tumours on the ventral side of mouse C57-1650-T2

description: Gene expression data from mouse tissue


title: Day 7 MESP1pos derivative replicate 2

description: replicate 2


title: NCI-HPN-F2K Colon p3 PreImmortal

description: female


title: Day 7 MESP1pos derivative replicate 1

description: replicate 1


title: Triple (SB/Tg/k5Cre) T857

description: Gene expression data from mouse tissue


title: Triple (SB/Tg/k5Cre) T627

description: Gene expression data from mouse tissue


title: Triple (SB/Tg/k5Cre) T817

description: Gene expression data from mouse tissue


title: Day 7 MESP1pos derivative replicate 3

description: replicate 3


title: NCI-HPN-F2K Colon p0 Uncultured

description: female


title: Day 7 MESP1neg derivative replicate 1

description: replicate 1


title: Quadruple (SB/Tg/K5Cre/Bcat) Q648-2

description: Gene expression data from mouse tissue


title: Triple (SB/Tg/k5Cre) T635-1

description: Gene expression data from mouse tissue


title: Triple (SB/Tg/k5Cre) T257

description: Gene expression data from mouse tissue


title: NCI-HPN-M1K Colon p8 Immortal

description: male


title: Triple (SB/Tg/k5Cre) T848

description: Gene expression data from mouse tissue


title: NCI-HPN-M2K Colon p0 Uncultured

description: male


title: NCI-HPN-F3K Colon p7 Immortal

description: female


title: Day 5 MESP1neg derivative replicate 2

description: replicate 2


title: Quadruple (SB/Tg/K5Cre/Bcat) Q190B

description: Gene expression data from mouse tissue


title: Bcat +/- 3 tumours on the ventral side of mouse C57-1650-T1

description: Gene expression data from mouse tissue


title: Quadruple (SB/Tg/K5Cre/Bcat) Q648-3

description: Gene expression data from mouse tissue


title: Quadruple (SB/Tg/K5Cre/Bcat) Q548

description: Gene expression data from mouse tissue


title: Day 5 MESP1neg derivative replicate 3

description: replicate 3


title: Day 5 MESP1neg derivative replicate 1

description: replicate 1


title: NCI-HPN-M1K Colon p58 Late Transformed

description: male


title: Quadruple (SB/Tg/K5Cre/Bcat) Q174

description: Gene expression data from mouse tissue


title: Quadruple (SB/Tg/K5Cre/Bcat) Q2164

description: Gene expression data from mouse tissue


title: NCI-HPN-F2K Colon p66 Late Tansformed

description: female


title: Day 5 MESP1pos derivative replicate 1

description: replicate 1


title: Quadruple (SB/Tg/K5Cre/Bcat) Q648-1

description: Gene expression data from mouse tissue


title: Day 5 MESP1pos derivative replicate 2

description: replicate 2


title: Day 5 MESP1pos derivative replicate 3

description: replicate 3


title: NCI-HPN-M2K Colon p55 Late Transformed

description: male


title: NCI-HPN-F1K Colon p51 Late Transformed

description: female


title: NCI-HPN-M1K Colon p5 PreImmortal

description: male


title: NCI-HPN-F1K Colon p0 uncultured

description: female


title: Quadruple (SB/Tg/K5Cre/Bcat) Q577

description: Gene expression data from mouse tissue


title: Quadruple (SB/Tg/K5Cre/Bcat) Q552

description: Gene expression data from mouse tissue


title: hlh-29 mutant, rep 3

city: Atlanta

first: Han Ting

last: Chou

state: GA

address: 1 University Park Drive

institute: Georgia State University

description:
Gene expression data from tm284 hlh-29 mutant young adults
TGT value =500; normalization factor (nf) = 1

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

data_processing: Data collection was carried out using GCOS 1.4 software (Affymetrix). analysis was performed using GeneSpring GX 11 Software (Aglient, Palo Alto,CA).  Probe intensity values were normalized to a target value of 500 with normalization factor equal to 1.

organism: Caenorhabditis elegans

source_name: hlh-29 mutant young adults, rep 3

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

growth_protocol: C. elegans animals were synchronized and grown to young adult stage at 20C

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

treatment_protocol: All animals were fed on NGM agar pads with OP50 bacteria lawn.

value: hermaphrodite

value: whole animal

value: young adult