title: development Pp-Pbl

city: Ribeirão Preto

first: Michelle

middle: Prioli Miranda

last: Soares

address: Bandeirantes avenue, 3900

department: Genetics

institute: USP

description:
honey bee workers (Africanized A. mellifera)
Slide number: 13775439, FileName: 13775439_2011-04-12.txt, Cy3: Pp, Cy5: Pbl
Slide number: 13775444, FileName: 13775444_2010-02-04.txt, Cy3: Pbl, Cy5: Pp
pools of ten thoracic integuments (dorsal portion) from each developmental phase

hyb_protocol: The RNA was dye-coupled and combined with hybridization buffer (49% Formamide, 49% SSC 20x and 0.2% SDS), pre-heated at 55° C for 3 min, applied to arrays, and hybridized for 17 h at 42 °C in single slide hybridization chambers placed in a water bath. A series of 30s shaking washes in 2× SSC plus 0.1% SDS; 2× SSC; 0.1× SSC and Milli-Q water at room temperature removed excess probe.

scan_protocol: The hybridized slides were  scanned using an Axon Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA) with GENEPIX software (Agilent Technologies, Santa Clara, CA), 10-micron resolution, Cy3 with Green Laser (532 nm), and Cy5 with Red Laser (635 nm). GenePix Pro 6.0 software was used for quantification of the spots and image analysis with default parameters.

data_processing: For the microarray data analysis, all normalizations and calculations were performed using the functions of Limma of the R-Biocondutor package (http://www.r-project.org/) (Smyth, 2005). Normexp method was used for background normalization adding an offset of 50 to the corrected intensities. Normalization within-arrays was done using print-tip loess to adjust imbalances between the green and red dyes due to spot intensity and spatial position on the slide. Average intensities were normalized between-arrays using the Aquantile method. After normalization, the Log2 ratio of gene expression differences between the developmental phases was calculated. Fold-change values and standard errors were estimated by fitting linear regression to the normalized expression data. The empirical Bayes statistics (moderated t-statistics) was used for significance analysis of the differential expression.

organism: Apis mellifera

source_name: Pp worker integument

label_protocol: RNA amplification was done with and according to Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). The amplified RNA samples (20 µg) were used for dual channel microarray hybridization with Cy3 and Cy5 dyes (dye swap). Dye swaps were done for each comparison and two slides were used to evaluate the differential expression.

extract_protocol: Two separate pools of 10 thoraces (only the dorsal portion) were prepared for each developmental phase (Pw, Pp and Pbl). Total RNA was extracted from the pooled samples using Trizol reagent and following manufacturer’s protocol. RNeasy Mini Kit, QIAGEN, Cat. 74104, was used to purify the extracted RNA, which was quantified in Nanodrop (ND 1000). RNA amplification was done with and according to Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion).

treatment_protocol: Bees were collected from colonies maintained at the Experimental Apiary of the University of São Paulo in Ribeirão Preto, SP, Brazil

tag: developmental stage

value: pink-eyed/white cuticle pupae, Pp phase

value: thoracic integument

source_name: Pbl worker integument

value: brown-eyed/light pigmented cuticle pupae, Pbl phase


title: Pancreatic islets_control_rep3

status: Public on Dec 29 2012

type: RNA

city: Beijing

first: yanchang

last: wei

address: #1 Beichen West Rd

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: This sample is the third of six control biological replicates used in this experiment, each from separate animals.

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

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

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

molecule: total RNA

organism: Mus musculus

source_name: Pancreatic islets

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

growth_protocol: At 16 weeks of age, fathers of type 2 diabetes or control were mated with normal females in standard conditions, to generate the F1 offspring.

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

treatment_protocol: Fathers type 2 diabetes vs control, mate with females in standard conditions, then the offspring's liver transcriptomics were analysed through microarray analysis.

tag: gender

value: Male

tag: strain

value: ICR

tag: cell type

value: Pancreatic islets

tag: disease status

value: control


title: Pancreatic islets_control_rep6

description: This sample is the last of six experimental biological replicates used in this experiment, each from separate animals.

value: Female


title: T cells Stimulated

city: Nanjing

first: Zichun

last: Hua

state: Jiangsu

address: Hankou Road

institute: Nanjing University

hyb_protocol: After labeling, the probes were purified, quantified and hybridized with Mouse Genome 430 2.0 Array chips (Affymetrix) for 16 h.

scan_protocol: The array chips were washed, stained and scanned with a G2500A GeneArray Scanner (Affymetrix).

data_processing: MAS 5

label: biotin

source_name: T cells stimulated with anti-CD3/CD28 antibodies

label_protocol: Probes were biotin-labeled with a BioArray High Yield RNA Transcript Labeling Kit (Affymetrix, P/N 900182).

growth_protocol: Purified T cells were cultured with fresh RPMI 1640 medium (Gibco, Grand Island, NY), supplemented with 20 % FBS, 2 mM L-glutamine, penicillin (100 U/ml) and streptomycin (100 mg/ml). Cells were incubated in a 37 ◦C incubator supplied with 95 % air and 5 % CO2 for 18 h.

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

treatment_protocol: Anti-CD3/CD28 antibodies were added to stimulate cells and triptolide(50ng/ml)were added to treat cells.

value: primary T cells

tag: treatment

value: anti-CD3/CD28 antibodies


title: Patient2_PBMC_rep1

status: Public on Dec 28 2012

city: Xi’an

first: Hao

last: Song

state: Shaanxi Province

address: NO.3 Xinong Road，Yangling

department: College of Veterinary Medicine

institute: Northwest A & F University

description: critically ill Patient with Influenza A (H1N2)

hyb_protocol: Samples of total RNA were labeled and hybridized with the miRNA Labeling Reagent and Hybridization Kit (Agilent, Santa Clara, CA USA) according to the manufacturer’s protocol. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 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 Microarray Scanner using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green(PMT100, PMT5).

data_processing: The scanned images were analyzed with Feature Extraction Software  (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Homo sapiens

source_name: Patient2, PBMC, replicate 1

extract_protocol: Blood samples were collected in EDTA-treated tubes and PBMCs were isolated by standard Ficoll density-gradient centrifugation. PBMCs were washed once in sterile phosphate-buffered saline (PBS) before RNA isolation. Total RNA was isolated from freshly obtained PBMCs using the mirVana miRNA PARIS kit (Ambion), in accordance with the manufacture’s protocol.

value: PBMC

tag: age (y)

tag: disease state

value: Influenza A (H1N1)


title: Control3_PBMC_rep1

description: healthy control

source_name: Control3, PBMC, replicate 1

label_protocol: Samples of total RNA were labeled and hybridized with the miRNA Labeling Reagent and Hybridization Kit (Agilent, Santa Clara, CA USA) according to the manufacturer’s protocol.

value: healthy


title: Patient5_PBMC_rep1

description: critically ill Patient with Influenza A (H1N5)

source_name: Patient5, PBMC, replicate 1


title: Patient4_PBMC_rep1

description: critically ill Patient with Influenza A (H1N4)

source_name: Patient4, PBMC, replicate 1


title: HybB-T22

city: Cincinnati

first: Nancy

last: Ratner

state: OH

address: 3333 Burnet Ave.

country: USA

institute: Cincinnati Children's Hospital Medical Center

description:
T22
SAMPLE 46

hyb_protocol: The hybridization cocktail was hybridized for 16 hr at 45 degrees C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450:FS450_0004.

scan_protocol: GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)

data_processing: Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R. A custom CDF was used for each species (mouse: Brainarray, Mouse4302_Mm_REFSEQ_11.0.1; Human, Brainarray, HGU133Plus2_Hs_REFSEQ_11.0.1).

source_name: mouse PNST

label_protocol: We generated biotinylated cDNA probes from a single round of DNA displacement synthesis amplification of 20ng total RNA (Ovation Biotin RNA Amplification and Labelling System; NuGen) for hybridization to the whole-genome Affymetrix GeneChips using the Affymetrix protocol.

extract_protocol: Total RNA was isolated from frozen human tissue and cells using the RNeasy kit (Qiagen) and verified RNA integrity with an Agilent Bioanalyser 2100 (with typical 28S/18S ratios = 2 +/- 0.1). For mouse, total RNA was isolated from nerves and tumors using the Qiagen fibrous tissue protocol (Qiagen, Inc. Valencia, CA).

tag: genotype/variation

value: T-NPcis

tag: tissue

value: peripheral nerve sheath tumors (PNST)


title: Control2_PBMC_rep1

description: healthy control

source_name: Control2, PBMC, replicate 1


title: Pancreatic islets_control_rep1

description: This sample is the first of six control biological replicates used in this experiment, each from separate animals.


title: development Pw-Pbl

country: Brazil

description:
honey bee workers (Africanized A. mellifera)
Slide number: 13802201, FileName: 13802201_2010-02-04.txt, Cy3: Pw, Cy5: Pbl
Slide number: 13802205, FileName: 13802205_2010-02-04.txt, Cy3: Pbl, Cy5: Pw
pools of ten thoracic integuments (dorsal portion) from each developmental phase

source_name: Pw worker integument

value: white-eyed/white cuticle pupae, Pw phase


title: Patient3_PBMC_rep1

description: critically ill Patient with Influenza A (H1N3)

source_name: Patient3, PBMC, replicate 1


title: Patient1_PBMC_rep1

description: critically ill Patient with Influenza A (H1N1)

source_name: Patient1, PBMC, replicate 1


title: development Pw-Pp

description:
honey bee workers (Africanized A. mellifera)
Slide number: 13802207, FileName: 13802207_2010-02-04.txt, Cy3: Pw, Cy5: Pp
Slide number: 13802203, FileName: 13802203_2010-02-04.txt, Cy3: Pp, Cy5: Pw
pools of ten thoracic integuments (dorsal portion) from each developmental phase


title: HybC-T23

description:
T23
SAMPLE 47


title: HybC-T25

description:
T25
SAMPLE 48


title: T cells stimulated and treated with triptolide

source_name: T cells stimulated with anti-CD3/CD28 antibodies and treated with triptolide


title: Control1_PBMC_rep1

description: healthy control

source_name: Control1, PBMC, replicate 1


title: HybC-T19

description:
T19
SAMPLE 44

value: T-P0CreB; Nf2 flox/flox; p53+/-


title: HybB-T18

description:
T18
SAMPLE 43


title: HybA-T21

description:
T21
SAMPLE 45


title: batch2c-MPNST.AS45

description:
AS45
SAMPLE 83

value: malignant peripheral nerve sheath tumors (MPNST)


title: HybA-T13

description:
T13
SAMPLE 39

value: T-P0CreB; Nf2 flox/flox; Nf1 flox/+


title: HybB-T16

description:
T16
SAMPLE 41


title: HybA-T17

description:
T17
SAMPLE 42


title: batch2b-MPNST.AS42

description:
AS42
SAMPLE 82


title: HybC-T7

description:
T7
SAMPLE 38

value: T-P0CreB; Nf2 flox/flox


title: U2OS_NS_rep3

status: Public on Dec 30 2012

city: Frederick

first: Zhi-Ming

last: Zheng

state: MD

department: HIV DRP Program

institute: National Cancer Institute

hyb_protocol: Standard methods following recommendations of the manufacturer were used to hybridize the samples to the SpliceArrays.  The arrays were washed and stained using the FS450-0001 Fluidics protocol.

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G

data_processing:
The .CEL files were imported into Partek® Genomics Suite and the data was processed using the Robust Multichip Average (RMA) method which only utilizes the PM values to correct background.  Quantile normalization was performed across all arrays, and then data was median polished for probeset summarization. ANOVA analysis was performed to identify probes that are differentially expressed between the sample groups specified.  For ease of analysis and interpretation, the “evidenced” and “discovery” probes (for known or unknown splice events) were input separately for the analysis. A false discovery rate (FDR) was applied to the ANOVA p-values to select significant probes for comparison of the sample types.
The results files titled, SpliceArray Analysis Results_ALL (Evidenced or Discovery) Probesets.txt contain the ANOVA data for all probes on the array, as well as probeset-specific annotation information.  These files are linked as supplementary files on the Series GSE22149 record.

source_name: U2OS cells treated with non-specific siRNA

label_protocol: the FL-Ovation cDNA Biotin Module v2 (NuGen, Inc., part # ‘s 4200-60)

growth_protocol: Dulbecco’s modified Eagle medium (DMEM, Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (FBS) (HyClone, Logan, UT), 2 mM L-glutamine, 100U/ml penicillin, and 100µg/ml streptomycin (Invitrogen).

extract_protocol: Total cell RNA was prepared from the cells using TRIzol (Invitrogen) following the manufacturer's instructions.

treatment_protocol: RNAi was conducted by two separate transfections, at intervals of 48 h, with 40 nM non-specific or SRp20 siRNA in the presence of Lipofectamine 2000.

tag: protocol

value: female

value: bone

tag: cell line

value: U2OS cells (originated from 15 year old female)

value: osteosarcoma


title: U2OS_NS_rep1

value: control


title: batch1a-MPNST_AS15

description:
AS15
SAMPLE 80


title: U2OS_SR_rep1

source_name: U2OS cells treated with SRp20 siRNA

value: SRp20 knockdown


title: HybA-T5

description:
T5
SAMPLE 36


title: HybB-T6

description:
T6
SAMPLE 37


title: batch1a-MPNST_AS10

description:
AS10
SAMPLE 78


title: batch1a-pNF_AS8

description:
AS8
SAMPLE 74

value: Neurofibroma


title: batch2a-pNF.AS38

description:
AS38
SAMPLE 76


title: batch1a-MPNST_AS13

description:
AS13
SAMPLE 79


title: HybC-T15

description:
T15
SAMPLE 40


title: U2OS_SR_rep2


title: batch2a-MPNST.AS37

description:
AS37
SAMPLE 81


title: HybB-T9

description:
T9
SAMPLE 35

value: T-P0CreB; Nf2 flox/+; Nf1 flox/flox


title: U2OS_NS_rep2


title: batch2a-pNF.AS12

description:
AS12
SAMPLE 75


title: HybA-T8

description:
T8
SAMPLE 34


title: Pancreatic islets_t2d_rep5

description: This sample is the fifth of six experimental biological replicates used in this experiment, each from separate animals.

value: Female

value: ICR

value: Pancreatic islets


title: batch2a-pNF.AS40

description:
AS40
SAMPLE 77


title: HybC-T10

description:
T10
SAMPLE 31

value: peripheral nerve sheath tumors (PNST)


title: HybC-T12

description:
T12
SAMPLE 33


title: U2OS_SR_rep3


title: HybA-T4

description:
T4
SAMPLE 30

source_name: mouse neurofibroma

value: T-P0CreB; Nf1 flox/flox

value: Mouse neurofibroma


title: HybB-T11

description:
T11
SAMPLE 32


title: batch1a-pNF_AS16

description:
AS16
SAMPLE 72


title: HybB-T2

description:
T2
SAMPLE 28


title: HybA-T1

description:
T1
SAMPLE 27


title: HybC-T3

description:
T3
SAMPLE 29


title: batch2c-pNF.AS33

description:
AS33
SAMPLE 69


title: HybM-T4

description:
T4
SAMPLE 25

value: T-DhhCre; Nf1 flox/flox


title: batch2c-pNF.AS34

description:
AS34
SAMPLE 70


title: batch2b-pNF.AS47

description:
AS47
SAMPLE 67


title: batch3a-pNF_AS48

description:
AS48
SAMPLE 71


title: HybJ-T6

description:
T6
SAMPLE 26


title: HybI-T28

description:
T28
SAMPLE 23


title: HybI-T29

description:
T29
SAMPLE 24


title: batch3c-dNF_AS50

description:
AS50
SAMPLE 64


title: batch2b-pNF.AS24

description:
AS24
SAMPLE 66


title: HybI-T27

description:
T27
SAMPLE 22


title: batch3c-DNF_LRS

description:
LRS
SAMPLE 63


title: batch1a-pNF_AS7

description:
AS7
SAMPLE 73


title: HybJ-T1

description:
T1
SAMPLE 20


title: HybI-T26

description:
T26
SAMPLE 21


title: batch3b-dNF_CSG95

description:
CSG95
SAMPLE 62


title: batch2b-pNF.AS23

description:
AS23
SAMPLE 65


title: batch2c-dNF.AS35

description:
AS35
SAMPLE 58


title: batch3b-dNF_CSG94

description:
CSG94
SAMPLE 61


title: HybM-T11

description:
T11
SAMPLE 17

value: T-DhhCre; Nf1 flox/-


title: batch2c-dNF.AS44

description:
AS44
SAMPLE 59


title: HybM-T12

description:
T12
SAMPLE 18


title: batch3a-dNF_AS55

description:
AS55
SAMPLE 60


title: HybJ-T13

description:
T13
SAMPLE 19


title: HybH-N14

description:
N14
SAMPLE 15

source_name: mouse control

value: Nf2 flox/flox

value: Mouse control


title: HybI-N12

description:
N12
SAMPLE 13


title: HybG-N13

description:
N13
SAMPLE 14


title: HybJ-T10

description:
T10
SAMPLE 16


title: batch2b-dNF.AS4

description:
AS4
SAMPLE 57


title: HybD-N01

description:
N01
SAMPLE 6

value: Nf1 flox/flox


title: HybH-N05

description:
N05
SAMPLE 10


title: HybD-N10

description:
N10
SAMPLE 11


title: batch2b-dNF.AS22

description:
AS22
SAMPLE 56


title: batch2a-dNF.AS3

description:
AS3
SAMPLE 54


title: HybE-N11

description:
N11
SAMPLE 12


title: batch1a-dNF_AS5

description:
AS5
SAMPLE 53


title: HybI-N03

description:
N03
SAMPLE 8


title: HybH-N19

description:
N19
SAMPLE 5


title: ventricle_right_E8_LAL_techrep2

city: Prague

first: David

last: Sedmera

address: U nemocnice 3

country: Czech Republic

institute: Charles University

hyb_protocol: Targets (4 μg) were hybridized to Affymetrix Chicken Genome arrays according to manufacturer protocols. Post hybridization washing and fluorescence labeling was done in an Affymetrix Fluidics Station 450 in accordance with manufacturer protocols.

scan_protocol: Microarrays were scanned using an Affymetrix 7G Scanner.

data_processing: Gene hybridization intensities were normalized by gcRMA algorithm (Wu et al., 2005) and detection calls generated by MAS5 algorithm, both implemented with the ArrayQuest webtool (Argraves et al., 2005).

organism: Gallus gallus

source_name: Heart, right ventricle, stage E8, left atrial ligation

label_protocol: Total RNA was converted into biotin-labeled cRNA targets using a SuperScript cDNA synthesis kit (Invitrogen) and Bioarray Hi Yield in vitro transcription kit (Enzo).

growth_protocol: Eggs were incubated in a force draft incubator at 37.5 °C and high humidity until the appropriate developmental stage.

extract_protocol: Tissues from normal and experimentally treated chicks was collected at the appropriate stage, and tissues were carefully dissected, collected and stored in RNAlater, and then pooled for RNA isolation. RNA was purified using RNeasy Mini columns (Qiagen) and evaluated by Agilent BIoanalyzer.

treatment_protocol: Conotruncal banding (CTB) or partial ligation of the left atrial appendage (LAL) was performed in ovo at embryonic day 4 (Stage 24), as described by Sedmera et al., 1999. Following experimental treatment, eggs were returned to the incubator until the appropriate developemental stage.

value: Heart, right ventricle

tag: experimental treatment

value: left atrial ligation


title: jan-N3

description:
N3
SAMPLE 51

source_name: normal human nerve

value: Normal human nerve


title: ventricle_right_E8_LAL_techrep1


title: batch2a-dNF.AS46

description:
AS46
SAMPLE 55


title: ventricle_right_E8_normal_techrep2

source_name: Heart, right ventricle, stage E8, normal

value: normal


title: ventricle_right_E8_normal_techrep1


title: HybE-N02

description:
N02
SAMPLE 7


title: HybG-N04

description:
N04
SAMPLE 9


title: batch1a-dNF_AS18

description:
AS18
SAMPLE 52

value: Neurofibroma


title: HybE-N16

description:
N16
SAMPLE 2


title: jan-N1

description:
N1
SAMPLE 49


title: HybD-N15

description:
N15
SAMPLE 1


title: ventricle_left_E8_LAL_techrep2

source_name: Heart, left ventricle, stage E8, left atrial ligation

value: Heart, left ventricle


title: HybG-N18

description:
N18
SAMPLE 4


title: ventricle_left_E8_techrep1

source_name: Heart, left ventricle, stage E8


title: ventricle_left_E8_techrep2


title: jan-N2

description:
N2
SAMPLE 50


title: HybI-N17

description:
N17
SAMPLE 3


title: ventricle_left_E8_LAL_techrep1


title: Subject_6 [Affymetrix]

city: Iowa City

first: Jeffrey

last: Plume

state: IA

address: 500 Newton Rd.

department: Psychiatry

institute: University of Iowa

description:
31_female_4-17-08_s2.CEL
Gene expression data isolated lymphoblasts

hyb_protocol: Hybridized under contract by the University of Iowa DNA Facility

scan_protocol: Scanned under contract by the University of Iowa DNA Facility using the 2 Model 3000 GeneArray scanners

data_processing: Quantile  normalized with Partek genomic suite using default settings then z-scored

source_name: Homo sapien lymphoblast

label_protocol: Labeled under contract by the University of Iowa DNA Facility

extract_protocol: RNA isolated using the Ambion PureLink™ RNA Mini Kit following the manufacurer's protocol

value: Lymphoblast

tag: subject

tag: phenotype

value: Control


title: ventricle_left_E6_normal_techrep2

source_name: Heart, left ventricle, stage E6, normal


title: iN(shp53)

city: Chengdu

first: chongkui

last: sun

state: Sichuan

address: No.14, Sec. 3, Renmin Road South

department: State key laboratory of oral diseases

institute: Sichuan University

description: Sample 6

hyb_protocol: Standard Illumina hybridization protocol. Immobilized, biotinylated amplified RNAs were then detected by staining with Cy3-steptavidin (1ug Cy3-SA per 1 ml of Illumina Block E1) for 10 minutes at room temperature.

scan_protocol: Illumina Scan protocol. Arrays were scanned on an Illumina BeadArray Reader. Laser power and PMT voltage were kept constant for Cy3 scans.

data_processing: Scanned images were quantitated by Illumina Beadscan, v3. Quantitated data was imported into Illumina GenomeStudio software. The data were normalised using Illumina's quantile normalisation method. Average signal of each probe was filtered using 50 as baseline. To each probe of different samples, select differently expressed probes using division of maximum and minimum signal values.

source_name: induced neurons from shRNA-p53-treated fibroblasts

label_protocol: RNA transcripts were amplified by T7 linear amplification (MessageAmp TotalPrep Amplification kit; Life Technologies). In vitro transcription was carried out by adding 10x T7 reaction buffer (2.5ul), T7 biotin-NTP mix (2.5ul), and T7 RNA polymerase enzyme mix (2.5ul) and incubating at 37C. The in vitro transcription reaction was carried out for 14 hours.

growth_protocol: Human fibroblast IMR90 grows in DMEM with 10% FBS. The induction process uses special neuron medium.

extract_protocol: Total RNA was extracted using the Trizol isolation system (Invitrogen) according to the manufacturer's instructions. Total RNA was treated with DNase I (Qiagen) to prevent DNA contamination. Total RNA concentration and purity were obtained from an absorbance ratio at 260nm and 280nm. Total RNA quality was then determined by the Agilent 2100 Bioanalyzer (Agilent Technologies) according to the manufacturer's recommendations.

treatment_protocol: Assemble lentivirus using shRNAs to knockdown the p16/p19 locus. Exogenous hTERT was transfected to IMR90 using retrovirus.

value: p53 shRNA

tag: condition

value: neuron-induction medium

value: induced neurons


title: Subject_7 [Affymetrix]

description:
4_female_ND_3-18-08_s1.CEL
Gene expression data isolated lymphoblasts

value: Nicotine Dependent


title: ventricle_right_E6_normal_techrep2

source_name: Heart, right ventricle, stage E6, normal


title: ventricle_right_E6_normal_techrep1


title: Subject_8 [Affymetrix]

description:
5_female_ND_3-18-08_s1.CEL
Gene expression data isolated lymphoblasts


title: Subject_5 [Affymetrix]

description:
34_female_4-17-08_s2.CEL
Gene expression data isolated lymphoblasts


title: Subject_4 [Affymetrix]

description:
3_female_ND_3-18-08_s2.CEL
Gene expression data isolated lymphoblasts


title: ventricle_both_E6_normal_techrep2

source_name: Heart, ventricles (right and left), stage E6, normal

value: Heart, ventricles (right and left)


title: iN(hTERT)

description: Sample 7

source_name: induced neurons from exogenous hTERT-overexpressing fibroblasts

value: exogenous hTERT overexpression


title: Subject_3 [Affymetrix]

description:
29_female_4-17-08_s2.CEL
Gene expression data isolated lymphoblasts


title: iN(miR9-124+ADM)

description: Sample 8

source_name: induced neurons from miR-9+miR-124+Ascl1+NeuroD2+Myt1l overexpressing fibroblasts

tag: sample type

value: positive control


title: SBI-0087702_treated

city: La Jolla

first: Eric

last: Lau

state: CA

address: 10901 North Torrey Pines Road, Rm 6207

department: Signal Transduction

institute: The Sanford-Burnham Medical Research Institute

description: sampleID: 8473515006_F

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.8.0). It was vst transformed and quantile normalized.

source_name: WM793 cells treated for 24 hours with 10 micromolar SBI-0087702.

label_protocol: standard as recommended by illumina

extract_protocol: Total RNA was extracted using GenElute Mammalian Total RNA Miniprep Kit (Sigma).

value: Human superficial spreading melanoma WM793

tag: agent


title: Subject_2 [Affymetrix]

description:
10_female_control_3-18-08_s1.CEL
Gene expression data isolated lymphoblasts


title: Subject_4 [NimbleGen]

type: genomic

hyb_protocol: Hybridization was performed under contract by Nimblegen (Madison, WS).

scan_protocol: Arrays were scanned with the MS 200 Microarray scanner and data collection software under contract by Nimblegen

data_processing: Arrays were processed following standard protocol under contract by Nimblegen

molecule: genomic DNA

source_name: Human Lymphoblasts

label_protocol: 5μg of genomic DNA was digested with MseI and  hybridized with 1 μg of monoclonal mouse anti-5-methyl cytidine antibody at 4C overnight; methylated regions magnetic seperation using  a conjugated of secondary antibody

extract_protocol: DNA was isolated from lymphblasts by cold protein precipitation (Lahiri and Schnabel, 1993)

tag: genotype

value: Lymphoblasts

tag: chip antibody

value: 5'methylcytosine (Calbiochem, Cat# NA81, Anti-5-methylcytosine mouse aAb (162 33 D3), lot#D00062056)

source_name: Lymphoblasts

value: none, input DNA


title: ventricle_left_E6_normal_techrep1

tag: developmental stage


title: Subject_6 [NimbleGen]

tag: cell type


title: Subject_2 [NimbleGen]


title: Subject_7 [NimbleGen]


title: ventricle_both_E6_normal_techrep1


title: DMSO_treated

description: sampleID: 8473515006_E

source_name: WM793 cells treated for 24 hours with 0.1% DMSO.

value: control


title: Subject_1 [Affymetrix]

description:
8_female_control_3-18-08_s2.CEL
Gene expression data isolated lymphoblasts


title: iN(shp16)

description: Sample 5

source_name: induced neurons from shRNA-p16-treated fibroblasts

tag: treatment

value: p16 shRNA


title: Gastric cancer 61T

city: Hong Kong

first: Alfred

middle: S

last: Cheng

address: Rm 707, LiKaShing Medical Sciences Building, Prince of Wales Hospital, Shatin

country: Hong Kong

institute: Institute of Digestive Disease, The Chinese University of Hong Kong

hyb_protocol: Labelled DNA was purified using a Qiaquick PCR purification column and then vacuum dried. Both dye-coupled DNAs were then resuspended together in 85 ul of DIG Easy Hyb solution (Roche Diagnostics) together with 5 ul of salmon sperm DNA (10 ug/ul) and denatured at 95 C for 5 min. The hybridization mixture was allowed to cool briefly and 5 ul of yeast tRNA (10 ug/ul) was added and the mixture was held at 65 C for 2 min and allowed to cool to room temperature. Hybridization to the microarray was carried out under a cover-slip in a humidified chamber at 37 C for 8 h. The cover slip was floated off in 1 x SSC and each slide was washed three times in 1x SSC, 0.1% SDS at 50 C for 15 min followed by removal of SDS at room temperature in 1 x SSC and 0.1 x SSC for 5 min each.

scan_protocol: The slides were dried by centrifugation at 500 r/min for 5 min and scanned immediately using the GenePix 4000A scanner (Axon). The settings for PMT gain were adjusted during the initial rapid scan to achieve a balance between the two channels and these settings were used for the high resolution scan. GenePix version 4.1 was used to perform image analysis and feature segmentation.

data_processing: Normalisation was performed using a subset of high-intensity methylated clones that demonstrated consistent log-ratios between replicate arrays.

source_name: MMASS_methylated DNA

label_protocol: 300 ng of PCR product together with 0.5 ng of control Arabidopsis thaliana cDNA (synthesized from pARAB obtained from the Microarray Centre, University Health Network, Toronto, Canada) were indirectly labeled using aminoallyl-dUTP and the the BioPrime Labeling Kit (Invitrogen).  300 ng of PCR product together with 0.5 ng of control Arabidopsis thaliana cDNA (synthesized from pARAB obtained from the Microarray Centre, University Health Network, Toronto, Canada) were indirectly labeled using aminoallyl-dUTP and the the BioPrime Labeling Kit (Invitrogen).

growth_protocol: Not applicable

extract_protocol: Genomic DNA was digested using MseI then ligated to linker. For representation of methylated sequences, the sample was restricted by a combination of BstUI, HhaI and HpaII. Then a linker PCR was carried out using the adaptor ligated to the MseI fragments. For representation of unmethylated sequences, subtraction hybrididzation was used to remove an amplicon of methylated sequences.

treatment_protocol: Not applicable

tag: Sex

value: male

tag: age

tag: survival

value: Short (< 5 years)

source_name: MMASS_unmethylated DNA


title: IMR90(shp53)

description: Sample 3

source_name: shRNA-p53-treated fibroblasts

value: fibroblasts


title: Gastric cancer 60T

value: female


title: Subject_3 [NimbleGen]

value: Control


title: Subject_1 [NimbleGen]


title: Subject_7 [Illumina]

description: Lymphoblast isolated from whole blood

hyb_protocol: Illumina standard protocol

scan_protocol: Illumina standard protocol

data_processing: Beta values were convereted to M-values using the Du et al.(2010) conversion then z-transformed (normalized data)

label: Cy5 and Cy3

source_name: Lymphoblast DNA

label_protocol: Illumina standard protocol

extract_protocol: DNA isolated using cold protein precipitation (Lahiri and Schnabel, 1993)


title: IMR90(WT)

description: Sample 1

source_name: wildtype fibroblasts, no treatment

value: negative control


title: IMR90(shp16)

description: Sample 2

source_name: shRNA-p16-treated fibroblasts


title: IMR90(hTERT)

description: Sample 4


title: Subject_8 [NimbleGen]


title: ventricle_both_E5_normal_techrep1

source_name: Heart, ventricles (right and left), stage E5, normal

tag: tissue

value: normal


title: Subject_4 [Illumina]

description: Lymphoblast isolated from whole blood

value: Nicotine Dependent


title: Gastric cancer 45T


title: Subject_2 [Illumina]

description: Lymphoblast isolated from whole blood


title: Subject_5 [NimbleGen]


title: Gastric cancer 17T


title: Gastric cancer 74T

value: Long (> 5 years)


title: Subject_6 [Illumina]

description: Lymphoblast isolated from whole blood


title: Subject_8 [Illumina]

description: Lymphoblast isolated from whole blood


title: Gastric cancer 47T


title: ventricle_both_E5_CTB_techrep1

source_name: Heart, ventricles (right and left), stage E5, conotruncal banded

value: Heart, ventricles (right and left)

value: contruncal banded


title: miR-214_replicate3

city: Salamanca

first: Norma

middle: Carmen

last: Gutierrez

department: Hematology

country: Spain

institute: University Hospital

description: H929 cell line transfected with non-targeting control

hyb_protocol: Labeled RNA was hybridized to Human Gene 1.0 ST Array

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: Expression value for each probe set was calculated using dChip program that uses Li and Wong algorithm.

label: Biotin

source_name: Myeloma cell line

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA).

extract_protocol: RNA was extracted from the cell lines using Trizol reagent (Invitrogen) according to the standard protocol. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Tech, Palo Alto, CA, USA).

tag: transfection


title: Subject_1 [Illumina]

description: Lymphoblast isolated from whole blood


title: ventricle_both_E4_normal_techrep1

source_name: Heart, ventricles (right and left), stage E4, normal


title: ventricle_right_E10_normal_techrep2

source_name: Heart, right ventricle, stage E10, normal

value: Heart, right ventricle


title: Subject_3 [Illumina]

description: Lymphoblast isolated from whole blood


title: ventricle_both_E5_CTB_techrep2


title: ventricle_right_E10_normal_techrep1


title: Gastric cancer 50T


title: Gastric cancer 52T


title: Subject_5 [Illumina]

description: Lymphoblast isolated from whole blood


title: N87 FOXD3 ChIP-chip Slide 2

description: Agilent Human Promoter ChIP-on-Chip Set 1 of 2

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

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Agilent Feature Extraction Software (9.7) was used for background subtraction and LOWESS normalization log2 ratio (test/reference).

source_name: N87 cells anti-FOXD3 Ab immunoprecipitated

label_protocol: DNA were amino-allyl labelled using randomly-primed, Klenow-based extension protocol. Cy5/3 dye was then incorporated into the DNA using in-direct labeling by incubating the dye with DNA for 3 hours.

growth_protocol: The gastric tumor cell line was maintained in RPMI1640 supplemented with 10% FBS.

extract_protocol: ChIP assays were performed by using Transcription Factor ChIP kit (Diagenode). IP and input DNA were then purified with standard phenol/chloroform method.

treatment_protocol: No treatment was performed. FOXD3 target genes in normal condition were identified.

value: Gastric cancer derived from a liver metastasis

tag: cell line

value: N87 cells

value: anti-FOXD3 Ab (Millipore, Catalog no.:AB5687, Lot no.:LV1473019)

source_name: N87 cells IgG immunoprecipitated

value: IgG


title: Anti_Sox2

city: Kyoto

first: Nobuyuki

last: Tanimura

address: Yoshida-Konoe-cho, Sakyo-ku

department: Graduate School of  Biostudies

country: Japan

institute: Kyoto University

description: Sox2 ChIP, E14, promoter

hyb_protocol: Labeled DNA was hybridized for 16 hr at 45°C on GeneChip Mouse Promoter 1.0R Array. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Using Tiling Analysis Software (TAS, Affymetrix), the CEL files were quantile-normalized, and the probe signals were calculated as the ratio relative to input (bandwidth = 250).
Bar files contain the fold difference of immunoprecipitated DNA signals relative to input DNA signals for each probe.

source_name: Sox2 ChIP DNA from E14 mouse ES cells

label_protocol: Fragmented DNA was labeled with biotin by Terminal deoxynucleotidyl Transferase (TdT).

growth_protocol: E14 mouse ES cells, cultured in feeder-free conditions, were maintained in Dulbecco’s modified Eagle’s medium, with 15% fetal bovine serum (FBS), 2 mM L-glutamine, 0.1 mM non-essential amino acid, 1 mM sodium pyruvate, 100 μM 2-mercaptoethanol, and LIF.

extract_protocol: Cells were cross-linked with 1% formaldehyde for 10 min at room temperature and then quenched with 125 mM glycine. Fixed cells were washed twice in cold 1x PBS and harvested using silicon scraper. Cells were re-suspended in Lysis Buffer 1 (50mM Hepes-KOH pH 7.8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, and 1x Complete EDTA-free (Roche)), rotated at 4°C for 10 min, and centrifuged. Cells were re-suspended in Lysis Buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5mM EGTA, and 1x Complete EDTA-free), rocked at room temperature for 10 min, and centrifuged. Cells were re-suspended in Lysis Buffer 3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, and 1x Complete EDTA-free) and sonicated. Triton X-100 was added to sonicated lysate (1% final concentration) and centrifuged. Supernatants were subjected to immunoprecipitation. Each antibody was pre-bound by incubating with Dynabeads Protein G in blocking buffer (1x PBS supplemented with 0.5% BSA) overnight at 4°C. Washed beads were added to the chromatin lysates and incubated overnight at 4°C. Immunoprecipitated beads were washed 5 times with Wash Buffer (50 mM Hepes-KOH pH 7.8, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate, and 1x Complete EDTA-free) and once with TE containing 50 mM NaCl, and then incubated in Elution Buffer (1% SDS, 10 mM EDTA, and 50 mM Tris-HCl pH 8.0) at 65°C. Immunoprecipitated beads in Elution Buffer were incubated at 65°C overnight and beads were spun down. Supernatant was diluted with TE and treated sequentially with RNaseA for 2 h and Proteinase K for 2 h. DNA was purified by phenol:chloroform:isoamyl alcohol extraction and precipitation with ethanol.

value: embryonic stem cells

tag: antibody

source_name: Input DNA from E14 mouse ES cells


title: Anti_Sall4

description: Sall4 ChIP, E14, promoter

source_name: Sall4 ChIP DNA from E14 mouse ES cells


title: Gastric cancer 12T


title: NC_replicate3

value: non-targeting control


title: Gastric cancer 8T

value: male


title: ventricle_left_E10_techrep2

source_name: Heart, left ventricle, stage E10

value: Heart, left ventricle

tag: experimental treatment


title: miR-214_replicate2

description: H929 cell line transfected with miR-214

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA)


title: batch2c-pNF.AS32

description:
AS32
SAMPLE 68

value: Neurofibroma


title: miR-214_replicate1

description: H929 cell line transfected with miR-214


title: H pylori-infected vs. control gastric tissues-1

description: Agilent Mouse CpG Island ChIP-on-Chip Microarray set 1 of 1

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction Software (9.10.3.7) was used for background subtraction and LOWESS normalization log2 ratio Cy5/Cy3.

source_name: H pylori-infected gastric tissue

growth_protocol: H pylori Sydney strain-1 (SS1) was cultured in Brucella broth with 5% fetal bovine serum under microaerobic condition for 48 hr at 37C with mild shaking (100 r.p.m.).

extract_protocol: Genomic DNA from gastric tissues was extracted using QIAamp DNA Mini Kit (Qiagen) and sonicated into fragments of 200-600 base-pair. Methylated DNA was isolated with affinity purification using MethylMinerTM Methylated DNA Enrichment kit (Invitrogen) according to the manufacturer’ protocol.

treatment_protocol: Male C57BL/6 mice were gavaged with H pylori SS1 or broth control. The mice were sacrificed after 40 weeks. Stomach tissues were collected for histological examination, H pylori confirmation and DNA methylation analysis.

tag: gender

tag: strain

value: stomach

value: adult

source_name: Control gastric tissue


title: H pylori-infected vs. control gastric tissues-2

description: Agilent Mouse CpG Island ChIP-on-Chip Microarray set 1 of 2


title: NC_replicate1


title: NC_replicate2


title: ventricle_left_E10_techrep1

value: normal


title: N87 FOXD3 ChIP-chip Slide 1

description: Agilent Human Promoter ChIP-on-Chip Set 1 of 1


title: Gan(BALB/c)2

status: Public on Dec 27 2012

city: kanazawa

first: masanobu

last: oshima

address: Kakuma-machi

institute: kanazawa university

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Single Array Analysis were calculated by  Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: adult gastric tumor in glandular stomach

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3'IVT Express Kit（Affymetrix) from 250 ng total RNA according to the manufacturer's instructions.  Biotinylated cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: All mice were maintained in SPF facility.

extract_protocol: Total RNA was extracted using ISOGEN according to the manufacture's protocol.

treatment_protocol: Tumor tissues or normal stomach were sampled at 40-50 weeks of age, and homegenized in ISOGEN (Nippon Gene, Japan).

value: BALB/c

value: Wnt1, Ptgs2, Ptges transgenic


title: ventricle_both_E4_normal_techrep2

value: Heart, ventricles (right and left)


title: Gan(TNF KO)2

value: Wnt1, Ptgs2, Ptges transgenic; TNF-alpha knockout

value: adult gastric tumor in glandular stomach


title: Gan(BALB/c)3


title: Gan3


title: Gan(TNF KO)1


title: Gan(TNF KO)3


title: Gan(BALB/c)1


title: Gan1


title: Gan2


title: WT1

source_name: adult normal glandular stomach

value: wild type

value: adult normal glandular stomach


title: Sox11 loss-of-function mutant retina at E18

city: Minato-ku, Tokyo

first: Sumiko

last: Watanabe

address: 4-6-1 Shirokane-dai

department: Institute of Medical Science

institute: University of Tokyo

hyb_protocol: 10 µg of fragmented cRNA were hybridized (45°C, 16 hours). Hybridization was controlled by adding cRNA cocktail (bioB, bioC, bioD, cre). Washing and staining were performed in a Fluidics Station 450 (Affymetrix) using the protocol EukGE-WS2v5.

scan_protocol: Scanning was performed in an Affymetrix GeneChip® Scanner 3000 7G. Chip analysis was performed using the Affymetrix GeneChip® Operating Software v1.4.

data_processing: Affymetrix GeneChip Operating Software v1.4. The average values were scaled to 100 so that all chips could be directly compared.

source_name: Sox11 KO retina

label_protocol: 500ng of total RNA was reverse transcribed using the SuperScript II system for cDNA synthesis (Invitrogen) according to the protocol Rev.3 recommended by Affymetrix. The oligonucleotide used for priming was 5'-ggccagtgaattgtaatacgactcactatagggaggcgg-(t)24-3' (Affymetrix). Double-stranded cDNA was cleaned up by the Sample Cleanup Module (Affymetrix). In vitro transcription was performed on all cDNAs using the GeneChip® IVT Labeling Kit (Affymetrix). The cRNA was cleaned up by using RNeasy Mini spin columns (QIAGEN). The cRNA was fragmented by metal-induced hydrolysis.

growth_protocol: Not applicable.

extract_protocol: Retinaes were dissected from all littermate embryos, and all samples were genotyped. From each retina of WT and Sox11 mutant embryo, RNA was extracted by the RNeasy Plus Micro kit (QIAGEN), and cDNA synthesis and amplification were performed using the cDNA Synthesis and Amplification kit (Affymetrix).

treatment_protocol: Not applicable.

tag: strain/background

tag: genotype/variation

value: retina


title: WT3

tag: genotype


title: WT2


title: HET Spleen 54d Mouse1

city: Notre Dame

first: Md Suhail

last: Alam

state: IN Indiana

address: 103 Galvin, University of Notre Dame, IN

department: Center for Rare and Neglected Diseases/Biological Sciences

institute: University of Notre Dame

description: Gene expression data from spleen of Npc1+/- mouse1 of age 54 days

hyb_protocol: Affymetrix mouse 430 2.0 array hybridization were performed by 'UCLA Clinical Microarray Core, UCLA, Los Angeles, CA, USA, according to manufacturer's instrcutions

scan_protocol: The acquisition if array image was undertaken by using Affymetrix GeneChip Command Console 1.1 (AGCC).

data_processing:
The data were analyzed using DNA-Chip Analyzer (D-Chip) with the .CEL files obtained from AGCC. We used a PM/MM difference model for estimating gene expression level and quantile approach for data normalization.
Thresholds for selecting significant genes were set at a relative difference ³1.5-fold, absolute difference ³100 signal intensity units and p<0.05. Genes that met all three criteria simultaneously were considered as significant change.

source_name: Spleen from 54 days Npc1+/- mouse1

label_protocol: Biotinylated cRNA were prepared using 'MessageAmpTM Premier Amplification Kit (Invitrogen)' according to the manufactureres instrcutions.

growth_protocol: Mouse were kept and breeding was done at Freimann Life Scinece Center, University of Notre Dame, IN.

extract_protocol: Total RNA from brain, liver and speleen was isolated using 'Roche MagNa Pure Compact automated System' according to the manufacturer's instructions.

value: Spleen

value: 54 days

tag: subject

tag: genetic background


title: HET Spleen 67d Mouse1

description: Gene expression data from spleen of Npc1+/- mouse1 of age 67 days

source_name: Spleen from 67 days Npc1+/- mouse1

value: 67 days


title: NPC Spleen 25d Mouse1

description: Gene expression data from spleen of Npc1-/- mouse1 of age 25 days

source_name: Spleen from 25 days Npc1-/- mouse1

value: 25 days


title: NPC Spleen 67 Mouse1

description: Gene expression data from spleen of Npc1-/- mouse1 of age 67 days

source_name: Spleen from 67 days Npc1-/- mouse1


title: HET Spleen 55d Mouse1

description: Gene expression data from spleen of Npc1+/- mouse1 of age 55 days

source_name: Spleen from 55 days Npc1+/- mouse1

value: 55 days


title: NPC Spleen 20d Mouse1

description: Gene expression data from spleen of Npc1-/- mouse1 of age 20 days

source_name: Spleen from 20 days Npc1-/- mouse1

value: 20 days


title: NPC Spleen 54d Mouse1

description: Gene expression data from spleen of Npc1-/- mouse1 of age 54 days

source_name: Spleen from 54 days Npc1-/- mouse1


title: HET Spleen 67d Mouse2

source_name: Spleen from 67 days Npc1+/- mouse2


title: HET Spleen 20d Mouse1

description: Gene expression data from spleen of Npc1+/- mouse1 of age 20 days

source_name: Spleen from 20 days Npc1+/- mouse1


title: NPC Spleen 55d Mouse1

description: Gene expression data from spleen of Npc1-/- mouse1 of age 55 days

source_name: Spleen from 55 days Npc1-/- mouse1


title: NPC Spleen 71d Mouse1

description: Gene expression data from spleen of Npc1-/- mouse1 of age 71 days

source_name: Spleen from 71 days Npc1-/- mouse1

value: 71 days


title: Wild type retina at E18

source_name: wild-type retina

value: wild-type


title: NPC Liver 71d Mouse1

description: Gene expression data from liver of Npc1-/- mouse1 of age 71 days

source_name: Liver from 71 days Npc1-/- mouse1

value: Liver


title: NPC Liver 55d Mouse1

description: Gene expression data from liver of Npc1-/- mouse1 of age 55 days

source_name: Liver from 55 days Npc1-/- mouse1

value: BALB/c


title: ventricle_both_E5_normal_techrep2

source_name: Heart, ventricles (right and left), stage E5, normal

tag: developmental stage

value: normal


title: HET Liver 54 Mouse1

description: Gene expression data from liver of Npc1+/- mouse1 of age 54 days

source_name: Liver from 54 days Npc1+/- mouse1


title: NPC Liver 20d Mouse1

description: Gene expression data from liver of Npc1-/- mouse1 of age 20 days

source_name: Liver from 20 days Npc1-/- mouse1


title: NPC Liver 67 Mouse1

description: Gene expression data from liver of Npc1-/- mouse1 of age 67 days

source_name: Liver from 67 days Npc1-/- mouse1


title: NPC Liver 54d Mouse1

description: Gene expression data from liver of Npc1-/- mouse1 of age 54 days

source_name: Liver from 54 days Npc1-/- mouse1


title: HET Liver 67d Mouse1

description: Gene expression data from liver of Npc1+/- mouse1 of age 67 days

source_name: Liver from 67 days Npc1+/- mouse1


title: HET Liver 67d Mouse2

source_name: Liver from 67 days Npc1+/- mouse2


title: HET Liver 25d Mouse1

description: Gene expression data from liver of Npc1+/- mouse1 of age 25 days

source_name: Liver from 25 days Npc1+/- mouse1


title: HET Spleen 25d Mouse1

description: Gene expression data from spleen of Npc1+/- mouse1 of age 25 days

source_name: Spleen from 25 days Npc1+/- mouse1


title: HET Liver 55d Mouse1

description: Gene expression data from liver of Npc1+/- mouse1 of age 55 days

source_name: Liver from 55 days Npc1+/- mouse1


title: NPC Liver 25d Mouse1

description: Gene expression data from liver of Npc1-/- mouse1 of age 25 days

source_name: Liver from 25 days Npc1-/- mouse1


title: HET Brain 81d Mouse1

description: Gene expression data from brain of Npc1+/- mouse1 of age 81 days

source_name: Brain from 81 days Npc1+/- mouse1

value: Brain

value: 81 days


title: HET Brain 82d Mouse1

description: Gene expression data from brain of Npc1+/- mouse1 of age 82 days

source_name: Brain from 82 days Npc1+/- mouse1

value: 82 days


title: HET Liver 20d Mouse1

description: Gene expression data from liver of Npc1+/- mouse1 of age 20 days

source_name: Liver from 20 days Npc1+/- mouse1


title: Thymus wt 4

city: Brisbane

first: Brendan

middle: John

last: O'Sullivan

state: Queensland

address: Level 6, 37 Kent Street Woolloongabba

country: Australia

institute: The University of Queensland Diamantina Institute Translational Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Array data were processed using the Illumina GenomeStudio software, transformed by variance stabilization transformation and normalized by robust spline normalization using Lumi.

source_name: Thymus

label_protocol: Biotinylated cRNA was generated from 500 ng of total RNA using the Illumina TotalPrep cRNA Amplification Kit® (ABI)

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

value: thymus

value: RelB+/-

value: 8 weeks


title: NPC Brain 82d Mouse1

description: Gene expression data from brain of Npc1-/- mouse1 of age 82 days

source_name: Brain from 82 days Npc1-/- mouse1


title: T47D-ELF5-rep1

city: Darlinghurst

first: Mark

last: Cowley

state: NSW

address: 384 Victoria St.

department: Genome Informatics & Clinical Genomics

institute: Garvan Institute of Medical Research

description:
MK_TV+1_(HuGene-1_0-st-v1).CEL
RNA from T47D cell line, dox treated, replicate 1

hyb_protocol: Labeled, fragmented RNA hybridized to Affymetrix Human Gene 1.0 ST Gene Arrays at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

scan_protocol: Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

data_processing: Within each batch, data was RMA normalised using NormalizeAffymetrixST (version 1) GenePattern module from the Peter Wills Bioinformatics Centre's GenePattern Server: http://pwbc.garvan.unsw.edu.au/gp. T47D and MCF7 arrays were normalised within the context of a larger set of microarrays, so if you re-normalise these data using the 8 arrays here, the value will differ slightly.

source_name: T47D, ELF5 induced

label_protocol: RNA was fragmented, biotin labeled at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

growth_protocol: Human breast carcinoma MCF7-EcoR and T47D-EcoR (Brummelkamp et al, 2002, Science 296) cell lines were grown in RPMI 1640 medium (Invitrogen) supplemented with 10 % Tet System Approved fetal bovine serum (FBS) (Clontech). Cells were infected with pHUSH-ProEX-based produced by the Platinum E cell line (Morita et al., 2000). Transient transfection with Elf5-containing plasmid constructs used FuGENE reagent (Roche) or Lipofectamine LTX (Invitrogen) according to manufacturer’s instructions. Cells were maintained in the presence of puromycin (Sigma) at a concentration of 1μg/ml for MCF7-EcoR and 2μg/ml for T47D-EcoR.

extract_protocol: Total RNA was extracted with the RNeasy Minikit (Qiagen) and DNase-treated with the DNase kit (Qiagen) according to manufacturer’s instructions. RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: T47D and MCF7 cells were treated with doxycycline (Clontech) at 0.1 μg/ml, R5020 (Du Pont) at 10 nM or 17β-estradiol (Sigma) at 10 mM. Dox-containing medium was changed every 24 hours to ensure optimum Dox activity.

tag: inducible vector

value: doxycycline inducible pHUSH ProEx vector containing ELF5

tag: phenotype

value: luminal

tag: treatment

value: doxycycline

tag: batch


title: T47D-ELF5-rep2

description:
MK_TV+3_(HuGene-1_0-st-v1).CEL
RNA from T47D cell line, dox treated, replicate 2


title: T47D-vehicle-rep1

description:
MK_TV-2_(HuGene-1_0-st-v1).CEL
RNA from T47D cell line, vehicle treated, replicate 1

source_name: T47D, untreated

value: vehicle


title: T47D-vehicle-rep2

description:
MK_T_V-3A_(HuGene-1_0-st-v1).CEL
RNA from T47D cell line, vehicle treated, replicate 2


title: Thymus ko 3

tag: tissue

value: RelB-/-

tag: age


title: NPC Brain 67d Mouse1

description: Gene expression data from brain of Npc1-/- mouse1 of age 67 days

source_name: Brain from 67 days Npc1-/- mouse1

value: 67 days


title: Bme_Control_rep2

type: mixed

city: College Station

first: Leslie

middle: Garry

last: Adams

state: TX

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

description: Biological replicate 2 of 2. Total RNA from BME at time 0 co-hybridized against BME gDNA

hyb_protocol: Slides were hybridized at 45ºC for ~20 h in a dark, humid chamber (Corning) and washed for 10 min at 45ºC with low stringency buffer [1X SSC, 0.2% SDS] followed by two 5-min washes in a higher stringency buffer [0.1X SSC, 0.2% SDS and 0.1X SSC] at room temperature with agitation. Slides were dried by centrifugation at 800X g for 2 min and immediately scanned. Prior to hybridization, microarrays were pre-treated by washing in 0.2% SDS, followed by 3 washes in distilled water and incubated in prehybridization buffer [5X SSC, 0.1% SDS; 1% BSA in 100ml of water] at 45ºC for at least 45 min. Immediately before hybridization, the slides were washed 4 times in distilled water, dipped in 100% isopropanol for 10 sec and dried by centrifugation at 1,000X g for 2 min.

scan_protocol: Microarrays were scanned using a commercial laser scanner (GenePix 4100; Axon Instruments Inc., Foster City, CA). The genes represented on the arrays were adjusted for background and normalized to internal controls using image analysis software (GenePixPro 6.0; Axon Instruments Inc.).

data_processing: Genes with fluorescent signal values below background were disregarded in all analyses. Pathogen arrays were normalized against B. melitensis genomic DNA as previously described (Talaat, 2002). Data were analyzed using GeneSifter (VizX Labs, Seattle, WA). The signal values of every gene (triplicate spots in 4 arrays = 12 spots) for each experiment (i.e. 4 and 12 h) were averaged, the fold-change calculated, and Student’s t test performed. At each time point, genes determined to be expressed at statistically significantly levels on pathogen arrays hybridized with probes generated from B. melitensis-infected cells (fold-change > 2 and P value < 0.05) were subtracted from the final list of differentially expressed genes.

organism: Brucella melitensis

source_name: B. melitensis 16M, total RNA, time 0, labeled with Cy3 (green)

label_protocol: Ten μg of total RNA were reverse transcribed overnight to amino-allyl cDNA using 1.5 μg of primers (BmGDPs), 0.6 μl 50X dNTPs/ aa-dUTP mix (2:3 aa-dUTP:dTTP) and 400U Superscript III. The reaction was stopped by incubating the samples with 1M NaOH at 65ºC for 15 min and neutralized with 1M HCl. Unincorporated aa-dUTPs and free amines were removed by column passage and dried using a Speed-Vac. Dried samples were re-hydrated in 0.1M Na2CO3 buffer (pH 9.0) and labeled with Cy3-ester. After one hour incubation in the dark, uncoupled dye was removed using PCR purification kit and dye incorporation calculated by NanoDrop® ND-1000 (NanoDrop). Dried, labeled cDNA samples were resuspended in nuclease–free water and mixed with 0.5 μg of labeled (Cy5) B. melitensis gDNA to the final volume of 35 μl. B. melitensis genomic DNA was labeled overnight by directed incorporation of Cy5-dCTP during reverse transcription using random primers solution and Klenow fragment from BioPrime DNA labeling system kit and 50X dNTPs (1:2 dCTP). The reaction was stopped by adding 5 μl of stop buffer from the BioPrime kit and unincorporated Cy dye was removed using PCR purification kit, eluted in 1mM Tris pH 8.0 and kept in the dark at 4ºC until used. Samples were heated at 95ºC for 5 min and then kept at 45ºC until hybridization. Following incubation at 45ºC, 35 μl of 2X formamide-based hybridization buffer [50% formamide; 10X SSC; 0.2% SDS] was mixed with each sample and applied to a custom 3.2K B. melitensis oligo-array.

extract_protocol: First, total RNA from B. melitensis-infected HeLa cells was extracted by TRI-Reagent® (Ambion, Austin, TX) according to manufacturer’s instructions. Then, intracellular B. melitensis total RNA was initially enriched and then amplified from 50 μg of total RNA from B. melitensis-infected HeLa cells at 4 and 12 h p.i. The enrichment procedure was performed using the MICROBEnrich® kit (Ambion) according to the manufacturer’s instructions. After enrichment, the remaining RNA was amplified in a 3 step-protocol. In the first step, the protocol utilizes genome-directed primers (GDPs) to bias the reverse transcription to bacterial transcripts and the overhang tailing activity of Moloney murine leukemia virus (MMLV) reverse transcriptase to add the T7 promoter to cDNAs during reverse transcription. Then, the second-strand cDNA is synthesized, and finally in vitro transcription is carried out using a T7 polymerase. Control B. melitensis total RNA was isolated by adding ice-cold ethanol/phenol solution to the culture and the bacteria recovered by centrifugation. The media was then removed and the pellet suspended in TE buffer–lysozyme solution containing 10% SDS. After 2 min of incubation, acid water-saturated phenol was added to the lysate and mixed, and the sample incubated for 6 min at 64ºC. Tubes were kept on ice for at least 2 min and then centrifuged at maximum speed. The upper layer, containing the RNA, was transferred to a new tube, mixed with an equal volume of chloroform and then separated by centrifugation. The aqueous phase was mixed with 100% cold ethanol and stored at -20ºC. After at least one hour of incubation, RNA was pelleted by centrifugation, washed in 80% ethanol and suspended in DEPC-treated water with 2% DTT and 1% RNase inhibitor. Contaminant genomic DNA was removed by RNase-free DNase I treatment and samples were stored at -80ºC until used.  B. melitensis genomic DNA was isolated from a pellet from a saturated culture of B. melitensis 16M grown on tryptic soy broth (TSB), washed with 25 ml of J-buffer [0.1M Tris pH 8.0; 0.1M EDTA; 0.15M NaCl] and then lysed in 1 ml of J-buffer containing 10% lysozyme solution (10mg/ml in 0.25M Tris, pH 8.0). After 10 min of incubation, DNA was released from the cells by sodium salt of N-lauroyl sarcosine followed by degradation of RNA by DNase-free RNase, and digestion of proteins with proteinase K. The resulting solution was transferred to a dialysis bag and dialyzed against TE [10mM Tris, pH 8.0 and 1mM EDTA] overnight at 37ºC. DNA was subsequently extracted twice using neutral water-saturated phenol first and then twice with ether before dialyzing overnight against TE. Genomic DNA was stored at 4ºC until used.

tag: Strain

value: 16M Biotype 1 (ATCC 23456)

source_name: Genomic DNA from Brucella melitensis 16M labeled with Cy5 (red).


title: HET Brain 67d Mouse1

description: Gene expression data from brain of Npc1+/- mouse1 of age 67 days

source_name: Brain from 67 days Npc1+/- mouse1


title: Bme-inf HeLa_12h_rep3_Bmel array

description: Biological replicate 3 of 4. Total RNA from BME-infected HeLa cells at 12h p.i. co-hybridized against BME gDNA

source_name: Bmel-infected HeLa cells, total RNA, 12h p.i., Cy3

tag: Cell line

value: S3 (ATCC; CCL 2.2)


title: NPC Brain 84d Mouse1

description: Gene expression data from brain of Npc1-/- mouse1 of age 84 days

source_name: Brain from 84 days Npc1-/- mouse1

value: 84 days


title: Thymus wt 3


title: Thymus ko 2


title: WT Brain 67d Mouse1

source_name: Brain from 67 days Npc1+/+ mouse1

value: BALB/c


title: Bme-inf HeLa_12h_rep4_Bmel array

description: Biological replicate 4 of 4. Total RNA from BME-infected HeLa cells at 12h p.i. co-hybridized against BME gDNA


title: Bme_Control_rep1

description: Biological replicate 1 of 2. Total RNA from BME at time 0 co-hybridized against BME gDNA


title: Bme-inf HeLa_12h_rep2_Bmel array

description: Biological replicate 2 of 4. Total RNA from BME-infected HeLa cells at 12h p.i. co-hybridized against BME gDNA


title: Bme-inf HeLa_12h_rep1_Bmel array

description: Biological replicate 1 of 4. Total RNA from BME-infected HeLa cells at 12h p.i. co-hybridized against BME gDNA


title: Thymus wt 2


title: MCF7-vehicle-rep2

description:
MK_MV-2_(HuGene-1_0-st-v1).CEL
RNA from MCF7 cell line, vehicle treated, replicate 2

source_name: MCF7, untreated

tag: cell line


title: MCF7-ELF5-rep1

description:
MK_MV+1_(HuGene-1_0-st-v1).CEL
RNA from MCF7 cell line, dox treated, replicate 1

source_name: MCF7, ELF5 induced


title: MCF7-ELF5-rep2

description:
MK_MV+3_(HuGene-1_0-st-v1).CEL
RNA from MCF7 cell line, dox treated, replicate 2


title: NPC Brain 62d Mouse1

description: Gene expression data from brain of Npc1-/- mouse1 of age 62 days

source_name: Brain from 62 days Npc1-/- mouse1

value: 62 days


title: Thymus wt 1


title: Intrac Bme_12h_rep4

description: Biological replicate 4 of 4. Enriched and amplified total RNA from intracellular Bmel at 12h post-infection co-hybridized against BME gDNA.

source_name: Enriched and amplified total RNA, intracellular Brucella melitensis 16M, 12h p.i., labeled with Cy3 (green).


title: HeLa_Control_12h_rep2

description: Biological replicate 2 of 4. Total RNA from HeLa cells, 12h control, co-hybridized against universal human reference RNA

data_processing: Genes with fluorescent signal values below background were disregarded in all analyses. Host arrays were initially normalized against universal human reference RNA (Weil et al., 2002) and resulting data analyzed using Seralogix’s suite of gene expression analysis and modeling tools (www.seralogix.com). Differentially expressed genes were found to be significant based on Seralogix’s Bayesian z-score method (z > 1.96 or equivalently p < 0.05). This method infers a given gene’s standard deviation by computing a local average standard deviation for genes showing similar expression levels. Genes are ordered within a treatment group according to their average expression levels. Then, for a given gene, the k next higher expressing genes and the k next lower expressing genes standard deviations are used to obtain an average standard deviation of these 2k + 1 genes. This approach results in a nonparametric smoothing function for inferring any given gene’s standard deviation from its expression level. For this study k = 50 was utilized. The inferred standard deviations are derived for each time point and condition (infected and controls) and used in a z-score method to identify significant differentially expressed genes.

source_name: Non infected HeLa cells, total RNA, 12h, Cy5

label_protocol: Ten μg of total RNA were reverse transcribed overnight to amino-allyl cDNA using 6 µg of random hexamer primers, 0.6 μl 50X dNTPs/ aa-dUTP mix (2:3 aa-dUTP:dTTP) and 400U Superscript III. The reaction was stopped by incubating the samples with 1M NaOH at 65ºC for 15 min and neutralized with 1M HCl. Unincorporated aa-dUTPs and free amines were removed by column passage and dried using a Speed-Vac. Dried samples were re-hydrated in 0.1M Na2CO3 buffer (pH 9.0) and labeled with Cy5-ester (experimental HeLa RNA) or Cy3-ester (reference HeLa RNA). After one hour incubation in the dark, uncoupled dye was removed using PCR purification kit and dye incorporation calculated by NanoDrop® ND-1000 (NanoDrop). The dried, labeled cDNA samples were re-suspended in 20 μl of nuclease-free water (experimental RNA) and human genomic DNA Cot1 (reference RNA), mixed and heated at 95ºC for 10 min, 60ºC for 10 min, and then 25ºC for 10 min. Samples were kept at 45ºC until hybridization. Immediately before hybridization, 40 μl of 2X formamide-based hybridization buffer was added to each sample.

extract_protocol: Total RNA from infected and non-infected HeLa cell cultures was extracted by TRI-Reagent® (Ambion, Austin, TX) according to manufacturer’s instructions. The resultant RNA pellet was re-suspended in DEPC-treated water with 2% DTT and 1% RNase inhibitor. Contaminant genomic DNA was removed by RNase-free DNase I treatment according to the manufacturer’s instructions, and samples were stored at -80ºC until used.

source_name: Universal Human Reference RNA labeled with Cy3 (green).

tag: Several human cell lines

tag: Comercial source (Stratagene)


title: HET Brain 62d Mouse1

description: Gene expression data from brain of Npc1+/- mouse1 of age 62 days

source_name: Brain from 62 days Npc1+/- mouse1

value: Brain


title: HET Brain 59d Mouse1

description: Gene expression data from brain of Npc1+/- mouse1 of age 59 days

source_name: Brain from 59 days Npc1+/- mouse1

value: 59 days


title: HeLa_Control_12h_rep3

description: Biological replicate 3 of 4. Total RNA from HeLa cells, 12h control, co-hybridized against universal human reference RNA


title: HeLa_Control_12h_rep4

description: Biological replicate 4 of 4. Total RNA from HeLa cells, 12h control, co-hybridized against universal human reference RNA


title: Thymus ko 1

source_name: Thymus


title: Intrac Bme_12h_rep2

description: Biological replicate 2 of 4. Enriched and amplified total RNA from intracellular Bmel at 12h post-infection co-hybridized against BME gDNA.


title: HCC1937-ELF5-rep3

description:
HL_1937S3_(HuGene-1_0-st-v1).CEL
RNA from HCC1937 cell line, siRNA-vs-ELF5 treated, replicate 3

source_name: HCC1937, ELF5 knockdown

growth_protocol: Human breast, basal A carcinoma HCC1937 cell lines were also grown in 10% FBS RPMI medium.

treatment_protocol: HCC1937 cells were transiently knocked down with siRNA-vs-Elf5, or mock transfected with the transfection reagent of LF2000 and Optimem.

value: basal

value: siRNA to ELF5


title: HCC1937-ELF5-rep2

description:
HL_1937S2_(HuGene-1_0-st-v1).CEL
RNA from HCC1937 cell line, siRNA-vs-ELF5 treated, replicate 2


title: Intrac Bme_12h_rep3

description: Biological replicate 3 of 4. Enriched and amplified total RNA from intracellular Bmel at 12h post-infection co-hybridized against BME gDNA.


title: HeLa_Control_12h_rep1

description: Biological replicate 1 of 4. Total RNA from HeLa cells, 12h control, co-hybridized against universal human reference RNA


title: HCC1937-ELF5-rep1

description:
HL_1937S1_(HuGene-1_0-st-v1).CEL
RNA from HCC1937 cell line, siRNA-vs-ELF5 treated, replicate 1


title: Bme-inf HeLa_12h_rep3_HeLa array

description: Biological replicate 3 of 4. Total RNA from BME-infected HeLa cells at 12h p.i. co-hybridized against universal human reference RNA

source_name: Bmel-infected HeLa cells, total RNA, 12h p.i., Cy5


title: MCF7-vehicle-rep1

description:
MK_MV-1_(HuGene-1_0-st-v1).CEL
RNA from MCF7 cell line, vehicle treated, replicate 1


title: Bme-inf HeLa_4h_rep4_Bmel array

description: Biological replicate 4 of 4. Total RNA from BME-infected HeLa cells at 4h p.i. co-hybridized against BME gDNA

source_name: Bmel-infected HeLa cells, total RNA, 4h p.i., Cy3


title: WT Brain 60d Mouse1

description: Gene expression data from brain of Npc1+/+ mouse1 of age 60 days

source_name: Brain from 60 days Npc1+/+ mouse1

value: 60 days


title: NPC Brain 55d Mouse1

description: Gene expression data from brain of Npc1-/- mouse1 of age 55 days

source_name: Brain from 55 days Npc1-/- mouse1

value: 55 days


title: HCC1937-mock-rep3

description:
HL_1937M3_(HuGene-1_0-st-v1).CEL
RNA from HCC1937 cell line, mock treated, replicate 3

source_name: HCC1937, mock transfected

value: mock


title: NPC Brain 54d MOuse1

description: Gene expression data from brain of Npc1-/- mouse1 of age 54 days

source_name: Brain from 54 days Npc1-/- mouse1

value: 54 days


title: WT Brain 60d Mouse2

description: Gene expression data from brain of Npc1+/+ mouse2 of age 60 days

source_name: Brain from 60 days Npc1+/+ mouse2


title: Bme-inf HeLa_4h_rep3_Bmel array

description: Biological replicate 3 of 4. Total RNA from BME-infected HeLa cells at 4h p.i. co-hybridized against BME gDNA

source_name: Genomic DNA from Brucella melitensis 16M labeled with Cy5 (red).


title: HCC1937-mock-rep1

description:
HL_1937M1_(HuGene-1_0-st-v1).CEL
RNA from HCC1937 cell line, mock treated, replicate 1


title: HET Brain 55d Mouse1

description: Gene expression data from brain of Npc1+/- mouse1 of age 55 days

source_name: Brain from 55 days Npc1+/- mouse1


title: HCC1937-mock-rep2

description:
HL_1937M2_(HuGene-1_0-st-v1).CEL
RNA from HCC1937 cell line, mock treated, replicate 2


title: Bme-inf HeLa_4h_rep2_Bmel array

description: Biological replicate 2 of 4. Total RNA from BME-infected HeLa cells at 4h p.i. co-hybridized against BME gDNA


title: Bme-inf HeLa_4h_rep1_Bmel array

description: Biological replicate 1 of 4. Total RNA from BME-infected HeLa cells at 4h p.i. co-hybridized against BME gDNA


title: HeLa_Control_4h_rep4

description: Biological replicate 4 of 4. Total RNA from HeLa cells, 4h control, co-hybridized against universal human reference RNA

source_name: Non infected HeLa cells, total RNA, 4h, Cy5


title: Intrac Bme_4h_rep4

description: Biological replicate 4 of 4. Enriched and amplified total RNA from intracellular Bmel at 4h post-infection co-hybridized against BME gDNA.

source_name: Enriched and amplified total RNA, intracellular Brucella melitensis 16M, 4h p.i., labeled with Cy3 (green).


title: Bme-inf HeLa_12h_rep2_HeLa array

description: Biological replicate 2 of 4. Total RNA from BME-infected HeLa cells at 12h p.i. co-hybridized against universal human reference RNA


title: HET Brain 54d Mouse1

description: Gene expression data from brain of Npc1+/- mouse1 of age 54 days

source_name: Brain from 54 days Npc1+/- mouse1


title: HeLa_Control_4h_rep3

description: Biological replicate 3 of 4. Total RNA from HeLa cells, 4h control, co-hybridized against universal human reference RNA

source_name: Universal Human Reference RNA labeled with Cy3 (green).


title: HeLa_Control_4h_rep2

description: Biological replicate 2 of 4. Total RNA from HeLa cells, 4h control, co-hybridized against universal human reference RNA


title: Bme-inf HeLa_12h_rep1_HeLa array

description: Biological replicate 1 of 4. Total RNA from BME-infected HeLa cells at 12h p.i. co-hybridized against universal human reference RNA


title: Intrac Bme_4h_rep2

description: Biological replicate 2 of 4. Enriched and amplified total RNA from intracellular Bmel at 4h post-infection co-hybridized against BME gDNA.


title: Intrac Bme_4h_rep1

description: Biological replicate 1 of 4. Enriched and amplified total RNA from intracellular Bmel at 4h post-infection co-hybridized against BME gDNA.


title: HeLa_Control_4h_rep1

description: Biological replicate 1 of 4. Total RNA from HeLa cells, 4h control, co-hybridized against universal human reference RNA


title: NPC Brain 40d MOuse1

description: Gene expression data from brain of Npc1-/- mouse1 of age 40 days

source_name: Brain from 40 days Npc1-/- mouse1

value: 40 days


title: Bme-inf HeLa_4h_rep4_HeLa array

description: Biological replicate 4 of 4. Total RNA from BME-infected HeLa cells at 4h p.i. co-hybridized against universal human reference RNA

source_name: Bmel-infected HeLa cells, total RNA, 4h p.i., Cy5


title: HET Brain 40d Mouse1

description: Gene expression data from brain of Npc1+/- mouse1 of age 40 days

source_name: Brain from 40 days Npc1+/- mouse1


title: Intrac Bme_4h_rep3

description: Biological replicate 3 of 4. Enriched and amplified total RNA from intracellular Bmel at 4h post-infection co-hybridized against BME gDNA.


title: Bme-inf HeLa_4h_rep3_HeLa array

description: Biological replicate 3 of 4. Total RNA from BME-infected HeLa cells at 4h p.i. co-hybridized against universal human reference RNA


title: NPC Brain 37d Mouse1

description: Gene expression data from brain of Npc1-/- mouse1 of age 37 days

source_name: Brain from 37 days Npc1-/- mouse1

value: 37 days


title: Bme-inf HeLa_4h_rep2_HeLa array

description: Biological replicate 2 of 4. Total RNA from BME-infected HeLa cells at 4h p.i. co-hybridized against universal human reference RNA


title: Bme-inf HeLa_4h_rep1_HeLa array

description: Biological replicate 1 of 4. Total RNA from BME-infected HeLa cells at 4h p.i. co-hybridized against universal human reference RNA


title: HET Brain 37d Mouse1

description: Gene expression data from brain of Npc1+/- mouse1 of age 37 days

source_name: Brain from 37 days Npc1+/- mouse1


title: HET Brain 25d Mouse1

description: Gene expression data from brain of Npc1+/- mouse1 of age 25 days

source_name: Brain from 25 days Npc1+/- mouse1

value: 25 days


title: NPC Brain 20d Mouse1

description: Gene expression data from brain of Npc1-/- mouse1 of age 20 days

source_name: Brain from 20 days Npc1-/- mouse1

value: 20 days


title: HET Brain 20d Mouse1

description: Gene expression data from brain of Npc1+/- mouse1 of age 20 days

source_name: Brain from 20 days Npc1+/- mouse1


title: NPC Brain 59d Mouse1

description: Gene expression data from brain of Npc1-/- mouse1 of age 59 days

source_name: Brain from 59 days Npc1-/- mouse1


title: WT Brain 20d Mouse1

description: Gene expression data from brain of Npc1+/+ mouse1 of age 20 days

source_name: Brain from 20 days Npc1+/+ mouse1


title: Rec12_Y98F_4h_1

status: Public on Dec 26 2012

city: San Francisco

first: Kyle

last: Fowler

state: California

address: 600 16th Street

institute: University of California San Francisco

description:
Rec12_Y98F_4h_1
Rec12-FLAG IP

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

scan_protocol: Slides were imaged on an Agilent G2565AA Microarray Scanner and quantified using Agilent Feature Extraction Software (v 10.1.1.1 or 10.5.1.1).

data_processing: Dark spot and control probes were removed, as were custom probes for repetitive DNA. Output ratios were then normalized to the genome median.

organism: Schizosaccharomyces pombe

source_name: IP Rec12-Y98F protein at 4 hours in meiosis

label_protocol: Immunoprecipitated material was PCR amplified to increase signal and incorporate Cy3/Cy5-labeled dUTPs.

growth_protocol: S. pombe cells were grown in minimal media without nitrogen for ~18 hours to synchronize the cells. Nitrogen was added and the temperature shifted to 34°C, marking the start of meiosis (t=0).

extract_protocol:
For DSB analysis, no exogenous crosslinking agent was used and cells were broken with a bead beater. Chromatin was sonicated to ~500-1000 bp and Rec12-FLAG was immunoprecipitated.
For other proteins, 200 ml culture was removed and formaldehyde was added to a final concentration of 1%. Chromatin was sonicated to ~1000 bp and the protein of interest was immunoprecipitated.

tag: strain/background

value: WT

tag: time since meiosis started

value: 4 hours

tag: chip antibody

value: monoclonal anti-FLAG M2 mouse antibody

tag: antibody vendor (catalog #)

value: Sigma (F3165)

source_name: Whole-cell input for Rec12-Y98F protein at 4 hours in meiosis


title: WT Brain 25d Mouse1

description: Gene expression data from brain of Npc1+/+ mouse1 of age 25 days

source_name: Brain from 25 days Npc1+/+ mouse1

tag: genotype

tag: subject

tag: genetic background

value: BALB/c


title: Rec12_rec27d_3.5h_1

description:
Rec12_rec27d_3.5h_1
Rec12-FLAG IP

source_name: IP Rec12 protein in rec27Δ at 3.5 hours in meiosis

tag: genotype/variation

value: 3.5 hours

source_name: Whole-cell input for Rec12 protein in rec27Δ at 3.5 hours in meiosis


title: Rec8_WT_3.5h_1

description:
Rec8_WT_3.5h_1
GFP-IP

source_name: IP Rec8 protein at 3.5 hours in meiosis

value: anti-GFP from mouse (clones 7.1 & 13.1)

source_name: Whole-cell input for Rec8 protein at 3.5 hours in meiosis


title: NPC Brain 25d Mouse1

description: Gene expression data from brain of Npc1-/- mouse1 of age 25 days

source_name: Brain from 25 days Npc1-/- mouse1

value: Brain


title: Rec12_WT_3.5h_1

description:
Rec12_WT_3.5h_1
Rec12-FLAG IP

source_name: IP Rec12 protein at 3.5 hours in meiosis

source_name: Whole-cell input for Rec12 protein at 3.5 hours in meiosis


title: Rec12_Y98F_3h_1

description:
Rec12_Y98F_3h_1
Rec12-FLAG IP

source_name: IP Rec12-Y98F protein at 3 hours in meiosis

value: 3 hours

source_name: Whole-cell input for Rec12-Y98F protein at 3 hours in meiosis


title: Rec25_WT_3.5h_1

description:
Rec25_WT_3.5h_1
GFP-IP

source_name: IP Rec25 protein at 3.5 hours in meiosis

source_name: Whole-cell input for Rec25 protein at 3.5 hours in meiosis


title: Rec25_WT_3.5h_2

description:
Rec25_WT_3.5h_2
GFP-IP


title: Rec11_WT_3.5h_1

description:
Rec11_WT_3.5h_1
GFP-IP

source_name: IP Rec11 protein at 3.5 hours in meiosis

source_name: Whole-cell input for Rec11 protein at 3.5 hours in meiosis


title: Rec10_WT_3.5h_1

description:
Rec10_WT_3.5h_1
GFP-IP
Dyes swapped relative to other experiments (normally IP=Cy5; Input=Cy3).

source_name: Whole-cell input for Rec10 protein at 3.5 hours in meiosis

source_name: IP Rec10 protein at 3.5 hours in meiosis


title: Rec27_rec8d_3.5h_1

description:
Rec27_rec8d_3.5h_1
GFP-IP

source_name: IP Rec27 protein in rec8Δ at 3.5 hours in meiosis

source_name: Whole-cell input for Rec27 protein in rec8Δ at 3.5 hours in meiosis


title: Rec27_rec12d_3.5h_1

description:
Rec27_rec12d_3.5h_1
GFP-IP

source_name: IP Rec27 protein in rec12Δ at 3.5 hours in meiosis

source_name: Whole-cell input for Rec27 protein in rec12Δ at 3.5 hours in meiosis


title: Mug20_WT_3.5h_1

description:
Mug20_WT_3.5h_1
GFP-IP

source_name: IP Mug20 protein at 3.5 hours in meiosis

source_name: Whole-cell input for Mug20 protein at 3.5 hours in meiosis


title: DSBs_rec11d_1

description:
DSBs_rec11d_1
Rec12-FLAG IP

source_name: IP DSBs (Rec12 covalently linked to DNA) in rec11Δ

value: 9 hours

source_name: Whole-cell input for DSBs (Rec12 covalently linked to DNA) in rec11Δ


title: Rec27_WT_3.5h_1

description:
Rec27_WT_3.5h_1
GFP-IP

source_name: IP Rec27 protein at 3.5 hours in meiosis

source_name: Whole-cell input for Rec27 protein at 3.5 hours in meiosis


title: DSBs_rec10-109_1

description:
DSBs_rec10-109_1
Rec12-FLAG IP

source_name: IP DSBs (Rec12 covalently linked to DNA) in rec10-109

value: 11 hours

source_name: Whole-cell input for DSBs (Rec12 covalently linked to DNA) in rec10-109


title: STA_STA23_02-15-07

city: Stanford

first: Minnie

last: Sarwal

address: 703 Welch Road

department: Pediatric Nephrology

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82425.gif

hyb_protocol: not provided

scan_protocol: Affymetrix protocol

data_processing: dChip

source_name: PB from kidney transplant recipients

label_protocol: not provided

extract_protocol: not provided

tag: Kidney, Peripheral Blood

tag: disease state


title: STA_STA05_04-25-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82447.gif

tag: Kidney, Peripheral Blood leukocyte


title: AR_AR03_03-29-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82348.gif


title: STA_STA26_02-21-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82427.gif


title: STA_STA22_02-15-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82424.gif


title: STA_STA04_04-25-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82446.gif


title: AR_AR05_05-25-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82440.gif


title: STA_STA01_03-29-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82402.gif


title: Rec27_WT_3.5h_2

description:
Rec27_WT_3.5h_2
GFP-IP


title: AR_AR19_02-20-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82368.gif


title: AR_AR35_04-02-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82355.gif


title: AR_AR01_04-23-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82430.gif


title: STA_STA16_02-15-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82419.gif


title: AR_AR05_04-12-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82360.gif


title: STA_STA09_04-25-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82451.gif


title: genomic DNA from twins 1 (RS-1M)

city: Chuoshi

first: Kunio

last: Miyake

state: Yamanashi

address: 1110 Shimokato

institute: Yamanashi University

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: GenomeStudio software v1.9

source_name: Skin fibroblast 1

label_protocol: Standard Illumina Protocol

growth_protocol: DMEM with 10% FBS

extract_protocol: genomic DNA was extracted and purified from skin fibroblast cells samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

tag: cell

value: Skin fibroblast cells

tag: disease

value: Rett syndrome


title: STA_STA05_02-15-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82410.gif


title: AR_AR32_04-02-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82352.gif


title: genomic DNA from twins 2 (RS-2T)

source_name: Skin fibroblast 2


title: STA_STA08_04-23-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82450.gif


title: AR_AR31_04-12-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82350.gif


title: STA_STA24_04-24-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82407.gif


title: Intrac Bme_12h_rep1

description: Biological replicate 1 of 4. Enriched and amplified total RNA from intracellular Bmel at 12h post-infection co-hybridized against BME gDNA.

source_name: Enriched and amplified total RNA, intracellular Brucella melitensis 16M, 12h p.i., labeled with Cy3 (green).

tag: Strain

value: 16M Biotype 1 (ATCC 23456)

source_name: Genomic DNA from Brucella melitensis 16M labeled with Cy5 (red).


title: WRKY45kd#15-BTH(12hr)-4

city: Tsukuba

first: Hiroshi

last: Takatsuji

state: Ibaraki

address: 2-1-2 Kannondai

department: Division of Plant Sciences

institute: National Institute of Agrobiological Sciences

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Slides were scanned immediately after washing on Agilent Scanner model G2505B and software G2565BA using default parameters

data_processing: The scanned images were analyzed with Feature Extraction software (version 9.1; Agilent Technologies)  using default parameters.

organism: Oryza sativa

source_name: leaves

label_protocol: The RNAs (400-ng aliquots) were labeled with a Low RNA Input Linear Amplification/Labeling Kit (Agilent Technologies)

growth_protocol: Rice plants were grown on soil from seeds.

extract_protocol: Total RNA was isolated using an RNeasy plant mini kit (Qiagen).

treatment_protocol: seedlings at the four-leaf stage were sprayed with 0.5 mM BTH in 0.5% acetone / 0.05% Tween20 (BTH) or the solvent only (mock)  for 24 h

tag: cultivar

value: Nipponbare

tag: tissue

value: leaf

tag: protocol

value: WRKY45kd#15 knockdown

tag: treatment

value: BTH

tag: developmental stage

value: 4th leaves at 4-leaf stage

tag: time


title: Bme-inf HeLa_12h_rep4_HeLa array

description: Biological replicate 4 of 4. Total RNA from BME-infected HeLa cells at 12h p.i. co-hybridized against universal human reference RNA

source_name: Bmel-infected HeLa cells, total RNA, 12h p.i., Cy5

tag: Cell line

value: S3 (ATCC; CCL 2.2)

source_name: Universal Human Reference RNA labeled with Cy3 (green).

tag: Several human cell lines

tag: Comercial source (Stratagene)


title: WRKY45kd#15-BTH(12hr)-3


title: STA_STA02_04-02-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82403.gif


title: WRKY45kd#15-BTH(12hr)-2


title: WRKY45kd#15-BTH(12hr)-1


title: NB-#15BTH(12hr)-4

value: control


title: NB-#15BTH(12hr)-2


title: NB-#15BTH(12hr)-3


title: AR_AR21_11-21-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82370.gif


title: STA_STA10_04-05-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82405.gif


title: WRKY45kd#15-Mock(12hr)-4

value: Mock


title: AR_AR34_04-02-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82353.gif


title: STA_STA08_04-12-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82404.gif


title: NB-#15BTH(12hr)-1


title: WRKY45kd#15-Mock(12hr)-3


title: STA_STA18_04-24-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82406.gif


title: AR_AR37_04-05-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82357.gif


title: BTNo, 3015

city: South San Francisco

first: Andrew

last: Melton

address: 310 Utah Suite 100

institute: BioSeek

description:
3015
Donor Pool 3.

hyb_protocol: The Illumina Direct Hybridization Assay was used for hybridization.

scan_protocol: The Illumina iScan system was used to scan the BeadChips.

data_processing: Data was exported from GenomeStudio and normalized using the defaults in GeneSpring.

source_name: B cell and PBMC co-culture, unstimulated

label_protocol: The TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System was used to label and amplify the RNA.

extract_protocol: QIAGEN RNeasy.

treatment_protocol: PBMC and CD19+ B cells were prepared by thawing and washing once in medium containing DMEM/F12 (CellGro, Manassas, VA), 10% heat-inactivated FBS (Hyclone, Logan, UT), 2 mM L-Glutamine (CellGro), 500 IU/ml Penicillin and 500 μg/ml Streptomycin (CellGro), 1 mM Na-Pyruvate (Gibco, Grand Island, NY), 55 μM 2-mercaptoethanol (Gibco), and 12.5 nM Hydrocortisone (Sigma, St. Louis, MO). Pooled B cells (25,000 cells/well) and PBMC (25,000 cells/well) from 3-5 donors were then added to round-bottom 96-well plates (Costar, Corning, NY) and stimulated with 5 μg/ml goat (Fab')2 anti-human IgM low endotoxin/azide-free (a-IgM, Southern Biotech, Birmingham, AL) and a cocktail of superantigens (SAg) containing 0.02 ng/ml Staphylococcal enterotoxin B (SEB, Toxin Technologies, Sarasota, FL) and 0.02 ng/ml Toxic shock syndrome toxin-1 (TSST-1, Toxin Technologies) for 3 days.

tag: cell type

value: co-culture of PBMCs and CD19+ B cells

tag: culture conditions

value: no stimulation


title: BTNo, 2015

description:
2015
Donor Pool 2.


title: WRKY45kd#15-Mock(12hr)-2


title: BTNo, 1015

description:
1015
Donor Pool 1.


title: AR_AR28_02-21-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82388.gif

tag: Kidney, Peripheral Blood

tag: disease state


title: BT, 3005

description:
3005
Donor Pool 3.

source_name: B cell and PBMC co-culture, stimulated

value: stimulation with anti-IgM and superantigens


title: AR_AR37_02-20-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82364.gif


title: NB-#15Mock(12hr)-4


title: STA_STA03_11-16-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82408.gif


title: BT, 2005

description:
2005
Donor Pool 2.


title: AR_AR29_11-16-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82390.gif


title: AR_AR30_11-21-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82396.gif


title: BT, 1005

description:
1005
Donor Pool 1.


title: AR_AR26_11-21-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82384.gif


title: STA_STA09_04-05-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82413.gif


title: AR_AR07_04-25-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82442.gif

tag: Kidney, Peripheral Blood leukocyte


title: WRKY45kd#15-Mock(12hr)-1


title: NB-#15Mock(12hr)-2


title: STA_STA15_04-12-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82418.gif


title: AR_AR39_04-05-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82359.gif


title: STA_STA28_02-15-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82429.gif


title: WRKY45kd#15-BTH(24hr)-4


title: STA_STA27_02-21-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82428.gif


title: STA_STA19_02-15-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82421.gif


title: STA_STA02_04-25-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82444.gif


title: STA_STA11_11-16-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82414.gif


title: NB-#15Mock(12hr)-3


title: WRKY45kd#15-BTH(24hr)-3


title: NB-#15Mock(12hr)-1


title: STA_STA20_04-24-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82422.gif


title: AR_AR22_02-20-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82371.gif


title: AR_AR36_04-05-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82356.gif


title: WRKY45kd#15-BTH(24hr)-2


title: NB-#15BTH(24hr)-4


title: WRKY45kd#15-BTH(24hr)-1


title: AR_AR02_04-25-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82431.gif


title: AR_AR17_04-12-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82366.gif


title: AR_AR14_02-15-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82363.gif


title: AR_AR16_04-12-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82365.gif


title: AR_AR25_02-20-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82377.gif


title: NB-#15BTH(24hr)-2


title: STA_STA06_04-23-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82448.gif


title: STA_STA04_04-02-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82409.gif


title: NB-#15BTH(24hr)-3


title: AR_AR31_02-20-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82401.gif


title: AR_AR01_04-12-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82346.gif


title: WRKY45kd#15-Mock(24hr)-4


title: NB-#15BTH(24hr)-1


title: AR_AR18_11-16-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82367.gif


title: STA_STA21_04-24-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82423.gif


title: STA_STA13_02-15-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82416.gif


title: STA_STA17_02-15-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82420.gif


title: AR_AR12_04-12-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82361.gif


title: STA_STA25_02-15-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82426.gif


title: STA_STA07_04-05-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82412.gif


title: AR_AR06_04-25-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82441.gif


title: AR_AR27_02-20-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82387.gif


title: WRKY45kd#15-Mock(24hr)-3


title: WRKY45kd#15-Mock(24hr)-1


title: WRKY45kd#15-Mock(24hr)-2


title: NB-#15Mock(24hr)-4


title: AR_AR24_02-20-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82373.gif


title: NB-#15Mock(24hr)-3


title: AR_AR38_04-05-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82358.gif


title: STA_STA06_11-21-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82411.gif


title: NB-#15Mock(24hr)-2


title: STA_STA06_04-25-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82443.gif


title: STA_STA03_04-23-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82445.gif


title: STA_STA12_04-05-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82415.gif


title: AR_AR04_04-23-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82439.gif


title: NB-#15Mock(24hr)-1


title: AR_AR20_02-20-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82369.gif


title: PBLc22_11yr

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45118.gif

scan_protocol: GenePix Results 3

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: aRNA by SH on 3/27/03 from cell lines

tag: aRNA by SH on 3/27/03 from cell lines

extract_protocol: lihua_extract preparation; RNA Isolation, Microarray Target Preparation and Hybridization: Total RNA extracted from peripheral blood was subject to microarray and Q-PCR experiments. Sample preparation for array hybridization was done following the manufactures recommended protocols, and hybridized on 75 GeneChip Human Genome U133 Plus2.0 arrays (Affymetrix Inc. Santa Clara, CA), 26 Agilent Human genome 44K arrays (Agilent, CA) and 21 cDNA arrays (Stanford, CA). Details of sample collection, RNA isolation, microarray target preparation and hybridization protocols are as followings: For total RNA extracted from whole blood, 2.5 ml of peripheral blood was collected in PAXgene Blood RNA Tubes (PreAnalytiX, Qiagen) and processed using the PAXgene Blood RNA Kit (PreAnalytiX, Qiagen). For RNA extracted from leukocyte, 5 -10 ml whole blood was collected in sodium heparin tubes.  Leukocytes were recovered by initial separation of the white blood cells by centrifugation and  lysis of erythrocytes (ref. Lily method paper). RNA was extracted using RNeasy Midi Kit (Qiagen Inc, Valencia, CA). RNA concentration was measured using NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE) and the integrity of RNA was assessed with the Agilent 2100 Bioanalyzer using RNA Nano Chips (Agilent Technologies, Santa Clara, CA). RNA was stored in -80 oC until further use for microarray and qPCR. Sample preparation for array hybridization was done using the T7 protocol (T7), which employs one-cycle cRNA synthesis by using T7-Oligo (dT) Primer. A total of 2 microg total RNA was used for the synthesis of cRNA as the final product following manufacturer's Technical manual, Affymetrix). cRNA were hybridized on GeneChip Human Genome U133 Plus 2.0 Arrays (Affymetrix Inc. Santa Clara, CA).; Protocol Type = Extract preparation; Performer: Minnie,,Sarwal

tag: Disease State

tag: LIhua_samples; Patients and Samples

value: 122 peripheral blood samples from pediatric and young adult kidney allograft recipients were collected at Stanford University and other SNS01 centers from 2002 to 2007. All blood samples were obtained at the time of matched clinically indicated or protocol graft biopsies, which were used to categorize the sample as acute rejection (AR) {Racusen, 1999 )or stable, if there was absence of AR or other substantive pathology (STA). AR samples were obtained prior to treatment intensification for rejection.; Protocol Type = Biological Sample; Performer:Minnie,,Sarwal


title: AR_AR03_04-23-07

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82434.gif


title: PBL483_D0

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45121.gif


title: AR_AR13_04-12-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82362.gif


title: WRKY45kd#3-BTH(24hr)-4

tag: cultivar

value: WRKY45kd#3 knockdown


title: AR_AR23_04-24-06

description: Image: http://smd.stanford.edu/MicroArray/gifs/2008-12/82372.gif


title: PBLc484_D0

description:
Simple annotation: Kidney transplant, Peripheral Blood
Image: http://smd.stanford.edu/MicroArray/gifs/2003-09/45124.gif


title: WRKY45kd#3-BTH(24hr)-3

tag: tissue