title: Zliver-72 h-rep 1

city: Bodø

first: Anusha

last: Dhanasiri

state: Nordland

address: Universitetsalleen 11

department: Faculty of biosciences and Aquaculture

institute: University of Nordland

description: Gene expression of liver during transport  (72 h)

hyb_protocol: Fragmentation of cRNA was carried out using the Fragmentation mix as described in the standard protocol (one color microarray-based gene expression analysis -Low input quick amp labeling) Agilent Technologies, at 60°C for 30 minutes. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Zebrafish Oligo Microarray (V3) (4x44K) (GPL14664) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed with gene expression wash buffer 1 (Agilent) for 1 minute at room temperature and gene expression wash buffer 2 (Agilent) at 37°C for 1 minute and then dried immediately by brief centrifugation.

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

data_processing:
Scanned images were analyzed with Feature Extraction Software 10.7.3 (Agilent) and raw data were first checked for overall quality using R (v2.14.1) with the Bioconductor framework and the Array Quality Metrics package. Then, they were imported into Genespring v12.1 (Agilent technologies) for analysis. The recommended standard normalizations and transformations for Agilent single color microarray were performed: threshold raw signals to 1, log base 2 transformation, percentile shift normalization algorithm targeted to 80th percentile.
The data was also filtered based on their signal intensity values. For that, the data was divided in to 4 groups (time points) and only probes that were in the 80th percentile of the distribution of intensities in 100% of the samples (all the 4 biological replicates at a particular time point) in any 1 out of 4 groups (sampling points) were considered for subsequnet analysis. The filtered data are linked as a supplementary file on the Series GSE44078 record.

organism: Danio rerio

source_name: Zebrafish liver, 72 h, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Agilent Low Input Quick Amp Kit (Agilent) according to the one color microarray-based gene expression analysis (Low input quick amp labeling) protocol from Agilent Technologies, followed by Qiagen’s RNeasy mini spin column purification. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Healthy adult zebrafish  of size range 4-4.3 cm were maintained in a benchtop recirculation system. A photoperiod regime of 12 h light: 12 h dark and water temperature of 26°C were used in the rearing system.

extract_protocol: Total RNA from 20 individual liver samples collected at each time point were extracted using the mirVana™ miRNA isolation kit (Ambion® Life Technologies, Carlsbad, California, USA) following the manufacturer's protocol.The quality of RNA was assessed by agarose gel electrophoresis and the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA, pooled liver RNA). Its quantity was determined spectrophotometrically using the nanodrop ND-100 (NanoDrop technologies, Inc., Wilmington, DE).

treatment_protocol: A mock transport was performed in 5 l plastic bags containing 1.5 l water and fish at a density of 30 per litre.  The bags were charged with 3.5 l pure oxygen. Mock transportation was conducted in a temperature-controlled dark room at 26°C for a duration of 72 h. Undisturbed fish from 4 individual tanks of the bench top system were sampled prior to the transport experiment, representing basal samples of unstressed fish. In addition, fish were sampled from four randomly selected bags at 0 h (immediately after packing), 48 and 72 h from the start of transport. Fish were terminally anaesthetized with a lethal dose (200 mg l-1) of tricaine methanesulfonate (MS222), immediately frozen in liquid nitrogen and stored at -80°C for analysis of microarray transcriptomics on liver (20 fish per sampling point).

tag: protocol

value: during mock transport

tag: time

value: liver


title: E176_11_Leptin_1_B

status: Public on Mar 04 2013

type: RNA

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

hyb_protocol: cRNA, according to manufacturer's recommendations

data_processing: RMA; RMA preprocessed log2 expression values

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

label_protocol: biotin, according to manufacturer's recommendations

extract_protocol: RNA was isolated from PBMCs using the manufacturer’s protocol for Trizol Reagent (Invitrogen, Grand Island, NY) and further purified using RNAeasy spin columns (Qiagen, Valencia, CA). RNA concentration and purity were determined from 260nm/280 nm absorbances. RNA integrity was determined using the Agilent 2100 BioChip (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Human PBMCs were isolated by stratifying of whole blood on Ficoll-Paque PREMIUM (GE Healthcare; Pscataway, NJ). Subjects were randomized in a 1:1 fashion to receive either metreleptin or placebo, for a period of 36 weeks in the form of a self-administered daily subcutaneous injection.

tag: sample

tag: treatment

value: Leptin

tag: weeks of treatment

tag: subject


title: Zliver-72 h-rep 3

country: Norway

source_name: Zebrafish liver, 72 h, replicate 3

tag: tissue


title: Zliver-72 h-rep 4

source_name: Zebrafish liver, 72 h, replicate 4


title: Zliver-72 h-rep 2

source_name: Zebrafish liver, 72 h, replicate 2


title: Tumor_MetTrp53_A66

type: genomic

city: St. Louis

first: Robert

last: Lesurf

state: MO

address: 4444 Forest Park Ave

department: McDonnell Genome Institute

country: USA

institute: Washington University in St. Louis

hyb_protocol: 2ug of sample and reference DNA were hybridised to Agilent 44K whole mouse genome CGH arrays (Agilent, G4414A). Samples were prepared using the direct method according to the manufacturer’s protocol, to which minor changes were incorporated.   Hybridization took place in a rotisserie oven for 72 hours, set to 65C and rotation speed of 20rpm.  The washing and scanning of the slides took place in an ozone free area to prevent the degradation of the  Cy5 dye.  In turn, the slides were washed according to the wash procedure B.

scan_protocol: Scanned on an Agilent High-Resolution C scanner. Feature extraction was performed using Agilent software (FE 9.5.3.1).

data_processing: Raw Cy5 and Cy3 intensities were background corrected using the Edwards log linear interpolation background correction algorithm. Data was transformed to log2 ratios and a weighted median subtraction was used to normalize within Arrays.  Duplicate probes were averaged and all probes were then reordered by genomic position.  The dataset was segmented using a Circular Binary Segmentation (CBS) algorithm.  Probes corresponding to the Met transgene were removed based on the peak observed in the MMTV-Met;Trp53fl/+ MFP sample

molecule: genomic DNA

organism: Mus musculus

source_name: Mammary tumor

label_protocol: DNA was prepared for array hybridisation using the Agilent Genomic DNA Enzymatic Labeling kit and labelled with Cy-5.   Cy3-labelled genomic DNA extracted from mouse spleen was used as a reference.

extract_protocol: Genomic DNA was isolated from snap frozen tissue pieces using the Qiagen Allprep kit (as described for RNA isolation).

tag: gender

value: Female

tag: strain

value: FVB

value: Tumor

tag: genotype

tag: pathology

value: Poorly Differentiated Adenocarcinoma

source_name: Normal Splenic DNA

value: Normal Splenic DNA


title: Tumor_MetTrp53_A1471

value: Spindloid


title: E176_07_Placebo_4_B

scan_protocol: according to manufacturer's recommendations

value: Placebo


title: E176_09_Placebo_1_B


title: Tumor_MetTrp53_A899

value: Other


title: Zliver-48 h-rep 4

description: Gene expression of liver during transport  (48 h)

source_name: Zebrafish liver, 48 h, replicate 4


title: E176_08_Placebo_2_B


title: Tumor_MetTrp53_A1221


title: E176_08_Placebo_1_B


title: Tumor_MetTrp53_A646


title: Tumor_Met_4691T

value: MMTV-Met

value: Solid Nodular Carcinoma


title: Zliver-48 h-rep 2

source_name: Zebrafish liver, 48 h, replicate 2


title: E176_07_Placebo_2_B


title: Tumor_Met_6030T


title: Tumor_MetTrp53_A1004


title: Zliver-48 h-rep 3

source_name: Zebrafish liver, 48 h, replicate 3


title: Tumor_Met_4164T


title: Tumor_Met_5482T


title: Tumor_Met_5154T


title: Tumor_Met_4695T


title: Zliver-0 h-rep 4

description: Gene expression of liver after packing (0 h)

source_name: Zebrafish liver, 0 h, replicate 4

value: after packing

value: 0 h


title: Zliver-0 h-rep 3

source_name: Zebrafish liver, 0 h, replicate 3


title: G1E_D218Y, biological rep 2

city: Aurora

first: Amy

middle: E.

last: Campbell

state: CO

institute: University of Colorado Anschutz Medical Campus

hyb_protocol: Affymetrix standard protocol. University of Pennsylvania Microarray Facillity.

data_processing: Affymetrix .CEL (probe intensity) files were imported into Partek Genomics Suite v6.6 where RMA normalization was performed yielding log2-transformed expression intensities for all transcript clusters on the array. RMA results were filtered to exclude control probesets. To find differentially expressed genes, a 1-way ANOVA was performed across the five conditions (each with three replicates) and all ten possible pairwise comparisons were performed, each yielding a p-value and a fold-change for all genes on the array. All p-values were corrected for False Discovery Rate (FDR) by the method of Benjamini and Hochberg as implemented in Partek. Genes with a p-value of less than 0.05 and a fold change more than or equal to 1.5 were used for further analysis. University of Pennsylvania Microarray Facillity.

source_name: GATA1-null G1E_GATA1(D218Y)-ER

growth_protocol: G1E cells were cultured as described previously [PMID: 9032291].

extract_protocol: Trizol extraction of total RNA followed by purification via Qiagen RNeasy kit was performed according to the manufacturer's instructions.

treatment_protocol: G1E cells expressing wild type or mutant versions of GATA1-ER were induced to differentiate for 24 hours with 100 nM estradiol.

tag: cell line background

tag: cell type

value: GATA1-deficient proerythroblast cells with erythrocyte differentiation potential

tag: genotype/variation

value: expressing GATA1(D218Y)-ER

tag: treated with

value: 100 nM estradiol for 24 hrs


title: Tumor_Met_4425T


title: Zliver-0 h-rep 1

source_name: Zebrafish liver, 0 h, replicate 1

value: liver


title: G1E_D218Y, biological rep 3

scan_protocol: Affymetrix standard protocol. University of Pennsylvania Microarray Facillity.


title: Tumor_Met_5156T


title: E176_07_Placebo_3_B


title: E176_05_Placebo_3_B


title: Zliver-0 h-rep 2

source_name: Zebrafish liver, 0 h, replicate 2


title: E176_05_Placebo_4_B


title: G1E_D218G, biological rep 3

source_name: GATA1-null G1E_GATA1(D218G)-ER

label_protocol: Affymetrix standard protocol. University of Pennsylvania Microarray Facillity.

value: expressing GATA1(D218G)-ER


title: E176_05_Placebo_2_B


title: E176_07_Placebo_1_B


title: G1E_D218G, biological rep 1


title: Zliver-48 h-rep 1

source_name: Zebrafish liver, 48 h, replicate 1

value: during mock transport


title: Zliver-basal-rep 4

description: Gene expression of liver prior to transport (basal)

source_name: Zebrafish liver, basal,replicate 4

value: prior to transport

value: basal


title: Zliver-basal-rep 3

source_name: Zebrafish liver, basal,replicate 3


title: E176_04_Leptin_4_B

source_name: PBMC

value: Leptin


title: G1E_D218G, biological rep 2


title: G1E_R216W, bioloical rep 3

source_name: GATA1-null G1E_GATA1(R216W)-ER

value: expressing GATA1(R216W)-ER


title: E176_04_Leptin_3_B


title: G1E_D218Y, biological rep 1


title: Zliver-basal-rep 2

source_name: Zebrafish liver, basal,replicate 2


title: G1E_R216W, bioloical rep 2


title: E176_04_Leptin_2_B


title: Test Legionella pneumophila CuO nanoparticle treated Replicate 1

type: mixed

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

hyb_protocol: Hybridization was performed as previously described (Hovel-Miner, G 2009. JB, 191:2461).

scan_protocol: Scanning and image acquisition was performed on a Scan Array Express (Perkin Elmer) using ScanArray 3.0 software as previously described (Hovel-Miner, G 2009. JB, 191:2461).

data_processing: The data was background subtracted and normalized by calculating the contribution of each spot to the total intensity and the ratio to gDNA was recorded. Excel and TigrMEV was used for processing.

label: Alexa 647

organism: Legionella pneumophila

source_name: genomic DNA, reference channel

label_protocol: RNA: 15 ug of Total RNA was labeled with amino-allyl dUTP during reverse transcriptase and subsequently coupled with the succinimidyl ester fluorescent dye AlexaFluor 546 as previously described (Hovel-Miner, G 2009. JB, 191:2461). Genomic DNA: 5 ug of genomic DNA was labeled with amino-allyl dUTP with klenow fragment and random hexamer as previously described (Porwollik, S. 2001. Mutat Res 483:1). Subsequently, the resulting DNA was coupled to the succinimidyl ester fluorescent dye AlexaFluor 647.

growth_protocol: BYE broth, 37°C shaking.

extract_protocol: RNA: TRIzol reagent, reverse-transcribed into cDNA. Genomic DNA: QIAamp kit.

treatment_protocol: 160 ug/ml CuO nanoparticles, 3h

tag: agent

value: CuO

tag: media

value: BYE broth, 37°C shaking

label: Alexa 546

source_name: 160 ug/ml CuO nanoparticles, 3h


title: Control Legionella pneumophila untreated Replicate 3

value: control

source_name: Untreated control


title: Test Legionella pneumophila CuO nanoparticle treated Replicate 2


title: E176_01_Leptin_4_B


title: G1E_R216W, bioloical rep 1


title: Control Legionella pneumophila untreated Replicate 2


title: Test Legionella pneumophila CuO nanoparticle treated Replicate 3


title: E176_01_Leptin_3_B


title: G1E_R216Q, biological rep 2

source_name: GATA1-null G1E_GATA1(R216Q)-ER

value: expressing GATA1(R216Q)-ER


title: G1E_GATA1, biological rep 1

source_name: GATA1-null G1E_GATA1-ER

value: expressing GATA1-ER


title: G1E_GATA1, biological rep 2


title: G1E_GATA1, biological rep 3


title: Control Group - CD1 bone marrow Cell Replicate 1

status: Public on Mar 02 2013

city: Rome

first: fiorella

last: ciaffoni

state: Italy

address: Viale Regina Elena 299

department: Cellular Biology and Neurosciences

country: Italy

institute: Istituto Superiore di Sanità

description: Control

data_processing:
Three different mice were analyzed per experimenalt point (replicate 1, 2 and 3). Differences in gene expression among groups were identified using the RT 2 Profiler PCR Array Data Analyses Web portal (QIAGEN) and considered statistically significant with a p<0.05 by two-tailed, Student’s t-test.
For the normalization it was used the average of Gapdh as housekeeping gene.
Target gene signals (Ct value cut-off 35) normalized to housekeeping gene; 2^-(Ave deltaCt), where deltaCt = (Ct_Target − Ave(Ct_HKG).
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Biological consequences of gene expression alterations were predicted with the David Bioinformatic Database (David Bioinformatics Resources 6.7 NIAID/NIH)
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., Group1/Control Group) ratios.

label: SYBR Green

source_name: CD1 bone marrow cells

label_protocol:
PCR assays were performed using the TGFβ/BMP Signaling Pathway PCR array (PAMM-035A - SABiosciences, Frederick, MD). Reverse transcription was performed from 100 ng total RNA using RT2 First Strand kit  (SABiosciences, Frederick, MD) following manufacturer's instructions.
RT-PCR was performed with RT2 SYBR ROX qPCR Mastermix(SABiosciences, Frederick,MD) following manufacturer's instructions
Absolute quantification was detected by 7300 Real-TimePCR System (Applied Biosystem).Termal cycling conditions were setted following manufacturer's instructions

extract_protocol: Total bone marrow cells were harvested by flushing the femoral cavity with colture media. Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Mice were injected intraperitoneally with TGF-β Signaling inhibitor SB431542 (60 µg/kg/day) or vehicle (same volume) for two cycles of five consecutive days two days apart, rested for one month, and then treated for two additional cycles.

value: CD1 bone marrow cells

value: wild-type mouse


title: G1E_R216Q, biological rep 1

value: GATA1-deficient proerythroblast cells with erythrocyte differentiation potential


title: Control Group - CD1 spleen cell Replicate 1

description: Control

data_processing:
Three different mice were analyzed per experimenalt point (replicate 1, 2 and 3). Differences in gene expression among groups were identified using the RT 2 Profiler PCR Array Data Analyses Web portal (QIAGEN) and considered statistically significant with a p<0.05 by two-tailed, Student’s t-test.
For the normalization it was used the average of Gapdh as housekeeping gene.
Target gene signals (Ct value cut-off 35) normalized to housekeeping gene; 2^-(Ave deltaCt), where deltaCt = (Ct_Target − Ave(Ct_HKG).
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Biological consequences of gene expression alterations were predicted with the David Bioinformatic Database (David Bioinformatics Resources 6.7 NIAID/NIH)
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., Group1/Control Group) ratios.
Biological consequences of gene expression alterations were predicted with the David Bioinformatic Database (David Bioinformatics Resources 6.7 NIAID/NIH)

source_name: CD1 spleen cells

label_protocol:
PCR assays were performed using the TGFβ/BMP Signaling Pathway PCR array (PAMM-035A - SABiosciences, Frederick, MD). Reverse transcription was performed from 100 ng total RNA using RT2 First Strand kit  (SABiosciences, Frederick, MD) following manufacturer's instructions.
RT-PCR was performed with RT2 SYBR ROX qPCR Mastermix(SABiosciences, Frederick,MD) following manufacturer's instructions.
Absolute quantification was detected by 7300 Real-TimePCR System (Applied Biosystem).Termal cycling conditions were setted following manufacturer's instructions

extract_protocol: Total spleen cells were lysed in Trizol. Total RNA extracted using Trizol following manufacturer's instructions.

value: CD1 spleen cells


title: Group2 - Vehicle treated Gata1 low spleen cell Replicate 1

description: Test

source_name: Vehicle treated Gata1 low spleen cells

value: Vehicle treated Gata1 low spleen cells

value: mouse model of myelofibrosis


title: Group1 - Untreated Gata1 low spleen cell Replicate 1

description: Test

source_name: Untreated Gata1 low spleen cells

value: Untreated Gata1 low spleen cells


title: Group3 - SB431542r treated Gata1 low spleen cell Replicate 1

description: Test

source_name: SB431542 treated Gata1 low spleen cells

value: SB431542 treated Gata1 low spleen cells


title: Control Legionella pneumophila untreated Replicate 1


title: Group1 - Untreated Gata1 low bone marrow Cell Replicate 1

description: Test

source_name: Untreated Gata1 low bone marrow cells

value: Untreated Gata1 low bone marrow cells


title: Group2 - Vehicle treated Gata1 low bone marrow Cell Replicate 1

description: Test

source_name: Vehicle treated Gata1 low bone marrow cells


title: Zliver-basal-rep 1

source_name: Zebrafish liver, basal,replicate 1

tag: protocol

value: prior to transport

value: basal

value: liver


title: RIL TK098, wet treatment

city: Austin

first: David

middle: Bryant

last: Lowry

state: TX

address: 1 University Station #C0930

department: Integrative Biology

institute: University of Texas at Austin

hyb_protocol: Hybridization to atSNPTILE array (Affymetrix) by proprietary Asuragen protocols using a GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Scan by proprietary Asuragen protocols using a GeneChip Scanner 3000 7G

data_processing: CEL file data were processed in JMP Genomics using log2 transformation and quantile normalization of probe intensities. Mean summary of probesets (defined by a custom CDF file based on TAIR version 9) were calculated for genes with three or more nonpolymorphic probes.

organism: Arabidopsis thaliana

source_name: Leaf_wet treatment

label_protocol: 7ug of RNA was converted without amplification to cDNA using GeneChip Whole Transcript (WT) Double-Stranded cDNA Synthesis Kit (Affymetrix). Fragmentation and end labeling with biotin were carried out using the GeneChip® WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).

growth_protocol: Grown in 2.5-inch pots in fritted clay. Daylength: 12 hours. Light period: 23°C and 40% humidity. Dark period: 20°C and 50% humidity. Light intensity: 330 µmol m-2 s-1.

extract_protocol: Tissue preserved in RNAlater (Ambion, Inc.) and stored at -80°C. Extraction by RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: Wet treatment was well watered to 100% field capacity. Dry treatment experienced 6 day drydown to 40% of field capacity.

tag: recombinant inbred line (ril) from

value: reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640)

value: leaf


title: Group3 - SB431542 treated Gata1 low bone marrow Cell Replicate 1

description: Test

source_name: SB431542 treated Gata1 low bone marrow cells


title: RIL TK098, dry treatment

source_name: Leaf_dry treatment


title: RIL TK095, dry treatment


title: Seq H3K56ac no ab I replicate1

city: Singapore

first: Archana

middle: P

last: Gupta

address: 60 Nanyang Drive

department: School Of Biological Sciences

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Scanning as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: Data was Lowess normailzed and further processed as described in Gupta AP, Hoe CW, Lei Z, Bozdech Z: Dynamics of epigenetic regulation of gene expression during Plasmodium falciparum life cycle (manuscript in prep.)

organism: Plasmodium falciparum

source_name: ChIP DNA extracted at ring stage

label_protocol: Labeling  carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

extract_protocol: Chromatin-immuno precipitation and RNA extraction was carried out as described in Gupta AP, ChIn WH, Zhu L, Bozdech Z: Dynamics of epigenetic regulation of gene expression during Plasmodium falciparum life

treatment_protocol: P. falciparum cells were harvested at 5% parasetemia in 2% hematocrit either directly  for RNA extraction or saponin lysed and formaldehyde cross linked for immuno-precipitation

tag: sample type

value: ChIP with anti-H3K56ac followed by no antibody

tag: chip antibody

value: anti-H3K56ac followed by no antibody

value: whole organism

source_name: input

value: Input DNA from ring stage parasites


title: Seq H3K56ac no ab II replicate2


title: Seq H3K56ac H3K9ac II replicate2

value: ChIP with anti-H3K56ac followed by anti-H3K9

value: anti-H3K56ac followed by anti-H3K9


title: RIL TK099, dry treatment


title: RIL TK099, wet treatment


title: Seq H3K56ac H3K9ac I replicate1


title: Seq H3K9ac only II replicate2

value: ChIP with anti-H3K9ac


title: Seq H3K9ac only I replicate1


title: H4R3me2 TP4-I replicate1

source_name: ChIP DNA extracted at time point 4

value: ChIP with anti-H4R3me2 from time point 4 (32 hpi)

tag: time

value: 32 hpi

source_name: input pool

value: amplified input consisting of genomic DNA from time point 1, 2, 3, 4, 5 and 6


title: RIL TK091, dry treatment


title: RIL TK095, wet treatment


title: RIL TK091, wet treatment


title: H4R3me2 TP5-I replicate1

source_name: ChIP DNA extracted at time point 5

value: ChIP with anti-H4R3me2 from time point 4 (40 hpi)

value: 40 hpi


title: RIL TK086, wet treatment


title: H4R3me2 TP6-I replicate1

source_name: ChIP DNA extracted at time point 6

value: ChIP with anti-H4R3me2 from time point 4 (48 hpi)

value: 48 hpi


title: H4R3me2 TP3-I replicate1

source_name: ChIP DNA extracted at time point 3

value: ChIP with anti-H4R3me2 from time point 3 (24 hpi)

value: 24 hpi


title: RIL TK082, wet treatment

value: reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640)

value: leaf


title: RIL TK086, dry treatment


title: RIL TK081, dry treatment


title: RIL TK084, dry treatment


title: Seq H3K56ac only II replicate2

value: ChIP with anti-H3K56ac


title: RIL TK082, dry treatment


title: RIL TK080, dry treatment


title: H4R3me2 TP1-I replicate1

source_name: ChIP DNA extracted at time point 1

value: ChIP with anti-H4R3me2 from time point 1 (8 hpi)

value: 8 hpi

value: whole organism


title: RIL TK084, wet treatment


title: RIL TK081, wet treatment


title: H4R3me2 TP2-I replicate1

source_name: ChIP DNA extracted at time point 2

value: ChIP with anti-H4R3me2 from time point 2 (16 hpi)

value: 16 hpi


title: H3K79me3 6-III replicate3

value: ChIP with anti-H3K79me3 from time point 4 (48 hpi)


title: RIL TK080, wet treatment


title: H3K79me3 6-II replicate2


title: Seq H3K56ac only I replicate1

value: Input DNA from ring stage parasites


title: G1E_R216Q, biological rep 3

source_name: GATA1-null G1E_GATA1(R216Q)-ER

value: GATA1-deficient proerythroblast cells with erythrocyte differentiation potential

value: expressing GATA1(R216Q)-ER

value: 100 nM estradiol for 24 hrs


title: RIL TK076, dry treatment


title: H3K79me3 4-II replicate2

value: ChIP with anti-H3K79me3 from time point 4 (32 hpi)

value: 32 hpi

value: amplified input consisting of genomic DNA from time point 1, 2, 3, 4, 5 and 6


title: RIL TK008, dry treatment


title: H3K79me3 4-III replicate3


title: H3K79me3 5-III replicate3

value: ChIP with anti-H3K79me3 from time point 4 (40 hpi)

value: 40 hpi


title: RIL TK008, wet treatment

value: reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640)

value: leaf


title: H3K79me3 6-I replicate1

value: 48 hpi


title: RIL TK071, dry treatment


title: H3K79me3 4-I replicate1


title: H3K79me3 5-II replicate2


title: H3K79me3 5-I replicate1


title: RIL TK070, dry treatment


title: RIL TK071, wet treatment


title: H3K79me3 3-I replicate1

value: ChIP with anti-H3K79me3 from time point 3 (24 hpi)

value: 24 hpi


title: RIL TK076, wet treatment


title: RIL TK070, wet treatment


title: H3K79me3 3-II replicate2

value: whole organism


title: H3K79me3 2-II replicate2

value: ChIP with anti-H3K79me3 from time point 2 (16 hpi)

value: 16 hpi


title: RIL TK063, dry treatment


title: RIL TK060, dry treatment


title: H3K79me3 1-I replicate1

value: ChIP with anti-H3K79me33 from time point 1 (8 hpi)

value: 8 hpi


title: RIL TK063, wet treatment


title: H3K4me3 TP6-II replicate2

value: ChIP with anti-H3K4me3 from time point 4 (48 hpi)


title: H3K4me3 TP6-III replicate3


title: H3K79me3 1-II replicate2

value: ChIP with anti-H3K79me3 from time point 1 (8 hpi)


title: RIL TK006, dry treatment


title: RIL TK058, dry treatment


title: H3K79me3 1-III replicate3


title: RIL TK057, dry treatment


title: RIL TK006, wet treatment


title: RIL TK060, wet treatment


title: RIL TK058, wet treatment


title: H3K4me3 TP6-I replicate1


title: RIL TK057, wet treatment


title: H3K79me3 2-I replicate1


title: H3K4me3 TP5-II replicate2

value: ChIP with anti-H3K4me3 from time point 4 (40 hpi)


title: met1-II_H3K9m2

city: Dallas

first: Hume

last: Stroud

address: 5323 Harry Hines Blvd

institute: UT Southwestern

description: Sample 2

hyb_protocol: According to standard NimbleGen protocols (www.nimblegen.com)

data_processing: Each probe in the array was assigned a score define by the log2 ratio between Cy5 and Cy3 signal. The mean score of all probes in the array was substracted from the individual scores.

source_name: H3K9m2 ChIP on met1

extract_protocol: As previously described (Bernatavichute et al., PLoS One. 2008 Sep 8;3(9):e3156.)

tag: ecotype

value: met1 deletant

value: 3 wk-old leaves

value: H3k9m2 (Anti-Histone H3 (di methyl K9))

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

source_name: H3 ChIP on met1

value: Anti-Histone H3


title: RIL TK054, wet treatment

value: reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640)

tag: tissue

value: leaf


title: H3K4me3 TP5-I replicate1

value: 40 hpi

value: amplified input consisting of genomic DNA from time point 1, 2, 3, 4, 5 and 6


title: H3K4me3 TP4-III replicate3

value: ChIP with anti-H3K4me3 from time point 4 (32 hpi)

value: 32 hpi

value: whole organism


title: H3K4me3 TP4-II replicate2


title: RIL TK042, wet treatment


title: RIL TK040, wet treatment


title: H3K4me3 TP5-III replicate3


title: RIL TK054, dry treatment


title: H3K4me3 TP4-I replicate1


title: RIL TK040, dry treatment


title: Col_for_met1-II_H3K27m3

description: Sample 5

scan_protocol: According to standard NimbleGen protocols (www.nimblegen.com)

source_name: H3K27m3 ChIP on wildtype

value: wild type

value: H3k27m3 (Anti-Histone H3 (di methyl K9))

value: Upstate

source_name: input genomic DNA from wildtype


title: RIL TK004, dry treatment


title: Col_for_ibm1-I_H3K9m2

description: Sample 3

source_name: H3K9m2 ChIP on wildtype

label_protocol: According to standard NimbleGen protocols (www.nimblegen.com)

source_name: H3 ChIP on wildtype


title: H3K4me3 TP3-III replicate3

value: ChIP with anti-H3K4me3 from time point 3 (24 hpi)

value: 24 hpi


title: H3K4me3 TP2-II replicate2

value: ChIP with anti-H3K4me3 from time point 2 (16 hpi)

value: 16 hpi


title: RIL TK034, dry treatment

source_name: Leaf_dry treatment


title: RIL TK036, dry treatment


title: H3K4me3 TP3-II replicate2


title: H3K4me3 TP3-I replicate1


title: RIL TK036, wet treatment

source_name: Leaf_wet treatment


title: H3K4me3 TP2-I replicate1


title: H3K4me3 TP2-III replicate3


title: RIL TK004, wet treatment


title: H3K4me3 TP1-II replicate2

value: ChIP with anti-H3K4me3 from time point 1 (8 hpi)

value: 8 hpi


title: RIL TK031, dry treatment


title: RIL TK030, dry treatment


title: Col_for_met1-II_H3K9m2

description: Sample 1

value: 3 wk-old leaves

value: H3k9m2 (Anti-Histone H3 (di methyl K9))

value: Abcam

value: Anti-Histone H3


title: met1-II_H3K27m3

description: Sample 6

source_name: H3K27m3 ChIP on met1

value: met1 deletant

source_name: input genomic DNA from met1


title: H4K20me3 TP6-II replicate2

value: ChIP with anti-H4K20me3 from time point 4 (48 hpi)

value: 48 hpi

source_name: input pool

value: amplified input consisting of genomic DNA from time point 1, 2, 3, 4, 5 and 6


title: ibm1-I_H3K9m2

description: Sample 4

source_name: H3K9m2 ChIP on ibm1

value: ibm1 deletant


title: H4K20me3 TP5-II replicate2

source_name: ChIP DNA extracted at time point 5

value: ChIP with anti-H4K20me3 from time point 4 (40 hpi)

value: 40 hpi

value: whole organism


title: RIL TK030, wet treatment

value: reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640)

value: leaf


title: H3K4me3 TP1-I replicate1


title: H4K20me3 TP5-I replicate1


title: RIL TK034, wet treatment


title: H4K20me3 TP4-I replicate1

source_name: ChIP DNA extracted at time point 4

value: ChIP with anti-H4K20me3 from time point 4 (32 hpi)

value: 32 hpi


title: RIL TK027, wet treatment


title: RIL TK024, dry treatment


title: H4K20me3 TP4-II replicate2


title: RIL TK024, wet treatment


title: RIL TK023, wet treatment


title: H3K4me3 TP1-III replicate3

source_name: ChIP DNA extracted at time point 1

value: ChIP with anti-H3K4me3 from time point 1 (8 hpi)

value: 8 hpi


title: RIL TK023, dry treatment


title: H4K20me3 TP2-II replicate2

source_name: ChIP DNA extracted at time point 2

value: ChIP with anti-H4K20me3 from time point 2 (16 hpi)

value: 16 hpi


title: RIL TK022, dry treatment


title: H4K20me3 TP6-I replicate1

source_name: ChIP DNA extracted at time point 6


title: RIL TK022, wet treatment


title: H4K20me3 TP3-I replicate1

source_name: ChIP DNA extracted at time point 3

value: ChIP with anti-H4K20me3 from time point 3 (24 hpi)

value: 24 hpi


title: H4K20me3 TP3-II replicate2


title: RIL TK214, dry treatment


title: H4K20me3 TP1-II replicate2

value: ChIP with anti-H4K20me3 from time point 1 (8 hpi)


title: RIL TK027, dry treatment


title: H4K20me1 TP6-III replicate3

value: ChIP with anti-H4K20me1 from time point 4 (48 hpi)

value: 48 hpi


title: H4K20me1 TP6-II replicate2

value: amplified input consisting of genomic DNA from time point 1, 2, 3, 4, 5 and 6


title: RIL TK210, dry treatment


title: H4K20me3 TP2-I replicate1


title: RIL TK214, wet treatment


title: H4K20me3 TP1-I replicate1


title: H4K20me1 TP6-I replicate1


title: RIL TK209, wet treatment


title: H4K20me1 TP3-III replicate3

value: ChIP with anti-H4K20me1 from time point 3 (24 hpi)


title: H4K20me1 TP4-III replicate3

value: ChIP with anti-H4K20me1 from time point 4 (32 hpi)


title: RIL TK209, dry treatment


title: H4K20me1 TP5-I replicate1

value: ChIP with anti-H4K20me1 from time point 4 (40 hpi)

value: 40 hpi

value: whole organism


title: RIL TK200, dry treatment

value: reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640)

value: leaf


title: H4K20me1 TP4-II replicate2

value: 32 hpi


title: H4K20me1 TP4-I replicate1


title: RIL TK195, wet treatment


title: H4K20me1 TP3-II replicate2


title: RIL TK200, wet treatment


title: RIL TK210, wet treatment


title: RIL TK195, dry treatment


title: RIL TK192, wet treatment


title: RIL TK192, dry treatment


title: H4K20me1 TP5-III replicate3


title: H4K20me1 TP5-II replicate2


title: RIL TK194, dry treatment


title: RIL TK194, wet treatment


title: RIL TK019, wet treatment


title: H4K20me1 TP2-II replicate2

value: ChIP with anti-H4K20me1 from time point 2 (16 hpi)


title: H4K20me1 TP2-I replicate1


title: RIL TK019, dry treatment


title: H4K20me1 TP1-III replicate3

value: ChIP with anti-H4K20me1 from time point 1 (8 hpi)

value: 8 hpi


title: RIL TK183, dry treatment


title: H3K56ac TP6-III replicate3

value: ChIP with anti-H3K56ac from time point 4 (48 hpi)


title: H4K20me1 TP3-I replicate1

value: 24 hpi


title: H3K56ac TP5-III replicate3

value: ChIP with anti-H3K56ac from time point 4 (40 hpi)


title: H4K20me1 TP1-I replicate1


title: RIL TK178, wet treatment


title: RIL TK180, wet treatment


title: H3K56ac TP6-II replicate2


title: H3K56ac TP5-II replicate2


title: RIL TK178, dry treatment


title: RIL TK176, dry treatment


title: H4K20me1 TP1-II replicate2


title: H3K56ac TP5-I replicate1


title: RIL TK183, wet treatment


title: RIL TK175, wet treatment


title: RIL TK031, wet treatment


title: RIL TK175, dry treatment


title: RIL TK168, dry treatment


title: H3K56ac TP4-III replicate3

value: ChIP with anti-H3K56ac from time point 4 (32 hpi)


title: RIL TK042, dry treatment


title: RIL TK176, wet treatment


title: H4K20me1 TP2-III replicate3

value: 16 hpi


title: RIL TK168, wet treatment


title: H3K56ac TP4-II replicate2

value: amplified input consisting of genomic DNA from time point 1, 2, 3, 4, 5 and 6


title: RIL TK180, dry treatment


title: H3K56ac TP6-I replicate1

value: 48 hpi


title: RIL TK167, dry treatment


title: RIL TK167, wet treatment


title: H3K56ac TP4-I replicate1


title: H3K56ac TP3-III replicate3

value: ChIP with anti-H3K56ac from time point 3 (24 hpi)


title: H3K56ac TP2-II replicate2

value: ChIP with anti-H3K56ac from time point 2 (16 hpi)


title: H3K56ac TP3-I replicate1


title: RIL TK164, dry treatment


title: H3K56ac TP3-II replicate2


title: RIL TK164, wet treatment


title: RIL TK161, dry treatment


title: RIL TK161, wet treatment


title: H3K56ac TP1-III replicate3

value: ChIP with anti-H3K56ac from time point 1 (8 hpi)


title: RIL TK159, dry treatment


title: H3K56ac TP2-I replicate1

value: whole organism


title: H3K14ac TP5 replicate1

value: ChIP with anti-H3K14ac from time point 4 (40 hpi)

value: 40 hpi


title: RIL TK158, dry treatment

value: reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640)

value: leaf


title: H3K14ac TP6 replicate1

value: ChIP with anti-H3K14ac from time point 4 (48 hpi)


title: RIL TK158, wet treatment


title: H3K14ac TP3 replicate1

value: ChIP with anti-H3K14ac from time point 3 (24 hpi)


title: H3K56ac TP1-II replicate2

value: 8 hpi


title: H3K56ac TP2-III replicate3


title: H3K14ac TP4 replicate1

value: ChIP with anti-H3K14ac from time point 4 (32 hpi)

value: 32 hpi


title: RIL TK156, dry treatment


title: RIL TK156, wet treatment


title: H3K56ac TP1-I replicate1


title: H3K14ac TP2 replicate1

value: ChIP with anti-H3K14ac from time point 2 (16 hpi)


title: RIL TK159, wet treatment


title: RIL TK151, dry treatment


title: RIL TK151, wet treatment


title: H3K14ac TP1 replicate1

value: ChIP with anti-H3K14ac from time point 1 (8 hpi)


title: RIL TK015, dry treatment


title: RIL TK152, wet treatment


title: RIL TK152, dry treatment


title: RIL TK015, wet treatment


title: H3K9ac TP6-II replicate2

value: ChIP with anti-H3K9ac from time point 4 (48 hpi)

value: amplified input consisting of genomic DNA from time point 1, 2, 3, 4, 5 and 6


title: H3K9ac TP5-II replicate2

value: ChIP with anti-H3K9ac from time point 4 (40 hpi)


title: H3K9ac TP5-III replicate3


title: H3K9ac TP6-I replicate1

value: 48 hpi


title: H3K9ac TP6-III replicate3


title: RIL TK146, dry treatment


title: H3K9ac TP4-II replicate2

value: ChIP with anti-H3K9ac from time point 4 (32 hpi)


title: H3K9ac TP3-III replicate3

value: ChIP with anti-H3K9ac from time point 3 (24 hpi)

value: 24 hpi

value: whole organism


title: H3K9ac TP4-III replicate3


title: H3K9ac TP3-I replicate1


title: H3K9ac TP5-I replicate1

value: 40 hpi


title: RIL TK144, dry treatment

value: reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640)

value: leaf


title: RIL TK145, wet treatment


title: H3K9ac TP2-I replicate1

value: ChIP with anti-H3K9ac from time point 2 (16 hpi)

value: 16 hpi


title: RIL TK141, wet treatment


title: H3K9ac TP2-II replicate2


title: RIL TK133, dry treatment


title: RIL TK145, dry treatment


title: H3K9ac TP3-II replicate2


title: RIL TK134, dry treatment


title: RIL TK133, wet treatment


title: H3K9ac TP4-I replicate1


title: RIL TK144, wet treatment


title: RIL TK141, dry treatment


title: RIL TK134, wet treatment


title: RIL TK143, wet treatment


title: RIL TK146, wet treatment


title: H3K9ac TP2-III replicate3


title: RIL TK143, dry treatment


title: H3K9ac TP1-III replicate3

value: ChIP with anti-H3K9ac from time point 1 (8 hpi)

value: 8 hpi


title: H3K9ac TP1-II replicate2


title: RIL TK128, dry treatment


title: RIL TK128, wet treatment


title: H4ac4 TP6-II replicate2

value: ChIP with anti-H4ac4 from time point 4 (48 hpi)


title: RIL TK125, dry treatment


title: H4ac4 TP6-III replicate3


title: H4ac4 TP5-II replicate2

value: ChIP with anti-H4ac4 from time point 4 (40 hpi)


title: H4ac4 TP6-I replicate1


title: RIL TK124, wet treatment


title: H4ac4 TP5-III replicate3


title: RIL TK124, dry treatment


title: H4ac4 TP5-I replicate1


title: RIL TK125, wet treatment


title: RIL TK120, dry treatment


title: H4ac4 TP4-III replicate3

value: ChIP with anti-H4ac4 from time point 4 (32 hpi)

value: 32 hpi


title: RIL TK115, dry treatment


title: RIL TK117, wet treatment


title: H3K9ac TP1-I replicate1

value: amplified input consisting of genomic DNA from time point 1, 2, 3, 4, 5 and 6


title: H4ac4 TP4-I replicate1


title: H4ac4 TP4-II replicate2


title: H4ac4 TP3-II replicate2

value: ChIP with anti-H4ac4 from time point 3 (24 hpi)


title: RIL TK115, wet treatment


title: RIL TK114, dry treatment


title: H4ac4 TP3-III replicate3


title: RIL TK114, wet treatment


title: H4ac4 TP3-I replicate1


title: RIL TK117, dry treatment


title: RIL TK120, wet treatment


title: RIL TK111, dry treatment


title: H4ac4 TP2-II replicate2

value: ChIP with anti-H4ac4 from time point 2 (16 hpi)


title: RIL TK111, wet treatment


title: H4ac4 TP1-III replicate3

value: ChIP with anti-H4ac4 from time point 1 (8 hpi)


title: H4ac4 TP1-II replicate2


title: H4ac4 TP1-I replicate1


title: H4K16ac TP6-III replicate3

value: ChIP with anti-H4K16ac from time point 4 (48 hpi)

value: 48 hpi


title: H4K16ac TP5-II replicate2

value: ChIP with anti-H4K16ac from time point 4 (40 hpi)

value: 40 hpi

value: whole organism


title: RIL TK011, dry treatment

value: reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640)

value: leaf


title: H4K16ac TP6-I replicate1


title: H4ac4 TP2-I replicate1

value: 16 hpi


title: H4ac4 TP2-III replicate3


title: H4K16ac TP5-III replicate3


title: RIL TK107, dry treatment


title: RIL TK103, dry treatment


title: RIL TK107, wet treatment


title: RIL KT262, dry treatment


title: RIL TK011, wet treatment


title: H4K16ac TP4-I replicate1

value: ChIP with anti-H4K16ac from time point 4 (32 hpi)


title: RIL KT259, dry treatment


title: H4K16ac TP3-II replicate2

value: ChIP with anti-H4K16ac from time point 3 (24 hpi)

value: 24 hpi


title: H4K16ac TP6-II replicate2


title: RIL TK102, wet treatment


title: RIL KT259, wet treatment


title: H4K16ac TP5-I replicate1


title: RIL KT262, wet treatment


title: RIL TK103, wet treatment


title: RIL TK102, dry treatment


title: RIL KT254, dry treatment


title: RIL KT254, wet treatment


title: H4K16ac TP3-I replicate1


title: H4K16ac TP3-III replicate3


title: H4K16ac TP2-II replicate2

value: ChIP with anti-H4K16ac from time point 2 (16 hpi)


title: RIL KT252, dry treatment


title: RIL KT252, wet treatment


title: RIL KT250, dry treatment


title: H4K16ac TP1-II replicate2

value: ChIP with anti-H4K16ac from time point 1 (8 hpi)

value: 8 hpi


title: H4K16ac TP1-I replicate1

value: amplified input consisting of genomic DNA from time point 1, 2, 3, 4, 5 and 6


title: RIL KT250, wet treatment


title: H4K12ac TP5-III replicate3

value: ChIP with anti-H4K12ac from time point 4 (40 hpi)


title: RIL KT249, dry treatment


title: H4K12ac TP6-III replicate3

value: ChIP with anti-H4K12ac from time point 4 (48 hpi)


title: H4K12ac TP6-I replicate1


title: H4K16ac TP2-I replicate1


title: H4K12ac TP6-II replicate2


title: RIL KT247, dry treatment


title: RIL KT247, wet treatment


title: RIL KT242, wet treatment


title: RIL KT242, dry treatment


title: RIL KT249, wet treatment


title: H4K12ac TP4-I replicate1

value: ChIP with anti-H4K12ac from time point 4 (32 hpi)

value: 32 hpi


title: H4K12ac TP3-III replicate3

value: ChIP with anti-H4K12ac from time point 3 (24 hpi)


title: H4K12ac TP4-III replicate3


title: H4K12ac TP3-II replicate2


title: H4K12ac TP5-I replicate1

value: 40 hpi


title: RIL KT232, dry treatment


title: H4K12ac TP2-III replicate3

value: ChIP with anti-H4K12ac from time point 2 (16 hpi)

value: whole organism


title: H4K12ac TP2-I replicate1


title: RIL KT231, dry treatment

value: reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640)

value: leaf


title: RIL KT235, wet treatment


title: RIL KT235, dry treatment


title: RIL KT232, wet treatment


title: RIL KT240, wet treatment


title: RIL KT240, dry treatment


title: RIL KT231, wet treatment


title: H4K12ac TP1-III replicate3

value: ChIP with anti-H4K12ac from time point 1 (8 hpi)


title: H4K12ac TP3-I replicate1


title: H4K12ac TP4-II replicate2


title: RIL KT227, dry treatment


title: H4K8ac TP6-III replicate3

value: ChIP with anti-H4K8ac from time point 4 (48 hpi)

value: 48 hpi


title: H4K8ac TP6-II replicate2


title: H4K12ac TP1-I replicate1


title: H4K12ac TP1-II replicate2


title: H4K8ac TP6-I replicate1


title: RIL KT211, wet treatment


title: H4K8ac TP5-I replicate1

value: ChIP with anti-H4K8ac from time point 4 (40 hpi)


title: H4K8ac TP5-III replicate3


title: RIL KT218, dry treatment


title: RIL KT211, dry treatment


title: RIL KT218, wet treatment


title: RIL KT204, dry treatment


title: H4K8ac TP5-II replicate2


title: RIL KT203, dry treatment


title: RIL KT196, wet treatment


title: RIL KT204, wet treatment


title: H4K8ac TP4-II replicate2

value: ChIP with anti-H4K8ac from time point 4 (32 hpi)


title: H4K8ac TP3-II replicate2

value: ChIP with anti-H4K8ac from time point 3 (24 hpi)

value: 24 hpi


title: RIL KT196, dry treatment


title: RIL KT227, wet treatment


title: H4K8ac TP3-I replicate1

value: amplified input consisting of genomic DNA from time point 1, 2, 3, 4, 5 and 6


title: H4K8ac TP2-III replicate3

value: ChIP with anti-H4K8ac from time point 2 (16 hpi)

value: 16 hpi


title: RIL KT203, wet treatment


title: RIL KT184, dry treatment


title: RIL KT180, dry treatment


title: H4K8ac TP3-III replicate3


title: H4K8ac TP4-I replicate1

value: 32 hpi


title: RIL KT180, wet treatment


title: H4K8ac TP2-I replicate1


title: RIL KT178, dry treatment


title: RIL KT178, wet treatment


title: H4K8ac TP2-II replicate2


title: RIL KT170, dry treatment


title: H4K8ac TP1-III replicate3

value: ChIP with anti-H4K8ac from time point 1 (8 hpi)

value: 8 hpi


title: H4K8ac TP1-II replicate2


title: RIL KT170, wet treatment


title: H4K8ac TP4-III replicate3


title: H4K5ac TP5-II replicate2

value: ChIP with anti-H4K5ac from time point 4 (40 hpi)

value: 40 hpi


title: RIL KT163, dry treatment

value: reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640)


title: RIL KT167, dry treatment

value: leaf


title: H4K5ac TP5-I replicate1

value: whole organism


title: RIL KT163, wet treatment


title: RIL KT164, wet treatment


title: RIL KT161, wet treatment


title: RIL KT164, dry treatment


title: H4K8ac TP1-I replicate1


title: RIL KT167, wet treatment


title: H4K5ac TP3-II replicate2

value: ChIP with anti-H4K5ac from time point 3 (24 hpi)


title: H4K5ac TP6-I replicate1

value: ChIP with anti-H4K5ac from time point 4 (48 hpi)

value: 48 hpi


title: H4K5ac TP3-I replicate1


title: H4K5ac TP4-II replicate2

value: ChIP with anti-H4K5ac from time point 4 (32 hpi)


title: H4K5ac TP2-III replicate3

value: ChIP with anti-H4K5ac from time point 2 (16 hpi)


title: H4K5ac TP4-I replicate1


title: H4K5ac TP4-III replicate3


title: H4K5ac TP3-III replicate3

value: 24 hpi


title: RIL KT161, dry treatment


title: H4K5ac TP2-II replicate2

value: amplified input consisting of genomic DNA from time point 1, 2, 3, 4, 5 and 6


title: RIL KT156, wet treatment


title: H4K5ac TP2-I replicate1


title: RIL KT156, dry treatment


title: N/TERT FSTL1 siRNA Replicate 3

first: Prabha

last: Sampath

state: Singapore

address: 8A Biomedical Grove

department: Institute of Medical Biology

institute: Institute of Medical Biology

description:
SAMPLE 6
Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was back ground substracted and quantile normalized using  Illumina Inc. GenomeStudio version 1.9.0.

source_name: N/TERT_FSTL1 siRNA

label_protocol: Biotinylated cRNA were prepared with the Target Amp-Nano labeling kit for Illumina arrays.

extract_protocol: Total RNA was extracted two days post transfection using Exiqon miRcury total RNA extraction kit.

treatment_protocol: N/TERT cells were transfected with 30nM of Dharmacon non targeting siRNA or On-target plus smart pool siRNA against human FSTL1.

value: N/TERT keratinocytes

tag: transfected with

value: Smartpool siRNA against FSTL1

tag: time point

value: Day2 post transfection


title: RIL KT140, dry treatment


title: N/TERT FSTL1 siRNA Replicate 1

description:
SAMPLE 4
Replicate 1


title: H4K5ac TP1-III replicate3

value: ChIP with anti-H4K5ac from time point 1 (8 hpi)


title: H4K5ac TP1-II replicate2

value: 8 hpi


title: RNA TP5

source_name: RNA extracted at time point 5

value: RNA from time point 5 (40 hpi)

source_name: reference pool

value: Reference pool consisting of time point 1, 2, 3, 4, 5 and 6 cDNA


title: Skin Sample 24 hr Post-injury Replicate 3

description: Replicate 3

data_processing: The data was back ground substracted and normalized using  Illumina Inc. GenomeStudio version 1.9.0

source_name: Human skin

label_protocol: Biotinylated cRNA were prepared with the Target Amp-Nano kit for Illumina arrays

growth_protocol: 8mm doughnut biopsies with an inner injury diameter of 2mm were incubated in Airliquid interface cultures for 24hrs

extract_protocol: Total RNA isolation was carried out using Trizol extraction procedure combined with Exiqon miRCURY total RNA isolation Kit

treatment_protocol: Total RNA was isolated either from biopsies snap frozen immediately in Trizol (0hr) or biopsies incubated in airliquid interface cultures for 24hrs.

value: Human skin

tag: model

value: Ex vivo organ culture model of injury

value: 24 hr Post-injury


title: H4K5ac TP1-I replicate1

value: whole organism


title: RNA TP6

source_name: RNA extracted at time point 6

value: RNA from time point 6 (48 hpi)


title: N/TERT non targeting siRNA Replicate 1

description:
SAMPLE 1
Replicate 1

source_name: N/TERT_non-targeting siRNA

tag: cell type

value: non-targeting siRNA


title: Skin Sample 24 hr Post-injury Replicate 2

description: Replicate 2


title: N/TERT non targeting siRNA Replicate 2

description:
SAMPLE 2
Replicate 2


title: N/TERT non targeting siRNA Replicate 3

description:
SAMPLE 3
Replicate 3


title: RIL KT140, wet treatment

source_name: Leaf_wet treatment

value: reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640)

value: leaf


title: N/TERT FSTL1 siRNA Replicate 2

description:
SAMPLE 5
Replicate 2


title: Skin Sample 0 hr Post-injury Replicate 1

description: Replicate 1

value: 0 hr Post-injury


title: RIL KT120, dry treatment

source_name: Leaf_dry treatment


title: RIL KT120, wet treatment


title: Skin Sample 0 hr Post-injury Replicate 3

description: Replicate 3


title: Skin Sample 24 hr Post-injury Replicate 1

description: Replicate 1


title: RIL KT160, dry treatment


title: RIL KT135, dry treatment


title: Skin Sample 0 hr Post-injury Replicate 2

description: Replicate 2


title: N/TERT miR-198 Replicate 3

description: Replicate 3

source_name: N/TERT keratinocytes

extract_protocol: Total RNA was extracted two days post transfection using Exiqon miRcury total RNA extraction kit

treatment_protocol: N/TERT cells were transfected with 20nM of Exiqon negative control or miR-198

tag: transfection

value: transfected with 20nM of miR-198


title: RNA TP4

source_name: RNA extracted at time point 4

value: RNA from time point 4 (32 hpi)

value: 32 hpi


title: N/TERT miR-198 Replicate 2

description: Replicate 2

value: N/TERT keratinocytes

value: Day2 post transfection


title: RIL KT135, wet treatment


title: RIL KT117, dry treatment


title: RIL KT184, wet treatment


title: RNA TP3

source_name: RNA extracted at time point 3

value: RNA from time point 3 (24 hpi)

value: 24 hpi


title: N/TERT miR-198 Replicate 1

description: Replicate 1


title: RIL KT117, wet treatment


title: RNA TP2

source_name: RNA extracted at time point 2

value: RNA from  time point 2 (16 hpi)

value: 16 hpi

value: Reference pool consisting of time point 1, 2, 3, 4, 5 and 6 cDNA


title: RNA TP1

source_name: RNA extracted at time point 1

value: RNA from time point 1 (8 hpi)

value: 8 hpi


title: N/TERT Control miR Replicate 2

description: Replicate 2

value: transfected with 20nM of Exiqon negative control


title: TAF3 siRNA, no doxorubicin, rep3

city: Frederick

first: Xiaolin

last: Wu

state: MD

address: 8560 Progress Drive, C3001

department: Cancer Research Technology Program

institute: Frederick National Laboratory for Cancer Research/SAIC-Frederick Inc

description:
TAF3 siRNA, no doxorubicin
Illumina HumanHT-12 v3 Beadchip

hyb_protocol: Standard Illumina hybridization protocol. 750 ng of aRNA in 5 ul was mixed with 10 ul of hybridization reagents and heated at 65C for 5 min. After cooled to room temperature, total 15 ul of the hybridization solution was applied to Illumina HumanHT-12 v3 chip. The chip was incubated for about 18 hours at 58C. Then washed and stained with streptavidin-Cy3.

scan_protocol: Standard Illumina scanning protocol usig Illumina BeadArray Reader.  The scanning was done using standard DirectHyb Gene Expression protocol with the following settings: Factor=1, PMT=587, Filter=100%.

data_processing: Raw data was extracted using Illumina BeadStudio software without normalization. Results were analyzed by GeneSpring GX 10.0.2 using simple median-scaling.  Genes were filtered on Flags Present or Marginal.

source_name: HCT116 cells

label_protocol: Biotinylated cRNA were prepared with the MessageAmp Premier RNA Amplification kit (Applied Biosystems, Foster City, CA). Briefly, 200 ng of total RNA was used to synthesize the first strand of cDNA using ArrayScript reverse transcriptase and an oligo(dT) primer bearing a T7 promoter. The single-stranded cDNA was then converted into a double-stranded DNA (dsDNA) by DNA polymerase I in the presence of E. coli RNase H and DNA ligase. The dsDNA was then served as a template for in vitro transcription in a reaction containing biotin-labeled UTP, unlabeled NTPs and T7 RNA Polymerase. The amplified, biotin-labeled antisense RNA (aRNA) was purified and the quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit.

growth_protocol: HCT116 cells were cultured on tissue culture plates in the Dulbecco's Modified Eagle Medium (DMEM, Gibco)

extract_protocol: Total RNAs were extracted using the Rneasy kit (Qiagen)

treatment_protocol: Cells were transfected with control or TAF3 siRNA.  48 hours after siRNA transfection, the cells were treated with 0.5 μM doxorubicin for 24 hours or left untreated.

tag: cell line

value: HCT116 cells

tag: sirna

value: TAF3 siRNA

tag: treatment

value: no doxorubicin


title: Columbia Clipped_Biol_Rep 2

city: Utbana

first: Madhura

middle: H

last: Siddappaji

state: IL

address: 515 Morrill Hall

institute: UIUC

description: Gene expression data from clipped Columbia ecotype plants

hyb_protocol: Following fragmentation, 2 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneArray Scanner G2500A.

data_processing: The data was analysed using R software

source_name: Arabidopsis ecotype Columbia

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 3 day cold treated seeds were planted in 3 inch circular pots containing sunshine plant mix. Plant were grown in greenhouse with 16:8 light and dark cycles.

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

treatment_protocol: Plants were clipped at bolting to simulate mammalian herbivore damage

value: Secondary meristem

value: Columbia

tag: stress

value: clipped at bolting stage


title: TAF3 siRNA, doxorubicin, rep4

description:
TAF3 siRNA, doxorubicin
Illumina HumanHT-12 v3 Beadchip

value: doxorubicin


title: N/TERT Control miR Replicate 1

description: Replicate 1

value: N/TERT keratinocytes


title: Landsberg erecta Clipped_Biol. Rep 2

description: Gene expression data from clipped landsberg ecotype plants

source_name: Arabidopsis ecotype Landsberg erecta

value: Landsberg erecta


title: Landsberg erecta Clipped_Biol. Rep 1


title: Columbia Clipped_Biol_Rep 1


title: TAF3 siRNA, doxorubicin, rep2


title: Columbia Clipped_Biol_Rep 3


title: non-targeting siRNA control, no doxorubicin, rep3

description:
non-targeting siRNA control, no doxorubicin
Illumina HumanHT-12 v3 Beadchip

value: non-targeting siRNA control


title: non-targeting siRNA control, doxorubicin, rep4

description:
non-targeting siRNA control, doxorubicin
Illumina HumanHT-12 v3 Beadchip


title: GF_preweaned_ileum

city: Chicago

first: Lei

last: Lu

state: Illinois

address: 900 E 57th Street

institute: University if Chicago

description: Phalanx Biotech Group's Mouse OneArray contains 31,082 features, 29,922 detection probes and 1880 control probes, spotted onto class slides using a proprietary non-contact printing method. Detection probes are annotated against the human genome and grouped into the following categories:

hyb_protocol: Phalanx Mouse One Array (MOA) v1.1 arrays were pre-heated at 60℃ for 10 mins, and rehydrated by 100% ethanol followed by deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hours. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridized on MOA in duplicate in Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by an Axon GenePix 4000B scanner (635nm power 100 PMT 550~570 ; 532nm power 10, PMT 460), and the fluoresence intensities were quantified.

data_processing:
The raw intensity was filtered (SNR>5), and normalized by the quantile normalization method using Matlab.  The average ratios of the hybridization replicates were calculated and the significant values for each gene were found by pairwise comparision (Ranking and hypothesis testing).
The average ratios of the hybridization replicates were calculated and the significant values for each gene were found by pairwise comparision (Ranking and hypothesis testing).

source_name: GF mouse ileum

label_protocol: 2.5 µg of total RNA was reverse-transcribed and amplified using the MessageAmp aRNA Amplification Kit (Ambion). Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amersham).

growth_protocol: GF are kept in germ free isolator, conventional mice are kept in specific pathogen free environment

extract_protocol: Total RNA extraction by Rnaeasy/Qiagen. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧8).

tag: strain

value: ileum

value: Germ free preweaned


title: MPI_preweaned_ileun

source_name: gnotobiotic mouse ileun

value: humanized gnotobiotic preweaned


title: SPF_Ileum_postweaned

source_name: SPF mouse ileum

value: Conventional postwened


title: Splenic CD8+ pmel-1 T cells_gp100/saline/covax_day 21

city: Houston

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

hyb_protocol: As per Illumina instructions, with detection by avidin-Cy5 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader.

data_processing: The non-normalized data were generated by GenomeStudio with background correction. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

source_name: Splenic CD8+ pmel-1 T cells, gp100/saline/covax, day 21

label_protocol: 100 ng or less of total RNA was amplified and biotin-labeled through a two-round Eberwine procedure using MessageAmp II and Illumina TotalPrep RNA Amplification kits (Ambion).

extract_protocol: Total RNA was extracted using the RNAqueous kit (Ambion, Austin, TX).

treatment_protocol: Mice received 1000 pmel-1 T cells i.v., and s.c. vaccination with gp100/saline or gp100/IFA followed by covax. Six and 21 days later, splenocyte suspensions were RBC-lysed and pmel-1 T cells were column-sorted using magnetic microbeads (Miltenyi Biotech) coated with CD90.1 mAb, followed by FACS-sorting pmel-1 T cells using CD8 and CD90.1.

value: splenic CD8+ T cells

tag: vaccination

value: day 21


title: SPF_Ileum_preweaned

source_name: SPF mouse Ileum

value: Conventional preweaned


title: Splenic CD8+ pmel-1 T cells_gp100/IFA/covax_day 21

source_name: Splenic CD8+ pmel-1 T cells, gp100/IFA/covax, day 21


title: Splenic CD8+ pmel-1 T cells_gp100/saline/covax_day 6

source_name: Splenic CD8+ pmel-1 T cells, gp100/saline/covax, day 6

value: day 6


title: non-targeting siRNA control, doxorubicin, rep2

value: HCT116 cells


title: TAF3 siRNA, no doxorubicin, rep1

value: TAF3 siRNA

value: no doxorubicin


title: Experimental Sample (WT vs QDR1/QDR2/QDR3 knockout) replicate 3

status: Public on Mar 01 2013

city: New Delhi

first: Rajendra

last: Prasad

state: Delhi

address: New Mehrauli Road

department: School of Life Sciences

country: India

institute: Jawaharlal Nehru University

description: Biological Replicate 3 of 3

hyb_protocol: Labeled cDNA was mixed with hybridization buffer and applied immediately on the microarray slide. It was covered with 24 * 60 mm coverslip, sealed in Corning hybridization chambers and allowed to incubate overnight at 42° C. Slides were washed and scanned.

scan_protocol: Scanned on Scan Array Express microarray scanner from Perkin Elmer.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Candida albicans

source_name: QDR1/QDR2/QDR3 knockout Candida albicans cells

label_protocol: 10 µg of total RNA were primed with 2 µg of oligo dT at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 800 U SuperScript II Gibco BRL.

growth_protocol: All Candida strains were grown at 30°C

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

treatment_protocol: Test Candida albicans QDR1/QDR2/QDR3 knockout cells were grown at 30°C till OD600 of 1.8 and harvested.

tag: genotype

value: QDR1/QDR2/QDR3 knockout

source_name: Wild type candida cells

value: wild type


title: Experimental Sample (WT vs QDR1/QDR2/QDR3 knockout) replicate 1

description: Biological Replicate 1 of 3


title: Experimental Sample (WT vs QDR3 knockout) replicate 2; Dye swap

description: Biological Replicate 2 of 3

source_name: Wild type Candida albicans cells

treatment_protocol: Test Candida albicans QDR3 knockout cells were grown at 30°C till OD600 of 1.8 and harvested.

source_name: QDR3 knockout

value: QDR3 knockout


title: Experimental Sample (WT vs QDR3 knockout) replicate 3

description: Biological Replicate 3 of 3

source_name: QDR3 knockout Candida albicans cells


title: Experimental Sample (WT vs QDR2 knockout) replicate 1

description: Biological Replicate 1 of 3

source_name: QDR2 knockout Candida albicans cells

treatment_protocol: Test Candida albicans QDR2 knockout cells were grown at 30°C till OD600 of 1.8 and harvested.

value: QDR2 knockout


title: Experimental Sample (WT vs QDR1/QDR2/QDR3 knockout) replicate 2; Dye Swap

description: Biological Replicate 2 of 3

source_name: QDR1/QDR2/QDR3 knockout


title: Experimental Sample (WT vs QDR3 knockout) replicate 1

description: Biological Replicate 1 of 3


title: GF_Ileum_postweaned

value: Germ free postweane


title: Experimental Sample (WT vs QDR2 knockout) replicate 2; Dye Swap

description: Biological Replicate 2 of 3

source_name: QDR2 knockout


title: RIL KT160, wet treatment

source_name: Leaf_wet treatment

tag: recombinant inbred line (ril) from

value: reciprocal crosses between A. thaliana (L.) Heynh. accessions Kas-1 (CS903) and Tsu-1 (CS1640)

value: leaf


title: GF_Ileum_preweaned

source_name: GF mouse Ileum

value: ileum

value: Germ free preweaned


title: N/TERT Control miR Replicate 3

description: Replicate 3

source_name: N/TERT keratinocytes

value: N/TERT keratinocytes

value: transfected with 20nM of Exiqon negative control

tag: time

value: Day2 post transfection


title: Experimental Sample (WT vs QDR1 knockout) replicate 3

description: Biological Replicate 3 of 3

source_name: QDR1 knockout Candida albicans cells

treatment_protocol: Test Candida albicans QDR1 knockout cells were grown at 30°C till OD600 of 1.8 and harvested.

value: QDR1 knockout


title: non-targeting siRNA control, no doxorubicin, rep1

source_name: HCT116 cells

value: non-targeting siRNA control


title: Splenic CD8+ pmel-1 T cells_gp100/IFA/covax_day 6

source_name: Splenic CD8+ pmel-1 T cells, gp100/IFA/covax, day 6

value: splenic CD8+ T cells

value: day 6


title: 31DAP embryo, biological replicate 3

city: Guelph

first: Gregory

middle: S

last: Downs

address: 50 Stone Road E

institute: University of Guelph

hyb_protocol: Labeled cRNAs were fragmented and applied to a maize custom GeneChip microarray for molecular hybridization.

scan_protocol: The array images with hybridization signals were acquired and quantified by GeneChip Operation System (GCOS) software (Affymetrix).

data_processing: CEL files were normalized using the Robust Multichip Average (RMA) method from the “affy” library of the BioConductor package (version 2.6) of the R statistical framework (version 2.11.0)

organism: Zea mays

source_name: 31DAP embryo

label_protocol: Labeling followed a standard protocol recommended by Affymetrix.

growth_protocol: An elite Syngenta Zea mays (maize) inbred (SRG200) was grown in a greenhouse at the University of Guelph during the summer of 2007. Growth conditions were 16 hour days (~600 μmol m-2 s-1) at 28°C, 8 hour nights at 23°C, and 50% relative humidity. Plants were grown semi-hydroponically in pots containing Turface® clay, watered with a modified Hoagland’s solution containing: 0.4 g/L 28-14-14 fertilizer, 0.4 g/L 15-15-30 fertilizer, 0.2 g/L NH4NO3, 0.4 g/L of MgSO4•7H2O and 0.03 g/L of micronutrient mix (S, Co, Cu, Fe, Mn, Mo and Zn).

extract_protocol: Total RNA was isolated and used for cDNA, cRNA synthesis.

treatment_protocol: Three biological replicates per sample were harvested in the middle of the day to minimize complications due to diurnal changes in C and N metabolism.

tag: developmental stage

value: embryo


title: 24DAP endosperm, biological replicate 1

source_name: 24DAP endosperm

value: endosperm


title: 24DAP embryo, biological replicate 2

source_name: 24DAP embryo


title: Experimental Sample (WT vs QDR1 knockout) replicate 2; Dye Swap

description: Biological Replicate 2 of 3

value: wild type

source_name: QDR1 knockout


title: Experimental Sample (WT vs QDR2 knockout) replicate 3

description: Biological Replicate 3 of 3

source_name: Wild type candida cells


title: VT anthers, biological replicate 3

source_name: VT anthers

value: VT

value: anthers


title: Experimental Sample (WT vs QDR1 knockout) replicate 1

description: Biological Replicate 1 of 3


title: CGH: IsoClark05_v_Clark

city: Saint Paul

middle: M

last: Stupar

state: MN

address: 1991 Upper Buford Circle

department: Agronomy and Plant Genetics

institute: University of Minnesota

hyb_protocol: Genomic DNA were hybridized to the microarray according to the manufacturer instructions (NimbleGen CGH User Guide Ver 9.1)

scan_protocol: Slides were scanned on the NimbleGen MS 200 Scanner (Roche/NimbleGen, Madison,WI) according to the array manufacturer instructions (NimbleGen CGH User Guild Ver 9.1)

data_processing: The segMNT algorithm in the NimbleScan software (verison 2.5) was used to extract the raw data and normalize into log2 ratio value according to the default settings.

organism: Glycine max

source_name: DNA from soybean NIL IsoClark05

label_protocol: 500 ng of genomic DNA was labeled and amplified using the NimbleGen Dual-Color Labeling Kit according to the NimbleGen CGH User Guide Ver 9.1.

extract_protocol: Genomic DNA samples were isolated using the Qiagen Plant DNeasy protocol

value: single plant leaf tissue

source_name: DNA from soybean line Clark

value: Clark


title: VT anthers, biological replicate 2


title: 24DAP endosperm, biological replicate 3


title: 31DAP embryo, biological replicate 2


title: 31DAP leaf, biological replicate 3

source_name: 31DAP leaf

value: leaf


title: 24DAP endosperm, biological replicate 2


title: 24DAP root, biological replicate 3

source_name: 24DAP root

value: root


title: VT anthers, biological replicate 1


title: 24DAP embryo, biological replicate 1


title: 24DAP leaf, biological replicate 1

source_name: 24DAP leaf


title: 31DAP leaf, biological replicate 1


title: 31DAP embryo, biological replicate 1


title: 31DAP leaf, biological replicate 2


title: CGH: IsoClark03_v_Clark

source_name: DNA from soybean NIL IsoClark03


title: 24DAP root, biological replicate 1


title: 24DAP leaf, biological replicate 3


title: 24DAP root, biological replicate 2


title: 24DAP pericarp, biological replicate 3

source_name: 24DAP pericarp

value: pericarp


title: 24DAP leaf, biological replicate 2


title: 24DAP pericarp, biological replicate 1


title: 24DAP pericarp, biological replicate 2


title: CGH: IsoClark06_v_Clark

source_name: DNA from soybean NIL IsoClark06


title: 24DAP embryo, biological replicate 3


title: CGH: IsoClark02_v_Clark

source_name: DNA from soybean NIL IsoClark02


title: CGH: IsoClark01_v_Clark

source_name: DNA from soybean NIL IsoClark01


title: CGH: Clark_v_Clark


title: 17DAP endosperm, biological replicate 3

source_name: 17DAP endosperm


title: 17DAP leaf, biological replicate 1

source_name: 17DAP leaf


title: 17DAP pericarp, biological replicate 2

source_name: 17DAP pericarp


title: 17DAP pericarp, biological replicate 3


title: Phaeodactylum 8 hour darkness, 3 hour light rep1

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

institute: Norwegian University of Science and Technology

description: Phaeodactylum, exposure to 3 hour light after 8h darkness

hyb_protocol: 1650 ng cRNA from each sample was fragmented and hybridized on 4x44K P. tricornutum whole-genome 60-mer oligonucleotide microarrays (Agilent Technologies) in an Agilent G2545A Hybridization rotary oven (10 rpm, 65°C, 17.5 h). Hybridization was performed with the Gene Expression Hybridization Kit (Agilent p/n 5188-5242). The slides were washed with buffer 1 & 2 from Gene Expression Wash Buffer kit (Agilent p/n 5188-5327)

scan_protocol: The microarray sides were scanned twice at 5 µm resolution on a laser scanner (G2505 B from Agilent Technologies), using the “dynamic range expander” option in the scanner software. The resulting images were processed using Agilent Feature Extraction software v9.5.

data_processing: The median signal intensities (gMedianSignal) were normalized using the quantile method, and no background subtraction was performed. Spots identified as feature outliers were excluded from analysis, and weak or non-detected spots were given reduced weight (0.5). Genes with statistically significant differential expression were identified using the Limma package (version 3.2.3) and R (version 2.10.1).

organism: Phaeodactylum tricornutum

source_name: Phaeodactylum, 8 hour darkness, 3 hour light

label_protocol: Total RNA (150 - 200 ng) was reverse transcribed, amplified and labelled with Cy3-CTP using the Low Input Quick Amp Labelling Kit, One-Color (Agilent p/n 5190-2305)

growth_protocol: Phaeodactylum tricornutum Bohlin (originating from the CCMP 632 strain) was grown in axenic cultures at 20C and illuminated with 150 µmol photons m-2 s-1 provided by fluorescent tubes (PHILIPS Master TL-D 36W/840) in cycles of 16/8 hour photoperiods. Growth medium was made from natural seawater filtered through 0.2 µm Tuffryn® membrane capsules (PALL GELMAN) before nutrients were added and the medium autoclaved. Nutrient addition was made according to Guillard’s f/2 recipe (Guillard, 1975), and P was increased to 1.1 of the f/2 recipe to prevent P limitation throughout the experimental period. Three cultures of each treatment were grown in 2000 ml Nalgene optically clear flasks, and aerated with a mixture of air and 1-2% CO2 (v/v) to prevent settling of cells and C limitation. Cultivation was performed in exponential fed-batch modus: Fresh medium was added to the cultures every minute by micro pumps (Bio-Chem Valve™ Inc.) and medium doses increased exponentially based on information on actual culture volume and the desired dilution rate. Maximum specific growth rate was determined from measurements of optical density at 750 nm (OD750). Both experimental cultures were filled and harvested several times until the optical density was relatively stable for several consecutive days and sampling was initiated.

extract_protocol: Diatom cultures were centrifuged at 4000 g for 10 min at 15°C. The supernatant was removed and the cell pellet was resuspended in 1 ml f/2 medium. The suspension was transferred to 2 ml tubes and centrifuged at 18000 g for 1 min at 4°C. Supernatants were removed and the cell pellets were flash frozen in liquid nitrogen and stored at -80°C. Precooled (-80°C) 5 mm stainless steel beads (QIAGEN) were added to the tubes with frozen cell pellets, and the samples were mechanically disrupted and homogenized using the TissueLyser system (QIAGEN). Disruption was carried out for 2 x 2 min at 25 Hz. The samples were placed in a precooled (-80°C) adapter set for the first shaking step. Before the second shaking step, the samples were transferred to a room temperate adapter set and 0.5 ml lysis buffer (SpectrumTM Plant Total RNA kit, Sigma-Aldrich) was added to each tube. Total RNA was isolated from the homogenized lysate using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich). On-column digestion of DNA with DNase I (QIAGEN) was included for all RNA preparations. The concentration of the RNA was determined by measuring the absorbance at 260 nm with the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies), and the purity of the RNA was estimated by the OD260/OD280 nm absorption ratio (all ratios were > 2.0). The integrity of the RNA was verified by denaturing agarose gel electrophoresis and ethidium bromide staining following the protocol described in the RNeasy Mini handbook (QIAGEN).

treatment_protocol: After a 8 hour dark period the cultures were exposed to 150 µmol photons m-2 s-1 provided by fluorescent tubes (PHILIPS Master TL-D 36W/840) and samples harvested after 0.5 h, 6 h, 10.5 h and 15.5h light exposure. After 16h light exposure the light was turned off and dark samples were collected after 0.5 h, 4 h and 7.5 h darkness. The final samples were harvested 3 hours after light was turned on after the 8 hour dark period. Two biological replicas for each of the eigth time points were harvested.

value: clone Pt 1 8.6 (CCMP632)


title: 17DAP leaf, biological replicate 3


title: CGH: IsoClark04_v_Clark

source_name: DNA from soybean NIL IsoClark04


title: 17DAP embryo, biological replicate 2

source_name: 17DAP embryo


title: 17DAP endosperm, biological replicate 2


title: 17DAP leaf, biological replicate 2


title: 17DAP embryo, biological replicate 1


title: Phaeodactylum 8 hour darkness, 3 hour light rep2

value: exposure to 3 hour light after 8h darkness


title: 17DAP endosperm, biological replicate 1


title: Phaeodactylum 16 hour light, 7.5 hour darkness rep2

description: Phaeodactylum, exposure to 7.5 hour darkness after 16 hour light exposure

source_name: Phaeodactylum, 16 hour light, 7.5 hour dark


title: Phaeodactylum 16 hour light, 7.5 hour darkness rep1

value: exposure to 7.5 hour darkness after 16 hour light exposure


title: Phaeodactylum 16 hour light, 4 hour darkness rep2

description: Phaeodactylum, exposure to 4 hour darkness after 16 hour light exposure

source_name: Phaeodactylum, 16 hour light, 4 hour dark


title: 10DAP leaf, biological replicate 2

source_name: 10DAP leaf


title: CGH: T203_v_Clark

source_name: DNA from soybean line T203

source_name: DNA from soybean line Clark


title: 17DAP embryo, biological replicate 3


title: 10DAP leaf, biological replicate 3


title: CGH: IsoClark07_v_Clark

source_name: DNA from soybean NIL IsoClark07


title: 10DAP leaf, biological replicate 1


title: 17DAP pericarp, biological replicate 1


title: Phaeodactylum 16 hour light, 30 min darkness rep2

description: Phaeodactylum, exposure to 30 min darkness after 16 hour light exposure

source_name: Phaeodactylum, 16 hour light, 30 min dark


title: Phaeodactylum 16 hour light, 4 hour darkness rep1

value: exposure to 4 hour darkness after 16 hour light exposure


title: Phaeodactylum 15.5 hour light rep1

description: Phaeodactylum, exposure to 15.5 hour light after 8h darkness

source_name: Phaeodactylum, 15.5 hour light


title: U251-miR-NC

city: Nanjing

first: Huibo

last: Wang

state: Jiangsu

address: 300# Guangzhou Rd.

department: Department of Neurosurgery

country: China

institute: First Affiliated Hospital of Nanjing Medical University

description: miRNA expression of U251 cells transfected with miR-NC

scan_protocol: Label, hybridization and scanning was performed in shanghai biotechnology corporation (http://www.ebioservice.com/) following standard Agilent protocol.Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to  Hi 100% and Lo 5%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014850_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Label, hybridization and scanning was performed in shanghai biotechnology corporation (http://www.ebioservice.com) following standard Agilent protocol.

growth_protocol: Huamn glioma cell lines (U87, LN229, and U251) was cultured in DMEM medium and supplied with 10% FBS..

treatment_protocol: Transfection was performed following standard protocol of Lipofectamine 2000 transfection.

value: human glioblastoma


title: U251-miR-139-5p

description: miRNA expression of U251 cells transfected with miR-139-5p

hyb_protocol: Label, hybridization and scanning was performed in shanghai biotechnology corporation (http://www.ebioservice.com/) following standard Agilent protocol.


title: LN229-miR-139-5p

description: miRNA expression of LN229 cells transfected with miR-139-5p


title: Phaeodactylum 15.5 hour light rep2

value: exposure to 15.5 hour light after 8h darkness


title: 10DAP endosperm, biological replicate 3

source_name: 10DAP endosperm


title: LN229-miR-NC

description: miRNA expression of LN229 cells transfected with miR-NC


title: 5DAP cob, biological replicate 2

source_name: 5DAP cob

value: cob


title: Phaeodactylum 16 hour light, 30 min darkness rep1

value: exposure to 30 min darkness after 16 hour light exposure


title: U87-miR-139-5p

description: miRNA expression of U87 cells transfected with miR-139-5p


title: Phaeodactylum 10.5 hour light rep2

description: Phaeodactylum, exposure to 10.5 hour light after 8h darkness

source_name: Phaeodactylum, 10.5 hour light


title: 5DAP cob, biological replicate 3


title: 10DAP endosperm, biological replicate 1

value: endosperm


title: Phaeodactylum 0.5 hour light rep2

description: Phaeodactylum, exposure to 30 min light after 8h darkness

source_name: Phaeodactylum, 0.5 hour light


title: Phaeodactylum 6 hour light rep1

description: Phaeodactylum, exposure to 6 hour light after 8h darkness

source_name: Phaeodactylum, 6 hour light


title: 5DAP ovule , biological replicate 2

source_name: 5DAP ovule

value: ovule


title: 5DAP cob, biological replicate 1


title: Phaeodactylum 0.5 hour light rep1

value: exposure to 30 min light after 8h darkness


title: 5DAP ovule , biological replicate 3


title: Phaeodactylum 10.5 hour light rep1

value: exposure to 10.5 hour light after 8h darkness


title: U87-miR-NC

description: miRNA expression of U87 cells transfected with miR-NC


title: Phaeodactylum 6 hour light rep2

value: exposure to 6 hour light after 8h darkness


title: 10DAP embryo, biological replicate 2

source_name: 10DAP embryo

value: embryo


title: 10DAP embryo, biological replicate 1


title: R1 stalk, biological replicate 3

source_name: R1 stalk

value: R1 (1d before pollination)

value: stalk


title: 10DAP embryo, biological replicate 3


title: R1 stalk, biological replicate 1


title: R1 stalk, biological replicate 2


title: R1 root, biological replicate 3

source_name: R1 root

value: root


title: R1 root, biological replicate 2


title: NCIH727

city: Brussels

first: Jean-Baptiste

last: Demoulin

address: av Hippocrate 75, B1.74.05

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description:
miRNA expression profiling of Bronchopulmonary neuroendocrine cell line
VG24_C6

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: Program: Genechip Command Console; program version: 2.0.0.1029; log2 intensities; summarization algorithm: median polish

label: Biotin

label_protocol: Affymetrix standard

growth_protocol: *** patient samples: frozen specimens from normal ileum (N), primary midgut carcinoid tumors (P), Mesenthery midgut carcinoid metastasis (M) and midgut carcinoid liver metastases (L). *** cell lines: Tumor cells cultured in medium and incubated at 37˚C with 5% CO2

extract_protocol: Total RNA was isolated from five human neuroendocrine cancer cell lines and 100 to 200 mg of tissue specimens by using mirVana miRNA isolation kit (Applied Biosystems) according to the manufacturer’s instructions.

treatment_protocol: Treated CNDT2.5 cells with 1µM of octreotide for 12 months

value: Lung

tag: disease state

value: tumor (cell line)

tag: tumor stage

value: primary

tag: treatment-duration


title: NCIH720

description:
miRNA expression profiling of Atypical bronchopulmonary neuroendocrine cell line
VG23_C5

tag: tissue


title: CNDT

description:
miRNA expression profiling of Ileum  neuroendocrine cell line
VG19_C1

source_name: Ileum  neuroendocrine cell line

value: Ileum


title: CNDT + Octreotide

description:
miRNA expression profiling of Ileum  neuroendocrine cell line treated with Octreotide
VG20_C2

value: 1 µM of Octreotide

value: everyday treatment for 12 months


title: LCM

description:
miRNA expression profiling of Enterochromaffin cells
VG25_EC

source_name: Enterochromaffin cells

value: Enterochromaffin cells

value: normal

value: non tumor


title: Midgut carinoid Liver Metastasis, L5

description:
miRNA expression profiling of Midgut carinoid Liver Metastasis tumor from patient, fifth replicate
VG18_L5

source_name: Midgut carinoid Liver Metastasis

value: Liver

value: tumor

value: metastasis


title: 5DAP ovule , biological replicate 1

value: ovule


title: KRJ-1

description:
miRNA expression profiling of Gastrointestinal neuroendocrine cell line
VG21_C3


title: R1 leaf, biological replicate 2

source_name: R1 leaf

value: leaf


title: R1 husk, biological replicate 2

source_name: R1 husk

value: R1 (1d before pollination)

value: husk


title: R1 husk, biological replicate 1


title: R1 husk, biological replicate 3


title: siIMP1

city: Taichung

first: yeunting

last: hsieh

address: Chugong Road Section3, 160

department: GYN

country: Taiwan

institute: TCVGH

hyb_protocol: The fragmented labeled cRNA was then pooled and hybridized to Agilent human whole genome oligo microarray 4 x 44K (Agilent Technologies) at 60°C for 17 h.

scan_protocol: With Agilent microarray scanner (Agilent Technologies) at 535 nm for Cy3 and 625 nm for Cy5.

data_processing:
Agilent Feature Extraction software (version 9.3; Agilent Technologies) was used to quantify signal and background intensity for each feature and substantially normalized the data by rank consistency linear LOWESS normalization method.
Fold ratios were obtained by the comparison of normalized data between groups. Only genes that were up- or down-regulated greater than 2-fold between the groups were filtered [*regulated_genes.txt available on Series records]

source_name: control JAR cells

label_protocol: 0.5 g of total RNA was amplified by a low RNA input fluor linear amp kit and labeled with Cy3 (contol) or Cy5 (IMP1 siRNA-treated).

growth_protocol: JAR cells were maintained in RPMI1640 with 10% FBS

treatment_protocol: siRNA was transfected into cells by Lipofectamine RNAi MAX  following manufacturer's instructions

value: JAR

value: human choriocarcinoma cell line

tag: transfected with

value: universal negtive control siRNA

source_name: siIMP1 transfected JAR cells

value: siRNA targeting IMP1


title: R1 silk, biological replicate 3

source_name: R1 silk

value: silk


title: QGP

description:
miRNA expression profiling of Pancreatic neuroendocrine cell line
VG22_C4

source_name: Pancreatic neuroendocrine cell line

value: Pancreas

value: tumor (cell line)

value: primary


title: R1 leaf, biological replicate 3


title: R1 root, biological replicate 1

value: root


title: R1 silk, biological replicate 2


title: Midgut carinoid Liver Metastasis, L4

description:
miRNA expression profiling of Midgut carinoid Liver Metastasis tumor from patient, forth replicate
VG17_L4


title: R1 silk, biological replicate 1


title: R1 cob, biological replicate 2

source_name: R1 cob

value: cob


title: R1 cob, biological replicate 3


title: R1 ovule, biological replicate 3

source_name: R1 ovule


title: Midgut carinoid Liver Metastasis, L3

description:
miRNA expression profiling of Midgut carinoid Liver Metastasis tumor from patient, third replicate
VG16_L3

value: Liver


title: Midgut carinoid Liver Metastasis, L1

description:
miRNA expression profiling of Midgut carinoid Liver Metastasis tumor from patient, first replicate
VG14_L1

value: tumor


title: R1 cob, biological replicate 1


title: Midgut carinoid Mesentary Metastasis, M3

description:
miRNA expression profiling of Midgut carinoid Mesentary Metastasis tumor from patient, third replicate
VG11_M3

source_name: Midgut carinoid Mesentary Metastasis

value: Mesentarium

value: metastasis


title: Midgut carinoid Mesentary Metastasis, M5

description:
miRNA expression profiling of Midgut carinoid Mesentary Metastasis tumor from patient, fifth replicate
VG13_M5


title: Midgut carinoid Mesentary Metastasis, M2

description:
miRNA expression profiling of Midgut carinoid Mesentary Metastasis tumor from patient, second replicate
VG10_M2


title: Midgut carinoid Liver Metastasis, L2

description:
miRNA expression profiling of Midgut carinoid Liver Metastasis tumor from patient, second replicate
VG15_L2


title: R1 leaf, biological replicate 1

value: leaf


title: 10DAP endosperm, biological replicate 2

source_name: 10DAP endosperm

value: endosperm


title: Midgut carinoid primary tumor, P5

description:
miRNA expression profiling of midgut cercinoid primary tumor from patient, fifth replicate
VG08_P5

source_name: Midgut carinoid primary tumor

value: Ileum


title: V16 tassel, biological replicate 3

source_name: V16 tassel

value: tassel


title: Midgut carinoid Mesentary Metastasis, M1

description:
miRNA expression profiling of Midgut carinoid Mesentary Metastasis tumor from patient, first replicate
VG09_M1


title: Midgut carinoid primary tumor, P4

description:
miRNA expression profiling of midgut cercinoid primary tumor from patient, forth replicate
VG07_P4


title: Midgut carinoid Mesentary Metastasis, M4

description:
miRNA expression profiling of Midgut carinoid Mesentary Metastasis tumor from patient, forth replicate
VG12_M4


title: Midgut carinoid primary tumor, P3

description:
miRNA expression profiling of midgut cercinoid primary tumor from patient, third replicate
VG06_P3


title: R1 ovule, biological replicate 2

value: R1 (1d before pollination)

value: ovule


title: V16 silk, biological replicate 1

source_name: V16 silk


title: Midgut carinoid primary tumor, P2

description:
miRNA expression profiling of midgut cercinoid primary tumor from patient, second replicate
VG05_P2


title: V16 silk, biological replicate 3


title: Normal Ileum Mucosa, N1

description:
miRNA expression profiling of Normal Ileum Mucosa from patient, first replicate
VG01_N1

source_name: Normal Ileum Mucosa

value: normal

value: non tumor


title: V16 tassel, biological replicate 2


title: V16 tassel, biological replicate 1


title: V16 silk, biological replicate 2

value: silk


title: Normal Ileum Mucosa, N2

description:
miRNA expression profiling of Normal Ileum Mucosa from patient, second replicate
VG02_N2


title: V16 cob, biological replicate 2

source_name: V16 cob


title: Midgut carinoid primary tumor, P1

description:
miRNA expression profiling of midgut cercinoid primary tumor from patient, first replicate
VG04_P1


title: V16 cob, biological replicate 1


title: V16 cob, biological replicate 3


title: V16 floret, biological replicate 3

source_name: V16 floret

value: floret


title: 6 h cyanamid-treated seedlings vs control: replicate1

city: Fuchu

first: Naoya

last: Wasano

state: Tokyo

address: Saiwai-cho 3-5-8

country: Japan

institute: Tokyo University of Agriculture & Technology

description:
US90500268_252116911405_S01_GE2_105_Dec08_1_3
Biological replicate 1 of 2

hyb_protocol: Mixtures of 0.825 µg of Cy3-labeled and Cy5-labeled cRNAs were co-hybridized at 65 °C for 17 h on an Agilent Technologies 4 × 44K Arabidopsis 4 60-mer oligo-microarray.

scan_protocol: The slides were then washed and scanned with an Agilent G2505B Scanner to detect fluorescence intensity.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Data represent the log ratio (treated/control). Features flagged in Feature Extraction software as non-uniform (IsFeatNonUnifOL and IsFeatPopnOL field), saturated (IsSaturated field) or low signal (IsWellAboveBG field) were omitted.

source_name: 6 h cyanamid-treated seedlings

label_protocol: Two-color spike mix was added to the total RNA, and the RNA was labeled with a Quick Amp Labeling Kit, two-color (Agilent Technologies), according to the manufacturer’s protocol. Fluorescent cRNA was generated from total RNA: 500 ng of RNA was reverse-transcribed with MMLV reverse transcriptase and an oligo(dT) primer containing the T7 promoter, and subsequently transcribed in vitro using T7 RNA polymerase, resulting in Cy3-labeled (control) and Cy5-labeled (cis-CA-treated) cRNAs. The cRNAs were purified through RNeasy Mini Spin columns (Qiagen) and then quantified with a NanoDrop ND-1000 UV-VIS spectrophotometer

growth_protocol: The sterilized seeds were placed on 0.8% agar (Nakalai Tesque, Inc., Kyoto, Japan) with Murashige and Skoog Plant Salt Mixture (Nihon Pharmaceutical Co., Ltd., Tokyo, Japan) and 1% sucrose (Wako Pure Chemical Industries, Osaka, Japan) in a sterilized Petri dish (90-mm diameter). The seeds were held at 4 °C overnight in darkness and then transferred to a growth chamber. Emerging plants were maintained in the growth chamber under a schedule of 16-h light (22 °C) and 8-h dark (20 °C).

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

treatment_protocol: After 14 d in the growth chamber, seedlings were removed from the agar and equilibrated for 1 h at 22 °C in 20 ml deionized water, and then transferred to 20 ml of deionized water containing 20 ppm cyanamid, and then incubated under light. Plants were collected at 0 (control), 2, and 6 h and immediately frozen in liquid nitrogen, and then stored at –80 °C before analysis.

value: Col. 0

tag: age

value: day 14

value: seedling

source_name: control seedlings


title: V16 floret, biological replicate 2


title: 6 h  trans-2-hexenal-treated seedlings vs control: replicate1

description: Biological replicate 1 of 2

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Data represent the log ratio treated/control). Features flagged in Feature Extraction software as non-uniform (IsFeatNonUnifOL and IsFeatPopnOL field),

source_name: 6 h trans-2-hexenal-treated seedlings

treatment_protocol: After 14 d in the growth chamber, seedlings were removed from the agar and  transferred to 20 ml of deionized water in petri-dish. Seedlings were put in a 2 L desiccator and incubated under light in 2.3 ppb trans-2-hexenal condition.  Plants were collected at 0 (control) and 6 h, and immediately frozen in liquid nitrogen, and then stored at –80 °C before analysis.


title: 6 h cyanamid-treated seedlings vs control: replicate2

description:
US90500268_252116911405_S01_GE2_105_Dec08_1_4
Biological replicate 2 of 2


title: V15 ear, biological replicate 1

source_name: V15 ear

value: ear


title: V15 ear, biological replicate 3


title: 2 h cyanamid-treated seedlings vs control: replicate1

description:
US90500268_252116911405_S01_GE2_105_Dec08_1_1
Biological replicate 1 of 2

source_name: 2 h cyanamid-treated seedlings


title: V15 tassel, biological replicate 3

source_name: V15 tassel


title: 6 h trans-2-hexenal-treated seedlings vs control: replicate 2

description: Biological replicate 2 of 2


title: 2 h cyanamid-treated seedlings vs control: replicate 2

description:
US90500268_252116911405_S01_GE2_105_Dec08_1_2
Biological replicate 2 of 2


title: V10 ear, biological replicate 3

source_name: V10 ear


title: V15 tassel, biological replicate 2


title: V10 ear, biological replicate 1


title: V10 ear, biological replicate 2


title: V15 tassel, biological replicate 1


title: Spinal cord wild type age 100 days rep4

city: Utrecht

first: C.

last: Saris

address: Heidelberglaan 100

department: Neurology

country: Netherlands

institute: UMC Utrecht

description:
SPCW100N04
replicate 4

data_processing: The data were normalised using quantile normalisation with Lumi in R

source_name: Mouse lumbar spinal cord

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

extract_protocol: Blood from mice was collected directly into a PreAnalytix PAXgene tube (Qiagen, Venlo, The Netherlands) and the RNA was isolated using the PreAnalytix PAXgene Blood RNA kit (Qiagen). Blood total mRNA samples were treated with the Ambion GLOBINclear Mouse/Rat kit (Ambion, Austin TX, USA) to remove mouse hemoglobin mRNA. In mice, the tibialis anterior muscles were removed; the left tibialis anterior was used for mRNA isolation. Lumbar spinal cord was homogenized in lysis buffer (RLT-β-mercaptoethanol) using a T25 Ultra-Turrax homogenizer (IKA Labor Technik, Staufen, Germany). mRNA was isolated using an RNeasy RNA isolation kit (Qiagen). All kits were used according to the manufacturers’ protocol.

tag: genotype/variation

value: Wild type littermate

value: 100 days

value: lumbar spinal cord


title: Spinal cord wild type age 100 days rep1

description:
SPCW100N01
replicate 1


title: Spinal cord wild type age 70 days rep8

description:
SPCW070N08
replicate 8

value: 70 days


title: Spinal cord wild type age 100 days rep5

description:
SPCW100N05
replicate 5


title: Spinal cord wild type age 100 days rep6

description:
SPCW100N06
replicate 6


title: Spinal cord wild type age 100 days rep2

description:
SPCW100N02
replicate 2


title: Spinal cord wild type age 70 days rep7

description:
SPCW070N07
replicate 7


title: Spinal cord wild type age 100 days rep3

description:
SPCW100N03
replicate 3


title: V10 tassel, biological replicate 2

source_name: V10 tassel


title: V10 tassel, biological replicate 3


title: Spinal cord wild type age 70 days rep4

description:
SPCW070N04
replicate 4


title: V5 tassel, biological replicate 2

source_name: V5 tassel


title: V5 tassel, biological replicate 1


title: Spinal cord wild type age 70 days rep3

description:
SPCW070N03
replicate 3


title: V4 tassel, biological replicate 3

source_name: V4 tassel


title: Spinal cord wild type age 70 days rep1

description:
SPCW070N01
replicate 1


title: V8-V9 ear, biological replicate 3

source_name: V8-V9 ear


title: Spinal cord wild type age 70 days rep2

description:
SPCW070N02
replicate 2


title: Spinal cord wild type age 70 days rep5

description:
SPCW070N05
replicate 5


title: V5 tassel, biological replicate 3


title: R1 ovule, biological replicate 1

source_name: R1 ovule


title: V16 floret, biological replicate 1


title: V4 tassel, biological replicate 2


title: V4 tassel, biological replicate 1


title: Spinal cord G93A-SOD1 age 100 days rep8

description:
SPCT100N08
replicate 8


title: Spinal cord wild type age 70 days rep6

description:
SPCW070N06
replicate 6


title: Normal Ileum Mucosa, N3

description:
miRNA expression profiling of Normal Ileum Mucosa from patient, third replicate
VG03_N3


title: V8-V9 ear, biological replicate 2


title: Spinal cord G93A-SOD1 age 100 days rep5

description:
SPCT100N05
replicate 5


title: Spinal cord G93A-SOD1 age 100 days rep2

description:
SPCT100N02
replicate 2


title: V8-V9 tassel, biological replicate 3

source_name: V8-V9 tassel


title: V15 ear, biological replicate 2


title: Spinal cord G93A-SOD1 age 100 days rep6

description:
SPCT100N06
replicate 6


title: V8-V9 ear, biological replicate 1


title: V10 tassel, biological replicate 1


title: V8-V9 tassel, biological replicate 2


title: Spinal cord G93A-SOD1 age 100 days rep4

description:
SPCT100N04
replicate 4


title: V7 tassel, biological replicate 2

source_name: V7 tassel


title: Spinal cord G93A-SOD1 age 100 days rep7

description:
SPCT100N07
replicate 7


title: Spinal cord G93A-SOD1 age 100 days rep3

description:
SPCT100N03
replicate 3


title: V7 tassel, biological replicate 3


title: Spinal cord G93A-SOD1 age 70 days rep8

description:
SPCT070N08
replicate 8