title: Irradiation+Ly+Su-2

city: Heidelberg

first: Manuel

last: Roehrich

state: Baden-Württemberg

address: INF 280

department: Molecular Radiation Oncology

institute: DKFZ Heidelberg

description: mRNA expression mouse lung tissue 24 days after irradiation (irradiated and treated with Ly+Su)

hyb_protocol: 500 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (GPL4133) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters.

data_processing: Data was analyzed with ChipSkipper Table Butler and SUMO software (http://angiogenesis.dkfz.de/oncoexpress/software/index.htm).

source_name: Mouse lung tissue, treated with irradiation+Ly+Su, replicate 2

label_protocol: 500 ng of total RNA were labeled with Cyanin-3 using the Agilent Low RNA Input Linear Amplification Kit following the detailed protocol described in the user´s manual.

growth_protocol: RNA was extracted from lung tissue. So there was in-vitro-no growth protocol.

extract_protocol: RNA was extracted from treated animals’ lung tissue. Lung tissue specimens were solubilized and homogenized in TRIzol (Invitrogen, Carlsbad, CA). Total RNA was isolated according to the manufacturer´s instruction and purity and integrity of the RNA was assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Mouse lung tissue specimens were shock-frozen (-80 °C) before RNA extraction.

tag: treatment

value: irradiated and treated with Ly+Su

value: lung


title: Petunia_hybrida_cold_treatment_24h_rep3

status: Public on Jan 15 2015

type: RNA

city: wuhan

first: wei

last: zhang

country: China

institute: Huazhong Agricultural University

description: This sample is selfing line of Petunia hybrida. It is the third of three 24h cold treatment at 2°C biological replicates used in this experiment.

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

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

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

molecule: total RNA

organism: Petunia x hybrida

source_name: Petunia hybrida selfing line_cold_24h

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

extract_protocol: Total RNA was extracted from both control and cold-treated samples with Trizol Reagent (Invitrogen,http://www.invitrogen.com). The RNA quality was checked on a 1.2% agarose gel using an RNase-free electrophoresis system.

tag: cultivar

tag: genotype

value: selfing line

tag: phenotype

value: normal


title: Irradiation+Ly+Su-1

country: Germany

organism: Mus musculus

source_name: Mouse lung tissue, treated with irradiation+Ly+Su, replicate 1

tag: tissue


title: Irradiation+Ly+Imatinib-2

description: mRNA expression mouse lung tissue 24 days after irradiation (irradiated and treated with Ly+Imatinib)

source_name: Mouse lung tissue, treated with irradiation+Ly+Imatinib, replicate 2

value: irradiated and treated with Ly+Imatinib


title: Irradiation+Ly+Imatinib-1

source_name: Mouse lung tissue, treated with irradiation+Ly+Imatinib, replicate 1


title: Gastric_Cancer_16

city: Los Angeles

first: David

last: Wong

address: 10833 Le Conte Ave

department: Dentistry

country: USA

institute: UCLA

description: Sample name: P17

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Affymetrix Expression Console

label: Biotin

organism: Homo sapiens

source_name: Saliva

label_protocol: Biotin

growth_protocol: Un-stimulated saliva collected from patients

extract_protocol: Total RNA was extracted by using Qiagen Rneasy kit

treatment_protocol: Saliva was spun down to collect cell-free saliva supernatant

tag: disease state

value: gastric cancer

tag: rna source

value: cell-free saliva supernatant


title: Arabidopsis_seedling_FN__Exp1

city: Potsdam-Golm

first: Rainer

last: Hoefgen

address: Am Mühlenberg 1

institute: Max-Planck Institute for Molecular Plant Physiology

description: Control rep1

hyb_protocol: ATH1 GeneChip hybridizations, were performed by RZPD (now ATLAS Biolabs, Berlin, Germany)

scan_protocol: Washing, staining, and scanning, were performed by RZPD (now ATLAS Biolabs, Berlin, Germany)

data_processing: Raw intensity values from the scanned ATH1 GeneChip were analyzed using RMAExpress.

label: biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis, seedling, FN (full nutrient condition)

label_protocol: Preparation and biotin labeling of cRNA, were performed by RZPD (now ATLAS Biolabs, Berlin, Germany)

growth_protocol: Arabidopsis seedlings (100-120 seeds) were grown in 30 ml of sterile liquid medium (250 mL Erlenmeyer glass flasks) on orbital shakers with constant, uniform fluorescent light (~50 µE in the flask) and temperature (22°C). Shaker speed was low (30 rpm) during the first three days, and then increased to 80 rpm.

extract_protocol: Frozen plant material (100-200 mg) was ground in liquid nitrogen in a pre-cooled mortar or homogenised using metal beads (Ø 5mm) in the MM200 homogenizer (Retsch). TRIzol reagent (Invitrogen) was then added and mixed well by vortexing. After 5 min incubation at room temperature the homogenate was centrifuged at 13,000 x g for 5 min at 4°C in pre-cooled centrifuge. The supernatant was removed to a fresh Eppendorf tube and 400 µL of chloroform was added and mixed by vortexing before incubation at RT for 5 min. After 10 min centrifugation at 13,000 x g, at 4°C, the aqueous phase (~1 mL) was transferred to a fresh Eppendorf tube. RNA was precipitated with 0.5 mL of isopropanol and 0.5 mL of HSS buffer (0.8 M sodium citrate and 1.2 M NaCl) per 1 mL of aqueous phase, overnight at -20°C. The precipitate was pelleted by centrifugation at 13,000 x g for 30 minutes at 4°C. The supernatant was removed and the pellet was washed twice with 1 mL 70% ethanol, air dried, and re-suspended in ca. 50 µL water (approx. 1 µg RNA/1 µL). RNA concentration, purity and integrity were determined by analysis with Bioanalyser (Agilent) according to the manufacturer’s instruction.

treatment_protocol: Arabidopsis seedlings were grown in 30 mL of sterile liquid full nutrition (FN) medium (3 mM sulphate) or 150 μM sulphate medium. Transferring pre-grown 7-days old seedlings to a sulphate depleted medium (0 μM sulphate) assured immediate and continued sulphate starvation during the next two days of plant cultivation. On day 9 subsets of the sulphate depleted cultures were supplied with sulphate (500 μM) and samples taken 30 min and 3 hours after re-supply.

value: seedling

tag: age


title: Gastric_Cancer_17

description: Sample name: P18


title: Petunia_hybrida_cold_treatment_24h_rep2

description: This sample is selfing line of Petunia hybrida. It is the second of three 24h cold treatment at 2°C biological replicates used in this experiment.


title: Petunia_hybrida_cold_treatment_24h_rep1

description: This sample is selfing line of Petunia hybrida. It is the first of three 24h cold treatment at 2°C biological replicates used in this experiment.


title: Irradiation+Su-2

description: mRNA expression mouse lung tissue 24 days after irradiation (irradiated and treated with Su)

source_name: Mouse lung tissue, treated with irradiation+Su, replicate 1

value: irradiated and treated with Su


title: Irradiation+Su-1


title: Arabidopsis_seedling_30 min S__Exp1

description: 30 min resupply rep1

source_name: Arabidopsis, seedling, 30 min S (sulphate re-supply condition)


title: Arabidopsis_seedling_-S__Exp1

description: sulphate starvation rep1

source_name: Arabidopsis, seedling, -S (sulphate starvation condition)


title: Petunia_hybrida_cold_treatment_2h_rep3

description: This sample is selfing line of Petunia hybrida. It is the third of three 2h cold treatment at 2°C biological replicates used in this experiment.

source_name: Petunia hybrida selfing line_cold_2h


title: Gastric_Cancer_15

description: Sample name: P16


title: Irradiation+Imatinib-2

description: mRNA expression mouse lung tissue 24 days after irradiation (irradiated and treated with Imatinib)

source_name: Mouse lung tissue, treated with irradiation+Imatinib, replicate 2

value: irradiated and treated with Imatinib


title: Gastric_Cancer_14

description: Sample name: P15


title: Gastric_Cancer_13

description: Sample name: P14


title: KO-nudx19 leaves, rep2

city: Matsue

first: Takanori

last: Maruta

address: 1060 Nishikawatsu

country: Japan

institute: Shimane University

description: Gene expression data from 3-week-old KO-nudx19 leaves

hyb_protocol: Labeled cRNA was fragmented and hybridized to Affymetrix ATH1 GeneChip arrays for 16 h at 45°C according to Affymetrix protocols.

scan_protocol: Arrays were washed on an Affymetrix Fluidics Station 450 and measured for fluorescence intensity with an Affymetrix GeneChip Scanner 3000.

data_processing: Raw data were processed using Affymetrix Gene Chip Operating Software (GCOS; Version 1.4.0.036).

source_name: Three-week-oldKO-nudx19 leaves

label_protocol: Total RNA samples were reverse-transcribed, yielding double-strand cDNA, which was transcribed in vitro in the presence of biotin-labeled nucleotides with an IVT Labeling Kit (Affymetrix Inc., Santa Clara, CA), and purified.

growth_protocol: Wild-type and KO-nudx19 plants were grown on MS medium containing 3% sucrose in a growth chamber kept at 25°C during 16 h of light (100 µmol/m2/s) and at 22°C during 8 h of darkness for 1 week, and then transferred to and further grown on soil for 2 weeks in the same chamber.

extract_protocol: Total RNA was semi-automatically purified from leaves using a QuickGene RNA cultured cell Kit and QuickGene-Mini80 (FUJIFILM corporation, Tokyo, Japan). The quality and purity of the RNA were confirmed for microarray analysis with an Ultrospec 2100 pro (GE Healthcare UK Ltd, Amersham Place, England).

treatment_protocol: At 3 weeks, leaves were collected as samples for microarray analysis.

value: rosette leaves

value: 3 weeks


title: Irradiation+Imatinib-1

source_name: Mouse lung tissue, treated with irradiation+Imatinib, replicate 1


title: Irradiation+Ly-2

description: mRNA expression mouse lung tissue 24 days after irradiation (irradiated and treated with Ly)

source_name: Mouse lung tissue, treated with irradiation+Ly, replicate 2

value: irradiated and treated with Ly


title: Petunia_hybrida_cold_treatment_2h_rep2

description: This sample is selfing line of Petunia hybrida. It is the second of three 2h cold treatment at 2°C biological replicates used in this experiment.


title: Petunia_hybrida_cold_treatment_2h_rep1

description: This sample is selfing line of Petunia hybrida. It is the first of three 2h cold treatment at 2°C biological replicates used in this experiment.


title: KO-nudx19 leaves, rep1


title: shuai-JT3_WR

city: New York

first: Kenneth

middle: David

last: Birnbaum

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

description: excised meristem only as control for jkd meristem

hyb_protocol: Labeled cDNA was hybridized, washed, and stained on an ATH-121501 Arabidopsis microarray using a Hybridization Control Kit, GeneChipHybridization, Wash, and Stain Kit, GeneChip Fluidics Station 450

scan_protocol: Standard scanning conditions were used on the GeneChip Scanner (Affymetrix).

data_processing: Data were normalized using the MAS 5.0 method with a scaling factor of 250. Analysis included only transcripts determined to be present (average expression of >=50 at any time point, as determined by empirical analysis).

source_name: meristem only of jkd plants

label_protocol: RNA quality and quantity was assessed using the Bioanalyzer (Agilent Technologies) and amplified and labeled using the WT-Ovation Pico RNA Amplification System and FL-Ovation cDNA Biotin Module V2, respectively (Nugen Technologies).

growth_protocol: For transdifferentiation time series’,plants were grown for twos day post germination seedlings before treatments began. All plants were grown on square plates.  For meristem and QC profiles based on pWOX5:GFP in wild type and jkd backgrounds, we collected roots three days after germination and sorted GFP positive cells following protocols in Nawy et al. (2005).

extract_protocol: Protoplasts were sorted directly into RNA extraction buffer, and RNA was extracted using the RNeasy Micro Kit with DNase treatment according to the instructions of the manufacturer (Qiagen).

treatment_protocol: For auxin treatments, two days after germination, plants were transferred to 1uM 2,4-D medium and treated for 0 to 4 days. Root tips were harvested by cutting at 250 μM from the distal tip under the dissecting microscope using superfine scissors. Root tips were released in protoplast solution immediately after cutting and GFP positive cells were sorted.

value: meristem

value: 3 days post germination


title: wild-type leaves, rep2

description: Gene expression data from 3-week-old wild-type leaves

source_name: Three-week-old wild-type leaves

value: wildtype


title: Petunia_hybrida_cold_treatment_0.5h_rep3

description: This sample is selfing line of Petunia hybrida. It is the third of three 0.5h cold treatment at 2°C biological replicates used in this experiment.

source_name: Petunia hybrida selfing line_cold_0.5h


title: Irradiation+Ly-1

source_name: Mouse lung tissue, treated with irradiation+Ly, replicate 1


title: wild-type leaves, rep1


title: shuai-JT2_WR


title: Gastric_Cancer_12

description: Sample name: P13


title: shuai-JT1_WR


title: Irradiation-1

description: mRNA expression mouse lung tissue 24 days after irradiation (irradiated)

source_name: Mouse lung tissue, treated with irradiation, replicate 1

value: irradiated


title: Petunia_hybrida_control_rep2

description: This sample is selfing line of Petunia hybrida. It is the second of three control biological replicates used in this experiment.

source_name: Petunia hybrida selfing line_control


title: Petunia_hybrida_cold_treatment_0.5h_rep1

description: This sample is selfing line of Petunia hybrida. It is the first of three 0.5h cold treatment at 2°C biological replicates used in this experiment.


title: Gastric_Cancer_11

description: Sample name: P12


title: Petunia_hybrida_control_rep3

description: This sample is selfing line of Petunia hybrida. It is the third of three control biological replicates used in this experiment.


title: Ly+Su-2

description: mRNA expression mouse lung tissue 24 days after irradiation (treated with Ly+Su)

source_name: Mouse lung tissue, treated with Ly+Su, replicate 2

value: treated with Ly+Su


title: Irradiation-2

source_name: Mouse lung tissue, treated with irradiation, replicate 2

value: lung


title: Gastric_Cancer_9

description: Sample name: P10

source_name: Saliva


title: Petunia_hybrida_cold_treatment_0.5h_rep2

description: This sample is selfing line of Petunia hybrida. It is the second of three 0.5h cold treatment at 2°C biological replicates used in this experiment.

value: selfing line


title: Gastric_Cancer_10

description: Sample name: P11


title: Gastric_Cancer_6

description: Sample name: P7


title: Shuai-CT1_WR

source_name: meristem only of WT plants


title: Ly+Imatinib-1

description: mRNA expression mouse lung tissue 24 days after irradiation (treated with Ly+Imatinib)

source_name: Mouse lung tissue, treated with Ly+Imatinib, replicate 1

value: treated with Ly+Imatinib


title: Shuai WOX5-3

description: harvested separately for a QC-specific cell type transcriptome

source_name: wild type sorted QC using WOX5 promoter

value: Quiescent Center


title: Shuai-CT2_WR


title: Gastric_Cancer_5

description: Sample name: P6

value: gastric cancer


title: Shuai-CT3_WR


title: Ly+Su-1

source_name: Mouse lung tissue, treated with Ly+Su, replicate 1


title: Ly+Imatinib-2

source_name: Mouse lung tissue, treated with Ly+Imatinib, replicate 2


title: Gastric_Cancer_8

description: Sample name: P9

value: cell-free saliva supernatant


title: SI27b

city: Pittsburgh

first: William

middle: Armand

last: LaFramboise

state: PA

address: 5230 Centre Avenue

department: Pathology

institute: University of Pittsburgh

hyb_protocol: Fifteen micrograms of purified, amplified, biotin labeled cRNA was fragmented and hybridized on to Affymetrix Human Genome HGU133A 2.0 arrays (Affymetrix Corp. Santa Clara, CA) for 18 hours.

scan_protocol: Washing, staining and scanning of arrays was performed on the Affymetrix Fluidics Station 450 and Scanner 3000 immediately after completion of hybridization.

data_processing:
Microarray data was processed using the Robust Multi-array Average by importing raw CEL files into Partek software (Partek Genomics Suite, St. Louis, MO) resulting in RMA background correction, log 2 transformation, quantile normalization, and median polish probeset summarization.
HG-U133A_2.cdf
HG-U133A_2.na32.annot

source_name: Epithelial tissue, small intestine

label_protocol: RNA was quantified with the Nanodrop (Thermo Scientific, IL). Reverse transcription was performed using iScript RT Supermix followed by PCR with SsoADV SYBR Green (Bio-Rad, CA) on an ABI StepOne Plus Real-Time PCR machine (Applied Biosystems, CA). Primers were designed using Primer Express software (Applied Biosystems, CA) and purchased from Life Technologies (NY) (Table 3).

growth_protocol: Not applicable

extract_protocol: Total RNA containing both miRNA and mRNA was extracted using the Qiagen miRNeasy kit (Qiagen Inc., Valencia, CA) according to the manufacturer’s protocol. Only total RNA of highest quality and integrity was subjected to further processing after purification as defined by an absorption ratio 260/280>1.8 by spectrophotometry on the NanoDrop 1000 (NanoDrop, Wilmington, DE) and a RIN value >8.0 via electrophoretic analysis on the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Not applicable

value: Small Intestine


title: Gastric_Cancer_7

description: Sample name: P8


title: SI26b


title: Shuai WOX5-2


title: Su-1

description: mRNA expression mouse lung tissue 24 days after irradiation (treated with Su)

source_name: Mouse lung tissue, treated with Su, replicate 1

value: treated with Su


title: Su-2

source_name: Mouse lung tissue, treated with Su, replicate 2


title: Gastric_Cancer_4

description: Sample name: P5


title: Gastric_Cancer_3

description: Sample name: P3


title: Petunia_hybrida_control_rep1

description: This sample is selfing line of Petunia hybrida. It is the first of three control biological replicates used in this experiment.

value: normal


title: Shuai WOX5-1


title: SCR 96hr-S2

description: treated with 2,4-D for four days

source_name: pSCR::GFP sorted cells; 96hr auxin treatment

value: endodermis

value: 2 days post germination


title: SI50


title: SCR 72hr-S3

description: treated with 2,4-D for three days

source_name: pSCR::GFP sorted cells; 72hr auxin treatment


title: SI2


title: SCR 48hr-S3

description: treated with 2,4-D for two days

source_name: pSCR::GFP sorted cells; 48hr auxin treatment


title: FB-c-15

city: Stockholm

first: Jesper

middle: Robert

last: Gådin

address: CMM, L8:02 Karolinska Universitetessjukhuset, Solna

department: Department of Medicine

country: Sweden

institute: Karolinska Institutet

hyb_protocol: User Manual GeneChip® Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: Scanning images were generated using using Affymetrix GeneChip® Command Console Software (AGCC)

data_processing:
Data were processed using Partek Genomics Suite 6.6 using the default Partek settings: RMA background correction, quantile normalization, median polish probeset summarization, and log2 transformation
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Myofibroblasts

growth_protocol: AoSMCs and FBs were obtained from fresh human tissue biopsies. Samples were incubated in 0.3% collagenase solution for 2 hours at 37°C on a shaker

extract_protocol: Total RNA was extracted with Triazol

treatment_protocol: Cells were cultured until passage 3 and treated with TGFb1 (20 ng/ml) for 6h in serum free medium

tag: ID

tag: gender

value: M

tag: aorta status

value: Dilated

tag: cuspidity

value: TAV

value: Un-treated

value: aortic valve


title: FB-t1-15

label_protocol: User Manual GeneChip® Whole Transcript (WT) Sense Target Labeling Assay

value: TGFb1 treated


title: Ly-2

description: mRNA expression mouse lung tissue 24 days after irradiation (treated with Ly)

source_name: Mouse lung tissue, treated with Ly, replicate 2

value: treated with Ly

value: lung


title: SCR 72hr-S2

description: treated with 2,4-D for three days


title: Imatinib-1

description: mRNA expression mouse lung tissue 24 days after irradiation (treated with Imatinib)

source_name: Mouse lung tissue, treated with Imatinib, replicate 1

value: treated with Imatinib


title: Imatinib-2

source_name: Mouse lung tissue, treated with Imatinib, replicate 2


title: Ly-1

source_name: Mouse lung tissue, treated with Ly, replicate 1


title: Gastric_Cancer_1

description: Sample name: P1

source_name: Saliva


title: SI36


title: SCR 48hr-S2

description: treated with 2,4-D for two days


title: AO-t1-12

source_name: AoSMCs

value: tunica media of ascending aorta


title: SI24


title: AO-c-12


title: FB-t1-14

value: F

value: Non-Dilated


title: LI39

source_name: Epithelial tissue, large intestine

value: Large Intestine


title: ctrl-1

description: mRNA expression mouse lung tissue 24 days after irradiation (untreated)

source_name: Mouse lung tissue, untreated, 24 days, replicate 1

value: untreated


title: ctrl-2

source_name: Mouse lung tissue, untreated, 24 days, replicate 2


title: LI50


title: LI27


title: LI38


title: LI24


title: SCR 24hr-S3

description: treated with 2,4-D for one day

source_name: pSCR::GFP sorted cells; 24hr auxin treatment


title: SCR 0hr-3

source_name: pSCR::GFP sorted cells; no auxin treatment


title: jkd-4 QC-3

description: previously published as cell type profile in Birnbaum et al. (2003) Science; 302(5652):1956-60.

source_name: jkd sorted QC using WOX5 promoter

value: Quiescent Center

value: 3 days post germination


title: AO-t1-11


title: AO-t1-10

value: BAV


title: AO-c-10

value: M


title: AO-c-11


title: SCR 96hr-S3

description: treated with 2,4-D for four days

value: endodermis

value: 2 days post germination


title: jkd-4 QC-2

source_name: jks sorted QC using WOX5 promoter


title: FB-t1-13


title: SCR 0hr-5


title: LI2


title: liver-5P-rep1

city: Kanagawa

first: Asako

last: Takenaka

address: Higashi-Mita 1-1-1, Tama-ku, Kawasaki

institute: Meiji University

hyb_protocol: Fragmentation and hybridization were performed using the GeneChip 3’ IVT express kit (Affymetrix, Santa Clara, CA, USA) according to the manifucture’s instructions.

scan_protocol: Fluorescence signals were scanned with the Affymetrix GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The raw data (.CEL files) were normalized by Robust Multichip Average (RMA) algorithm using R.

organism: Rattus norvegicus

source_name: liver of rat fed low protein diet

label_protocol: Biotinylated aRNA were prepared using the GeneChip 3’ IVT express kit (Affymetrix, Santa Clara, CA, USA) according to the manifucture’s instructions.

growth_protocol: Six-week-old male Wistar strain rats weighing approximately 150 g were purchased (Japan Laboratory Animals, Tokyo, Japan), housed individually in cages, and kept at 22–24 °C under a 12 h (06:00–18:00) light–dark cycle. The animals were fed ad libitum a commercial pellet feed (certified diet MF; Oriental Yeast, Tokyo, Japan) for the first 4 d in order to adjust them to their new environment. All the animals were allowed free access to water throughout the experiment.

extract_protocol: Total RNA was extracted using RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Rats were trained to eat a control diet (15P) between 10:00 and 18:00 for 4 d, after which they were divided into two treatment groups: the 15P group and the isoenergetic low protein diet (5P) group. Rats were fed the respective diet for 8 hours, and their livers were collected after 16 hours of starvation.

tag: strain

value: Wistar

value: male

value: six weeks old

value: liver


title: jkd-4 QC-1


title: FB-c-13

value: Un-treated

value: aortic valve


title: liver-15P-rep3

source_name: liver of rat fed control diet


title: FB-c-14

value: TAV


title: Col-0 QC-3

description: grown alongside the jkd mutant WOX5::GFP plants as controls

source_name: wild type sorted QC using WOX5 promoter


title: AO-t1-9

value: Dilated

value: TGFb1 treated

value: tunica media of ascending aorta


title: liver-5P-rep2


title: SCR 0hr-1


title: AO-c-9


title: Col-0 QC-2


title: liver-5P-rep3


title: Col-0 QC-1


title: liver-15P-rep2


title: liver-15P-rep1


title: FB-t1-12

source_name: Myofibroblasts

value: Non-Dilated


title: FB-t1-10

value: F


title: FB-c-11


title: AO-t1-8


title: FB-t1-11


title: FB-c-10


title: FB-c-12


title: AO-c-7


title: AO-t1-7


title: Gastric_Cancer_2

description: Sample name: P2

value: gastric cancer

value: cell-free saliva supernatant


title: FB-t1-9

value: M

value: BAV


title: AO-c-8


title: chl1-9 10mM NH4NO3 rep3

city: Montpellier

first: Gabriel

last: Krouk

address: 2 Place Pierre Viala

country: France

institute: CNRS

description: chl1-9 10mM NH4NO3 rep3

hyb_protocol: Affymetrix recommendation

scan_protocol: Affymetrix recommendation

data_processing: Mas5 [R]

label_protocol: GeneChip 3'IVT Express Kit (Affymetrix)

growth_protocol: Plants are grown in vitro on 10mM NH4NO3 for 8 days

extract_protocol: TRIzol reagent

value: Root


title: T101A 10mM NH4NO3 rep3

description: T101A 10mM NH4NO3 rep3


title: T101D 10mM NH4NO3 rep3

description: T101D 10mM NH4NO3 rep3


title: chl1-5 10mM NH4NO3 rep3

description: chl1-5 10mM NH4NO3 rep3


title: T101D 10mM NH4NO3 rep2

description: T101D 10mM NH4NO3 rep2


title: FB-t1-8


title: chl1-12 10mM NH4NO3 rep3

description: chl1-12 10mM NH4NO3 rep3


title: chl1-12 10mM NH4NO3 rep2

description: chl1-12 10mM NH4NO3 rep2


title: FB-c-9


title: FB-c-8


title: AO-t1-6


title: T101D 10mM NH4NO3 rep1

description: T101D 10mM NH4NO3 rep1


title: col 10mM NH4NO3 rep3

description: col 10mM NH4NO3 rep3

source_name: col

value: col


title: T101A 10mM NH4NO3 rep2

description: T101A 10mM NH4NO3 rep2


title: chl1-9 10mM NH4NO3 rep2

description: chl1-9 10mM NH4NO3 rep2


title: col 10mM NH4NO3 rep2

description: col 10mM NH4NO3 rep2


title: T101A 10mM NH4NO3 rep1

description: T101A 10mM NH4NO3 rep1


title: FB-c-7


title: FB-t1-7


title: CC5_mRNA

city: St. Louis

first: Jacqueline

last: Payton

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

description: Gene expression analysis was performed for centrocytes using Affymetrix Human Gene 2.0 ST arrays

hyb_protocol: Products were hybridized to Affymetrix Human Gene 1.0 ST arrays according to the manufacturer’s protocol

data_processing: Gene expression levels were determined using the Affymetrix Expression Console software (v1.2.0.20) with exon-level RMA analysis and default settings

source_name: CD19+/CD10+/CD44low/CXCR4- B cells

label_protocol: Purified RNA was amplified using Nugen Ovation Pico SL or Ovation Pico kits and labeled using Nugen Encore Biotin kit

extract_protocol: RNA was purified using Qiagen RNeasy Kits according to the manufacturer’s protocol.

value: Tonsil

tag: tumor

tag: previously treated for nhl

tag: cell type

value: centrocytes


title: chl1-5 10mM NH4NO3 rep2

description: chl1-5 10mM NH4NO3 rep2


title: CC4_mRNA


title: chl1-9 10mM NH4NO3 rep1

description: chl1-9 10mM NH4NO3 rep1


title: chl1-5 10mM NH4NO3 rep1

description: chl1-5 10mM NH4NO3 rep1


title: FB-c-6


title: FB-t1-6


title: AO-t1-5


title: AO-c-5


title: AO-c-4


title: LvM3b over-expressing miR-483

first: Jia Min

last: Loo

address: 1230 York Avenue #342

institute: The Rockefeller University

description: replicate 1

hyb_protocol: Standard Illumina Protocol.

scan_protocol: Standard Illumina Protocol.

data_processing: The data was median normalized using Microsoft Excel.

source_name: LvM3b colon cancer cells_miR-483

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

growth_protocol: Cells were routinely passaged in DMEM media supplemented with 10% FBS, glutamine, sodium pyruvate, pen-strep and fungizone.

extract_protocol: RNA was extracted using Ambion miRVANA total RNA isolation kit according to manufacturer's protocol.

treatment_protocol: Cells were used for RNA extraction at about 70% confluency on a 10cm dish.

tag: cell line

value: colon

value: adenocarcinoma


title: DiPSC

city: Seongnam

first: Kangin

last: lee

address: 335 Pankyoro, Bundanggu

department: Biomedical Science

country: South Korea

institute: CHA University

description: replicate 1

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina HumanHT-12   Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader  Confocal  Scanner

data_processing: Raw data preparation and Statistic analysis  The quality of hybridization and overall chip performance were monitored by visual inspection of both internal quality control checks and the raw scanned data. Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)).   Array probes that have detection p-value ≥ 0.05 (similar to signal to noise) in over 50% samples were filtered out. (We applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05) Selected gene signal value was transformed by logarithm and normalized by quantile method.  Statistical significance of the expression data was determined using Fold Change.  Hierarchical cluster analysis was performed using complete linkage and Euclidean distance as a measure of similarity.  Gene-Enrichment and Functional Annotation analysis for significant probe list was performed using DAVID (http://david.abcc.ncifcrf.gov/home.jsp).  All data analysis and visualization of differentially expressed genes was conducted using R 2.15.1 (www.r-project.org).

source_name: disc cell-derived iPSC

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep   RNA Amplification Kit (Ambion, Austin,TX).

growth_protocol: Dissected disc tissue was washed with 1X phosphate buffered saline (1XPBS) (Wellgene, Daegu, Korea, http://www.welgene.com), followed by incubation with collagenase A (Roche, Mannheim, Germany, http://www.roche.com) for 4 hours with shaking every hour. The enzyme-treated tissue was filtered through a 100 µm mesh, washed three times with 1X PBS, and finally resuspended in DMEM/F12 (Invitrogen, Carlsbad, CA, USA, http://www.lifetechnologies.com) supplement with 10% FBS (Hyclone, Logan, UT, USA, www.thermoscientific.com) and 1% penicillin/streptomycin (Invitrogen) for incubation in a humidified chamber (37oC, 5% CO2).

extract_protocol: Total RNA was isolated using the NucleoSpin RNA II Kit (Macherey-Nagel, Duren, Germany)  according to the manufacturer’s suggestions, and 2ug of total RNA was utilized for a genome-wide  gene expression profiling experiment using the Illumina array (Illumina, San Diego, CA, USA) at  Macrogen (Macrogen, Seoul, Korea).

value: disc cell-derived iPSC


title: FB-c-5

tag: treatment

value: Un-treated

value: aortic valve


title: FB-c-4

value: TAV


title: AO-c-6

value: Dilated

value: tunica media of ascending aorta


title: chl1-12 10mM NH4NO3 rep1

description: chl1-12 10mM NH4NO3 rep1


title: FB-t1-4

value: F

value: Non-Dilated

value: TGFb1 treated


title: LvM3b over-expressing miR-551a

description: replicate 1

source_name: LvM3b colon cancer cells_miR-551a


title: AO-t1-4

source_name: AoSMCs

value: M


title: H9 on MEF

description: replicate 1

source_name: Human embryonic stem cell

value: embryonic stem cell


title: Ls-Parental Control

description: replicate 1

source_name: Ls-Parental colon cancer cells


title: col 10mM NH4NO3 rep1

description: col 10mM NH4NO3 rep1

value: Root


title: CC2_mRNA


title: FB-t1-5

value: BAV


title: LvM3b Control

description: replicate 1

source_name: LvM3b colon cancer cells_control


title: LvM3b- over-expressing miR-551a

description: replicate 1

source_name: LvM3b colon cancer cells

tag: genotype/variation

value: over-expressing miR-551a


title: LvM3b- over-expressing miR-483

description: replicate 1

value: over-expressing miR-483


title: LvM3b_control_

description: replicate 1

value: colon


title: CB5_mRNA

description: Gene expression analysis was performed for centroblasts using Affymetrix Human Gene 2.0 ST arrays

source_name: CD19+/CD10+/CD44low/CXCR4+ B cells

value: Tonsil

value: centroblasts


title: CB4_mRNA


title: CB3_mRNA


title: CB2_mRNA


title: AO-t1-3


title: CC3_mRNA

value: centrocytes


title: FB-t1-2

value: aortic valve


title: SCR 24hr-S2

description: treated with 2,4-D for one day

source_name: pSCR::GFP sorted cells; 24hr auxin treatment

value: endodermis

value: 2 days post germination


title: FB-c-3

value: Un-treated


title: FB-t1-3


title: CC1_mRNA


title: PC3_siDEK 2

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

hyb_protocol: 600ng labeled cRNA was hybridized on Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID 028004)

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution using the one colour and 20 bit tiff file settings

data_processing: Image files were processed with Agilent Feature Extraction 11.0.1.1 to produce spatially detrended and background subtracted gProcessedSignal intensities. Data were normalized by the quantile method. Genespring output with quantile-normalized data and gene annotation can be found on the series record.

source_name: Prostate Tumor

label_protocol: 100ng of total RNA was used as input for generation of Cyanine-3-labeled cRNA following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0.

extract_protocol: not provided


title: Disc cell

description: replicate 1

source_name: human disc cells

value: intervertebral disc


title: FB-c-1

value: F

value: Non-Dilated


title: FB-t1-1

value: TGFb1 treated


title: FB-c-2

value: TAV


title: PC3_si Control 1


title: WiDR Pre-Selection-2

description:
miRNA present in reference sample
Pre-2

hyb_protocol: Genoexplorer miRNA arrays (human) were used for hybridization. One miRNA microarray chip were used for each sample. The hybrization was performed at 42 dgrees celcius for 16hrs, then stained by streptavidin-Cy5 dye. After washes, the arrays were dried and scanned.

scan_protocol: Arrays were scanned using Axon 400B. Raw data with signal intensity were analyzed by GenePix Software.

data_processing: Raw intensity values for each of the three probes for every miRNA or control were averaged and standard deviation was also calculated. Array background was calculated as the average of signal intensity of all negative controls and buffers, and a signal threshold was determined by array background + 2x background's standard deviation, for each array; only averaged miRNA intensities higher than the signal threshold were considered. Across individual samples, raw data was median normazlized.

source_name: WiDR Pre-Injection Sample-2

label_protocol: Labeling was performed by Genosensor using in-house protocol.

growth_protocol: WiDR cells were routinely cultured in DMEM media supplemented with 10% FBS, glutamine, pyruvate, pen-strep and fungizone.

extract_protocol: Genomic DNA was extracted from reference samples and from liver nodule using Qiagen Dneasy Kit and lenti-viral derived miRNA were enriched by vector specific PCR and in vitro transcription according to manufacturer's protocol. RNA was cleaned up using Ambion's Mega Clear kit and sent to Genosensor for profiling.

treatment_protocol: WiDR cells were cultured in DMEM media and transduced with the Lenti-miR library (System Biosciences). A portion of cells were saved as reference samples. A separate portion was injected into the liver of immunodeficient mice to allow for in vivo selection. The resulting liver nodule was extracted after 3-5 weeks.

value: WiDR

tag: transduced with

value: Lenti-miR library

tag: time point

value: before in vivo selection


title: CB1_mRNA

tag: tissue


title: AO-t1-2

value: M

value: BAV

value: tunica media of ascending aorta


title: PC3_si Control 2


title: AO-c-3


title: AO-c-2


title: WiDR Post-Selection-2

description:
miRNA present after intrahepatic selection
Post-2

source_name: WiDR Post-Intrahepatic Sample-2

tag: injected into

value: liver of immunodeficient mice

value: after in vivo selection


title: WiDR Post-Selection-1

description:
miRNA present after intrahepatic selection
Post-1

source_name: WiDR Post-Intrahepatic Sample-1


title: AO-t1-1


title: WiDR Pre-Selection-1

description:
miRNA present in reference sample
Pre-1

source_name: WiDR Pre-Injection Sample-1


title: AO-c-1


title: PC3_siDEK 1


title: Cordblood_19

status: Public on Jan 14 2015

type: genomic

city: Memphis

first: Khyobeni

last: Mozhui

state: TN

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

description: Normal newbord cord blood

hyb_protocol: Standard Illumina Humanmethylation27 array protocol

data_processing: Raw data was processed using the Illumina GenomeStudio (version 2009.1). Beta values with detection p-value ≥ 0.001 were considered as missing data. One probe with a median detection p-value ≥ 10-6 across all samples was dropped from analysis. The data was then corrected for batch effects using the COMBAT R package. Following the batch correction, the β values were converted to M-values using a logit transform.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Cordblood

extract_protocol: Newborn umbilical cord blood was collected at delivery. Whole blood was centrifuged and buffy coat layer isolated and frozen until processed for nucleic acid purification. DNA extraction was performed with Wizard genomics DNA purification reagents (Promega; http://www.promega.com).

value: Male

tag: race

value: AA

tag: batch


title: Cordblood_22

description: Normal newbord cord blood

scan_protocol: Standard Illumina Humanmethylation27 array protocol


title: Cordblood_7

description: Normal newbord cord blood

label_protocol: Standard Illumina Humanmethylation27 array protocol

value: Female


title: Cordblood_17

description: Normal newbord cord blood


title: Cordblood_23

description: Normal newbord cord blood


title: Cordblood_21

description: Normal newbord cord blood


title: Cordblood_5

description: Normal newbord cord blood


title: Cordblood_1

description: Normal newbord cord blood


title: Cordblood_27

description: Normal newbord cord blood


title: Cordblood_15

description: Normal newbord cord blood


title: Cordblood_2

description: Normal newbord cord blood


title: Cordblood_3

description: Normal newbord cord blood


title: Cordblood_216

description: Normal newbord cord blood


title: Cordblood_16

description: Normal newbord cord blood

value: Mixed


title: Cordblood_14

description: Normal newbord cord blood


title: Cordblood_20

description: Normal newbord cord blood


title: Cordblood_202

description: Normal newbord cord blood


title: Cordblood_10

description: Normal newbord cord blood


title: Cordblood_12

description: Normal newbord cord blood


title: Cordblood_211

description: Normal newbord cord blood

value: EA


title: Cordblood_18

description: Normal newbord cord blood


title: Cordblood_158

description: Normal newbord cord blood


title: Cordblood_8

description: Normal newbord cord blood


title: Cordblood_205

description: Normal newbord cord blood


title: Cordblood_214

description: Normal newbord cord blood


title: Cordblood_209

description: Normal newbord cord blood


title: Cordblood_191

description: Normal newbord cord blood


title: Cordblood_147

description: Normal newbord cord blood


title: Cordblood_207

description: Normal newbord cord blood


title: Cordblood_199

description: Normal newbord cord blood


title: Cordblood_204

description: Normal newbord cord blood


title: Cordblood_208

description: Normal newbord cord blood


title: Cordblood_145

description: Normal newbord cord blood


title: Cordblood_212

description: Normal newbord cord blood


title: Cordblood_189

description: Normal newbord cord blood


title: Cordblood_138

description: Normal newbord cord blood


title: Cordblood_187

description: Normal newbord cord blood


title: Cordblood_136

description: Normal newbord cord blood


title: Cordblood_210

description: Normal newbord cord blood


title: Cordblood_123

description: Normal newbord cord blood


title: Cordblood_198

description: Normal newbord cord blood


title: Cordblood_203

description: Normal newbord cord blood


title: Cordblood_200

description: Normal newbord cord blood


title: Cordblood_195

description: Normal newbord cord blood


title: Cordblood_206

description: Normal newbord cord blood


title: Cordblood_194

description: Normal newbord cord blood


title: Cordblood_201

description: Normal newbord cord blood


title: Cordblood_165

description: Normal newbord cord blood


title: Cordblood_185

description: Normal newbord cord blood


title: Cordblood_196

description: Normal newbord cord blood


title: Cordblood_213

description: Normal newbord cord blood


title: Cordblood_161

description: Normal newbord cord blood


title: Cordblood_163

description: Normal newbord cord blood


title: Cordblood_188

description: Normal newbord cord blood


title: Cordblood_105

description: Normal newbord cord blood


title: Cordblood_186

description: Normal newbord cord blood


title: Cordblood_183

description: Normal newbord cord blood


title: Cordblood_157

description: Normal newbord cord blood


title: Cordblood_181

description: Normal newbord cord blood


title: Cordblood_193

description: Normal newbord cord blood


title: Cordblood_164

description: Normal newbord cord blood


title: Cordblood_197

description: Normal newbord cord blood


title: Cordblood_159

description: Normal newbord cord blood


title: Cordblood_180

description: Normal newbord cord blood


title: Cordblood_156

description: Normal newbord cord blood


title: Cordblood_148

description: Normal newbord cord blood


title: Cordblood_167

description: Normal newbord cord blood


title: Cordblood_146

description: Normal newbord cord blood


title: Cordblood_192

description: Normal newbord cord blood


title: Cordblood_101

description: Normal newbord cord blood


title: Cordblood_154

description: Normal newbord cord blood


title: Cordblood_215

description: Normal newbord cord blood


title: Cordblood_184

description: Normal newbord cord blood


title: Cordblood_103

description: Normal newbord cord blood


title: Cordblood_178

description: Normal newbord cord blood


title: Cordblood_99

description: Normal newbord cord blood


title: Cordblood_152

description: Normal newbord cord blood


title: Cordblood_107

description: Normal newbord cord blood


title: Cordblood_78

description: Normal newbord cord blood


title: Cordblood_153

description: Normal newbord cord blood


title: Cordblood_94

description: Normal newbord cord blood


title: Cordblood_97

description: Normal newbord cord blood


title: Cordblood_128

description: Normal newbord cord blood


title: Cordblood_190

description: Normal newbord cord blood


title: Cordblood_149

description: Normal newbord cord blood


title: Cordblood_90

description: Normal newbord cord blood


title: Cordblood_126

description: Normal newbord cord blood


title: Cordblood_81

description: Normal newbord cord blood


title: Cordblood_182

description: Normal newbord cord blood


title: Cordblood_122

description: Normal newbord cord blood


title: Cordblood_91

description: Normal newbord cord blood


title: Cordblood_150

description: Normal newbord cord blood


title: Cordblood_96

description: Normal newbord cord blood


title: Cordblood_95

description: Normal newbord cord blood


title: Cordblood_124

description: Normal newbord cord blood


title: Cordblood_140

description: Normal newbord cord blood


title: Cordblood_89

description: Normal newbord cord blood


title: Cordblood_118

description: Normal newbord cord blood


title: Cordblood_116

description: Normal newbord cord blood


title: Cordblood_74

description: Normal newbord cord blood


title: Cordblood_92

description: Normal newbord cord blood


title: Cordblood_88

description: Normal newbord cord blood


title: Cordblood_176

description: Normal newbord cord blood


title: Cordblood_151

description: Normal newbord cord blood


title: Cordblood_120

description: Normal newbord cord blood


title: Cordblood_142

description: Normal newbord cord blood


title: Cordblood_86

description: Normal newbord cord blood


title: Cordblood_83

description: Normal newbord cord blood


title: Cordblood_144

description: Normal newbord cord blood


title: Cordblood_114

description: Normal newbord cord blood


title: Cordblood_93

description: Normal newbord cord blood


title: Cordblood_82

description: Normal newbord cord blood


title: Cordblood_80

description: Normal newbord cord blood


title: Cordblood_85

description: Normal newbord cord blood


title: Cordblood_84

description: Normal newbord cord blood


title: Cordblood_76

description: Normal newbord cord blood


title: Cordblood_54

description: Normal newbord cord blood


title: Cordblood_79

description: Normal newbord cord blood


title: Cordblood_112

description: Normal newbord cord blood


title: Cordblood_56

description: Normal newbord cord blood


title: Cordblood_53

description: Normal newbord cord blood


title: Cordblood_174

description: Normal newbord cord blood


title: Cordblood_170

description: Normal newbord cord blood


title: Cordblood_172

description: Normal newbord cord blood


title: Cordblood_55

description: Normal newbord cord blood


title: Cordblood_87

description: Normal newbord cord blood


title: Cordblood_51

description: Normal newbord cord blood


title: Cordblood_58

description: Normal newbord cord blood


title: Cordblood_57

description: Normal newbord cord blood


title: Cordblood_115

description: Normal newbord cord blood


title: Cordblood_110

description: Normal newbord cord blood


title: Cordblood_49

description: Normal newbord cord blood


title: Cordblood_59

description: Normal newbord cord blood


title: Cordblood_119

description: Normal newbord cord blood


title: Cordblood_77

description: Normal newbord cord blood


title: Cordblood_50

description: Normal newbord cord blood


title: Cordblood_117

description: Normal newbord cord blood


title: Cordblood_179

description: Normal newbord cord blood


title: Cordblood_177

description: Normal newbord cord blood


title: Cordblood_72

description: Normal newbord cord blood


title: Cordblood_52

description: Normal newbord cord blood


title: Cordblood_131

description: Normal newbord cord blood


title: Cordblood_175

description: Normal newbord cord blood


title: Cordblood_162

description: Normal newbord cord blood


title: Cordblood_64

description: Normal newbord cord blood


title: Cordblood_75

description: Normal newbord cord blood


title: Cordblood_173

description: Normal newbord cord blood


title: Cordblood_62

description: Normal newbord cord blood


title: Cordblood_68

description: Normal newbord cord blood


title: Cordblood_109

description: Normal newbord cord blood


title: Cordblood_108

description: Normal newbord cord blood


title: Cordblood_60

description: Normal newbord cord blood


title: Cordblood_70

description: Normal newbord cord blood


title: Cordblood_166

description: Normal newbord cord blood


title: Cordblood_134

description: Normal newbord cord blood


title: Cordblood_127

description: Normal newbord cord blood


title: Cordblood_143

description: Normal newbord cord blood


title: Cordblood_113

description: Normal newbord cord blood


title: Cordblood_171

description: Normal newbord cord blood


title: Cordblood_168

description: Normal newbord cord blood


title: Cordblood_73

description: Normal newbord cord blood


title: Cordblood_111

description: Normal newbord cord blood


title: Cordblood_129

description: Normal newbord cord blood


title: Cordblood_102

description: Normal newbord cord blood


title: Cordblood_106

description: Normal newbord cord blood


title: Cordblood_125

description: Normal newbord cord blood


title: Cordblood_66

description: Normal newbord cord blood


title: Cordblood_71

description: Normal newbord cord blood


title: Cordblood_141

description: Normal newbord cord blood


title: Cordblood_104

description: Normal newbord cord blood


title: Cordblood_139

description: Normal newbord cord blood


title: Cordblood_100

description: Normal newbord cord blood


title: Cordblood_137

description: Normal newbord cord blood


title: Cordblood_42

description: Normal newbord cord blood


title: Cordblood_98

description: Normal newbord cord blood


title: Cordblood_155

description: Normal newbord cord blood


title: Cordblood_46

description: Normal newbord cord blood


title: Cordblood_48

description: Normal newbord cord blood


title: Cordblood_121

description: Normal newbord cord blood


title: Cordblood_37

description: Normal newbord cord blood


title: Cordblood_160

description: Normal newbord cord blood


title: Cordblood_169

description: Normal newbord cord blood


title: Cordblood_29

description: Normal newbord cord blood


title: Cordblood_133

description: Normal newbord cord blood


title: Cordblood_130

description: Normal newbord cord blood


title: Cordblood_44

description: Normal newbord cord blood


title: Cordblood_135

description: Normal newbord cord blood


title: Cordblood_25

description: Normal newbord cord blood


title: Cordblood_67

description: Normal newbord cord blood


title: Cordblood_24

description: Normal newbord cord blood

value: Other


title: Cordblood_61

description: Normal newbord cord blood


title: Cordblood_69

description: Normal newbord cord blood


title: Cordblood_132

description: Normal newbord cord blood


title: Cordblood_63

description: Normal newbord cord blood


title: Cordblood_45

description: Normal newbord cord blood


title: Cordblood_28

description: Normal newbord cord blood


title: Cordblood_40

description: Normal newbord cord blood


title: Cordblood_30

description: Normal newbord cord blood


title: Cordblood_36

description: Normal newbord cord blood


title: Cordblood_26

description: Normal newbord cord blood


title: Cordblood_34

description: Normal newbord cord blood


title: Cordblood_65

description: Normal newbord cord blood


title: Cordblood_41

description: Normal newbord cord blood


title: Cordblood_38

description: Normal newbord cord blood


title: Cordblood_9

description: Normal newbord cord blood


title: Cordblood_31

description: Normal newbord cord blood


title: Cordblood_6

description: Normal newbord cord blood


title: Cordblood_43

description: Normal newbord cord blood


title: Cordblood_33

description: Normal newbord cord blood


title: Cordblood_32

description: Normal newbord cord blood


title: Cordblood_4

description: Normal newbord cord blood


title: Cordblood_39

description: Normal newbord cord blood


title: Cordblood_47

description: Normal newbord cord blood


title: Cordblood_35

description: Normal newbord cord blood


title: Cordblood_13

description: Normal newbord cord blood


title: heart_48hr-recover_heat_rep6

city: Ft. Detrick

first: Christine

last: Baer

state: MD

address: 568 Doughten Drive

department: Environmental Health Program

institute: Excet, Inc. / USACEHR

hyb_protocol: Fragmented, labeled cDNA were hybridized to Affymetrix RatGene 1.1 ST array plates on an Affymetrix GeneTitan following manufacturer’s instructions using the GeneTitan Hybridization, Wash and Stain Kit for WT array plates (Affymetrix, #901622).

scan_protocol: Array plates were scanned immediately after hybridization, wash and staining by the Affymetrix GeneTitan using default settings.

data_processing: Microarray data was processed for background adjustment, normalization, and summarization using the interPLIER gene level method (background = PM-GCBG, normalization method = Sketch-Quantile) in Affymetrix Expression Console software (Version 1.1).

label_protocol: An initial input of 100 ng total RNA per sample was synthesized to cRNA using the Ambion Whole Transcript (WT) Expression Kit (Ambion, #4411974) according to manufacturer’s recommendations. Then 10 µg cRNA was used as a template to synthesize cDNA which were fragmented and labeled using the GeneChip WT Terminal Labeling Kit (Affymetrix, #901524).

growth_protocol: Briefly, rats were housed under standard laboratory conditions (22°C, 12:12 hours light:dark cycle, lights on at 6:00AM) in an Association for Assessment and Accreditation of Laboratory Animal Care-accredited facility. Chow (Harlan Teklad, LM-485; Madison, WI) and water were provided ad libitum. Rats were implanted with TL11M2-C50-PXT PhysioTel® Multiplus Transmitters (Data Sciences International, St. Paul, MN) to measure core temperature (Tc; ±0.25°C), heart rate (HR; bpm), and mean arterial pressure (MAP; ±3 mmHg).

extract_protocol: Heart tissues were pulverized under liquid nitrogen using a SPEX 6750 freezer mill (SPEX Sample Prep, Metuchen, NJ). Total RNA was isolated from the pulverized heart and other tissues (liver, kidney and lung) using Trizol (Invitrogen, Carlsbad, CA) followed by column purification with RNeasy Mini kits (Qiagen, GmbH, Germany) to remove residual salt and organic solvents. Total RNA quality and quantity were evaluated using an Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA) and verified using the NanoDrop ND-1000 Spectrophotometer (NanoDrop, Wilmington, DE).

treatment_protocol: Briefly, rats in the heat-stress arm of the experiment were placed in a floor-standing incubator (Thermo Scientific, Ashville, NC) set at room temperature (RT, 22 °C) 24 hours prior to initiation of heat stress experiments. Rats in the control arm (n=18) were introduced to the incubator environment briefly at ambient temperature until Tc stabilized at ≤ 37.3°C, then weighed and returned to their original cages. Rats in the heat-stress arm were heated in the incubator at 37.0 ± 0.2°C until reaching a Tc of 41.8°C (Tc,Max). Six heat-stressed rats were weighed at Tc,Max and euthanized. The remaining rats were placed in a new cage at ambient housing temperature (22.0 ± 0.2°C) and euthanized at 24 hours (n=6) or 48 hours (n=6). Six time-matched controls were euthanized at times corresponding to Tc,Max, 24 hours, and 48 hours in the heat stress arm. Control and experimental animals were provided food and water ad libitum throughout recovery.

value: Fischer 344

tag: Sex

value: male

tag: age

value: ~2-3 months

value: heart


title: heart_48hr-recover_heat_rep5


title: heart_48hr-recover_heat_rep4


title: Cordblood_11

description: Normal newbord cord blood

tag: gender


title: heart_48hr-recover_control_rep6


title: heart_48hr-recover_heat_rep1


title: heart_48hr-recover_control_rep4


title: heart_48hr-recover_heat_rep2


title: heart_48hr-recover_control_rep2


title: heart_48hr-recover_control_rep3


title: heart_48hr-recover_control_rep5


title: heart_24hr-recover_heat_rep2


title: heart_24hr-recover_control_rep6


title: heart_24hr-recover_heat_rep3


title: heart_24hr-recover_heat_rep5


title: heart_24hr-recover_control_rep5


title: heart_24hr-recover_heat_rep4


title: heart_24hr-recover_control_rep4


title: heart_24hr-recover_control_rep3


title: heart_48hr-recover_control_rep1


title: heart_24hr-recover_heat_rep6


title: heart_48hr-recover_heat_rep3


title: heart_TcMax_heat_rep4


title: heart_TcMax_heat_rep5


title: heart_24hr-recover_control_rep2


title: heart_TcMax_heat_rep3


title: heart_TcMax_heat_rep2


title: heart_TcMax_heat_rep1


title: heart_24hr-recover_heat_rep1


title: heart_24hr-recover_control_rep1


title: heart_TcMax_control_rep3


title: heart_TcMax_control_rep4


title: heart_TcMax_control_rep2


title: heart_TcMax_control_rep1


title: heart_TcMax_control_rep6


title: kidney_48hr-recover_heat_rep4

value: kidney


title: heart_TcMax_control_rep5


title: kidney_48hr-recover_heat_rep6


title: kidney_48hr-recover_heat_rep5


title: kidney_48hr-recover_heat_rep2


title: kidney_48hr-recover_heat_rep1


title: kidney_48hr-recover_control_rep4


title: kidney_24hr-recover_heat_rep4


title: kidney_48hr-recover_control_rep1


title: kidney_24hr-recover_heat_rep6


title: kidney_48hr-recover_control_rep5


title: kidney_24hr-recover_control_rep6


title: kidney_48hr-recover_control_rep3


title: kidney_48hr-recover_control_rep6


title: kidney_24hr-recover_heat_rep5


title: kidney_24hr-recover_heat_rep1


title: kidney_24hr-recover_control_rep5


title: kidney_48hr-recover_heat_rep3


title: kidney_24hr-recover_control_rep1


title: kidney_24hr-recover_control_rep4


title: kidney_24hr-recover_control_rep3


title: kidney_48hr-recover_control_rep2


title: kidney_24hr-recover_heat_rep2


title: kidney_24hr-recover_control_rep2


title: kidney_24hr-recover_heat_rep3


title: kidney_TcMax_heat_rep6


title: kidney_TcMax_heat_rep3


title: kidney_TcMax_heat_rep2


title: kidney_TcMax_heat_rep1


title: kidney_TcMax_heat_rep5


title: kidney_TcMax_heat_rep4


title: kidney_TcMax_control_rep3


title: kidney_TcMax_control_rep5


title: lung_48hr-recover_heat_rep5

value: lung


title: kidney_TcMax_control_rep1


title: kidney_TcMax_control_rep2


title: kidney_TcMax_control_rep6


title: lung_48hr-recover_control_rep6


title: lung_48hr-recover_heat_rep1


title: kidney_TcMax_control_rep4


title: lung_48hr-recover_heat_rep3


title: lung_48hr-recover_heat_rep2


title: lung_48hr-recover_control_rep1


title: lung_48hr-recover_control_rep3


title: lung_48hr-recover_heat_rep4


title: lung_48hr-recover_control_rep4


title: lung_24hr-recover_heat_rep5


title: lung_24hr-recover_heat_rep6


title: lung_24hr-recover_heat_rep1


title: lung_48hr-recover_control_rep5


title: lung_24hr-recover_heat_rep2


title: lung_24hr-recover_control_rep5


title: lung_48hr-recover_control_rep2


title: lung_24hr-recover_control_rep3


title: lung_24hr-recover_heat_rep4


title: lung_24hr-recover_control_rep2


title: lung_24hr-recover_heat_rep3


title: lung_24hr-recover_control_rep4


title: lung_TcMax_heat_rep2


title: lung_TcMax_heat_rep4


title: lung_24hr-recover_control_rep6


title: MycPIDD_rep3

city: Innsbruck

first: Tatsiana

last: Aneichyk

state: - Please choose -

address: Innrain 80/82

department: Molecular Pathophysiology

country: Austria

institute: Medical University Innsbruck

hyb_protocol: Target samples were hybridized to Mouse MoGene 1.0 ST v.1 microarrays according to the manufacturer's protocols in a Affymetrix hybridization oven.

scan_protocol: Microarrays were scanned in Affymetrix 3000 scanner and image analysis was made with the Affymetrix GeneChip Command Console software (AGCC)

data_processing: The raw microarray data was pre-processed using “generalgcrma” package from R and our custom transcript-level “CEL definition file” (CDF). Transcripts for all genes have been defined using Ensembl version 71. Background adjustment, normalization and summarization of the microarray data were performed using the GCRMA method

source_name: spleen derived B220+IgM+IgD-

label_protocol: 250 ng of high quality RNA per sample was processed using the Ambion Affymetrix GeneChip WT Expression Kit (Part no. 308 4411974, Ambion) and the Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: preB cells were isolated from 2 mouse femora

extract_protocol: samples were snap frozen after sorting and later RNA was isolated by using TRIzol extraction protocol.

treatment_protocol: B cells were stained for B220, IgM and negativeley selected for IgD and DAPI. 1 Million cells were sorted.

tag: genotype

value: Eµ-Myc/PIDD-/-


title: lung_TcMax_heat_rep6

tag: strain


title: MycPIDD_rep2


title: lung_24hr-recover_control_rep1


title: lung_TcMax_heat_rep3


title: MycRAIDD_rep1

value: Eµ-Myc/RAIDD-/-


title: MycCasp2_rep4

value: Eµ-Myc/Caspase-2 -/-


title: lung_TcMax_control_rep6


title: Myc_rep3

value: Eµ-Myc


title: MycRAIDD_rep2


title: Myc_rep2


title: lung_TcMax_heat_rep5


title: lung_TcMax_control_rep4


title: lung_TcMax_control_rep5


title: MycPIDD_rep1


title: MycRAIDD_rep3


title: MycCasp2_rep3


title: Myc_rep1


title: Myc_rep4


title: lung_TcMax_control_rep3


title: mouse pSN_GTO_biol. repl. 3

first: Joriene

middle: C

last: de Nooij

address: 650 West 168th Street

department: Neurology

institute: Columbia University

hyb_protocol: Hybridization of fragmented biotin-labeled cRNA was carried out by the Herbert Irving Cancer Center Genomics Technologies core facility (Columbia University). The Affymetrix GeneChip Hybridization control kit and GeneChip Hybridization, Wash, and Stain kit were used to hybridize samples to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix). Fluidics were performed on the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Raw data from CEL files was analyzed with Partek Genomic Suite 6.6 software (Partek), using GCRMA background correction. Because of the high variability between GTO samples (as assessed using PCA), we limited the analysis to genes that were enriched in the MS neuronal subset when compared to the GTO neuronal subset, arbitrarily set the stringency levels of the statistical threshold for all our analysis to p<0.08, and used a cut-off of 5-fold or higher (MS-pSN_enriched_probesets.txt).

source_name: GTO-pSN enriched neuronal subset isolated by FACS

label_protocol: RNA was amplified using the Ovation Pico RNA amplification (NuGen), and double stranded cDNA was converted into Biotin-labeled cRNA using the Biotin Module V2 kit (NuGen).

growth_protocol: Dorsal root ganglia (DRG) were collected from Egr3::WGA-cherry; PV:Cre; Thy1-lsl-YFP mice, at postnatal day 7-10.

extract_protocol: Sorted cell samples were thawed in RNA lysis buffer and pooled to reach a (roughly) similar number of neurons for each of the three samples (~1250 neurons for MS; ~725 neurons for GTO). Total RNA was extracted using the Absolutely Rneasy nanoprep kit (Agilent Technologies) according to the manufacturer’s instructions.

treatment_protocol: DRG were collected in ice cold Hank's Buffered Saline Solution (HBSS) supplemented with 1% DNase. DRG were dissociated by enzymatic digestions with Papain (22 U/ml for 15 min. at 37oC.; Wortingthon), followed by Collagenase/Dispase (4 mg/ml and 4.5 mg/m,l respectively, for 15 min. at 37oC; Wortingthon).  Enzymatic digestion was halted by 20% bovine serum in HBSS (1% DNase) and neurons were dissociated by gentle trituration using a p200 pipet. Titurated cells were passed through 35 mm gauze filters to clear suspension from remaining cellular aggregates and immediatedly sorted by FACS into neuronal populations enriched in Cherry+YFP+ (MS) and Cherry-YFP+ (GTO) pSNs. Collected cells were pelleted and stored at -80oC until RNA extractions.

tag: strain background

value: mixed C57bl/129sv

value: male and female

tag: developmental stage

value: early postnatal day 7-10

value: DRG sensory neurons


title: liver_48hr-recover_heat_rep5

value: liver


title: liver_48hr-recover_heat_rep3


title: liver_48hr-recover_heat_rep4


title: liver_48hr-recover_heat_rep2


title: liver_48hr-recover_control_rep5


title: mouse pSN_MS_biol. repl. 1

source_name: MS-pSN enriched neuronal subset isolated by FACS


title: lung_TcMax_heat_rep1


title: lung_TcMax_control_rep1


title: lung_TcMax_control_rep2


title: MycCasp2_rep2


title: mouse pSN_GTO_biol. repl. 1


title: liver_48hr-recover_heat_rep1


title: mouse pSN_MS_biol. repl. 2


title: MycCasp2_rep1


title: mouse pSN_MS_biol. repl. 3


title: liver_48hr-recover_control_rep4


title: 858 Kras;p53

city: Boston

first: Chunxiao

last: Xu

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer Institute

description: Gene expression data primary mouse NSCLC cell line

hyb_protocol: 1. The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The cRNA is quantified spectrophotometrically and purity of the cRNA is also assessed by spectrophometric measurements. 2. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step. 3. The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed. 4. The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: The data were analyzed in R (v 3.0.1) using the oligo package in which RMA normalization was applied.

source_name: primary mouse NSCLC cell line with KrasG12D;p53-/- mutation

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

growth_protocol: Mouse cohorts were all maintained in virus-free conditions on a mixed 129/FVB background. DDR2 DOX induced lung cancer cell lines (3941 and 3942) were  were cultured in RPMI 1640 (Invitrogen) and 10% fetal bovine serum (Gibco). DDR2 expression was induced by treating cells with 2 ug/ml DOX every 2 to 3 days.  Kras mutated cell lines (634, 855 and 858) werecultured in the same conditions without DOX induction.

extract_protocol: Trizol reagent followed by additional purification using RNeasy from Qiagen

treatment_protocol: Cell lines were washed with PBS and trypsinized and then filtered (40 μm).

value: mixed 129/FVB

tag: tissue type

value: lung adenocarcinoma

tag: cell type

value: epithelial

tag: genotyping

value: adult


title: 3942 DDR2L63V;p53

source_name: primary mouse NSCLC cell line with DDR2l63v;p53-/- mutation


title: liver_48hr-recover_control_rep2

value: Fischer 344

value: male

value: ~2-3 months


title: liver_48hr-recover_control_rep3


title: 634 Kras;p53


title: P9 MG56-KO heart

city: Kyoto city

first: Atsuhiko

last: Ichimura

state: Kyoto

address: 46-29, Yoshida Shimoadachi-cho, Sakyo-ku

department: Department of Biological Chemistry

institute: Kyoto University

hyb_protocol: The labeled cRNA were then hybridized on Affimetrix gene chip and stained.

scan_protocol: The probe arrays were scanned with the GeneChip(R) Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Normalisation and data analyses were performed by using Affymetrix GeneChip Command Console Software 6.

source_name: Heart, MG56-KO, P9

label_protocol: cRNA labeling was performed according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted by guanidine hydrochloride-phenol-chloroform method and transcribed to cRNA.

value: heart

tag: genetic background

value: day 9 of postnatal


title: P9 WT heart

source_name: Heart, wild-type, P9

value: wild-type


title: 3941 DDR2L63V;p53


title: liver_48hr-recover_control_rep1


title: P9 MG56-KO Tibialis anterior

source_name: Tibialis anterior, MG56l-KO, P9

value: tibialis anterior (TA) muscle


title: 855 Kras;p53


title: P9 WT Tibialis anterior

source_name: Tibialis anterior, wild-type, P9


title: liver_24hr-recover_heat_rep6


title: liver_24hr-recover_heat_rep5


title: tumor cells HCC [5_HCC_TP]

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: GeneChip® miRNA 2.0 arrays (Affymetrix) were hybridized with 50 ng labelled microRNA, Hybridisation time was 40 hours.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
UnsupportedGeneChip® miRNA 2.0 Array CDF Files
miRNA 2.0 Annotations, Unsupported, CSV format from Affymetrix

source_name: hepatocellular carcinoma

label_protocol: miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

extract_protocol: miRNA was extracted with the miRNeasy FFPE Kit from Qiagen

treatment_protocol: Cells were microdissected from H&E stained FFPE sections

tag: tumor localisation

value: TP


title: tumor cells HCC [5_HCC_TC]

value: TC


title: tumor cells HCC [5_HCC_LC]

value: LC


title: tumor cells HCC [6_HCC_LC]


title: tumor cells HCC [6_HCC_TP]


title: liver_24hr-recover_heat_rep3


title: liver_24hr-recover_control_rep5


title: tumor cells HCC [6_HCC_TC]


title: liver_24hr-recover_heat_rep4


title: tumor cells HCC [5_HCC_LP]

value: LP


title: tumor cells HCC [6_HCC_LP]


title: liver_24hr-recover_heat_rep1


title: liver_24hr-recover_control_rep4


title: BRG1_48hr rep2

city: La Jolla

first: Roy

middle: M

last: Williams

state: CA

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: As recommended  by manufacturer

scan_protocol: As recommended  by manufacturer

data_processing: The data was quantiles normalized in Illumina Genomestudio V2009.1

label: streptavidin Cy3

label_protocol: As recommended  by manufacturer

growth_protocol: Growth medium (GM): RPMI 20% FBS, Differentiation medium (DM): RPMI 2%HS + ITS

extract_protocol: RNA extraction was performed by Trizol

treatment_protocol: siRNAs 100nM final concentraion were transfected by Dharmafect3 reagent

tag: cell line

value: myoblasts

tag: transfected with

tag: incubated in

value: Differentiation medium (DM) for 48hr


title: tumor cells HCC [4_HCC_TP]


title: tumor cells HCC [4_HCC_LP]


title: SCR_18hr rep2

value: siSCR

value: Differentiation medium (DM) for 18hr


title: SCR_48hr rep2


title: liver_24hr-recover_control_rep3

tag: tissue

value: liver


title: BRG1_18hr rep2


title: BRM_18hr rep2

value: siBRM


title: liver_24hr-recover_control_rep6

value: Fischer 344


title: tumor cells HCC [4_HCC_LC]


title: liver_24hr-recover_control_rep2

value: male


title: BRM_48hr rep2


title: tumor cells HCC [4_HCC_TC]


title: mouse pSN_GTO_biol. repl. 2

value: mixed C57bl/129sv

value: male and female

value: early postnatal day 7-10

value: DRG sensory neurons


title: BRG1_48hr rep1


title: liver_24hr-recover_control_rep1

value: ~2-3 months


title: tumor cells HCC [3_HCC_TP]

value: TP


title: tumor cells HCC [3_HCC_TC]

value: TC


title: tumor cells HCC [3_HCC_LP]


title: tumor cells HCC [3_HCC_LC]

value: LC


title: SCR_18hr rep1


title: FLS_PlGF siRNA_rep4

city: Daejeon

first: Ji-Hwan

last: Park

address: 125 Gwahak-ro, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology (KRIBB)

description: FLS treated with PlGF siRNA

hyb_protocol: Following the standard Agilent protocols, RNA was reverse-transcribed, amplified, and then hybridized onto the Agilent SurePrint G3 Human Gene Expression 8x60K v2 microarray

scan_protocol: cRNA on Agilent SurePrint G3 Human Gene Expression 8x60K v2 microarray chip was scanned by SureScan Microarray Scanner

data_processing: Quantile-normalization was performed for the log2-value of gMedianSignal

source_name: FLS_PlGF siRNA

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared, followed by RNAeasy Mini Kit (QIAGEN). cRNA was quantified and normalized by using NanoDrop

extract_protocol: Total RNA was isolated from RA-FLS 12 hours after PlGF siRNA or control siRNA treatment. RNA integrity was evaluated by Bioanalyzer 2100 (Agilent, Santa Clara, CA). The RNA integrity number in all the samples was larger than 9.5.

treatment_protocol: PlGF siRNA or control siRNA was treated to FLS

tag: treatment

value: PlGF siRNA

value: Fibroblast like synoviocyte (FLS)

tag: passaged culture


title: SCR_48hr rep1

value: myoblasts

value: Differentiation medium (DM) for 48hr


title: tumor cells HCC [2_HCC_LP]

value: LP


title: liver_TcMax_heat_rep4

tag: Sex

tag: age

value: liver


title: liver_TcMax_heat_rep2


title: liver_TcMax_heat_rep3


title: BRM_48hr rep1

value: siBRM


title: BRG1_18hr rep1

value: Differentiation medium (DM) for 18hr


title: tumor cells HCC [2_HCC_TC]


title: FLS_PlGF siRNA_rep3

description: FLS treated with PlGF siRNA


title: liver_TcMax_heat_rep1

value: Fischer 344

value: male


title: FLS_PlGF siRNA_rep2

description: FLS treated with PlGF siRNA


title: BRM_18hr rep1


title: liver_TcMax_heat_rep5


title: FLS_PlGF siRNA_rep1

description: FLS treated with PlGF siRNA


title: liver_TcMax_control_rep5


title: tumor cells HCC [2_HCC_LC]


title: liver_TcMax_heat_rep6


title: FLS_Control siRNA_rep4

description: FLS treated with control siRNA

source_name: FLS_Control siRNA

value: control siRNA


title: liver_TcMax_control_rep6


title: tumor cells HCC [2_HCC_TP]


title: tumor cells HCC [1_HCC_TP]


title: liver_TcMax_control_rep4


title: FLS_Control siRNA_rep3

description: FLS treated with control siRNA


title: liver_TcMax_control_rep3


title: tumor cells HCC [1_HCC_TC]


title: tumor cells HCC [1_HCC_LP]


title: liver_TcMax_control_rep2


title: FLS_Control siRNA_rep1

description: FLS treated with control siRNA


title: FLS_Control siRNA_rep2

description: FLS treated with control siRNA


title: liver_TcMax_control_rep1


title: 1321_SM

status: Public on Jan 13 2015

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

description: Sample name: 1321

hyb_protocol: cRNA was quantified and normalized to 77 ng/μl, and then 850 ng was hybridized to Beadchips

scan_protocol: The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner. cRNA synthesis, hybridization and scanning was performed at the UCLA Neuroscience Genomics Core (UNGC).

data_processing: Data processing done in R using the following packages: limma (excluding probes with detection p value >0.05 in all samples) and normalizing with neqc using the control probes.

source_name: skeletal muscle

label_protocol: Biotin-labeled cRNA was synthesized by the total prep RNA amplification kit from Ambion (Austin, TX)

growth_protocol: 16 week mice maintained on 12 hr light dark cycle fed chow diet for 8 weeks followed by high-fat/high-sucrose diet for 8 weeks

extract_protocol: After sacrifice, an approximately 50-mg piece of the quadriceps muscle was excised and disrupted and homogenized using a TissueRupter.  Total RNA was isolated using Qiazol and Rneasy spin columns. RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

value: skeletal muscle (quadriceps)

tag: gender

value: M

value: 16 weeks


title: 1307_SM

description: Sample name: 1307

tag: strain

value: CE/J


title: 1161_SM

description: Sample name: 1161


title: 1243_SM

description: Sample name: 1243


title: 1114_SM

description: Sample name: 1114


title: 1346_SM

description: Sample name: 1346


title: 1149_SM

description: Sample name: 1149


title: 1358_SM

description: Sample name: 1358


title: 1076_SM

description: Sample name: 1076


title: 1146_SM

description: Sample name: 1146


title: 1353_SM

description: Sample name: 1353

value: SM/J


title: 1027_SM

description: Sample name: 1027


title: 1080_SM

description: Sample name: 1080


title: tumor cells HCC [1_HCC_LC]

value: LC


title: 1261_SM

description: Sample name: 1261


title: 1198_SM

description: Sample name: 1198


title: 1270_SM

description: Sample name: 1270

value: NZW/LacJ


title: 1127_SM

description: Sample name: 1127


title: 1217_SM

description: Sample name: 1217


title: 1059_SM

description: Sample name: 1059


title: 1071_SM

description: Sample name: 1071


title: liver_24hr-recover_heat_rep2

value: ~2-3 months


title: 969_SM

description: Sample name: 969


title: 891_SM

description: Sample name: 891


title: Homo_control

city: Harbin

first: Liwen

last: Wu

state: Heilongjiang

address: #37 Yiyuan Street

department: Department of Orthopedics

institute: The Fourth Affiliated Hospital of Harbin Medical University

description: pooled plasma samples from 10 healthy controls

data_processing: The Ct (cycle threshold) was automatically given by SDS 2.3 software (Applied Biosystems) and is defined as the fractional cycle number at which the fluorescence passes the fixed threshold. U6 embedded in the TaqMan Human MicroRNA Arrays was used as an internal control. The relative expression levels of miRNAs were calculated using the comparative ΔΔCt method.

label: FAM

source_name: Human plasma

label_protocol: For cDNA synthesis, 30 ng of total RNA was subjected to reverse transcription using a TaqMan® microRNA Reverse Transcription Kit (#4366596; Applied Biosystems) and Megaplex RT primers (Human Pool A + B; Applied Biosystems) following the manufacturer’s protocol, allowing simultaneous reverse transcription of 739 mature human miRNAs to generate a miRNA cDNA library corresponding to each plasma sample. Reverse transcription was performed with the following cycling conditions: 40 cycles at 16°C for 2 min, 42°C for 1 min and 50°C for 1 s followed by a final step of 80°C for 5 min to inactivate reverse transcriptase. Thereafter, to generate enough miRNA cDNA template for the following real-time PCR, the cDNA libraries were pre-amplified using Megaplex PreAmp primer and PreAmp Master Mix (Applied Biosystems) following the manufacturer’s instructions. The PreAmp primer pool used here consisted of forward primers specific for each of the 739 human miRNAs and a universal reverse primer. The pre-amplification cycling conditions were as follows: 95°C for 10 min, 55°C for 2 min, 72°C for 2 min followed by 12 cycles at 95°C for 30 s and 60°C for 4 min; the samples were then held at 99.9°C for 10 min. After the preamplification step, the products were diluted with RNase-free water, combined with TaqMan gene expression Master Mix and then loaded into TaqMan TaqMan Low Density Array (TLDA) (Applied Biosystems), which are two 384-well formatted plates and real-time PCR-based microfluidic cards with embedded TaqMan primers and probes in each well for the 739 different mature human miRNAs. Real-time PCR was performed on an ABI PRISM 7900HT sequence detection system (Applied Biosystems) with the following cycling conditions: 50°C for 2 min, 94.5°C for 10 min followed by 40 cycles at 95°C for 30 s and 59.7°C for 1 min.

extract_protocol: Total RNA was isolated from each pool of plasma samples using the mirVana miRNA Isolation Kit (Applied Biosystems, Foster City, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: The pre-operative blood samples were obtained from 90 patients prior to surgery and/or chemotherapy. The control blood samples were obtained from healthy people. All extracted plasma samples were stored in phased liquid nitrogen. To minimize the effect of freeze-thaw on circulating miRNAs, we only used plasma samples which had not been previously thawed.

tag: disease state

value: healthy control

value: plasma (extracted from blood)


title: 997_SM

description: Sample name: 997


title: 898_SM

description: Sample name: 898


title: Homo_osteosarcoma

description: pooled plasma samples from 10 pre-operative osteosarcoma patients

value: osteosarcoma


title: 872_SM

description: Sample name: 872


title: 883_SM

description: Sample name: 883


title: 915_SM

description: Sample name: 915


title: 811_SM

description: Sample name: 811

value: BTBR T<+> tf/J


title: 880_SM

description: Sample name: 880


title: 927_SM

description: Sample name: 927


title: 977_SM

description: Sample name: 977


title: 697_SM

description: Sample name: 697


title: 848_SM

description: Sample name: 848


title: 765_SM

description: Sample name: 765


title: 799_SM

description: Sample name: 799


title: TCE_2mM(3)_24h

city: Maastricht

first: Lize

last: Deferme

state: Limburg

address: Universiteitssingel 50

department: TGX

country: Netherlands

institute: Maastricht University

description:
Effect of Tetrachloroethylene on mRNA levels in HepG2 cells
K_24h_TCE_3

hyb_protocol: 12.5µg of cRNA was used. The GeneTitan arrays were hybridized, washed and stained using the GeneTitan hybridization, wash and stain kit for 3’ IVT Arrays and GeneTitan Operating Software and scanned by means of an Affymetrix GeneTitan scanner

scan_protocol: Arrays were scanned with the GeneTitan scanner

data_processing: Obtained data sets were re-annotated to the MBNI Custom CDF-files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the NuGOExpressionFileCreator, an enhanced version of the standard ExpressionFileCreator module that is present in GenePattern (De Groot et al., 2008).

source_name: hepatocellular carcinoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit

growth_protocol: HepG2 cells were cultured in 6-well plates in the presence of minimal essential medium (MEM) supplemented with 1% non-essential amino acids, 1% sodium-pyruvate, 2% penicillin/streptomycin and 10% fetal bovine serum (FBS) (all from Gibco BRL, Breda, The Netherlands). The cells were incubated at 37 C and 5% CO2.

extract_protocol: Qiazol extraction was performed using the miRNAeasy kit from Qiagen according to the manufacturer’s protocol

treatment_protocol: When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing, or fresh medium containing a genotoxic of non-genotoxic carcinogen

value: hepatocellular carcinoma

value: liver

tag: compound and dose

value: 2mM tetrachloroethylene_24h_Biological replicate 3

tag: time (h)


title: 691_SM

description: Sample name: 691

value: CBA/J


title: 831_SM

description: Sample name: 831


title: 763_SM

description: Sample name: 763

value: NOD/ShiLtJ


title: 786_SM

description: Sample name: 786

value: skeletal muscle (quadriceps)


title: 669_SM

description: Sample name: 669

value: M


title: 668_SM

description: Sample name: 668

value: 16 weeks


title: TCE_2mM(1)_48h

description:
Effect of Tetrachloroethylene on mRNA levels in HepG2 cells
L_48h_TCE_1

tag: cell type

value: 2mM tetrachloroethylene_48h_Biological replicate 1


title: TCE_2mM(3)_48h

description:
Effect of Tetrachloroethylene on mRNA levels in HepG2 cells
L_48h_TCE_3

value: 2mM tetrachloroethylene_48h_Biological replicate 3


title: EtOH_Cont(3)_48h

description:
Effect of ethanol control on mRNA levels in HepG2 cells
L_48h_EtOH_3

value: 0.5% ethanol control 48h_Biological replicate 3


title: 606_SM

description: Sample name: 606


title: TCE_2mM(2)_48h

description:
Effect of Tetrachloroethylene on mRNA levels in HepG2 cells
L_48h_TCE_2

value: 2mM tetrachloroethylene_48h_Biological replicate 2


title: 608_SM

description: Sample name: 608


title: TCE_2mM(1)_24h

description:
Effect of Tetrachloroethylene on mRNA levels in HepG2 cells
K_24h_TCE_1

value: 2mM tetrachloroethylene_24h_Biological replicate 1


title: TCE_2mM(2)_24h

description:
Effect of Tetrachloroethylene on mRNA levels in HepG2 cells
K_24h_EtOH_2

value: 2mM tetrachloroethylene_24h_Biological replicate 2


title: EtOH_Cont(3)_24h

description:
Effect of ethanol control on mRNA levels in HepG2 cells
K_24h_EtOH_3

value: 0.5% ethanol control 24h_Biological replicate 3


title: 644_SM

description: Sample name: 644


title: 599_SM

description: Sample name: 599


title: 605_SM

description: Sample name: 605


title: HBSS_Cont(2)_48h

description:
Effect of PBS solvent control on mRNA levels in HepG2 cells
C_48h_PBS_2

value: 0.5% HBSS control 48h_Biological replicate 2


title: HBSS_Cont(2)_24h

description:
Effect of PBS solvent control on mRNA levels in HepG2 cells
C_24h_PBS_2

value: 0.5% HBSS control 24h_Biological replicate 2


title: EtOH_Cont(1)_24h

description:
Effect of ethanol control on mRNA levels in HepG2 cells
K_24h_EtOH_1

value: hepatocellular carcinoma

value: 0.5% ethanol control 24h_Biological replicate 1


title: 602_SM

description: Sample name: 602


title: 603_SM

description: Sample name: 603


title: HBSS_Cont(1)_24h

description:
Effect of PBS solvent control on mRNA levels in HepG2 cells
C_24h_PBS_1

value: liver

value: 0.5% HBSS control 24h_Biological replicate 1


title: EtOH_Cont(2)_48h

description:
Effect of ethanol control on mRNA levels in HepG2 cells
L_48h_EtOH_2

value: 0.5% ethanol control 48h_Biological replicate 2


title: HBSS_Cont(3)_48h

description:
Effect of PBS solvent control on mRNA levels in HepG2 cells
C_48h_PBS_3

value: 0.5% HBSS control 48h_Biological replicate 3


title: EtOH_Cont(2)_24h

description:
Effect of ethanol control on mRNA levels in HepG2 cells
K_24h_EtOH_2

value: 0.5% ethanol control 24h_Biological replicate 2


title: EtOH_Cont(1)_48h

description:
Effect of ethanol control on mRNA levels in HepG2 cells
L_48h_EtOH_1

value: 0.5% ethanol control 48h_Biological replicate 1


title: HBSS_Cont(3)_24h

description:
Effect of PBS solvent control on mRNA levels in HepG2 cells
C_24h_PBS_3

value: 0.5% HBSS control 24h_Biological replicate 3


title: HBSS_Cont(1)_48h

description:
Effect of PBS solvent control on mRNA levels in HepG2 cells
C_48h_PBS_1

value: 0.5% HBSS control 48h_Biological replicate 1


title: 579_SM

description: Sample name: 579

value: skeletal muscle (quadriceps)

value: M

value: 16 weeks


title: Dman_250uM(3)_48h

description:
Effect of D-mannitol on mRNA levels in HepG2 cells
C_48h_Dman_3

value: 250µM D-mannitol_48h_Biological replicate 3


title: 592_SM

description: Sample name: 592

value: BALB/cJ


title: 572_SM

description: Sample name: 572


title: Dman_250uM(3)_24h

description:
Effect of D-mannitol on mRNA levels in HepG2 cells
C_24h_Dman_3

value: 250µM D-mannitol_24h_Biological replicate 3


title: TPA_500nM(2)_48h

description:
Effect of Tetradecanoyl-phorbol-acetate on mRNA levels in HepG2 cells
E_48h_TPA_2

value: 500nM Tetradecanoyl phorbol acetate_48h_Biological replicate 2


title: TPA_500nM(3)_24h

description:
Effect of Tetradecanoyl-phorbol-acetate on mRNA levels in HepG2 cells
D_24h_TPA_3

value: hepatocellular carcinoma

value: 500nM Tetradecanoyl phorbol acetate_24h_Biological replicate 3


title: TPA_500nM(1)_48h

description:
Effect of Tetradecanoyl-phorbol-acetate on mRNA levels in HepG2 cells
E_48h_TPA_1

value: liver

value: 500nM Tetradecanoyl phorbol acetate_48h_Biological replicate 1


title: Dman_250uM(1)_24h

description:
Effect of D-mannitol on mRNA levels in HepG2 cells
C_24h_Dman_1

value: 250µM D-mannitol_24h_Biological replicate 1


title: Dman_250uM(1)_48h

description:
Effect of D-mannitol on mRNA levels in HepG2 cells
C_48h_Dman_1

value: 250µM D-mannitol_48h_Biological replicate 1


title: TPA_500nM(1)_24h

description:
Effect of Tetradecanoyl-phorbol-acetate on mRNA levels in HepG2 cells
D_24h_TPA_1

value: 500nM Tetradecanoyl phorbol acetate_24h_Biological replicate 1


title: Dman_250uM(2)_24h

description:
Effect of D-mannitol on mRNA levels in HepG2 cells
C_24h_Dman_2

value: 250µM D-mannitol_24h_Biological replicate 2


title: TPA_500nM(3)_48h

description:
Effect of Tetradecanoyl-phorbol-acetate on mRNA levels in HepG2 cells
E_48h_TPA_3

value: 500nM Tetradecanoyl phorbol acetate_48h_Biological replicate 3


title: 534_SM

description: Sample name: 534


title: 867_SM

description: Sample name: 867


title: 528_SM

description: Sample name: 528

value: SEA/GnJ


title: 547_SM

description: Sample name: 547

value: skeletal muscle (quadriceps)


title: 557_SM

description: Sample name: 557

value: M


title: Fu_2mM(2)_48h

description:
Effect of Furan on mRNA levels in HepG2 cells
I_48h_FU_2

value: 2mM Furan_48h_Biological replicate 2


title: Fu_2mM(3)_24h

description:
Effect of Furan on mRNA levels in HepG2 cells
I_24h_FU_3

value: 2mM Furan_24h_Biological replicate 3


title: Dman_250uM(2)_48h

description:
Effect of D-mannitol on mRNA levels in HepG2 cells
C_48h_Dman_2

value: 250µM D-mannitol_48h_Biological replicate 2


title: TPA_500nM(2)_24h

description:
Effect of Tetradecanoyl-phorbol-acetate on mRNA levels in HepG2 cells
D_24h_TPA_2

value: 500nM Tetradecanoyl phorbol acetate_24h_Biological replicate 2


title: 562_SM

description: Sample name: 562

value: 16 weeks


title: Fu_2mM(1)_24h

description:
Effect of Furan on mRNA levels in HepG2 cells
H_24h_FU_1

value: hepatocellular carcinoma

value: 2mM Furan_24h_Biological replicate 1


title: Fu_2mM(2)_24h

description:
Effect of Furan on mRNA levels in HepG2 cells
H_24h_FU_2

value: liver

value: 2mM Furan_24h_Biological replicate 2


title: Fu_2mM(1)_48h

description:
Effect of Furan on mRNA levels in HepG2 cells
I_48h_FU_1

value: 2mM Furan_48h_Biological replicate 1


title: Fu_2mM(3)_48h

description:
Effect of Furan on mRNA levels in HepG2 cells
J_48h_FU_3

value: 2mM Furan_48h_Biological replicate 3


title: 542_SM

description: Sample name: 542


title: 501_SM

description: Sample name: 501


title: 517_SM

description: Sample name: 517


title: 495_SM

description: Sample name: 495


title: DZN_250uM(3)_48h

description:
Effect of Diazinon on mRNA levels in HepG2 cells
I_48h_DZN_3

value: 250µM Diazinon_48h_Biological replicate 3


title: DZN_250uM(3)_24h

description:
Effect of Diazinon on mRNA levels in HepG2 cells
H_24h_DZN_3

value: 250µM Diazinon_24h_Biological replicate 3


title: 492_SM

description: Sample name: 492


title: DMSO_Cont(2)_24h

description:
Effect of DMSO control on mRNA levels in HepG2 cells
H_24h_DMSO_2

value: 0.5% DMSO control 24h_Biological replicate 2


title: DZN_250uM(2)_24h

description:
Effect of Diazinon on mRNA levels in HepG2 cells
H_24h_DZN_2

value: 250µM Diazinon_24h_Biological replicate 2


title: DZN_250uM(2)_48h

description:
Effect of Diazinon on mRNA levels in HepG2 cells
I_48h_DZN_2

value: 250µM Diazinon_48h_Biological replicate 2


title: 457_SM

description: Sample name: 457

value: skeletal muscle (quadriceps)

value: M


title: AZA_250uM(3)_48h

description:
Effect of Azathriopine on mRNA levels in HepG2 cells
I_48h_AZA_3

value: 250µM Azathriopine_48h_Biological replicate 3


title: DMSO_Cont(2)_48h

description:
Effect of DMSO control on mRNA levels in HepG2 cells
I_48h_DMSO_2

value: 0.5% DMSO control 48h_Biological replicate 2


title: DMSO_Cont(3)_24h

description:
Effect of DMSO control on mRNA levels in HepG2 cells
H_24h_DMSO_3

value: 0.5% DMSO control 24h_Biological replicate 3


title: 438_SM

description: Sample name: 438

value: 16 weeks


title: 447_SM

description: Sample name: 447


title: 452_SM

description: Sample name: 452


title: DMSO_Cont(3)_48h

description:
Effect of DMSO control on mRNA levels in HepG2 cells
I_48h_DMSO_3

value: hepatocellular carcinoma

value: 0.5% DMSO control 48h_Biological replicate 3


title: AZA_250uM(2)_48h

description:
Effect of Azathriopine on mRNA levels in HepG2 cells
I_48h_AZA_2

value: liver

value: 250µM Azathriopine_48h_Biological replicate 2


title: AZA_250uM(3)_24h

description:
Effect of Azathriopine on mRNA levels in HepG2 cells
H_24h_AZA_3

value: 250µM Azathriopine_24h_Biological replicate 3


title: DZN_250uM(1)_24h

description:
Effect of Diazinon on mRNA levels in HepG2 cells
H_24h_DZN_1

value: 250µM Diazinon_24h_Biological replicate 1


title: DZN_250uM(1)_48h

description:
Effect of Diazinon on mRNA levels in HepG2 cells
I_48h_DZN_1

value: 250µM Diazinon_48h_Biological replicate 1


title: DMSO_Cont(1)_24h

description:
Effect of DMSO control on mRNA levels in HepG2 cells
H_24h_DMSO_1

value: 0.5% DMSO control 24h_Biological replicate 1


title: 436_SM

description: Sample name: 436


title: 463_SM

description: Sample name: 463

value: RIIIS/J


title: 377_SM

description: Sample name: 377


title: DMSO_Cont(1)_48h

description:
Effect of DMSO control on mRNA levels in HepG2 cells
I_48h_DMSO_1

value: 0.5% DMSO control 48h_Biological replicate 1


title: 369_SM

description: Sample name: 369


title: AZA_250uM(1)_24h

description:
Effect of Azathriopine on mRNA levels in HepG2 cells
H_24h_AZA_1

value: 250µM Azathriopine_24h_Biological replicate 1


title: 357_SM

description: Sample name: 357

value: skeletal muscle (quadriceps)


title: 422_SM

description: Sample name: 422

value: M


title: AZA_250uM(2)_24h

description:
Effect of Azathriopine on mRNA levels in HepG2 cells
H_24h_AZA_2

value: 250µM Azathriopine_24h_Biological replicate 2


title: 367_SM

description: Sample name: 367


title: AZA_250uM(1)_48h

description:
Effect of Azathriopine on mRNA levels in HepG2 cells
I_48h_AZA_1

value: 250µM Azathriopine_48h_Biological replicate 1


title: 401_SM

description: Sample name: 401

value: BUB/BnJ


title: 340_SM

description: Sample name: 340

value: 16 weeks


title: 311_SM

description: Sample name: 311


title: 318_SM

description: Sample name: 318

value: LG/J


title: E. coli incubated with GST-fused Drosophila immune proteins for 10 min, biological rep3

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

hyb_protocol: Following fragmentation, 1.0-1.7 µg of cDNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip E. coli Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with Distribution Free Weighted method (DFW), using the statistical language R (R-2.7.2) and Bioconductor 2.2.

organism: Escherichia coli

label_protocol: The cDNA was purified using MinElute PCR Purification Kit (Qiagen), fragmented into 50~200 bp with DNase I (Takara-Bio, Kyoto, Japan) (0.06 units/μg DNA), labeled with biotin using terminal deoxynucleotidyl transferase (Promega KK, Tokyo, Japan) and GeneChip Labeling Reagent (Affymetrix, Santa Clara, CA, USA).

growth_protocol: E. coli BW25113 were maintained in Luria-Bertani medium at 37ºC for about 14 h until they reached the stationary phase of cell growth before treatment.

extract_protocol: Total RNA was purified with an RNeasy micro kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: The E. coli strain BW25113 (2 x 10^9) suspended with insect saline (0.13 M NaCl, 4.7 mM KCl, 1.9 mM CaCl2), was incubated with GST or GST-fused Drosophila immune proteins for 10 min at room temperature.

tag: genotype/variation

value: wild type

tag: incubated with

value: Drosophila immune proteins

tag: incubation duration

value: 10 min


title: E. coli incubated with GST-fused Drosophila immune proteins for 10 min, biological rep1


title: 321_SM

description: Sample name: 321


title: 297_SM

description: Sample name: 297


title: 285_SM

description: Sample name: 285


title: E. coli incubated with GST-fused Drosophila immune proteins for 10 min, biological rep2


title: E. coli incubated with GST protein for 10 min, biological rep1

source_name: E. coli incubated with GST protein alone for 10 min

value: GST alone (3 μM; control)


title: 287_SM

description: Sample name: 287


title: 276_SM

description: Sample name: 276


title: 271_SM

description: Sample name: 271


title: 263_SM

description: Sample name: 263