title: RA treated 2hpf embryo replicate 2

description:
2hpf biological replicate 2 of 2
RA2h-2

value: whole embryo

tag: dna fragmentation


title: X6055432102_R03C02_genomic DNA from whole blood_array

status: Public on Dec 09 2013

type: genomic

city: London

first: Jordana

last: Bell

address: St Thomas' Hospital, Westminster Bridge Rd

department: Department of Twin Research and Genetic Epidemiology

country: United Kingdom

institute: King's College London

description: Family 23 monozygotic twin 2

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

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

data_processing: BeadStudio software for 450k data.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: whole blood

label_protocol: Standard Illumina Protocol

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

tag: individual

value: Family 23 monozygotic twin 2

tag: gender

value: Female

tag: pain temperature

tag: age

tag: medip-seq id

tag: 450k chip

tag: order on 450k chip


title: X6057825005_R01C01_genomic DNA from whole blood_array

description: Family 24 monozygotic twin 1

value: Family 24 monozygotic twin 1


title: X6055432102_R02C02_genomic DNA from whole blood_array

description: Family 23 monozygotic twin 1

value: Family 23 monozygotic twin 1


title: X6057825033_R03C02_genomic DNA from whole blood_array

description: Family 21 monozygotic twin 2

value: Family 21 monozygotic twin 2


title: Untreated 6hpf embryo replicate 1

city: Worcester

first: Steven

last: Weicksel

state: Massachusetts

address: 55 Lake Ave

department: BMP

country: USA

institute: UMass Medical School

description:
6hpf biological replicate 1 of 2
WT6h-1

hyb_protocol: Adapted from Yuan et al 2005 Science

scan_protocol: Scanned on an Agilent High-Resolution C Scanner or an Axon 4000B. Images were quantified and background subtraction was done using Agilent Feature Extraction Software.

data_processing: Mean singals of the background subtracted data from two replicates for each sample was assigned to each probe location.  Signals were then taillied using a 30bp sliding window with a 10bp step. A Lowess fitting line (f=.05) then plotted to show the trend of the aggregated signals.

organism: Danio rerio

source_name: pooled whole zebrafish embryo 6hpf_untreated

label_protocol: Adapted from Yuan et al 2005 Science

extract_protocol: Adapted from Dennis et al 2007 Genome Research

tag: tissue

tag: developmental stage

value: 6 hr post fertilization

tag: treated with

value: none (untreated)

value: Micrococcal Nuclease

source_name: pooled whole zebrafish embryo 6hpf

value: Sonication


title: HBV - related acute liver failure group rep2

status: Public on Dec 10 2013

city: Wuhan

first: Lin

last: Ju-Sheng

state: Hubei

address: 1095 Jiefang Road

department: Gastroenterology

country: China

institute: Tongji Hospital

description: Hybridized to Affymetrix SNP6.0 Array

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations 450, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: CEL files and TXT files were analyzed using Birdseed algorithm, an evolution of the RLMM genotype-calling algorithm (Rabbee and Speed, 2006) by Affymetrix Genotyping Console software, which makes genotype calls by fitting a Gaussian mixture model in the two-dimensional A-signal vs. B-signal space, using SNP-specific models to increase performance.

label: Biotin

source_name: HBV - related acute liver failure patients

label_protocol: standard Affymetrix protocol

extract_protocol: Genomic DNA was extracted from EDTA-anticoagulated peripheral blood using a QuickGene DNA whole blood kit S (DB-S) as instruction. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: peripheral blood

tag: pools

value: 86 patients

tag: group

value: case 1

tag: disease state


title: Untreated 4hpf embryo replicate 2

description:
4hpf biological replicate 2 of 2
WT4h-2

source_name: pooled whole zebrafish embryo 4hpf_untreated

value: 4 hr post fertilization

source_name: pooled whole zebrafish embryo 4hpf


title: eMCAo 72hrs

type: RNA

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

description:
5320724053_E.AVG_Signal
400ng of total RNA was detected by beadchip

hyb_protocol: Hybridization was performed in 15ul volume by using illumina hybridization kit.

scan_protocol: Data were scanned and analysed with the BeadStudio software (v.1.8.0).

data_processing: Differentially expressed genes were selected based on p value < 0.05, differential score > 20, average signal intensity > 100, and normalize to endo-control and baseline (Illumina Inc. GenomeStudio Version 1.8.0).

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: ischemic brain

label_protocol: Biotin-labelled complementary RNA probes were synthesized with the Illumina TotalPrep RNA Amplification kit (Ambion).

growth_protocol: All animals were handled according to the Council for International Organisation of Medical Sciences on Animal Experimentation (World Health Organisation, Geneva, Switzerland) and the National University of Singapore (IACUC/NUS) guidelines for laboratory animals. The protocol was approved by the Committee on the Ethics of Animal Experiments of the National University of Singapore (Protocol Number: 081/09 and 025/11). All surgery was performed using ketamine/xylazine as anesthesia, and all efforts were made to minimize suffering.

extract_protocol: Total RNA (+ miRNA) was extracted from brain tissues by a single-step method using Trizol reagent (Invitrogen, Life Technologies, USA) according to manufacturers’ protocol.

treatment_protocol: no treatment

tag: species

value: Wistar rat

value: male

tag: weight

value: ischemic brain


title: Untreated 4hpf embryo replicate 1

description:
4hpf biological replicate 1 of 2
WT4h-1

value: whole embryo


title: eMCAo 48hrs

description:
5320724053_D.AVG_Signal
400ng of total RNA was detected by beadchip


title: X6057825033_R02C02_genomic DNA from whole blood_array

description: Family 21 monozygotic twin 1

value: Family 21 monozygotic twin 1


title: HBV - related acute liver failure group rep1

description: Hybridized to Affymetrix SNP6.0 Array

value: HBV - related acute liver failure patients


title: X6055432102_R01C01_genomic DNA from whole blood_array

description: Family 20 monozygotic twin 1

value: Family 20 monozygotic twin 1

value: Female


title: Untreated 9hpf embryo replicate 2

description:
9hpf biological replicate 2 of 2
WT9h-2

source_name: pooled whole zebrafish embryo 9hpf_untreated

value: 9 hr post fertilization

source_name: pooled whole zebrafish embryo 9hpf


title: X6055432099_R04C01_genomic DNA from whole blood_array

description: Family 19 monozygotic twin 2

value: Family 19 monozygotic twin 2


title: X6055432102_R03C01_genomic DNA from whole blood_array

description: Family 20 monozygotic twin 2

value: Family 20 monozygotic twin 2


title: Untreated 2hpf embryo replicate 2

description:
2hpf biological replicate 2 of 2
WT2h-2

source_name: pooled whole zebrafish embryo 2hpf_untreated

value: 2 hr post fertilization

value: none (untreated)

value: Micrococcal Nuclease

source_name: pooled whole zebrafish embryo 2hpf


title: RA treated 4hpf embryo replicate 1

description:
4hpf biological replicate 1 of 2
RA4h-1

source_name: pooled whole zebrafish embryo 4hpf_RA treated

value: Retinoic acid (RA)

value: Sonication


title: Untreated 2hpf embryo replicate 1

description:
2hpf biological replicate 1 of 2
WT2h-1


title: Untreated 9hpf embryo replicate 1

description:
9hpf biological replicate 1 of 2
WT9h-1


title: X6055432099_R03C01_genomic DNA from whole blood_array

description: Family 19 monozygotic twin 1

value: Family 19 monozygotic twin 1


title: X6057825006_R04C01_genomic DNA from whole blood_array

description: Family 18 monozygotic twin 2

value: Family 18 monozygotic twin 2


title: eMCAo 12hrs

description:
5320724053_B.AVG_Signal
400ng of total RNA was detected by beadchip

value: Wistar rat

value: male


title: 6tumor

city: shanghai

first: wei

last: gu

address: No.197,Rui Jin Er Road

institute: ruijin hospital

description: lncRNA expression

hyb_protocol: 1.5 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 Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies)

source_name: human gastric adenocarcinoma tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from two pool of snap frozen colon cancer tissues and one pool of normal tissues using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.

tag: sample pair

value: gastric adenocarcinoma tissue

value: female


title: eMCAo 24hrs

description:
5320724053_C.AVG_Signal
400ng of total RNA was detected by beadchip

value: ischemic brain


title: 6normal

description: lncRNA expression

source_name: human normal gastic tissue

value: normal gastric tissue


title: 4tumor

description: lncRNA expression


title: 3tumor

description: lncRNA expression


title: 4normal

description: lncRNA expression


title: 5normal

description: lncRNA expression


title: HBV - related acute liver failure group rep3

description: Hybridized to Affymetrix SNP6.0 Array

value: peripheral blood

value: 86 patients

value: case 1

value: HBV - related acute liver failure patients


title: 5tumor

description: lncRNA expression


title: wild type-batch-4-rep-11

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from wild type-batch-4-rep-11

hyb_protocol: All cRNAs were hybridized to a custom Affymetrix GeneChip

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

data_processing: The data were analyzed with Expression Console

organism: Borrelia hermsii

source_name: wild type-batch-4-rep-11

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

growth_protocol: Samples were prepared from 4 biological replicates of 50 ml broth cultures (5 x 107 cells/ml) of Borrelia hermsii

extract_protocol: Total RNA was isolated from 50 ml B. hermsii DAH cultures (5 x 107 cells/ml) using the RNeasy kit (Qiagen, Inc., Valencia, CA) and contaminating DNA was removed using the DNA-free kit (Ambion, Inc, Austin, TX).

treatment_protocol: no treatments, just strain differences

tag: genotype/variation

value: DAH wild type


title: wild type-batch-4-rep-10

description: Gene expression data from wild type-batch-4-rep-10

source_name: wild type-batch-4-rep-10


title: 3normal

description: lncRNA expression


title: X6057825006_R01C01_genomic DNA from whole blood_array

description: Family 18 monozygotic twin 1

tag: individual

value: Family 18 monozygotic twin 1

value: Female


title: wild type-batch-3-rep-8

description: Gene expression data from wild type-batch-3-rep-8

source_name: wild type-batch-3-rep-8


title: 1tumor

description: lncRNA expression

tag: gender


title: Untreated 6hpf embryo replicate 2

description:
6hpf biological replicate 2 of 2
WT6h-2

value: whole embryo

value: 6 hr post fertilization

value: none (untreated)

tag: dna fragmentation

value: Micrococcal Nuclease


title: eMCAo normal

description:
5320724053_A.AVG_Signal
400ng of total RNA was detected by beadchip

value: Wistar rat


title: 2tumor

description: lncRNA expression

value: male


title: wild type-batch-3-rep-7

description: Gene expression data from wild type-batch-3-rep-7

source_name: wild type-batch-3-rep-7


title: X6055432140_R06C02_genomic DNA from whole blood_array

description: Family 17 monozygotic twin 1

source_name: whole blood

value: Family 17 monozygotic twin 1

tag: pain temperature

tag: age


title: 2normal

description: lncRNA expression


title: wild type-batch-3-rep-9

description: Gene expression data from wild type-batch-3-rep-9

source_name: wild type-batch-3-rep-9


title: wild type-batch-2-rep-6

description: Gene expression data from wild type-batch-2-rep-6

source_name: wild type-batch-2-rep-6


title: 1normal

description: lncRNA expression


title: X6055432144_R01C01_genomic DNA from whole blood_array

description: Family 17 monozygotic twin 2

value: Family 17 monozygotic twin 2

tag: medip-seq id

tag: 450k chip


title: X6042308075_R03C02_genomic DNA from whole blood_array

description: Family 15 monozygotic twin 2

value: Family 15 monozygotic twin 2

tag: order on 450k chip


title: RA treated 9hpf emrbyo RNA expression

description:
ra9_v_wt2
RA9h-expression

hyb_protocol: Followed Agilent protocol

scan_protocol: Scanned on an Agilent High-Resolution C Scanner or an Axon 4000B. Images were quantified using Agilent Feature Extraction Software.

data_processing: Images were quantified and normalized (Lowess) using Agilent Feature Extraction Software v10.7.1.1. Active genes were filtered from maternal transcripts based on wt2_v_wt2 (control) experiment.

source_name: pooled whole zebrafish embryo 9hpf_RA treated

label_protocol: Followed Agilent protocol substituting COT DNA with salmon sperm DNA at 10ug/ul

extract_protocol: Trizol following manufactors specifications

tag: tissue

tag: developmental stage

value: 9 hr post fertilization

value: Retinoic acid

value: 2 hr post fertilization


title: RA treated 4hpf embryo RNA expression

description:
ra4_v_wt2
RA4h-expression

value: 4 hr post fertilization

tag: treated with


title: X6042308075_R06C01_genomic DNA from whole blood_array

description: Family 15 monozygotic twin 1

value: Family 15 monozygotic twin 1


title: wild type-batch-2-rep-5

description: Gene expression data from wild type-batch-2-rep-5

source_name: wild type-batch-2-rep-5

value: DAH wild type


title: X6057825025_R02C01_genomic DNA from whole blood_array

description: Family 14 monozygotic twin 1

value: Family 14 monozygotic twin 1


title: RA treated 6hpf embryo RNA expression

description:
ra6_v_wt2
RA6h-expression

source_name: pooled whole zebrafish embryo 6hpf_RA treated


title: X6042316131_R03C01_genomic DNA from whole blood_array

description: Family 16 monozygotic twin 1

value: Family 16 monozygotic twin 1

value: Female


title: Untreated 9hpf embryo RNA expression

description:
wt9_v_wt2
WT9h-expression

source_name: pooled whole zebrafish embryo 9hpf_untreated

value: whole embryo


title: X6057825033_R04C01_genomic DNA from whole blood_array

description: Family 12 monozygotic twin 1

value: Family 12 monozygotic twin 1


title: X6057825025_R03C01_genomic DNA from whole blood_array

description: Family 14 monozygotic twin 2

value: Family 14 monozygotic twin 2


title: X6042308075_R02C02_genomic DNA from whole blood_array

description: Family 13 monozygotic twin 2

value: Family 13 monozygotic twin 2


title: wild type-batch-1-rep-2

description: Gene expression data from wild type-batch-1-rep-2

source_name: wild type-batch-1-rep-2


title: Untreated 2hpf embryo RNA expression

description:
wt2_v_wt2
WT2h-expression

source_name: pooled whole zebrafish embryo 2hpf_untreated

value: none (untreated)


title: wild type-batch-2-rep-4

description: Gene expression data from wild type-batch-2-rep-4

source_name: wild type-batch-2-rep-4


title: Untreated 4hpf embyro RNA expression

description:
wt4_v_wt2
WT4h-expression

source_name: pooled whole zebrafish embryo 4hpf_untreated

source_name: pooled whole zebrafish embryo 2hpf


title: Untreated 6hpf embryo RNA expression

description:
wt6_v_wt2
WT6h-expression

source_name: pooled whole zebrafish embryo 6hpf_untreated

value: 6 hr post fertilization


title: X6055432089_R02C02_genomic DNA from whole blood_array

description: Family 7 monozygotic twin 1

value: Family 7 monozygotic twin 1


title: mutant-batch-3-rep-8

description: Gene expression data from mutant-batch-3-rep-8

value: DAH motility mutant


title: mutant-batch-3-rep-7

description: Gene expression data from mutant-batch-3-rep-7


title: wild type-batch-1-rep-1

description: Gene expression data from wild type-batch-1-rep-1

source_name: wild type-batch-1-rep-1


title: mutant-batch-4-rep-12

description: Gene expression data from mutant-batch-4-rep-12


title: mutant-batch-3-rep-9

description: Gene expression data from mutant-batch-3-rep-9


title: mutant-batch-4-rep-11

description: Gene expression data from mutant-batch-4-rep-11


title: wild type-batch-1-rep-3

description: Gene expression data from wild type-batch-1-rep-3

source_name: wild type-batch-1-rep-3


title: X6057825033_R05C01_genomic DNA from whole blood_array

description: Family 12 monozygotic twin 2

value: Family 12 monozygotic twin 2


title: X6042308075_R05C01_genomic DNA from whole blood_array

description: Family 13 monozygotic twin 1

value: Family 13 monozygotic twin 1


title: mutant-batch-2-rep-6

description: Gene expression data from mutant-batch-2-rep-6


title: Muscle taken at slaughter, M_1134

status: Public on Dec 08 2013

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: miRNA expression data from muscle of commercial pig breed Pix(DLxDE).

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip miRNA arrays. GeneChips were washed and processed to detect biotin-containing transcripts by Streptavidin-PE (Phycoerythrin) conjugate.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols.

data_processing: Data were analysed using the RMA algorithm.

organism: Sus scrofa

source_name: muscle, mean end weight of 110 kg

label_protocol: Biotinylated cRNA were prepared from miRNA according to the FlashTag™ Biotin RNA Labeling Kit for Affymetrix GeneChip miRNA arrays (Genisphere, Hatfield, PA, USA) according to the manufacturer's recommendations in Affymetrix® GeneChip® miRNA Array protocols (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Muscles were taken at slaughter.

extract_protocol: Total RNA was isolated using the Qiagen miRNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol for small-RNA. Then, small RNA was cleaned up using the RNeasy MinElute Clean-up kit (Qiagen, Hilden, Germany).

tag: breed

value: crossbreed Pix(DLxDE)

value: muscle


title: mutant-batch-4-rep-10

description: Gene expression data from mutant-batch-4-rep-10


title: X6042316146_R06C02_genomic DNA from whole blood_array

description: Family 11 monozygotic twin 2

value: Family 11 monozygotic twin 2


title: Muscle taken at slaughter, M_1138


title: Muscle taken at slaughter, M_1131


title: Muscle taken at slaughter, M_1130


title: mutant-batch-2-rep-4

description: Gene expression data from mutant-batch-2-rep-4


title: mutant-batch-1-rep-3

description: Gene expression data from mutant-batch-1-rep-3


title: X6055432155_R03C02_genomic DNA from whole blood_array

description: Family 9 monozygotic twin 1

value: Family 9 monozygotic twin 1


title: mutant-batch-1-rep-2

description: Gene expression data from mutant-batch-1-rep-2


title: X6042316146_R04C02_genomic DNA from whole blood_array

description: Family 11 monozygotic twin 1

value: Family 11 monozygotic twin 1


title: X6057825006_R02C01_genomic DNA from whole blood_array

description: Family 4 monozygotic twin 2

value: Family 4 monozygotic twin 2


title: Muscle taken at slaughter, M_1126


title: mutant-batch-1-rep-1

description: Gene expression data from mutant-batch-1-rep-1


title: Muscle taken at slaughter, M_1125


title: X6042308068_R02C02_genomic DNA from whole blood_array

description: Family 9 monozygotic twin 2

value: Family 9 monozygotic twin 2

value: Female


title: wild type-batch-4-rep-12

description: Gene expression data from wild type-batch-4-rep-12

source_name: wild type-batch-4-rep-12

value: DAH wild type


title: Muscle taken at slaughter, M_1114


title: Muscle taken at slaughter, M_1115


title: Muscle taken at slaughter, M_1117


title: Muscle taken at slaughter, M_1123


title: X6055432140_R02C01_genomic DNA from whole blood_array

description: Family 6 monozygotic twin 2

source_name: whole blood

value: Family 6 monozygotic twin 2


title: X6042316074_R06C02_genomic DNA from whole blood_array

description: Family 8 monozygotic twin 2

value: Family 8 monozygotic twin 2


title: X6055432089_R03C02_genomic DNA from whole blood_array

description: Family 7 monozygotic twin 2

value: Family 7 monozygotic twin 2


title: Muscle taken at slaughter, M_1106


title: Muscle taken at slaughter, M_1112


title: Muscle taken at slaughter, M_1109


title: Muscle taken at slaughter, M_1088


title: Muscle taken at slaughter, M_1092


title: Muscle taken at slaughter, M_1086


title: X6055432120_R05C02_genomic DNA from whole blood_array

description: Family 6 monozygotic twin 1

value: Family 6 monozygotic twin 1


title: Muscle taken at slaughter, M_1105


title: X6055432102_R05C02_genomic DNA from whole blood_array

description: Family 5 monozygotic twin 1

value: Family 5 monozygotic twin 1


title: Muscle taken at slaughter, M_1135


title: X6055432099_R06C02_genomic DNA from whole blood_array

description: Family 5 monozygotic twin 2

value: Family 5 monozygotic twin 2


title: X6042316145_R03C01_genomic DNA from whole blood_array

description: Family 3 monozygotic twin 2

value: Family 3 monozygotic twin 2


title: mutant-batch-2-rep-5

description: Gene expression data from mutant-batch-2-rep-5

value: DAH motility mutant


title: X6057825005_R05C02_genomic DNA from whole blood_array

description: Family 4 monozygotic twin 1

value: Family 4 monozygotic twin 1


title: Muscle taken at slaughter, M_1071

value: crossbreed Pix(DLxDE)

value: muscle


title: Muscle taken at slaughter, M_1080


title: Muscle taken at slaughter, M_1074


title: Muscle taken at slaughter, M_1072


title: Muscle taken at slaughter, M_1083


title: Muscle taken at slaughter, M_1082


title: Muscle taken at slaughter, M_1075


title: Muscle taken at slaughter, M_1079


title: Muscle taken at slaughter, M_1068


title: Muscle taken at slaughter, M_1066


title: Muscle taken at slaughter, M_726


title: Muscle taken at slaughter, M_759


title: X6042316131_R06C02_genomic DNA from whole blood_array

description: Family 3 monozygotic twin 1

value: Family 3 monozygotic twin 1


title: Muscle taken at slaughter, M_1073


title: Muscle taken at slaughter, M_1070


title: Muscle taken at slaughter, M_708


title: Muscle taken at slaughter, M_725


title: Muscle taken at slaughter, M_711


title: Muscle taken at slaughter, M_706


title: Muscle taken at slaughter, M_710


title: Muscle taken at slaughter, M_728


title: Muscle taken at slaughter, M_705


title: Muscle taken at slaughter, M_704


title: Muscle taken at slaughter, M_695


title: Muscle taken at slaughter, M_693


title: Muscle taken at slaughter, M_675


title: Muscle taken at slaughter, M_659


title: Muscle taken at slaughter, M_598


title: Muscle taken at slaughter, M_596


title: Muscle taken at slaughter, M_594


title: Muscle taken at slaughter, M_587


title: Muscle taken at slaughter, M_586


title: Muscle taken at slaughter, M_1120


title: Muscle taken at slaughter, M_592


title: Muscle taken at slaughter, M_635


title: Muscle taken at slaughter, M_622


title: Muscle taken at slaughter, M_614


title: Muscle taken at slaughter, M_615


title: Muscle taken at slaughter, M_624


title: Muscle taken at slaughter, M_628


title: Muscle taken at slaughter, M_629


title: Muscle taken at slaughter, M_580


title: X6042316145_R05C01_genomic DNA from whole blood_array

description: Family 2 monozygotic twin 2

value: Family 2 monozygotic twin 2


title: Muscle taken at slaughter, M_573


title: Muscle taken at slaughter, M_604


title: Muscle taken at slaughter, M_579


title: Muscle taken at slaughter, M_575


title: Muscle taken at slaughter, M_568


title: X6042316131_R03C02_genomic DNA from whole blood_array

description: Family 2 monozygotic twin 1

value: Family 2 monozygotic twin 1


title: Muscle taken at slaughter, M_571


title: Muscle taken at slaughter, M_551


title: Muscle taken at slaughter, M_559


title: Muscle taken at slaughter, M_543


title: Muscle taken at slaughter, M_600


title: Muscle taken at slaughter, M_545


title: Muscle taken at slaughter, M_557


title: Muscle taken at slaughter, M_560


title: Muscle taken at slaughter, M_447


title: Muscle taken at slaughter, M_478


title: Muscle taken at slaughter, M_484


title: Muscle taken at slaughter, M_474


title: Muscle taken at slaughter, M_443


title: Muscle taken at slaughter, M_476


title: Muscle taken at slaughter, M_489


title: Muscle taken at slaughter, M_482


title: Muscle taken at slaughter, M_497


title: Muscle taken at slaughter, M_485


title: Muscle taken at slaughter, M_438


title: Muscle taken at slaughter, M_428


title: Muscle taken at slaughter, M_425


title: Muscle taken at slaughter, M_424


title: Muscle taken at slaughter, M_419


title: Muscle taken at slaughter, M_421


title: Muscle taken at slaughter, M_423


title: Muscle taken at slaughter, M_418


title: Muscle taken at slaughter, M_475


title: Muscle taken at slaughter, M_499


title: Muscle taken at slaughter, M_510


title: Muscle taken at slaughter, M_530


title: Muscle taken at slaughter, M_538


title: Muscle taken at slaughter, M_536


title: Muscle taken at slaughter, M_541


title: Muscle taken at slaughter, M_542


title: Muscle taken at slaughter, M_532


title: A549_non-invasive_7_biological rep2

city: Kuala Lumpur

first: ho

middle: chai

last: san

state: Wilayah Persekutuan

address: Jalan Universiti

department: Department of Genetics and Molecular Biology

country: Malaysia

institute: University of Malaya

description: miRNA expression data from low invasive A549 non-small cell lung adenocarcinoma

hyb_protocol: 100.0μl biotin-labeled RNA were hybridized on GeneChip® miRNA array for 16 hours at 48°c in Affymetrix Hybridization Oven 640. GeneChips were washed and stained with GeneChip Fluidics Station 450 using fluidics script FS450_0003 program.

scan_protocol: GeneChips were scanned with GeneChip® scanner 3000 7G and digitized using GeneChip Operating Software (GCOS) and GeneChip Command Console Software (AGCC) v3.0.1. Raw data extracted from the scanned images were quality checked using Affymetrix miRNA QC Tool Software v1.0.33.0.

data_processing: MiRNA microarray raw CEL file format data were imported into Partek Genomic v6.4 using default parameters including robust-multichip average (RMA) for data normalization between triplicate samples, which includes background adjustments, normalization and summarization. Statistical analysis was performed using Analysis of Variance (ANOVA) approach. The differentially expressed miRNAs were filtered with p-value ≤ 0.05 and fold change ≥ 2.00, between high invasiveness and low invasiveness A549 cells.

source_name: A549 non-small cell lung adenocarcinoma, low invasive

label_protocol: Biotinylated RNA were prepared from 1.5μg total RNA. 4.0μl 5x FlashTag Ligation Mix Biotin and 2.0μl T4 DNA Ligase were added into the poly (A) tailed RNA tube. The mixture was incubated at room temperature for 30 minutes. 2.5μl Stop Solution was added.

growth_protocol: Cells were maintained in T-25 culture flasks containing RPMI 1640 culture medium supplemented with 10.0% (v/v) FBS. They were incubated at 37°c in 5.0% carbon dioxide incubator with 95.0% humidity and pH 7.0-7.6.

extract_protocol: Total RNA were extracted using Qiagen miRNeasy mini kit according to manufacturer's instructions.

treatment_protocol: Spent media were discarded and washed with 5.0ml 1x PBS. 1.0ml 0.1% (v/v) trypsin-0.53mM EDTA was added and incubated at 37°c for 10 minutes. 2.0ml culture media with 10.0% (v/v) FBS were added. Cells were centrifuged for 10 minutes and flicked thoroughly.

tag: cell line

value: A549 lung adenocarcinoma


title: A549_non-invasive_7_biological rep1


title: Muscle taken at slaughter, M_409


title: Muscle taken at slaughter, M_403


title: Muscle taken at slaughter, M_413


title: Muscle taken at slaughter, M_415


title: Muscle taken at slaughter, M_393


title: Muscle taken at slaughter, M_405


title: Muscle taken at slaughter, M_391


title: Muscle taken at slaughter, M_392


title: A549_invasive_7_biological rep2

description: miRNA expression data from high invasive A549 non-small cell lung adenocarcinoma

source_name: A549 non-small cell lung adenocarcinoma, high invasive


title: A549_non-invasive_7_biological rep3


title: A549_invasive_7_biological rep1


title: Muscle taken at slaughter, M_386


title: Muscle taken at slaughter, M_388


title: A549_invasive_7_biological rep3


title: Muscle taken at slaughter, M_375


title: Muscle taken at slaughter, M_376


title: Muscle taken at slaughter, M_380


title: Muscle taken at slaughter, M_378


title: Muscle taken at slaughter, M_364


title: 9341927023_A [Atf3]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Partek Genomic Suite.

organism: Mus musculus

source_name: Carotid artery ATF3 KO PBS

label_protocol: please see Material and Methods section

growth_protocol: Bone marrow-derived macrophages (BMDMs) were obtained by culturing bone marrow cells from 6 to 8 week old wildtype C57BL/6 mice in DMEM supplemented with 10% FCS, 10 mg ml-1 Ciprobay-500 and 40 ng ml-1 M-CSF (R & D Systems).

extract_protocol: please see Material and Methods section

treatment_protocol: BMDMs of wt mice were pretreated for 6 h with HDL (2 mg ml-1 ) then stimulated with CpG (100 nM) for 4 h. Further wild type or Atf3-deficient BMDMs were pretreated with 2 mg ml-1 HDL for 6 h and subsequently stimulated with CpG (100 nM) or P3C (50 ng ml-1) for 4 h.

tag: strain

tag: genotype

tag: treatment

value: carotid injury - 3 h later PBS

tag: stimulation period


title: 9341927023_F [WT]

source_name: Carotid artery WT PBS

value: WT


title: 9322863039_F [Atf3]


title: 9341927023_C [WT]


title: Muscle taken at slaughter, M_367


title: 9341927023_D [WT+HDL]

source_name: Carotid artery WT HDL

value: carotid injury - 3 h later HDL (20mg/kg)


title: Muscle taken at slaughter, M_368


title: 9341927023_B [WT+HDL]


title: 9322863039_C [WT]


title: 9322863039_E [Atf3+HDL]

source_name: Carotid artery ATF3 KO HDL


title: 9322863039_B [WT+HDL]


title: Muscle taken at slaughter, M_361


title: Muscle taken at slaughter, M_360


title: Muscle taken at slaughter, M_358


title: Muscle taken at slaughter, M_343


title: Muscle taken at slaughter, M_354


title: 9322863039_D [Atf3]


title: 9341927023_E [Atf3+HDL]


title: Muscle taken at slaughter, M_346


title: 8784129081_F [CpG]

description: Fig 4; Supp Fig 13

source_name: BMDM

tag: differentiation

value: 6d M-CSF

value: CpG 0.1uM

tag: condition

value: CpG


title: Muscle taken at slaughter, M_335


title: 8784129081_C [HDL]

description: Fig 4; Supp Fig 13

value: HDL 2mg/ml

value: HDL


title: 8784129081_E [con]

description: Fig 4; Supp Fig 13

value: con


title: 8784129081_D [HDL+P3C]

description: Fig 4; Supp Fig 13

value: HDL 2mg/ml + P3C 50ng/ml


title: Muscle taken at slaughter, M_333


title: 9322863039_A [Atf3+HDL]


title: Muscle taken at slaughter, M_326


title: Muscle taken at slaughter, M_328


title: Muscle taken at slaughter, M_324


title: Muscle taken at slaughter, M_325


title: Muscle taken at slaughter, M_322


title: 8784129081_B [P3C]

description: Fig 4; Supp Fig 13

value: P3C 50ng/ml


title: 8784129020_D [HDL+CpG]

description: Fig 4; Supp Fig 13

value: HDL 2mg/ml + CpG 0.1uM

value: HDL+CpG


title: 8784129020_E [HDL+P3C]

description: Fig 4; Supp Fig 13


title: 8784129081_A [HDL+P3C]

description: Fig 4; Supp Fig 13


title: 8784129020_B [HDL]

description: Fig 4; Supp Fig 13


title: 8784129020_F [HDL]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_319

value: crossbreed Pix(DLxDE)

value: muscle


title: 8784129020_C [CpG]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_309


title: Muscle taken at slaughter, M_311


title: Muscle taken at slaughter, M_307


title: Muscle taken at slaughter, M_315


title: Muscle taken at slaughter, M_305


title: Muscle taken at slaughter, M_303


title: Muscle taken at slaughter, M_306


title: Muscle taken at slaughter, M_262


title: 8784129010_D [HDL+P3C]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_288


title: 8784129020_A [P3C]

description: Fig 4; Supp Fig 13


title: 8784129010_C [P3C]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_261


title: 8784129010_F [P3C]

description: Fig 4; Supp Fig 13


title: 8784129010_A [CpG]

description: Fig 4; Supp Fig 13


title: 8784129004_E [HDL+CpG]

description: Fig 4; Supp Fig 13


title: DDC 24h biological replicate 2

city: Southampton

first: Marta

middle: Ewa

last: Polak

state: Hampshire

address: Southampton General Hospital, Mailpoint 813, LE59,

department: Clinical and Experimental Sciences

institute: University of Southampton

description: gene expression data from primary human skin DCs

hyb_protocol: hybridisation was carried out according to the standard Affymetrix protocol

scan_protocol: gene expression analysis was carried out using the Human Genome U-219 Affymetrix platform by ARK-Genomics Centre, The Roslin Institute, Edinburgh.

data_processing: Expression data were normalised using the Robust Multichip Average (RMA) package

source_name: human skin donor 2

growth_protocol: human skin epidermal and dermal dendritic cells were isolated by 48h migration followed by density gradient centrifugation on the Optiprep density gradient media (Axis Shield), followed by purification with CD1a (Langerhans cells) and CD11c (dermal dendritic cells) magnetic beads (MIltenyi Biotech)

extract_protocol: RNA was isolated using RNeasy mini kits (Qiagen, UK) as per the manufacturer’s protocol. RNA concentration and integrity was determined with an Agilent Bioanalyser (RIN of 7.0 or above)

treatment_protocol: human skin migratory CD1a+ LCs and CD11c+ DDCs were stimulated in culture with 25ng/ml of TNF-α for 0, 2, 8 and 24h (250,000 cell per time point). Harvested cells were cryopreserved at -80C in RLT buffer (Qiagen, UK) + 1% β-mercaptoethanol

value: dermis

tag: time

value: TNF-alpha


title: 8784129004_C [CpG]

description: Fig 4; Supp Fig 13


title: DDC 24h biological replicate 3

source_name: human skin donor 3


title: 8784129010_E [HDL+CpG]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_259


title: 8784129010_B [HDL+CpG]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_247


title: Muscle taken at slaughter, M_294


title: 8784129004_F [HDL+CpG]

description: Fig 4; Supp Fig 13


title: LC 24h biological replicate 3

value: epidermis


title: Muscle taken at slaughter, M_241


title: Muscle taken at slaughter, M_245


title: DDC 24h biological replicate 1

source_name: human skin donor 1


title: 8784129004_B [HDL]

description: Fig 4; Supp Fig 13

value: WT


title: 8784129004_D [CpG]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_240


title: LC 24h biological replicate 2


title: Muscle taken at slaughter, M_321


title: Muscle taken at slaughter, M_232


title: 8615616023_F [con]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_229


title: Muscle taken at slaughter, M_218


title: Muscle taken at slaughter, M_227


title: Muscle taken at slaughter, M_221


title: 8784129004_A [HDL]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_216


title: DDC 8h biological replicate 3


title: Muscle taken at slaughter, M_215


title: 8615616023_D [HDL+P3C]

description: Fig 4; Supp Fig 13


title: 8615616023_B [HDL+P3C]

description: Fig 4; Supp Fig 13


title: 8615616023_C [P3C]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_214


title: Muscle taken at slaughter, M_206


title: Muscle taken at slaughter, M_208


title: 8615616023_E [P3C]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_200


title: LC 24h biological replicate 1


title: DDC 8h biological replicate 2


title: Muscle taken at slaughter, M_198


title: Muscle taken at slaughter, M_204


title: 8615616023_A [con]

description: Fig 4; Supp Fig 13


title: DDC 8h biological replicate 1


title: LC 8h biological replicate 1


title: LC 8h biological replicate 2


title: Muscle taken at slaughter, M_195


title: Muscle taken at slaughter, M_191


title: Muscle taken at slaughter, M_194


title: DDC 2h biological replicate 3


title: LC 8h biological replicate 3


title: Muscle taken at slaughter, M_185


title: Muscle taken at slaughter, M_186


title: 8615616020_F [HDL]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_193


title: DDC 2h biological replicate 2


title: 8615616020_E [con]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_184


title: 8615616020_C [CpG]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_180


title: LC 2h biological replicate 3


title: Muscle taken at slaughter, M_171


title: Muscle taken at slaughter, M_115


title: Muscle taken at slaughter, M_176


title: Muscle taken at slaughter, M_109


title: 8615616020_D [con]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_104


title: LC 2h biological replicate 2


title: Muscle taken at slaughter, M_93


title: Muscle taken at slaughter, M_108


title: Muscle taken at slaughter, M_52


title: DDC 2h biological replicate 1


title: 8615616020_B [HDL+CpG]

description: Fig 4; Supp Fig 13


title: Muscle taken at slaughter, M_51


title: LC 2h biological replicate 1


title: Muscle taken at slaughter, M_50


title: DDC at T0 biological rep3a


title: 7911819006_D [Control]

description: Fig 3; Supp Fig 8, 9

value: Control


title: DDC at T0 biological rep3b


title: 7911819006_F [HDL + CpG]

description: Fig 3; Supp Fig 8, 9

value: 6d M-CSF

value: HDL + CpG


title: 7911819006_B [CpG]

description: Fig 3; Supp Fig 8, 9

value: CpG 0.1uM

value: CpG


title: Muscle taken at slaughter, M_48


title: 7911819006_E [HDL]

description: Fig 3; Supp Fig 8, 9

value: HDL 2mg/ml

value: HDL


title: Muscle taken at slaughter, M_63


title: Muscle taken at slaughter, M_42


title: DDC at T0 biological rep2a


title: Muscle taken at slaughter, M_49


title: DDC at T0 biological rep2b


title: 7911819006_A [HDL]

description: Fig 3; Supp Fig 8, 9


title: 7911819006_C [HDL + CpG]

description: Fig 3; Supp Fig 8, 9


title: Muscle taken at slaughter, M_29


title: Muscle taken at slaughter, M_38


title: Muscle taken at slaughter, M_20


title: Muscle taken at slaughter, M_45


title: Muscle taken at slaughter, M_39


title: LC at T0 biological rep3b


title: Muscle taken at slaughter, M_16


title: 8615616020_A [con]

description: Fig 4; Supp Fig 13

value: con


title: Muscle taken at slaughter, M_14


title: 7911798003_D [CpG]

description: Fig 3; Supp Fig 8, 9


title: 7911798003_F [CpG]

description: Fig 3; Supp Fig 8, 9


title: DDC at T0 biological rep1a


title: 7911798003_C [Control]

description: Fig 3; Supp Fig 8, 9


title: 7911798003_E [Control]

description: Fig 3; Supp Fig 8, 9


title: LC at T0 biological rep1a


title: LC at T0 biological rep2a


title: LC at T0 biological rep1b


title: KT2440(pCAR1DpmrDpnd)

status: Public on Dec 07 2013

city: Tokyo

first: Hideaki

last: Nojiri

address: 1-1-1 Yayoi, Bunkyo-ku

department: Biotechnology Research Center

country: Japan

institute: The University of Tokyo

description: This is an Affymetrix custom-commercial tiling array that covers the Pseudomonas putida KT2440 chromosome (RefSeq: NC_002947) at 11-bp density. BPMAP files are provided as supplementary files. KT2440b520511FR-3.bpmap represents  the forward strand of KT2440 chromosome, and KT2440b520511FF-3.bpmap represents the reverse strand of KT2440 chromosome.

hyb_protocol: Labeled cDNA was mixed with 50 pM control oligonucleotide B2 (Affymetrix), 1× Hybridization Mix (Affymetrix), and 7% DMSO in a total volume of 200 µl and denatured at 95˚C for 5 min. Per array, 200 µl of the hybridization cocktail was hybridized at 50˚C for 16 h with a rotation rate of 60 rpm using a GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained using a Hybridization, Wash, and Stain Kit (Affymetrix) according to the the modified FleX450-0005 protocol (for chromosomal tiling array, changed temperature of ‘the Post Hyb Wash #2” to 50˚C) of GeneChip Fluidics station 450 (Affymetrix).

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment. The intensities were linearly scaled so that the median was 100. Each CEL file was converted into the BAR files using KT2440b520511FR-3.bpmap for the forward strand and KT2440b520511FF-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of KT2440 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.

organism: Pseudomonas putida

source_name: cDNA prepared from succinate culture of KT2440(pCAR1DpmrDpnd)

label_protocol: Single-strand cDNA was synthesized in 60 µl of 1× First Strand Buffer (Invitrogen, Carlsbad, CA) containing 12  µg of total RNA, 360ng of actinomycin D (A1410, SIGMA, St.Louis, USA), 750 ng of random primers (Invitrogen), 1500 units of SuperScript II (Invitrogen), 60 units of RNaseOUT (Invitrogen), 10 mM DTT (Invitrogen), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.4 mM dTTP, and 0.1 mM dUTP (Roche Applied Science, Mannheim, Germany). After the RNA and random primers were denatured at 70˚C for 10 min and annealed at 25˚C for 10 min, the remaining reagents were added, and the reaction mixture was then incubated at 25˚C for 10 min, 37˚C for 60 min, 42˚C for 60 min, and 70˚C for 10 min. After cDNA synthesis, template RNA was degraded with one-third volume of 1N NaOH at 65˚C for 30 min; one-third volume of 1N HCl was added to neutralize the reaction mixture before cleanup. The cDNA was purified using a QIAquick PCR Purification Kit (Qiagen). The cDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). The purified single-stranded cDNA (~3.3 µg) was fragmented in 48 µl of 1× cDNA Fragmentation Buffer containing 15 units of Uracil DNA Glycosylase (UDG) and 225 units of Apurinic/apyrimidinic Endonuclease 1 (APE1) at 37˚C for 60 min, and incubated at 93˚C for 2 min. The fragmented cDNA was labeled in 60 µl of 1× TdT Buffer containing 60 units of Terminal Deoxynucleotidyl Transferase (TdT) and 0.083 mM GeneChip DNA Labeling Reagent at 37˚C for 60 min, and incubated at 70˚C for 2 min.

growth_protocol: Each strain was grown in 5 ml of LB at 300 strokes/min for 14-14.5 h (pre-culture) and then washed and transferred into 100-ml of NMM-4 buffer (Miyakoshi et al. Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 2007 Oct;189(19):6849-60. PMID: 17675379) supplemented with 0.1% succinate adjusting its turbidity (600 nm) at 0.05. The resultant culture was incubated on a rotary shaker at 120 rpm and cell growth was monitored in by measuring its turbidity (600 nm).

extract_protocol: Cells were treated with RNA Protect Bacteria reagent (Qiagen, CA, USA) to stabilize RNA of them.Total RNA was extracted using NucleoSpin RNA II (Macherey-Nagel GmbH & Co. KG, Düren, Germany). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI) at 37˚C for 30 min. After inactivation of DNase by the addition of the provided stop reagent and subsequent incubation at 65˚C for 10 min, total RNA was repurified using NucleoSpin RNA Clean-up (Macherey-Nagel).


title: KT2440(pCAR1DpmrDphu)

source_name: cDNA prepared from succinate culture of KT2440(pCAR1DpmrDphu)


title: LC at T0 biological rep3a


title: KT2440(pCAR1Dphu)

source_name: cDNA prepared from succinate culture of KT2440(pCAR1Dphu)


title: KT2440(pCAR1Dpnd)

source_name: cDNA prepared from succinate culture of KT2440(pCAR1Dpnd)


title: LC at T0 biological rep2b


title: KT2440(pCAR1Dpnd)

description: This is an Affymetrix custom-commercial tiling array that covers the IncP-7 carbazole-degradative plasmid pCAR1  (RefSeq: NC_004444.1) at 9-bp density. BPMAP files are provided as supplementary files. pCAR1_8b520435FR-3.bpmap represents  the forward strand of pCAR1, and pCAR1_8b520435FF-3.bpmap represents the reverse strand of pCAR1.

data_processing: The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.

label_protocol: Single-strand cDNA was synthesized in 60 µl of 1× First Strand Buffer (Invitrogen, Carlsbad, CA) containing 12 µg of total RNA, 360ng of actinomycin D (A1410, SIGMA, St.Louis, USA), 750 ng of random primers (Invitrogen), 1500 units of SuperScript II (Invitrogen), 60 units of RNaseOUT (Invitrogen), 10 mM DTT (Invitrogen), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.4 mM dTTP, and 0.1 mM dUTP (Roche Applied Science, Mannheim, Germany). After the RNA and random primers were denatured at 70˚C for 10 min and annealed at 25˚C for 10 min, the remaining reagents were added, and the reaction mixture was then incubated at 25˚C for 10 min, 37˚C for 60 min, 42˚C for 60 min, and 70˚C for 10 min. After cDNA synthesis, template RNA was degraded with one-third volume of 1N NaOH at 65˚C for 30 min; one-third volume of 1N HCl was added to neutralize the reaction mixture before cleanup. The cDNA was purified using a QIAquick PCR Purification Kit (Qiagen). The cDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). The purified single-stranded cDNA (~3.3 µg) was fragmented in 48 µl of 1× cDNA Fragmentation Buffer containing 15 units of Uracil DNA Glycosylase (UDG) and 225 units of Apurinic/apyrimidinic Endonuclease 1 (APE1) at 37˚C for 60 min, and incubated at 93˚C for 2 min. The fragmented cDNA was labeled in 60 µl of 1× TdT Buffer containing 60 units of Terminal Deoxynucleotidyl Transferase (TdT) and 0.083 mM GeneChip DNA Labeling Reagent at 37˚C for 60 min, and incubated at 70˚C for 2 min.


title: KT2440(pCAR1DpmrDpnd)


title: 7166151005_A [HDL + CpG]

description: Fig 3; Supp Fig 8, 9


title: KT2440(pCAR1DpmrDphu)


title: KT2440(pCAR1Dpmr)

source_name: cDNA prepared from succinate culture of KT2440(pCAR1Dpmr)


title: 7166151005_F [HDL]

description: Fig 3; Supp Fig 8, 9


title: Normal thyroid, fresh-frozen, biological rep2

city: Lisboa

first: Branca

middle: Maria

last: Cavaco

address: Rua Prof. Lima Basto

department: Unidade de Investigação de Patobiologia Molecular (UIPM)

country: Portugal

institute: Instituto Português de Oncologia de Lisboa Francisco Gentil (IPOLFG)

hyb_protocol: Labelling, hybridization and scanning protocols were done in a certified Affymetrix Core Facility at Instituto Gulbenkian de Ciência (Oeiras, Portugal)

data_processing: The data were analyzed with DNA-Chip Analyzer (dChip) 2010.01 software. Arrays were normalized with the invariant set normalization method and gene-level expression was determined by summarizing the multiple probes across the gene (median of 26 probes per gene) into a single gene level-probe set expression, using model-based expression analysis with perfect match-only model.

source_name: fresh-frozen normal thyroid tissue from contralateral lobe of thyroid tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

extract_protocol: Total RNA was extracted and purified using the RNeasy Mini kit (Quiagen) according to the manufacturer’s instructions.

tag: gender

value: female

tag: age at diagnosis (yrs)

tag: tissue type

value: normal thyroid


title: KT2440(pCAR1)

source_name: cDNA prepared from succinate culture of KT2440(pCAR1)


title: ATC, fresh-frozen, biological rep3

scan_protocol: Labelling, hybridization and scanning protocols were done in a certified Affymetrix Core Facility at Instituto Gulbenkian de Ciência (Oeiras, Portugal)

source_name: fresh-frozen ATC

value: anaplastic thyroid carcinomas (ATC)


title: Muscle taken at slaughter, M_19

source_name: muscle, mean end weight of 110 kg

value: crossbreed Pix(DLxDE)


title: KT2440(pCAR1Dpmr)


title: Normal thyroid, fresh-frozen, biological rep3


title: KT2440(pCAR1Dphu)


title: Normal thyroid, fresh-frozen, biological rep1


title: Normal thyroid, commercial RNA pool

source_name: Commercial total RNA pool of normal thyroid tissues

value: female/male (pooled)


title: ATC, fine-needle aspiration biopsy, biological rep4

source_name: fine-needle aspiration biopsy ATC


title: ATC, fine-needle aspiration biopsy, biological rep5

value: male


title: nitrogen(-)/nitrogen(+)

city: Tsukuba

first: Myco

last: Umemura

state: Ibaraki

address: Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description:
The values are log2(nitrogen(-)/nitrogen(+)) ratio after dye swap and normalized as a pair of files.
nitrogen(-)_Cy3(070713-1s.gpr), nitrogen(-)_Cy5(070713-2s.gpr)
nitrogen(+)_Cy5(070713-1s.gpr), nitrogen(+)_Cy3(070713-2s.gpr)

hyb_protocol: Mixture of the labeled probes was re-suspended in a 60 uL of hybridization solution prepared by mixing 10.2 uL of 20xSSC, 21 uL of formamide, 0.6 uL of salmon testes, 1.8 uL of 10% SDS, and 26.4 uL of distilled water. After heat denaturation at 95C for 5 min and incubation at room temperature for 30 min, the labeled-cDNA mixture was applied onto the 11 K A. oryzae oligonucleotide microarrays (Fermlab, Tokyo, Japan) (http://www.fermlab.com/). After hybridization at 42C for 15 h, the array slide was washed at room temperature using the slide washer SW-4 (Juji Field, Tokyo, Japan) in a solution containing 2xSSC and 0.03% SDS for 15 min, then in a solution containing 0.2xSSC for 5 min, and finally in a solution containing 0.05xSSC for 5 min. The remaining buﬀer was dried up with air.

scan_protocol: The acquired microarray images were analyzed with GenePix Pro 6.0 (Axon Instruments at Molecular Devices). Duplicated measurements were performed for each sample using the dye-swap  method for determining the average. It should be noted that gene expression was compared based on two disparate culture conditions and the average fluorescence intensities for the two dyes were adjusted to be nearly identical, therefore that the total amount of mRNA per cell was different. After automatic segmentation of the spots, subtracting the local background, and calculating the ratio between the two fluorescence intensities, the reliability for each gene expression was evaluated using two DNA microarray slides from the dye-swap experiment according to the software’s instructions.

data_processing:
The resulting data file was analyzed using the R package (R Development Core Team) and Bioconductor. Data was normalized by setting the baseline measurement per spot and per segment of the chip via intensity dependent (LOESS) normalization using the marray module. Duplicated data files generated by the dye-swap experiment for an individual test were merged using the limma module. NA values were calculated according to the default setting of R modules.  The evaluated values were also NA when the flag values from GenePix Pro were negative.  Note that NA values are represented as 'null' in the Sample data table below.
Two values concerning expression level and induction for each gene were obtained for each experiment using a two-color platform.  The value is the logarithmic induction ratio (M-value) defined as log 2 (Value1) / log 2 (Value2), where Value1 and Value2 are normalized intensities for each transcript under the KA-producing and the KA-non-producing conditions, respectively.

organism: Aspergillus oryzae

source_name: nitrogen(-)

label_protocol: Approximately one microgram of mRNA determined by the absorbance at 260 nm was subjected to labeling with Cy3-dUTP for reference RNA or Cy5-dUTP for experimental RNA with CyScribe cDNA Post Labeling Kit (GE Healthcare, Buckinghamshire, UK) according to the manufacturer’s instruction. The labeled complementary DNA (cDNA) was purified by CyScribe GFX Puriﬁcation Kit (GE Healthcare, Buckinghamshire, UK). The purified Cy3- and Cy5-labeled cDNA probes were mixed with an equal amount and dried up to a pellet using a vacuum pump in an Eppendorf tube.

growth_protocol: KA production of A. oryzae is usually observed within 3 to 4 days after inoculation, and stops with a small amount of sodium nitrate in the medium.  According to this, 10^5 conidia/mL were inoculated into the liquid medium (pH 6.0) contained 0.25% yeast extract, 0.1% K2HPO4, 0.05% MgSO4-7H2O, and 10% glucose, and cultured for 2, 4, or 7 days at 30°C, 180 rpm.  Nitrogen(-) and nitrogen(+) systems were cultured for 4 d, in the latter of which 0.1% sodium nitrate was added.

extract_protocol: Mycelia were ground in liquid nitrogen to a ﬁne powder, and approximately 3 g was mixed with 15 mL ISOGEN solution, followed by the addition of 3 mL chloroform. The mixture was left at room temperature for 3 min and centrifuged at 2300g for 20 min. The supernatant was transferred to a fresh tube and mixed with 7.5 mL isopropanol. The mixture was left at room temperature for 10 min and centrifuged at 2300g for 20 min. The pellet was dried and dissolved in 300 lL RNase-free water. mRNA was purified from approximately 200 lg total RNA using an OligotexTM-dT30 <Super> mRNA Purification kit (Takara, Shiga, Japan) according to the manufacturer’s instructions.

tag: culture protocol

value: nitrogen(-)

value: mycelia

source_name: nitrogen(+)

value: nitrogen(+)


title: 4d/2d

description:
The values are log2(4d/2d) ratio after dye swap and normalized as a pair of files.
4d_Cy3(070808-1s.gpr), 4d_Cy5(070808-2s.gpr)
2d_Cy5(070808-1s.gpr), 2d_Cy3(070808-2s.gpr)


title: 7d/4d

description:
The values are log2(7d/4d) ratio after dye swap and normalized as a pair of files.
7d_Cy3(070808-4s.gpr), 7d_Cy5(070808-3s.gpr)
4d_Cy5(070808-4s.gpr), 4d_Cy3(070808-3s.gpr)


title: ATC, fresh-frozen, biological rep1


title: ATC, fresh-frozen, biological rep2


title: 17 2h labelled rep2

city: Exeter

last: Penfield

address: Stocker Raod

department: Biosciences

institute: University or Exeter

description: 1.5mM 4SU added at 0h

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit standard protocol

scan_protocol: GeneChip® Scanner 3000, ACOS

data_processing: MAS 5.0

organism: Arabidopsis thaliana

source_name: 10 day old seedlings

label_protocol: Affymetrix GeneChip IVT labelling kit

growth_protocol: Plants were germinated at 22°C  for three days, grown at the experimental temperature for 7 days on 0.9% MS agar plates in 12 hour white light 12 hour dark cycles. Plants were floated on MS medium 12 hours before the expeimental start time (time 0h).

extract_protocol: RNA was extracted uding Qiagen Plant Rneasy mini kit

treatment_protocol: 1.5mM 4SU was added to indicated samples at time 0h.

value: whole seedlings floating on MS medium

tag: experimental temperature

value: 1.5mM 4SU added at 0h


title: drought acclimated plants dehydrated for 48h rep-2

city: Beijing

first: Xin

last: Deng

address: No.20 Nanxincun, Xiangshan

institute: Institute of Botany, the Chinese Academy of Science

hyb_protocol: 0.6 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 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) 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: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized using limma package of R.

organism: Dorcoceras hygrometricum

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Boea hygrometrica plants grown in a greenhouse (approximately 25°C, 16 h/8 h light period) with regular irrigation for 3 months were used for the treatments.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's

treatment_protocol: For rapid desiccation, fully hydrated plants were removed from the soil to Petri dishes and dried under 50% relative humidity and moderate illumination at 25°C for 2 h and 48 h in a climate chamber. For slow dehydration (SD), soil-grown plants were dehydrated in pot for 5 to 14 days until RWC decreased to less than 10%. For rehydration, SD14d-treated plants were re-watered for 3 days.

tag: tissue

value: euphylla


title: drought acclimated plants dehydrated for 48h rep-3


title: MIT9313 stress applications

city: Freiburg

first: Karsten

last: Voigt

address: Schänzlestr. 1

institute: University of Freiburg

description: Gene expression data from Prochlorococcus cells

hyb_protocol: Hybridization was performed according to Affymetrix protocols for E. coli (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) and (Steglich et al., 2006).

scan_protocol: Scanning was performed according to Affymetrix protocols for E. coli (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) and (Steglich et al., 2006).

data_processing: Microarray expression data of single probes were quantile-normalized using the R package LIMMA (Smyth 2005). The expression threshold value was individually evaluated for MED4 and MIT9313 and was set to 250 and 400, respectively.

organism: Prochlorococcus marinus str. MIT 9313

source_name: Prochlorococcus marinus MIT9313 cells treated with various stresses

label_protocol: Synthesis of complementary DNA (cDNA), labeling, hybridization, staining and scanning was carried out according to Affymetrix protocols for E.coli (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) with minor changes. Total RNA (2 µg) was denatured at 70 °C and annealed to random hexamer primers (25 ng/µl) at 25 °C for 10 min. The RNA was reverse transcribed to produce cDNA with Superscript II (25 U/µl – Invitrogen Life Technologies) and 0.5 mM dNTPs in the presence of 1 U/µl RNase Out RNase Inhibitor (Invitrogen). The mix was incubated at 25 °C for 10 min followed by 60 min incubations at 37 °C and 42 °C respectively. Superscript II was inactivated with a 10 min incubation at 70 °C. Sodium hydroxide (0.25 N) was used to remove RNA during a 30 min incubation at 65 °C, followed by neutralization with HCl. The cDNA was purified with MinElute PCR purification columns (Qiagen). Fragments of cDNA, 50-200 nt long, were produced from a 10 min incubation at 37 °C with DNase I (0.6 U per µg cDNA), followed by heat inactivation of the DNase I enzyme (10 min at 98 °C). The cDNA fragments were end-labeled with biotin using the BioArray Terminal Labeling Kit (Enzo) during a 60 min incubation at 37 °C. The reaction was stopped by freezing at –20 °C.

growth_protocol: Cells were grown at 22°C in AMP1 medium (Moore et al., 2007) under 10-30 µmol quanta m-2 s-1 continuous white cool light.

extract_protocol: Total RNA was extracted from the cells via filtration following the hot phenol method (Steglich et al., 2006) or a modified protocol using PGTX buffer.

treatment_protocol: The cells were subjected to several stress conditions for 30 min: light stress (light shifts from 10 µE to 100 µE or darkness, respectively, or from 30 µE to 300 µE) and temperature stress (shifts from 22°C to 12°C or 32°C, respectively). For nitrogen and iron starvation, the cells were washed twice in nitrogen- or iron-free medium and grown in minus N or minus Fe medium for 2, 3 or 6 days. Alternatively, iron depletion was induced via the addition of 0.6 µM DFB for 24 – 48 hours.

value: Prochlorococcus marinus str. MIT 9313


title: MIT9313 standard growth conditions -rRNA

source_name: Prochlorococcus marinus MIT9313 cells growing at standard growth conditons


title: fresh plants dehydrated for 14 days rep-1

description: fresh plants dehydrated for 14 days


title: drought acclimated plants dehydrated for 2h rep-1


title: drought acclimated plants dehydrated for 48h rep-1


title: drought acclimated plants dehydrated for 2h rep-2


title: MIT9313 standard growth conditions


title: drought acclimated plants dehydrated for 2h rep-3


title: DDC at T0 biological rep1b

source_name: human skin donor 1

value: dermis

value: TNF-alpha


title: fresh plants dehydrated for 14 days rep-2

description: fresh plants dehydrated for 14 days


title: plants rehydrated from drought acclimation rep-1


title: fresh plants dehydrated for 14 days rep-3

description: fresh plants dehydrated for 14 days


title: plants rehydrated from drought acclimation rep-2


title: plants rehydrated from drought acclimation rep-3


title: fresh plants dehydrated for 5 days rep-2

description: fresh plants dehydrated for 5 days


title: fresh plants dehydrated for 5 days rep-3

description: fresh plants dehydrated for 5 days


title: fresh plants dehydrated for 5 days rep-1

description: fresh plants dehydrated for 5 days


title: fresh plants dehydrated for 48h rep-3

description: fresh plants dehydrated for 48h

source_name: fresh plants dehydrated for 48h rep-3


title: fresh plants dehydrated for 48h rep-2

description: fresh plants dehydrated for 48h

source_name: fresh plants dehydrated for 48h rep-2


title: fresh plants dehydrated for 48h rep-1

description: fresh plants dehydrated for 48h

source_name: fresh plants dehydrated for 48h rep-1


title: Control 0h at NIES (Cy5)_Control 0h at ITF (Cy3)

first: RANDEEP

last: RAKWAL

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description: Dye-swap (Cy3/Cy5) of Cont 0h at ITF vs Control 0h at NIES

hyb_protocol: Agilent: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent Microarray scanner G2505C

data_processing: For detection of significantly differentially expressed genes between control and treatment, each slide image was processed by Agilent Feature Extraction Software (version 11.0.1.1). The program measures Cy3 and Cy5 signal intensities of whole probes. Dye-bias tends to be signal intensity dependent therefore the software selects probes using a set by rank consistency filter for dye-normalization. Said normalization was performed by LOWESS (locally weighted linear regression) that calculates the log ratio of dye-normalized Cy3- and Cy5-signals, as well as the final error of log ratio. The significance (P) value is based on the propagate error and universal error models. In this analysis, the threshold of significant differentially expressed genes was <0.01 (for the confidence that the feature was not differentially expressed). In addition, erroneous data generated due to artifacts were eliminated prior to data analysis using the software.

organism: Oryza sativa

source_name: Control 0h at ITF

label_protocol: Manual: Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Japonica-type rice (Oryza sativa L.) cv. Nipponbare was used as the test material. The seeds were received from National Institute for Environmental Sciences (NIES), Tsukuba, Japan. Rice seedlings were grown in the commercial soil (nursery soil for rice seedling growth and transplantation purchased from JA Zen-Noh, Japan; http//www.zennoh.or.jp/) with recommended NPK (nitrogen, phosphorus, and potash) doses at a controlled (25 °C, 70% relative humidity and natural light condition) greenhouse at NIES, Tsukuba, Japan during July, August, and September 2012.

extract_protocol: QIAGEN, RNeasy Plant Mini Kit

treatment_protocol: The experimental/treatment plot was at Iitate Farm (ITF) in Iitate village, Fukushima. A leveled ground was overlaid with a blue tarpaulin sheet in the designated area whose contamination level (ground137Cs) was on average - 700 kBq/m2, and emitting a constant dose of ~ 5 microSv/h. This area was defined as a low-level gamma field. Three cylindrical boxes were placed at a distance of 2 m apart, and shielded with a recently fabricated shielding material (Nihon Matai Co., Ltd., Moriyama, Shiga, Japan) to control the amount of radiation reaching inside the target area, namely rice seedlings at the center of the box. The effect of the shielding material around and below the boxes 1 (double shield, ~ 1.6 microSv/h: low dose) and 2 (single shield, ~ 2.6 microSv/h: middle dose) can be seen by the amount of gamma ray dose reaching inside. Box number 3 was not shielded and served as the high dose (~ 4.2 microSv/h) condition. The rice seedlings in three seedling cases were placed in the center of each box, and the gamma ray dose was recorded by two MYDOSE mini electronic pocket dosimeters placed near the 3rd fully opened leaf. Gamma ray exposure times were set at 6, 12, 24, 48, and 72 h after arrival at ITF, and the rice leaves at the 3rd position (from the base) from 6 to 10 seedlings were sampled, by cutting the 3rd leaf at the base of attachment to the sheath, for each dose (low, middle, and high). Post-cutting, the leaves were placed in an aluminum foil under dry ice followed by storing the samples in a deep freezer (-30 °C).

tag: cultivar

value: Nipponbare

tag: developmental stage

value: mature plant

source_name: Control 0h at NIES


title: Control 0h at NIES (Cy3)_Control 0h at ITF (Cy5)


title: MED4 stress applications

organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

source_name: Prochlorococcus marinus MED4 cells treated with various stresses


title: Control 0h at NIES (Cy5)_Control 72h at NIES (Cy3)

description: Dye-swap (Cy3/Cy5) of Cont 0h at ITF vs Control 72h at NIES

source_name: Control 72h at NIES


title: MED4 standard growth conditions

source_name: Prochlorococcus marinus MED4 cells growing at standard growth conditons

value: Prochlorococcus marinus subsp. pastoris str. CCMP1986


title: Control 0h at NIES (Cy3)_Control 72h at NIES (Cy5)


title: Control 0h at ITF (Cy3)_Low-Level Gamma ray 72h (Cy5)

description: Dye-swap (Cy3/Cy5) of Cont 0h at ITF vs Low-Level Gamma ray 72h

source_name: Low-Level Gamma ray 72h


title: control fresh plants rep-2

description: gene expression in controls

source_name: control fresh plants rep-2


title: OBD02 Leaf and stem

status: Public on Dec 06 2013

type: SRA

city: NEWARK

first: Dong-Hoon

last: Jeong

state: DE

address: 15 Innovation Way

institute: University of Delaware

description: small RNA

library_source: transcriptomic

data_processing:
The raw sequencing data was converted to SCARF format, trimmed of adapters, matched to the Brachypodium Genome 8X Assembly (ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Bdistachyon/)  by custom Perl scripts
Genome_build: 8X
Supplementary_files_format_and_content: Text containing distinct small RNAs or mRNAs with their raw abundance after removing the adapter sequences

organism: Brachypodium distachyon

source_name: Leaf and stem

growth_protocol: Brachypodium (Line Bd21) was used for all libraries. For the BDI small RNA and PARE libraries, seeds were germinated in soil and the plants were grown in a growth chamber at a constant 20°C, under a 20 h-light, 4 h-dark cycle. Leaf, stem, and panicle tissues were harvested from six-week old plants. Leaf tissue was the blade of first and second leaf from the top, not including the leaf sheath.  Stem tissue was harvested from just above the first top node to just below the second node, including both nodes as well as the leaf sheath of the second leaf.  Panicle tissue was harvested from plants with immature, unfertilized flowers from the tip of the spikelet to just above, but not including, the panicle node at approximately 10 h into the subjective day. To collect root tissue, seeds were husked, surface-sterilized with a 50% bleach solution, rinsed with sterile water, and germinated on half-strength Murashige and Skoog (MS) medium containing 0.2% (w/v) Phytagel in sterile plastic boxes. Root tissue was harvested from three-week old plants from the tip of the root to just below, but not including the seed. For the OBD set of small RNA libraries from tissues, Brachypodium plants were grown with supplemental light on a 16 h photoperiod at 25°C. For OBD02, leaf and stem tissues were collected at day 7-8, 14-15, and 27-28 and pooled. Panicle tissue was collected at day 28-35 at 4 time point intervals of 0700 (dawn), 1300, 1900, 0100 hours. For OBD03 seedlings, the following whole seedlings including roots were pooled. Two samples were soil grown under a 16 h photoperiod and tissues were collected from 3- and 4-day old plants. Two additional samples included 5-day old etiolated seedlings and light-grown seedlings grown on moistened filter paper.

extract_protocol:
Total RNAs were isolated using Trizol reagent (Molecular Research Center).
Small RNA libraries were constructed as previously described (Lu et al., 2007) and PARE libraries were constructed as described (German et al., 2008). All the libraries were sequenced on llumina IIGX analyzer. Sequencing was performed at Illumina or the Delaware Biotechnology Institute.

treatment_protocol: Stress treatments and controls except phosphate starvation and its control for BDI small RNA libraries were done using three-week old plants planted in soil under normal growth conditions with a 20 h photoperiod as above. Stresses began 5-6 h after the lights came on.  For heat stress, plants were moved to 40°C for 12 h.  For cold stress, plants were moved to 4°C in a cold room for 12 h.  For drought stress, plants were removed from the soil and rinsed, blotted dry with paper towels, and air-dried for 12 h.  For salt stress, the base of the plant pot was submerged in 300mM NaCl solution for 12 h to the depth of approximately 1 inch, not covering the soil.  For submergence stress, plants were fully submerged in 20°C water for 24 h.  For phosphate starvation stress, seeds were planted in MS media with KH2PO4 omitted, and control plants were planted in MS media; plants were harvested at three weeks, 5-6 h after lights on.  Control plants were sampled at the same time as the stress treatments. For OBD04, tissues from plants treated with abiotic, biotic, and mechanical stresses were pooled. For abiotic stress, leaves and stems were collected from plants subjected to heat (37°C), cold (4°C), salt (200 mM NaCl), and osmotic (300 mM Mannitol) treatments. For biotic stress, leaves were collected from plants with the following treatments: Bacterial treatments were (Pseudomonas fluorescens and Pseudomonas syringae pv. tomato DC3000 [Pto DC3000]) delivered to 28-29 day old Brachypodium leaves under vacuum at 1x107 cfu/mL. Leaves of four-week old plants were placed in a 1.5 ml microcentrifuge tube containing 20 µg/mL victorin. Tissue was harvested 24 h after treatment with victorin. Mechanical stress was applied by crushing the leaves of 29-30 day old plants with tweezers. Unless otherwise indicated, libraries were made from a pool of samples collected every 4 h after the stress began, i.e. 4h+8h+12h+16h+20h+24h.

value: leaf and stem

tag: plant line

value: untreated


title: control fresh plants rep-3

description: gene expression in controls

source_name: control fresh plants rep-3


title: BDI03 Drought-stressed shoot

description: small RNA

source_name: Shoot

value: shoot

value: drought


title: BDI01 Cold-stressed shoot

description: small RNA

value: cold


title: BDI06 Stem

description: small RNA

source_name: Stem

value: stem


title: BDI02 Shoot control for stress

description: small RNA


title: OBD04 Pooled Stresses

description: small RNA

value: Diverse stresses


title: BDI04 Leaf 1

description: small RNA

source_name: Leaf

value: leaf


title: fresh plants dehydrated for 2h rep-1

description: gene expression in fresh plants dehydrated for 2h

source_name: fresh plants dehydrated for 2h rep-1


title: fresh plants dehydrated for 2h rep-3

source_name: fresh plants dehydrated for 2h rep-3


title: Control 0h at ITF (Cy5)_Low-Level Gamma ray 72h (Cy3)


title: fresh plants dehydrated for 2h rep-2

source_name: fresh plants dehydrated for 2h rep-2


title: Seedling

description: small RNA

source_name: Seedling

value: seedling


title: control fresh plants rep-1

description: gene expression in controls

source_name: control fresh plants rep-1


title: Control 0h at ITF (Cy5)_Low-Level Gamma ray 6h (Cy3)

description: Dye-swap (Cy3/Cy5) of Cont 0h at ITF vs Low-Level Gamma ray 6h

source_name: Low-Level Gamma ray 6h

source_name: Control 0h at ITF


title: Control 0h at ITF (Cy3)_Low-Level Gamma ray 6h (Cy5)


title: OCI Ly3 nonSP rep2

city: Goettingen

first: Raphael

last: Koch

address: Robert Koch Str

department: Hematology

institute: University Medicine of Goettingen

description: non Side Population Cells

hyb_protocol: Biotinilated RNA was hybridized 16hrs at 45°C with rotation (60rpm) into individual Affymetrix Gene Human Assays 1.0 ST. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) according to GeneChip® Whole Transcript (WT) Sense Target Labeling Assay manual (Affymetrix) instructions.

scan_protocol: Microarrays were scanned in a GeneChip® Scanner 3000 7G (Affymetrix) and quality control was evaluated by Affymetrix software (Expression ConsoleTM)

data_processing: For microarray analysis quality control, quantile normalization and analysis of differentially expressed genes was performed using the software R. Differences in expression levels were considered significant in case of false discovery rate (fdr) < 0.05.

source_name: DLBCL Cell line OCI Ly3

label_protocol: 300ng of purified RNA were labelled with biotin according to the Affymetrix Gene Human Arrays 1.0 ST protocoll.

growth_protocol: Cells were cultured in IMDM-medium containing 20%FCS.

extract_protocol: RNA was isolated using QIAGEN® RNA Extraction Kit

treatment_protocol: Cells were stained using 10µg/ml of Hoechst33342. Incubation for 90min in 37°C. Afterwards washing twice in PBS.

tag: cell line

value: OCI Ly3

tag: phenotype

value: non-side population

tag: cell type

value: activated b-cell


title: OCI Ly3 SP rep2

description: Side Population Cells

value: side population


title: OCI Ly3 SP rep1

description: Side Population Cells


title: OCI Ly3 nonSP rep1

description: non Side Population Cells


title: Side Population rep1

hyb_protocol: 200 ng DNA was applied per BeadChip according to the manufacturer’s instructions.

scan_protocol: BeadChips were scanned using a Illumina Bead Array Reader®

data_processing: Initial data analysis was performed with the BeadStudio Methylation Module. DNA methylation values, described as beta values, were recorded for each locus in each sample. Only few CpG sites did not reveal reliable signals, as determined by their detection P-value, and were therefore excluded from further analysis. Raw data were quantile normalized. Statistical analysis and clustering by Euclidian distance was performed using the MultiExperiment Viewer (MeV, TM4)

label: biotin / DNP

label_protocol: After extraction of gDNA, bisulfite treatment was performed to convert the unmethylated cytosine into uracil. The bisulfite treated DNA is subjected to whole genome amplification (WGA) via random hexamer priming and Phi29 DNA polymerase, which has a proofreading activity resulting in error rates 100 times lower than the Taq polymerase. The products are then enzymatically fragmented, purified from dNTPs, primers and enzymes, and applied to the chip

growth_protocol: DLBCL Cell Line OCI Ly3 was cultured in IMDM medium containing 20% FCS.

extract_protocol: gDNA of Side Population and Non Side Population cells was extracted using Qiagen® DNA extraction Kit according to the manufacturer's instructions.

treatment_protocol: Cells were stained with 10µg/ml Hoechst33342 for 90min in 37°C. Afterwards cells were washed twice in PBS. FACS analysis showed a pattern of Side Population an Non Side Population cells whcih were sorted separately.

tag: dlbcl subtype

value: ABC


title: WM_K1

city: Gliwice

first: Magdalena

last: Olbryt

address: Wybrzerze AK 15

department: Center for Translational Research and Molecular Biology of Cancer

country: Poland

institute: Cancer Center and Institute of Oncology

description: WM793B melanoma cells cultured in control conditions (21% oxygen), biological replica 1

hyb_protocol: Following fragmentation, 16 μg of cRNA were hybridized for 16 hr at 45ºC on GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Arrays were scanned by GeneChip Scanner 3000 and the data was acquired using GCOS 1.2 software (Affymetrix).

data_processing: The CEL files were pre-processed using the GC-RMA algorithm available in R environment as the Bioconductor gcrma package.

source_name: control WM793B cells

label_protocol: Total RNA (5 μg) was used for synthesis of double stranded cDNA according to manufacturer's instructions. Half of the cDNA volume was used for synthesis of biotynylated cRNA with reagents recommended by Affymetrix.

growth_protocol: The human cancer cells were grown in CO2 incubator at 37°C in the following culture media: PC-3 - RPMI (Sigma-Aldrich) supplemented with 10% fetal bovine serum (FBS; Gibco BRL), SK-OV-3 - McCoy’s medium (Sigma-Aldrich) supplemented with 10% FBS (Gibco BRL), WM793B - 2% Tu medium (Sigma-Aldrich) supplemented with 2% FBS (Gibco BRL), bovine insulin (0.005 mg/ml) and 1.68 mmol/l CaCl2 (Sigma-Aldrich).

extract_protocol: Total RNA was isolated using Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Hypoxic conditions were introduced by incubating the cells in 1% oxygen using oxygen flow-regulated incubator for 72 h (chronic hypoxia) or for 4/12 hour periods of 1% oxygen interchanged with periods of 21% oxygen (cycling hypoxia). Control cells were cultured in standard conditions (21% oxygen) for 72 h.

value: WM793B human melanoma cell line

value: ATCC, CRL-2812


title: WM_H1

description: WM793B melanoma cells exposed to experimental chronic hypoxia (1% oxygen) for 72 h, biological replica 1

source_name: WM793B cells exposed to chronic hypoxia

value: ATCC, CRL-2809


title: non Side Population rep2

value: non side population


title: Side Population rep2


title: WM_C3

description: WM793B melanoma cells  exposed to experimental cycling hypoxia (interchanging 1% and 21% oxygen) for 72 h, biological replica 3

source_name: WM793B cells exposed to cycling hypoxia

value: ATCC, CRL-2808


title: WM_C2

description: WM793B melanoma cells  exposed to experimental cycling hypoxia (interchanging 1% and 21% oxygen) for 72 h, biological replica 2

value: ATCC, CRL-2807


title: non Side Population rep1


title: WM_K3

description: WM793B melanoma cells cultured in control conditions (21% oxygen), biological replica 3

value: ATCC, CRL-2814


title: SK_K1

description: SK-OV-3 cancer cells cultured in control conditions (21% oxygen), biological replica 1

source_name: control SK-OV-3 cells

value: SK-OV-3 human ovarian cancer cell line

value: ATCC, HTB-83


title: WM_K2

description: WM793B melanoma cells cultured in control conditions (21% oxygen), biological replica 2

value: ATCC, CRL-2813


title: WM_H2

description: WM793B melanoma cells exposed to experimental chronic hypoxia (1% oxygen) for 72 h, biological replica 2

value: ATCC, CRL-2810


title: WM_C1

description: WM793B melanoma cells  exposed to experimental cycling hypoxia (interchanging 1% and 21% oxygen) for 72 h, biological replica 1

value: ATCC, CRL-2806


title: WM_H3

description: WM793B melanoma cells exposed to experimental chronic hypoxia (1% oxygen) for 72 h, biological replica 3

value: ATCC, CRL-2811


title: SK_H3

description: SK-OV-3 ovarian cancer cells exposed to experimental chronic hypoxia (1% oxygen) for 72 h, biological replica 3

source_name: SK-OV-3 cells exposed to chronic hypoxia

value: ATCC, HTB-82


title: SK_C3

description: SK-OV-3 ovarian cancer cells   exposed to experimental cycling hypoxia (interchanging 1% and 21% oxygen) for 72 h, biological replica 3

source_name: SK-OV-3 cells exposed to cycling hypoxia

value: ATCC, HTB-79


title: SK_C1

description: SK-OV-3 ovarian cancer cells   exposed to experimental cycling hypoxia (interchanging 1% and 21% oxygen) for 72 h, biological replica 1

value: ATCC, HTB-77


title: Recovery 3

city: Cork

first: Christine

middle: Elizabeth

last: O'Carroll

address: University College Cork

country: Ireland

institute: Alimentary Pharmabiotic Centre, University College Cork

description: Replicate # 3:Gene expression of recovered (88 hour rest) macrophage re-stimulated with LPS for 4 hours

hyb_protocol: Cy3-labeled cRNA (600 ng) from each sample was hybridized to an Agilent Mouse 8x60k Microarray.  The hybridized array was then washed and scanned and data was extracted from the scanned image  using Feature Extraction version 10.7 (Agilent Technologies).

data_processing: Gene expression analysis was performed on Agilent 8x60k mouse arrays (Agilent-028005). All data processing was carried out using Bioconductor packages (Genome Biol. 2004; 5(10): R80) in the R software environment. The data was background corrected using Limma package (Stat Appl Genet Mol Biol. 2004;3). The data was then corrected for batch effects using the ComBat script (Biostatistics. 2007 Jan;8(1):118-27). The corrected data was then normalised between arrays using quantile normalisation (Stat Appl Genet Mol Biol. 2004;3)

source_name: bone marrow derived macrophage

label_protocol: Two hundred nanograms of total RNA was converted into labeled cRNA with nucleotides coupled to  fluorescent dye Cy3 using the Low Input Quick Amp Kit (Agilent Technologies, Palo Alto, CA) following  the manufacturer’s protocol.

growth_protocol: Bone marrow derived macrophages were isolated from female 6 - 8 week C57BL/6 mice and differentiated for 7 days in L929 conditioned growth medium

extract_protocol: Total RNA was extracted using Rneasy mini kit in combination with Qiashredders and a DNase step according to the manufacturers instructions (Qiagen).

treatment_protocol: BMDM s were stimulated with LPS for 8 hours followed by rest for 16 hours prior to re-stimulation with LPS for 4 hours to induced LPS tolerance. LPS tolerance was induced in Recovered cells with the rest period extending from 2 - 4 days before re-stimulation with LPS for 4 hours. The acute response to LPS was induced by stimulating BMDMs with LPS for 4 hours. Control BMDMs were left untreated.

value: bone marrow derived macrophage

tag: cell state

value: Recovery

tag: strain


title: Recovery 1

description: Replicate # 1: Gene expression of recovered (88 hour rest) macrophage re-stimulated with LPS for 4 hours

scan_protocol: Cy3-labeled cRNA (600 ng) from each sample was hybridized to an Agilent Mouse 8x60k Microarray.  The hybridized array was then washed and scanned and data was extracted from the scanned image  using Feature Extraction version 10.7 (Agilent Technologies).


title: SK_K2

description: SK-OV-3 cancer cells cultured in control conditions (21% oxygen), biological replica 2

value: ATCC, HTB-84


title: SK_H2

description: SK-OV-3 ovarian cancer cells exposed to experimental chronic hypoxia (1% oxygen) for 72 h, biological replica 2

value: ATCC, HTB-81


title: Recovery 2

description: Replicate # 2:Gene expression of recovered (88 hour rest) macrophage re-stimulated with LPS for 4 hours


title: SK_H1

description: SK-OV-3 ovarian cancer cells exposed to experimental chronic hypoxia (1% oxygen) for 72 h, biological replica 1

value: ATCC, HTB-80


title: SK_C2

description: SK-OV-3 ovarian cancer cells   exposed to experimental cycling hypoxia (interchanging 1% and 21% oxygen) for 72 h, biological replica 2

value: ATCC, HTB-78


title: KT2440(pCAR1)

description: This is an Affymetrix custom-commercial tiling array that covers the IncP-7 carbazole-degradative plasmid pCAR1  (RefSeq: NC_004444.1) at 9-bp density. BPMAP files are provided as supplementary files. pCAR1_8b520435FR-3.bpmap represents  the forward strand of pCAR1, and pCAR1_8b520435FF-3.bpmap represents the reverse strand of pCAR1.

source_name: cDNA prepared from succinate culture of KT2440(pCAR1)


title: SK_K3

description: SK-OV-3 cancer cells cultured in control conditions (21% oxygen), biological replica 3

value: ATCC, HTB-85


title: LPS Tolerance 3

description: Replicate # 3: Gene expression of LPS tolerant macrophage re-stimulated with LPS for 4 hours

value: LPS Tolerance


title: Acute response to LPS 3

description: Replicate # 3:Gene expression of macrophage treated with LPS for 4 hours only

value: Acute response to LPS


title: LPS Tolerance 2

description: Replicate # 2: Gene expression of LPS tolerant macrophage restimulated with LPS for 4 hours


title: LPS Tolerance 1

description: Replicate # 1: Gene expression of LPS tolerant macrophage re-stimulated with LPS for 4 hours


title: Untreated 2

description: Replicate # 2: Gene expression of untreated macrophage

value: control


title: Acute response to LPS 2

description: Replicate # 2:Gene expression of macrophage treated with LPS for 4 hours only


title: Untreated 3

description: Replicate # 3:Gene expression of untreated macrophage


title: Untreated 1

description: Replicate # 1: Gene expression of untreated macrophage


title: WholeBloodPostASA AR022

city: Durham

first: Deepak

last: Voora

state: NC

address: 905 S. Lasalle St, 2004 Snyderman Building, DUMC 3445

department: Institute for Genome Sciences & Policy

institute: Duke University

description: WholeBloodPostASA

hyb_protocol: cDNA was hybridized to an Affymetrix GeneChip Human Genome U133 Plus 2.0 Array for 18 hours

scan_protocol: The arrays were washed and then fluorescence was quantitated on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: RMA normalization in R

source_name: Whole blood after 7-10 days 81mg/day aspirin

label_protocol: Purified RNA (100 ng) was reversed transcribed with SuperScript III using random hexamers and the cDNA was amplified with Ovation RNA Amplification System V2 kit (NuGEN Technologies).  The cDNA was purified with DNA Clean & Concentrator-25 (Zymo Research) and 3.75 ug of cDNA was fragmented and labeled with FL-Ovation cDNA Biotin Module V2 kit (NuGEN Technologies)

extract_protocol: Total RNA was purified from whole blood using PAXgene Blood RNA kit (PreAnalytiX), including an on-column DNAse treatment.  RNA samples were further purified using RNAeasy Mini kit (Qiagen Sciences).

value: Whole Blood

tag: group

value: aspirin resistant


title: WholeBloodPostASA AR081

description: WholeBloodPostASA


title: WholeBloodPostASA AR060

description: WholeBloodPostASA


title: WholeBloodPostASA AR168

description: WholeBloodPostASA

value: high normal


title: WholeBloodPostASA AR039

description: WholeBloodPostASA


title: Organoid_Ileum2

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

library_source: genomic

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI37) using BWA package (-c, –l 25, -k 2, -n 10). Multiple reads mapping to same location and strand have been collapsed to single read and only uniquely placed reads were used for peak-calling.
Cisgenome v.2 software package (-e 50, -maxgap 200, -minlen 200) was used for peak-calling from the ChIP-seq against the common input sample.
Genome_build: hg19
Supplementary_files_format_and_content: txt file are aligned files with chr/start/end/strand format
Supplementary_files_format_and_content: cod files are peak coordinate files

Sensitive human data. Raw data has not been provided in order to protect the pivacy of patients.

source_name: Epithelial organoid terminal ileum

growth_protocol: Human organoids were maintained as describe previously (Sato et al, Gastroenterology 2011). In brief, organoids were embedded into matrigel (BD Biosciences) and maintained in medium containing Rspo-1, Noggin, EGF, ALK4/5/7 inhibitor A83–01, Nicotinamide, SB202190 and Wnt3. We used conditioned media for Rspo-1, Noggin and Wnt3a (stably transfected Rspo-1 HEK293T cells were kindly provided by Dr. C. J. Kuo, Department of Medicine, Stanford, CA).

extract_protocol:
Chromatin IP was performed using MAGnify ChIP kit (Invitrogen) according manufacturers’ recommendations; with these exceptions: crypts or organoids were cross-linked by 2% formaldehyde in PBS for 10 minutes, reaction was quenched with excess of glycine. Samples were washed with ice cold PBS and subsequently fragmented in 50ul of lysis buffer. 20 µl of chromatin was used per single IP. One µl anti H3K27ac (ab4729, Abcam) was used per IP.
Sequencing libraries from immunoprecipitated chromatin were prepared as described previously (Mokry et al. NAR 2012). brief, the chromatin was additionally sheared , blunt ended and phosphorylated. The sequencing adaptors were ligated and the resulting library was PCR amplified using ligation-mediated PCR. The libraries were sequenced on SOLiD 5500 or WildFire sequencer in a multiplexed way to produce 40-50-bp long reads.

value: normal terminal ileum


title: WholeBloodPostASA AR099

description: WholeBloodPostASA


title: Organoid_Ileum1

description: Sensitive human data. Raw data has not been provided in order to protect the pivacy of patients.


title: WholeBloodPostASA AR044

description: WholeBloodPostASA


title: Acute response to LPS 1

description: Replicate # 1: Gene expression of macrophage treated with LPS for 4 hours only


title: WholeBloodPostASA AR067

description: WholeBloodPostASA


title: WholeBloodPostASA AR046

description: WholeBloodPostASA


title: Epithelial crypt colon input

source_name: Epithelial crypt colon

value: inflamed descending colon


title: WholeBloodPostASA AR049

description: WholeBloodPostASA


title: Organoid_Colon

source_name: Epithelial organoid Colon

value: normal caecum


title: WholeBloodPostASA AR030

description: WholeBloodPostASA


title: Crypt4

value: normal sigma


title: Involution Adipose Stroma, biological rep 3

city: Worcester

first: Jessica

last: McCready

state: MA

address: 500 Salisbury St

institute: Assumption College

hyb_protocol: Samples were hybridized for 16 hr at 45C. The array was then washed and stained using the fluidics station.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with Autoloader

data_processing: Normalization and differential expression were carried out with Affy, gcrma and Limma packages in the Bioconductor suite of programs

source_name: Involution day 3

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

growth_protocol: Female Balb/c mice were bred to generate lactating or involuting mice.  Nulliparous mice were not exposed to male mice.

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

treatment_protocol: Adipose stroma was isolated from the mouse mammary gland via a collagenase hyaluronidase digestion and subsequent centrifugation.

value: Balb/c

tag: development stage

value: Involution

value: mammary gland stroma


title: WholeBloodPostASA AR051

description: WholeBloodPostASA


title: WholeBloodPostASA AR073

description: WholeBloodPostASA


title: WholeBloodPostASA AR027

description: WholeBloodPostASA


title: Crypt3

value: inflamed sigma


title: WholeBloodPostASA AR161

description: WholeBloodPostASA


title: Involution Adipose Stroma, biological rep 2


title: WholeBloodPostASA AR092

description: WholeBloodPostASA

value: aspirin sensitive


title: WholeBloodPostASA AR028

description: WholeBloodPostASA


title: Crypt2


title: Crypt1

value: inflamed caecum


title: WholeBloodPostASA AR015

description: WholeBloodPostASA


title: Lactation Adipose Stroma, biological rep 2

source_name: Lactation day 5

value: Lactation


title: Involution Adipose Stroma, biological rep 1


title: Lactation Adipose Stroma, biological rep 3


title: WholeBloodPostASA AR066

description: WholeBloodPostASA


title: WholeBloodPostASA AR103

description: WholeBloodPostASA


title: Nulliparous Adipose Stroma, biological rep 3

source_name: 8 week Nulliparous Mammary Gland

value: Nulliparous


title: WholeBloodPostASA AR097

description: WholeBloodPostASA


title: Lactation Adipose Stroma, biological rep 1


title: WholeBloodPostASA AR089

description: WholeBloodPostASA


title: Nulliparous Adipose Stroma, biological rep 1


title: WholeBloodPostASA AR075

description: WholeBloodPostASA


title: WholeBloodPostASA AR072

description: WholeBloodPostASA


title: WholeBloodPostASA AR078

description: WholeBloodPostASA


title: WholeBloodPostASA AR109

description: WholeBloodPostASA


title: Nulliparous Adipose Stroma, biological rep 2


title: MEFs

status: Public on Dec 05 2013

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description:
Total RNA was extracted from MEFs between passages 2 and 4.
Cultured in vitro cells.

hyb_protocol: MOA v2.0 arrays were pre-heated at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Agilent G2505C scanner (at 100% laser power, 635nm PMT 10 ; 532nm PMT 10) and quantify the fluoresence intensity by GenePix Pro software (4.1.1.44).

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). Intensity normalized by median scaling method performed on data set without flagged (probes that flag<0 within all arrays) and control data. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

source_name: mouse embryonic fibroblasts

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion). Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: The mouse embryonic fibroblasts were cultured in fibroblast medium (high glucose DMEM, 10% FBS, 2 mM Glutamax). Induced neurons and primary neurons were cultured in neural medium (Neural Basal/DMEM-F12 1:1, 1×B-27, 5 ng/ml BDNF).

extract_protocol: RNA extraction by Trizol Reagent. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6.5).

treatment_protocol: MEFs were used between passages 2 and 4, and primary neurons were cultured within one week. Induced neurons were induced from MEFs by ABN+Rarg+Nr5a2 through adenovirus. Induced neurons for the array experiment were the total final cells population including converted iN cells and non-converted cells and formed a mixed population.

value: mouse embryonic fibroblasts