title: MM034 gapmer3 rep3

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

hyb_protocol: Labeled RNA was hybridized to a Agilent human gene expression microarray according to the manufacturer's instructions.

scan_protocol: Arrays were scanned using the Agilent G2565CA Microarray Scanner and Scan Control Software 8.5 according to the manufacturer's instructions.

data_processing: Probe intensities were extracted using Feature Extraction software (Agilent).

source_name: short term culture

label_protocol: Total RNA (100 ng) was labeled using the low input Quick Amp WT labeling kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol: RNA was extracted using the miRNeasy mini kit (Qiagen)

treatment_protocol: Cells were treated with a control gapmer or GapmeR3 targeting LINC01212. Alternatively, LINC01212 was overexpressed.

value: melanoma short term culture


title: MM034 gapmer3 rep2

status: Public on Jan 15 2016

type: RNA

molecule: total RNA

organism: Homo sapiens

tag: treatment

tag: cell type


title: AMed 55

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

description:
Aorta intima-media from patient undergoing valve surgery and/or surgery for aortic aneurysm
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

hyb_protocol: GeneChip® Fluidics Station 450

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Affymetrix Power tools 1.10.0 apt-probeset-summarize using pre-defined function RMA with no further arguments

label: biotin

source_name: Aorta intima-media

label_protocol: Whole Transcript Sense Target Labeling

growth_protocol: Biopsies were obtained at surgery from mammary artery and dilated and non-dilated ascending aorta.

extract_protocol: Total RNA was isolated using Trizol (BRL-Life Technologies) and RNeasy Mini kit (Qiagen, Crawley, UK) including treatment with RNase-free DNase set (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Incubated with RNAlater (Ambion, Austin, TX) and homogenized with a FastPrep using Lysing Matrix D tubes (Qbiogene, Irvine, CA).

tag: number of aortic cusps

tag: aorta dilation

value: No


title: MM034 gapmer3 rep4


title: AMed 38


title: MM034 gapmer3 rep1


title: AMed 32

value: Borderline


title: MM034 control rep3

value: control


title: AMed 45


title: AMed 34


title: MM034 control rep2


title: AMed 17

value: Yes


title: MM034 control rep4


title: AMed 183


title: AMed 51


title: MM034 control rep1


title: SKMEL28 LINC01212 rep3

source_name: cell line

value: LINC01212 overexpression

tag: cell line


title: SKMEL28 LINC01212 rep2


title: SKMEL28 control rep4b


title: AMed 177


title: SKMEL28 LINC01212 rep4


title: SKMEL28 LINC01212 rep1


title: AMed 28


title: AMed 131


title: SKMEL28 control rep2b


title: SKMEL28 control rep1b


title: AMed 130


title: AMed 112


title: AMed 11


title: SKMEL28 gapmer3 rep3


title: AMed 120


title: SKMEL28 control rep3b


title: AMed 161


title: SKMEL28 control rep4


title: SKMEL28 gapmer3 rep2


title: AMed 106


title: SKMEL28 control rep1


title: AMed 297


title: AMed 13


title: SKMEL28 gapmer3 rep1


title: AMed 105


title: SKMEL28 gapmer3 rep4


title: AMed 111


title: AMed 116


title: MM057 gapmer3 rep3


title: AMed 301


title: AMed 286


title: SKMEL28 control rep3


title: MM057 gapmer3 rep1


title: MM057 gapmer3 rep2


title: AMed 222


title: AMed 283


title: SKMEL28 control rep2


title: AMed 52


title: MM057 control rep3


title: AMed 265


title: MM057 control rep2


title: MM087 gapmer3 rep4


title: AMed 266


title: AMed 262


title: MM087 control rep4


title: MM057 control rep1


title: MM087 control rep1


title: MM087 control rep3


title: MM087 gapmer3 rep1


title: AMed 188


title: TC32_siHNRNPH1 A3_rep2

city: Bethesda

first: Suntae

last: Kim

state: MD

address: Bldg 37, room 6128

department: Genetics Branch

country: USA

institute: CCR, NCI, NIH

description: TC32 cells treated with siHNRNPH1, replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Gene expression array signal intensities were Log2 transformed and quantile normalized using GenomeStudio (Illumina) and R v.3.0.2 with lumi package (Du et al., 2008). Differential expression between groups was assessed using an empirical Bayes method for the moderated T-statistics; all probes were corrected for multiple testing using Benjamini and Hochberg’s false discovery rate (FDR).

label: Biotin

source_name: TC32 cells, siHNRNPH1

label_protocol: Biotinylated cRNAs were prepared using the Ambion Illumina TotalPrep-96 RNA Amplification Kit (Cat #4393543)

growth_protocol: All cell lines were grown in RPMI-1640 (Invitrogen, Carlsbad, CA) supplemented with 10% FBS (Invitrogen).

extract_protocol: RNA was extracted with Trizol reagent. RNA quantity was measured using Nanodrop.

treatment_protocol: To generate expression profiles of TC32 cells, total RNA was purified from untransfected or siRNA-transfected TC32 cells (400,000 cells at plating in six-well plates) 48 hours post siRNA-transfection.

value: Ewing sarcoma

value: siHNRNPH1 A3

tag: treatment duration

tag: dose

value: 20 nM


title: MM087 control rep2


title: AMed 191


title: TC32_siHNRNPH1 A3_rep3

description: TC32 cells treated with siHNRNPH1, replicate 3


title: AMed 232


title: TC32_siHNRNPH1 Q3_rep3

value: siHNRNPH1 Q3


title: MM087 gapmer3 rep3


title: TC32_siHNRNPH1 Q3_rep1

description: TC32 cells treated with siHNRNPH1, replicate 1


title: AMed 184


title: CD14 monocytes - M.tb infected - 6 hrs [ZI.Mtb]

city: Seattle

first: Chetan

last: Seshadri

state: WA

address: 750 Republican Street

department: Medicine

institute: University of Washington

description: ZI.Mtb

data_processing: Signal intensities were quantile normalized using the Bioconductor package “lumi”

source_name: TST_POS_CD14+ monocytes_M.tb infected

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

growth_protocol: Archived peripheral blood mononuclear cells (PBMC) were thawed and washed twice with RPMI supplemented with 10% fetal calf serum (Atlas Biologicals).  Monocytes expressing CD14 were isolated by positive selection (Miltenyi).

extract_protocol: After a six hour incubation at 37C, 5% CO2, the mycobacteria were killed and total RNA harvested using TRIzol-LS (Invitrogen).  TRIzol samples were stored at -80C until all infections were completed.  To minimize batch effects, equal numbers of TSTPOS and TSTNEG subjects were processed on each of six days and frozen aliquots of M.tb were used for infections. TRIzol samples were thawed and the contents transferred to Phase Lock Gel tubes (5PRIME GmbH) and supplemented with 0.2 ml chloroform (Fisher Scientific).  Phase Lock Gel tubes were spun at 12,000g for 15 minutes at 4C and the upper aqueous layer transferred to a 2ml Eppendorf tube.  An equal volume of 70% ethanol was added dropwise and mixed by tapping.  The contents of this Eppendorf tube were then processed using RNeasy Mini Kit (Qiagen) according the manufacturer’s instructions with the following modifications.  DNA digestion was performed with DNAse I (Qiagen) and the final elution was performed twice with 30ul RNase-free water to maximize the yield.  Subsequently, RNA was dried down in a Speedvac and resuspended in 10ul water before assessing purity, integrity, and yield.

treatment_protocol: Cells were mock-infected or infected with virulent M. tuberculosis strain H37Rv at a multiplicity of infection (MOI) 10:1.

tag: cohort

tag: Sex

value: F

tag: age (yrs)

tag: cell subtype

value: CD14+ monocytes

tag: infected with

value: virulent M. tuberculosis strain H37Rv for 6hrs


title: TC32_siHNRNPH1 A3_rep1


title: CD14 monocytes - M.tb infected - 6 hrs [ZE.Mtb]

description: ZE.Mtb

value: peripheral blood mononuclear cells (PBMC)


title: pdx gapmer3 rep5

source_name: patient derived xenograft

label_protocol: Total RNA (100ng) was labeled using the low input Quick Amp WT labeling kit (Agilent Technologies) according to the manufacturer’s instructions.

treatment_protocol: Mice were treated with a control gapmer of GapmeR3 targeting LINC01212

tag: tissue type

value: patient derived melanoma xenograft


title: TC32_siHNRNPH1 A2_rep3

value: siHNRNPH1 A2


title: CD14 monocytes - M.tb infected - 6 hrs [ZH.Mtb]

description: ZH.Mtb

value: M


title: TC32_siNeg_rep5

description: TC32 cells treated with siNeg, replicate 2

source_name: TC32 cells, siNeg

value: siNeg


title: CD14 monocytes - M.tb infected - 6 hrs [ZG.Mtb]

description: ZG.Mtb

source_name: TST_NEG_CD14+ monocytes_M.tb infected


title: GCT44 - Yolk Sac Tumour cell line

type: genomic

city: Nottingham

first: Paul

middle: J

last: Scotting

address: Queen's Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

hyb_protocol: hybridization to the Infinium HumanMethylome450 arrays (Illumina) performed by the Queen Mary University of London Genome Centre, using the Illumina Infinium HD Assay Methylation Protocol.

scan_protocol: Illumina iScan with Autoloader2 to scan the arrays, and data has been analysed using the Illumina GenomeStudio Methylation Module v1.9 performed by the Queen Mary University of London Genome Centre.

data_processing: The Excel tool PivotTable was used to assign average methylation and differential methylation measurements to each gene according to various combinations of locations with respect to CpG islands and gene regions. Probes labelled by multiple gene names were excluded from the analysis.  Unmethylated and methylated signal intensities are available on the series record.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Yolk Sac Tumour (Roach, 1994)

label_protocol: Illumina Infinium HD Assay Methylation Protocol using the HumanMethylation450 BeadChip.

growth_protocol: Cell lines were cultured in Dulbecco’s Modified Eagle Medium (EC, Teratoma and YST) and RPMI-1640 media (Seminoma) (Sigma-Aldrich). containing 10% fetal bovine serum (Sigma-Aldrich). and 1% Penicillin/Streptomycin (Sigma-Aldrich).

extract_protocol: Bisulphite conversion of the DNA (1µg) was performed using EZ DNA methylation kit (Zymo),

tag: histological_subtype_primary tumor

value: Yolk Sac Tumour

tag: anatomical localisation

value: human testicular GCT


title: CD14 monocytes - M.tb infected - 6 hrs [ZF.Mtb]

description: ZF.Mtb


title: TC32_siHNRNPH1 A2_rep2


title: TC32_siNeg_rep4

description: TC32 cells treated with siNeg, replicate 1


title: TC32_siHNRNPH1 A2_rep1


title: pdx gapmer3 rep4


title: TCam-2 - Seminoma cell line

source_name: Seminoma (de Jong, 2008)

value: Seminoma


title: GCT27 - Embryocarcinoma cell line

source_name: Embryocarcinoma (Andrews, 1998)

value: Embryocarcinoma


title: CD14 monocytes - M.tb infected - 6 hrs [X.Mtb]

description: X.Mtb


title: CD14 monocytes - M.tb infected - 6 hrs [ZD.Mtb]

description: ZD.Mtb


title: TC32_siNeg_rep6

description: TC32 cells treated with siNeg, replicate 3


title: pdx gapmer3 rep2


title: pdx gapmer3 rep3


title: NT2D1 - Teratoma cell line

source_name: Teratoma (Andrews, 1998)

value: Teratoma

value: human testicular GCT lung metastasis


title: TC32_siSF3B1 Q3_rep2

description: TC32 cells treated with siSF3B1, replicate 2

source_name: TC32 cells, siSF3B1

value: Ewing sarcoma

value: siSF3B1 Q3


title: CD14 monocytes - M.tb infected - 6 hrs [S.Mtb]

description: S.Mtb


title: TC32_siSF3B1 Q3_rep3

description: TC32 cells treated with siSF3B1, replicate 3

value: 20 nM


title: pdx gapmer3 rep1


title: CD14 monocytes - M.tb infected - 6 hrs [U.Mtb]

description: U.Mtb


title: CD14 monocytes - M.tb infected - 6 hrs [V.Mtb]

description: V.Mtb


title: CD14 monocytes - M.tb infected - 6 hrs [T.Mtb]

description: T.Mtb

value: F


title: pdx control rep4

value: control


title: CD14 monocytes - M.tb infected - 6 hrs [R.Mtb]

description: R.Mtb

value: CD14+ monocytes

value: virulent M. tuberculosis strain H37Rv for 6hrs


title: pdx control rep3

value: patient derived melanoma xenograft


title: TC32_siSF3B1 A3_rep3

value: siSF3B1 A3


title: pdx control rep2


title: TC32_siHNRNPH1 Q3_rep2

value: siHNRNPH1 Q3


title: TC32_siSF3B1 Q3_rep1

description: TC32 cells treated with siSF3B1, replicate 1


title: TC32_siSF3B1 A3_rep2


title: TC32_siSF3B1 A3_rep1


title: TC32_siSF3B1 A2_rep3

value: siSF3B1 A2


title: CD14 monocytes - M.tb infected - 6 hrs [Q.Mtb]

description: Q.Mtb

value: peripheral blood mononuclear cells (PBMC)


title: CD14 monocytes - M.tb infected - 6 hrs [O.Mtb]

description: O.Mtb


title: CD14 monocytes - M.tb infected - 6 hrs [P.Mtb]

description: P.Mtb


title: CD14 monocytes - M.tb infected - 6 hrs [N.Mtb]

description: N.Mtb


title: Male wild-type littermate control-intact 4179

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

description: Mid-ventricular 20-30 mg ring of cardiac tissue; homogenized using desintegrator with Lysing Matrix D beads

hyb_protocol: Purified and labeled cRNA (28 pmol of Cy3 labeled cRNA) was hybridised on Agilent Mouse Whole Genome 4x44k array (design 014868) followed by (manual) washing, according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 9.5.1.1).

data_processing: The dataset contains the Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v9.5.1.1) after an additional quantile normalization. Intensities were base 2 log-transformed.

organism: Mus musculus

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 1 µg of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

extract_protocol:
1. 20-30 mg mid-ventricular section (previously stored at -80 C) has been placed into 600 µL RLT buffer in a tissue disintegration tube (Lysing Matrix D, MP Biomedicals, Cat. Nr. 6913-100 )
2. Disintegration was performed using RiboLyser for 40s at maximal power “6".  Samples were stored on ice during the transfers.
3. Lysing matrixtubes were centrifuged for 1 min at 10 000 x g at room temperature and supernatant transferred into a new tube.
4. Lysing matrix was washed using additional 290 µL RNase free water, centrifuged for 1 min at 10 000x g  supernatants were joined.
5.  Proteinase K (provided in the RNeasy Fibrous tissue Mini kit) was added (10 µL per sample) and mixed thoroughly.
6. Extraction continued with the RNeasy FibrousTissue Mini Kit; Qiagen; Cat Nr: 74704 according to manufacturer's manual

tag: strain

value: C57BL/6 N background

tag: genotype

value: wild-type littermate

tag: gender

value: Male

tag: tissue

value: Heart-left ventricle

tag: Stage

value: Control-intact


title: Female alpha-MHC-NOS3 control-intact 4177

value: Female


title: CD14 monocytes - M.tb infected - 6 hrs [M.Mtb]

description: M.Mtb

tag: cell type


title: CD14 monocytes - M.tb infected - 6 hrs [K.Mtb]

description: K.Mtb


title: CD14 monocytes - M.tb infected - 6 hrs [H.Mtb]

description: H.Mtb

value: M


title: Female alpha-MHC-NOS3 10 weeks TAC 4185

value: 10 weeks TAC


title: Female wild-type littermate 10 weeks TAC 4189


title: Male alpha-MHC-NOS3 10 weeks TAC 4183


title: MM087 gapmer3 rep2

tag: treatment

value: melanoma short term culture


title: AMed 199

tag: number of aortic cusps

tag: aorta dilation

value: Yes


title: Female wild-type littermate 10 weeks TAC 4188


title: TC32_siSUPT6H Q3_rep3

description: TC32 cells treated with siSUPT6H, replicate 3

source_name: TC32 cells, siSUPT6H

tag: cell line

value: Ewing sarcoma

value: siSUPT6H Q3

tag: treatment duration

tag: dose

value: 20 nM


title: TC32_siSF3B1 A2_rep1


title: TC32_siSF3B1 A2_rep2


title: Male alpha-MHC-NOS3 control-intact 4175


title: TC32_Untreated_rep2

description: TC32 cells, Untreated, replicate 2

source_name: TC32 cells, Untreated

value: Untreated


title: CD14 monocytes - M.tb infected - 6 hrs [L.Mtb]

description: L.Mtb

tag: cohort

tag: Sex

value: F

tag: age (yrs)

tag: cell subtype

value: CD14+ monocytes

value: virulent M. tuberculosis strain H37Rv for 6hrs


title: Male wild-type littermate 10 weeks TAC 4187

value: C57BL/6 N background


title: TC32_Untreated_rep1

description: TC32 cells, Untreated, replicate 1


title: CD14 monocytes - M.tb infected - 6 hrs [J.Mtb]

description: J.Mtb

value: peripheral blood mononuclear cells (PBMC)

tag: infected with


title: TC32_siSUPT6H A3_rep3

value: siSUPT6H A3


title: CD14 monocytes - M.tb infected - 6 hrs [I.Mtb]

description: I.Mtb


title: TC32_siSUPT6H Q3_rep1

description: TC32 cells treated with siSUPT6H, replicate 1


title: TC32_siSUPT6H Q3_rep2

description: TC32 cells treated with siSUPT6H, replicate 2


title: CD14 monocytes - M.tb infected - 6 hrs [E.Mtb]

description: E.Mtb


title: CD14 monocytes - M.tb infected - 6 hrs [G.Mtb]

description: G.Mtb


title: Female alpha-MHC-NOS3 10 weeks TAC 4184

tag: strain

value: Heart-left ventricle


title: Female wild-type littermate control-intact 4181

tag: genotype

value: wild-type littermate

value: Control-intact


title: CD14 monocytes - M.tb infected - 6 hrs [D.Mtb]

description: D.Mtb


title: Male alpha-MHC-NOS3 10 weeks TAC 4182

tag: gender

value: Male


title: Male wild-type littermate 10 weeks TAC 4186

tag: tissue

value: 10 weeks TAC


title: Female wild-type littermate control-intact 4180

value: Female

tag: Stage


title: TC32_siSUPT6H A3_rep2

tag: cell type


title: Male wild-type littermate control-intact 4178


title: CD14 monocytes - Media treated - 6 hrs [ZH.media]

description: ZH.media

source_name: TST_POS_CD14+ monocytes_media treated

value: M

value: media (mock-infected) for 6hrs


title: CD14 monocytes - M.tb infected - 6 hrs [A.Mtb]

description: A.Mtb


title: TC32_siSUPT6H A1_rep3

value: Ewing sarcoma

tag: treatment

value: siSUPT6H A1


title: TC32_siSUPT6H A3_rep1

value: 20 nM


title: TC32_Untreated_rep3

description: TC32 cells, Untreated, replicate 3

value: Untreated


title: TC32_siSUPT6H A1_rep1


title: TC32_siSUPT6H A1_rep2


title: CD14 monocytes - M.tb infected - 6 hrs [C.Mtb]

description: C.Mtb

value: F

value: CD14+ monocytes


title: TC32_siNeg_rep2

value: siNeg


title: Female alpha-MHC-NOS3 control-intact 4176

value: C57BL/6 N background


title: SA_tumor_exper2_rep2

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

data_processing: The data were quantile normalized without background subtraction using Illumina GenomeStudio V1.8

source_name: MC38mRFP colon adenocarcinoma, 21 days post-injection

label_protocol: Biotin labeled complementary RNA (cRNA) was made using the EpiCentre TargetAmp-Nano kit

growth_protocol: Either whole tumors or sorted cancer cells or sorted stromal cells were recovered directly from mice and used for the transcriptional analysis by microarray

extract_protocol: Whole tumors or sorted cells from digested tumors were processed directly for RNA extraction using the Qiagen miRNeasy kit

treatment_protocol: Sorted cells or whole tumors were analyzed directly from mice, without any additional treatments.

value: sorted mRFP positive cells (cancer)


title: SA_tumor_exper2_rep1


title: CD14 monocytes - M.tb infected - 6 hrs [B.Mtb]

description: B.Mtb

value: peripheral blood mononuclear cells (PBMC)

value: virulent M. tuberculosis strain H37Rv for 6hrs


title: CD14 monocytes - Media treated - 6 hrs [ZF.media]

description: ZF.media

source_name: TST_NEG_CD14+ monocytes_media treated


title: WT_tumor_exper2_rep1


title: CD14 monocytes - Media treated - 6 hrs [ZE.media]

description: ZE.media


title: WT_tumor_exper2_rep2


title: RDES_5nM_PlaB_24h_rep3

description: RDES cells treated with 5nM PlaB 24h, replicate 3

source_name: RDES cells, 5nM Pladienolide B (PlaB) 24h treated

treatment_protocol: To generate expression profiles, total RNA was purified from untreated cells or cells exposed to 5nM Pladienolide B (PlaB) for 24 hours (400,000 cells at plating in six-well plates)

value: RDES

value: 5nM PlaB

value: 5 nM


title: Male alpha-MHC-NOS3 control-intact 4174

data_processing: The dataset contains the Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v9.5.1.1) after an additional quantile normalization. Intensities were base 2 log-transformed. Probes below background were removed and intensities duplicate probes were averaged.

value: Male

value: Heart-left ventricle

value: Control-intact


title: CD14 monocytes - Media treated - 6 hrs [ZG.media]

description: ZG.media

value: media (mock-infected) for 6hrs


title: CD14 monocytes - Media treated - 6 hrs [ZI.media]

description: ZI.media


title: TC32_siNeg_rep1

value: Ewing sarcoma


title: CD14 monocytes - Media treated - 6 hrs [ZD.media]

description: ZD.media


title: CD14 monocytes - Media treated - 6 hrs [X.media]

description: X.media


title: CD14 monocytes - Media treated - 6 hrs [U.media]

description: U.media

value: M


title: RDES_Vehicle_rep3

description: RDES cells treated with DMSO vehicle control, replicate 3

source_name: RDES cells, 0.1% DMSO vehicle 24h treated

value: Vehicle control


title: RDES_Vehicle_rep2

description: RDES cells treated with DMSO vehicle control, replicate 2


title: RDES_5nM_PlaB_24h_rep2

description: RDES cells treated with 5nM PlaB 24h, replicate 2


title: CD14 monocytes - Media treated - 6 hrs [V.media]

description: V.media


title: TC32_siNeg_rep3

value: 20 nM


title: WT_stroma_exper2_rep2

value: sorted mRFP negative cells (stroma)


title: pdx control rep1

value: control

tag: tissue type

value: patient derived melanoma xenograft


title: SA_stroma_exper2_rep2


title: RDES_5nM_PlaB_24h_rep1

description: RDES cells treated with 5nM PlaB 24h, replicate 1


title: WT_tumor_exper1_rep3

source_name: MC38 colon adenocarcinoma, 9 days post-injection

value: whole tumor


title: WT_stroma_exper2_rep1


title: SA_stroma_exper2_rep1


title: TC71_5nM_PlaB_24h_rep2

description: TC71 cells treated with 5nM PlaB 24h, replicate 2

source_name: TC71 cells, 5nM Pladienolide B (PlaB) 24h treated


title: CD14 monocytes - Media treated - 6 hrs [S.media]

description: S.media

value: peripheral blood mononuclear cells (PBMC)

value: CD14+ monocytes


title: RDES_Vehicle_rep1

description: RDES cells treated with DMSO vehicle control, replicate 1

value: RDES


title: TC71_5nM_PlaB_24h_rep3

description: TC71 cells treated with 5nM PlaB 24h, replicate 3

value: 5nM PlaB


title: TC71_Vehicle_rep3

description: TC71 cells treated with DMSO vehicle control, replicate 3

source_name: TC71 cells, 0.1% DMSO vehicle 24h treated


title: TC71_5nM_PlaB_24h_rep1

description: TC71 cells treated with 5nM PlaB 24h, replicate 1

value: 5 nM


title: WT_tumor_exper1_rep2


title: CD14 monocytes - Media treated - 6 hrs [R.media]

description: R.media

value: F


title: CD14 monocytes - Media treated - 6 hrs [O.media]

description: O.media


title: SA_tumor_exper1_rep1


title: CD14 monocytes - Media treated - 6 hrs [T.media]

description: T.media


title: SA_tumor_exper1_rep3


title: SA_tumor_exper1_rep2


title: CD14 monocytes - Media treated - 6 hrs [M.media]

description: M.media


title: CD14 monocytes - Media treated - 6 hrs [N.media]

description: N.media


title: CD14 monocytes - Media treated - 6 hrs [P.media]

description: P.media


title: TC32_5nM_PlaB_24h_rep3

description: TC32 cells treated with 5nM PlaB 24h, replicate 3

source_name: TC32 cells, 5nM Pladienolide B (PlaB) 24h treated


title: TC32_5nM_PlaB_24h_rep2

description: TC32 cells treated with 5nM PlaB 24h, replicate 2


title: CD14 monocytes - Media treated - 6 hrs [K.media]

description: K.media


title: CD14 monocytes - Media treated - 6 hrs [Q.media]

description: Q.media


title: WT_tumor_exper1_rep1


title: CD14 monocytes - Media treated - 6 hrs [H.media]

description: H.media


title: TC32_5nM_PlaB_24h_rep1

description: TC32 cells treated with 5nM PlaB 24h, replicate 1


title: CD14 monocytes - Media treated - 6 hrs [I.media]

description: I.media


title: TC71_Vehicle_rep2

description: TC71 cells treated with DMSO vehicle control, replicate 2


title: CD14 monocytes - Media treated - 6 hrs [L.media]

description: L.media


title: TC32_Vehicle_rep2

description: TC32 cells treated with DMSO vehicle control, replicate 2

source_name: TC32 cells, 0.1% DMSO vehicle 24h treated


title: CD14 monocytes - Media treated - 6 hrs [J.media]

description: J.media


title: Siglec-E knockout 3

city: La Jolla

first: Ajit

last: Varki

state: California

address: 9500 Gilman Drive

institute: UC San Diego

hyb_protocol: standard Illumina

scan_protocol: standard Illumina

data_processing: Illumina GenomeStudio: cubic spline normalization

source_name: liver

label_protocol: standard Illumina

growth_protocol: Resected liver samples were placed immediately into RNALater (Qiagen) on ice.

extract_protocol: Tissues were homogenized using a Kinematica homogenizer. RNA was isolated from tissues using RNeasy kit (Qiagen). Concentration and quality of RNA were measured by a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies) and by a 2100 Bioanalyzer (Agilent).

value: male

tag: age

value: 55 wk

value: liver

value: Siglec-E KO


title: SKNMC_5nM_PlaB_24h_rep2

description: SKNMC cells treated with 5nM PlaB 24h, replicate 2

source_name: SKNMC cells, 5nM Pladienolide B (PlaB) 24h treated

tag: cell line

value: SKNMC

value: Ewing sarcoma


title: TC32_Vehicle_rep1

description: TC32 cells treated with DMSO vehicle control, replicate 1

value: Vehicle control

tag: treatment duration


title: SKNMC_5nM_PlaB_24h_rep1

description: SKNMC cells treated with 5nM PlaB 24h, replicate 1

tag: dose


title: CD14 monocytes - Media treated - 6 hrs [G.media]

description: G.media

tag: cohort

value: media (mock-infected) for 6hrs


title: CD14 monocytes - Media treated - 6 hrs [D.media]

description: D.media

tag: Sex


title: CD14 monocytes - Media treated - 6 hrs [C.media]

description: C.media

tag: age (yrs)


title: CD14 monocytes - Media treated - 6 hrs [E.media]

description: E.media

value: M

tag: cell subtype


title: 3rdNS_TPB4

status: Public on Jan 14 2016

city: Shinjuku-ku

first: Takuya

last: Matsumoto

state: Tokyo

address: 35 Shinanomachi

country: Japan

institute: Keio University School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.  Normalized data matrices available on the series record contain MAS5.0 signal. Normalizations were performed on sample subsets.

source_name: neurosphere

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

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

value: neurosphere

tag: donor

value: PB

tag: cell source

value: T-cell


title: 3rdNS_TPB8


title: 3rdNS_PB20

value: aHDF


title: 3rdNS_PB2


title: 3rdNS_eKA3

value: KA


title: SKNMC_5nM_PlaB_24h_rep3

description: SKNMC cells treated with 5nM PlaB 24h, replicate 3

value: 5nM PlaB


title: 3rdNS_KA23


title: TiPS_TPB8

source_name: iPSC

value: iPSC

tag: iPSc source


title: TC32_Vehicle_rep3

description: TC32 cells treated with DMSO vehicle control, replicate 3


title: TiPS_TPB4


title: TiPS_eTKA5


title: Siglec-E knockout 2

tag: gender

tag: genotype


title: TiPS_eTKA4


title: TiPS_TKA7(DNAVEC)


title: TiPS_TKA14(DNAVEC)


title: iPS_PB2


title: TC71_Vehicle_rep1

description: TC71 cells treated with DMSO vehicle control, replicate 1


title: SKNMC_Vehicle_rep2

description: SKNMC cells treated with DMSO vehicle control, replicate 2

source_name: SKNMC cells, 0.1% DMSO vehicle 24h treated


title: Wild-type 3

tag: tissue

value: wild type


title: SKNMC_Vehicle_rep3

description: SKNMC cells treated with DMSO vehicle control, replicate 3

tag: cell type


title: Wild-type 2

value: male


title: Siglec-E knockout 1

value: 55 wk


title: 3rdNS_TKA9(AIST)


title: 3rdNS_TKA4(AIST)


title: Wild-type 1

value: liver


title: SKNMC_Vehicle_rep1

description: SKNMC cells treated with DMSO vehicle control, replicate 1

tag: treatment


title: CD14 monocytes - Media treated - 6 hrs [B.media]

description: B.media

value: F

value: peripheral blood mononuclear cells (PBMC)

value: CD14+ monocytes

tag: infected with


title: TiPS_TKA9(AIST)


title: CD14 monocytes - Media treated - 6 hrs [A.media]

description: A.media


title: TiPS_TKA4(AIST)


title: iPS_eKA3


title: iPS_eKA4


title: iPS_KA11


title: Tcell_KA

value: Tcell


title: ES_KhES1

source_name: ESC

value: ES


title: fibroblast_KA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

value: fibroblast


title: iPS_PB20


title: iPS_KA23


title: ZR75B_T2_B

city: Toronto

first: Pamela

last: Ohashi

state: Ontario

address: 610 University Ave

country: Canada

institute: Princess Margaret Cancer Centre

hyb_protocol: Hybridization solutions consisted of 2 μg of probe for 78 k shRNA pools (2.3 μg for 90 k shRNA pools) in buffer containing 1x MES, 0.89M NaCl, 20 mM EDTA, 0.0001% Tween 20, 0.5 mg/ml BSA, 0.1 mg/ml herring sperm DNA, 0.05 nM biotinylated B2 oligo (Affymetrix), 10% DMSO, 20 μM each blocking oligos (Block_1 5'-AATGGACTATCATATGCTTACCGTAACTTGAA-3', Block_2 5'-TTCAAGTTACGGTAAGCATATGATAGTCCATT-3', Block_3 5'-GTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCG-3', Block_4 5'-CGGTGTTTCGTCCTTTCCACAAGATATATAAAGCCAAGAAATCGAAATAC-3'), and sterile water to a final volume of 138 μl. Samples in buffer were denatured at 95°C for 10 minutes, incubated at 40°C for 5 minutes, collected by centrifugation then applied to arrays, which were incubated for 16 hours at 40°C at 60 rpm. Arrays were stained with SAPE labeling mix (1x MES staining buffer, 2 mg/ml BSA, 10 μg/ml streptavidin-phycoerythrin), and washed on an Affymetrix fluidics station, then scanned. (see PMID: 21548937)

scan_protocol: As described in PMID: 21548937

data_processing: Feature signal was extracted from the GMAP arrays using Affymetrix Power Tools (APT, http://www.affymetrix.com webcite). The GMAP chip contains triplicate features per shRNA, which we summarized by using the median value. GC-background (GCbg) correction for non-specific probe binding was performed with APT, using feature signals derived from 33,894 GC-background probes on the array. Normalization of replicate arrays was performed with the Bioconductor affy package in R, using Cyclic Loess based on the 'MA-plot' of pairs of arrays. As a further normalization step, all T0 samples were normalized using Quantile Normalization. This normalization was also applied to all T1 and (separately) T2 samples. The log2 measurement values are present in the processed matrix.

source_name: breast cancer cell line

label_protocol: Affymetrix protocol

growth_protocol: Each cell line was grown to a population size of ~2 x 10^8 cells in the appropriate medium (see PMID: 22585861)

extract_protocol: Genomic DNA was prepared from cell pellets using the QIAmp Blood Maxi kit (Qiagen #51194). Genomic DNA was precipitated using ethanol and sodium chloride and resuspended at 400 ng/L in 10 mmol/L Tris-HCl, pH 7.5. shRNA populations from cell lines were amplified via PCR and prepared and applied to GMAP arrays. (see PMID: 22585861)

treatment_protocol: Cells were washed with warm PBS, trypsinized, resuspended in warm medium, and counted. An aliquot of the 80k human shRNA lentivirus pool and either polybrene (4–8 g/mL) or protamine sulfate (5 g/mL) were added such that an MOI of 0.3 to 0.4 would be achieved (determined by prior testing of each cell line). Cell–lentivirus mixtures were plated into 15-cm-diameter culture dishes and incubated at 37°C with 5% CO2. Twenty-four hours postinfection, the medium was replaced with fresh medium containing puromycin (puromycin concentration determined by prior tests on each cell line), and cells were incubated for an additional 48 hours. Culture dishes were washed with warm PBS to remove dead cells, and surviving cells were collected by trypsinization and resuspended in warm medium. Cell populations were quantified, aliquots of 2 x 10^7 cells were removed and pelleted by centrifugation, and 3 replicate populations of 2 x 10^7 cells were plated at appropriate density into 15-cm-diameter culture dishes. When replicate populations reached 80% to 90% confluency, cells from each replicate were collected by trypsinization and mixed (cells from different replicates were not comingled). From these mixtures, 2 aliquots of 2 x 10^7 cells were removed, pelleted, and frozen down, while one aliquot of 2 x 10^7 cells was replated for further growth. This step was repeated until a minimum of 6 to 8 doublings for each replicate cell population was obtained. (see PMID: 22585861)

tag: time point


title: ZR751_T2_B

tag: cell line


title: ZR75B_T1_B


title: ZR751_T0_A


title: ZR75B_T0_B


title: ZR75B_T1_C


title: ZR751_T0_C


title: ZR751_T2_A


title: T47D_T2_C


title: UACC893_T1_C


title: ZR751_T1_B


title: UACC893_T1_B


title: UACC893_T0_B


title: UACC893_T2_A


title: T47D_T2_B


title: ZR75B_T2_C


title: T47D_T1_C


title: UACC893_T1_A


title: ZR75B_T2_A


title: UACC893_T2_C


title: ZR751_T2_C


title: UACC893_T2_B


title: ZR75B_T1_A


title: T47D_T2_A


title: ZR751_T0_B


title: UACC893_T0_A


title: ZR75B_T0_A


title: ZR751_T1_C


title: ZR751_T1_A


title: T47D_T1_B


title: T47D_T0_C


title: SW527_T2_A


title: T47D_T0_B


title: T47D_T0_A


title: SW527_T0_A


title: SW527_T0_C


title: SUM52_T2_B


title: SW527_T2_C


title: T47D_T1_A


title: SUM52_T0_A


title: SW527_T1_B


title: SUM52_T0_B


title: SUM44_T0_C


title: SUM52_T1_A


title: SUM44_T2_C


title: SUM52_T1_B


title: SUM52_T1_C


title: SUM44_T1_C


title: SW527_T1_C


title: SW527_T2_B


title: SUM44_T1_A


title: SUM44_T2_B


title: SW527_T0_B


title: SUM52_T2_C


title: SUM52_T2_A


title: SUM44_T2_A


title: SUM44_T1_B


title: SUM44_T0_B


title: SUM229_T1_B


title: SUM225_T0_A


title: SUM225_T2_C


title: SUM229_T2_B


title: SUM229_T1_A


title: SUM225_T1_B


title: SUM225_T0_B


title: SUM225_T2_B


title: SUM190_T2_C


title: SUM229_T0_B


title: SUM229_T0_A


title: SUM229_T2_A


title: SUM229_T2_C


title: SUM190_T1_A


title: SUM225_T1_A


title: SUM190_T2_B


title: SUM190_T2_A


title: SUM190_T0_A


title: SUM225_T1_C


title: SUM185_T2_C


title: SUM190_T1_C


title: SUM185_T2_A


title: SUM185_T2_B


title: SUM190_T1_B


title: SUM225_T2_A


title: SUM229_T1_C


title: SUM190_T0_B


title: SUM185_T0_B


title: SUM159_T0_A


title: SUM185_T1_C


title: SUM185_T1_B


title: SUM149_T2_B


title: SUM159_T2_C


title: SUM159_T1_B


title: SUM159_T2_B


title: SUM185_T0_A


title: SUM149_T2_C


title: SUM1315_T2_B


title: SUM149_T1_C


title: SUM149_T1_B


title: SUM149_T0_B


title: SUM1315_T2_A


title: SUM1315_T0_B


title: SUM1315_T1_B


title: SUM159_T1_C


title: SUM1315_T2_C


title: SUM149_T2_A


title: SUM159_T1_A


title: SUM1315_T0_A


title: SUM159_T2_A


title: SUM159_T0_B


title: SUM1315_T1_A


title: SUM149_T0_A


title: SUM185_T1_A


title: SUM149_T1_A


title: SUM1315_T1_C


title: SW527_T1_A


title: SUM102_T2_C


title: SUM102_T2_B


title: SKBR7_T1_A


title: SKBR7_T2_A


title: SKBR5_T2_C


title: SUM102_T2_A


title: SUM102_T0_A


title: SUM102_T1_A


title: SUM102_T1_C


title: SKBR7_T0_A


title: SKBR7_T2_B


title: SUM102_T0_B


title: SKBR5_T0_B


title: SKBR5_T1_A


title: SKBR3_T2_A


title: SKBR5_T2_B


title: SKBR5_T2_A


title: SKBR5_T1_C


title: SKBR5_T1_B


title: SKBR7_T2_C


title: SKBR3_T2_C


title: SKBR3_T2_B


title: SKBR7_T0_B


title: SUM102_T1_B


title: SKBR7_T1_C


title: SKBR7_T1_B


title: SKBR5_T0_A


title: SKBR3_T1_C


title: SKBR3_T1_A


title: OCUBM_T2_C

value: OCUBM


title: OCUBM_T2_B


title: SKBR3_T1_B


title: OCUBM_T1_A


title: OCUBM_T2_A


title: MX1_T1_A


title: OCUBM_T1_C


title: SKBR3_T0_A


title: MX1_T1_B


title: MX1_T0_B


title: MFM223_T2_C


title: MX1_T2_C


title: SKBR3_T0_B


title: MFM223_T1_C


title: MX1_T2_A


title: SKBR3_T0_C


title: MFM223_T1_A


title: OCUBM_T0_A


title: MFM223_T0_B


title: MDAMB468_T2_C


title: MDAMB468_T2_B


title: OCUBM_T1_B


title: MFM223_T2_B


title: MFM223_T0_A


title: MX1_T0_A


title: MFM223_T1_B


title: MFM223_T2_A


title: MX1_T1_C


title: OCUBM_T0_B


title: MX1_T2_B


title: MDAMB453_T1_C


title: MDAMB468_T0_A


title: MDAMB415_T2_B


title: MDAMB468_T0_B


title: MDAMB453_T0_A


title: MDAMB436_T2_B


title: MDAMB436_T1_C


title: MDAMB453_T1_A


title: MDAMB453_T1_B


title: MDAMB453_T2_B


title: MDAMB436_T2_C


title: MDAMB453_T2_A


title: MDAMB436_T0_A


title: MDAMB468_T1_A


title: MDAMB436_T1_B


title: MDAMB436_T1_A


title: MDAMB436_T0_C


title: MDAMB436_T0_B


title: MDAMB453_T2_C


title: MDAMB415_T2_C


title: MDAMB415_T1_B


title: MDAMB436_T2_A


title: MDAMB415_T2_A


title: MDAMB453_T0_B


title: MDAMB468_T1_B


title: MDAMB415_T1_A


title: MDAMB468_T1_C


title: MDAMB415_T0_A


title: MDAMB361_T0_C


title: MDAMB361_T1_B


title: MDAMB330_T2_C


title: MDAMB468_T2_A


title: MDAMB361_T0_B


title: MDAMB361_T1_C


title: MDAMB361_T0_A


title: MDAMB361_T2_A


title: MDAMB330_T2_B


title: MDAMB330_T0_B


title: MDAMB415_T1_C


title: MDAMB231_T2_B


title: MDAMB330_T1_B


title: MDAMB330_T0_A


title: MDAMB361_T1_A


title: MDAMB415_T0_B


title: MDAMB361_T2_B


title: MDAMB231_T2_C


title: MDAMB231_T0_B


title: MDAMB330_T1_A


title: MDAMB361_T2_C


title: MDAMB231_T1_C


title: MDAMB231_T2_A


title: MDAMB330_T1_C


title: MDAMB330_T2_A


title: MDAMB231_T0_C


title: MDAMB231_T1_A


title: MDAMB231_T1_B


title: MDAMB134VI_T2_B


title: MDAMB157_T1_B


title: MDAMB231_T0_A


title: MDAMB157_T2_A


title: MDAMB134VI_T2_A


title: MDAMB157_T2_C


title: MDAMB157_T0_B


title: MDAMB157_T2_B


title: MDAMB134VI_T2_C


title: MDAMB157_T1_C


title: MCF7_T2_C


title: MCF7_T2_B


title: MDAMB134VI_T1_B


title: MDAMB134VI_T0_A


title: MDAMB134VI_T1_C


title: MDAMB134VI_T0_B


title: MCF7_T0_B


title: MCF12A_T2_A


title: MCF7_T0_A


title: MCF7_T1_C


title: MDAMB157_T1_A


title: MCF12A_T2_B


title: MDAMB468_T0_C


title: MDAMB157_T0_A


title: MCF7_T1_A


title: MCF7_T0_C


title: MCF7_T1_B


title: MCF7_T2_A


title: MDAMB134VI_T1_A


title: MCF12A_T0_B


title: MCF10A_T1_B


title: MCF10A_T1_C


title: MCF12A_T1_B


title: MCF10A_T0_A


title: MB157_T2_B


title: MCF10A_T2_B


title: MCF10A_T1_A


title: MCF12A_T1_C


title: MCF12A_T0_A


title: MCF10A_T2_A


title: MB157_T2_A


title: MACLS2_T2_B


title: MACLS2_T1_A


title: MB157_T0_B


title: MB157_T1_C


title: MB157_T1_A


title: MACLS2_T0_A


title: MCF12A_T1_A


title: MCF12A_T2_C


title: MB157_T2_C


title: MACLS2_T2_C


title: MACLS2_T2_A


title: MACLS2_T1_C


title: MACLS2_T1_B


title: MB157_T1_B


title: MCF10A_T2_C


title: MACLS2_T0_B


title: MB157_T0_A


title: MCF10A_T0_B


title: LY2_T2_A


title: LY2_T2_C


title: LY2_T1_C


title: LY2_T0_B


title: LY2_T1_A


title: LY2_T1_B


title: KPL1_T1_B


title: KPL1_T2_B


title: KPL1_T2_C


title: KPL1_T0_C


title: KPL1_T1_A


title: KPL1_T1_C


title: LY2_T2_B


title: LY2_T0_A


title: JIMT1_T2_C


title: JIMT1_T2_A


title: KPL1_T2_A


title: JIMT1_T1_C


title: JIMT1_T1_A


title: JIMT1_T2_B


title: JIMT1_T1_B


title: JIMT1_T0_B


title: KPL1_T0_A


title: KPL1_T0_B


title: HS578T_T2_B


title: HS578T_T1_A


title: HS578T_T1_B


title: JIMT1_T0_A


title: HS578T_T0_A


title: HS578T_T1_C


title: HS578T_T2_A


title: HS578T_T2_C


title: HDQP1_T1_B


title: HDQP1_T1_C


title: HDQP1_T2_C


title: HDQP1_T2_B


title: HDQP1_T2_A


title: HDQP1_T0_B


title: HCC70_T2_C


title: HS578T_T0_B


title: HCC38_T2_B


title: HCC70_T1_C


title: HCC70_T0_A


title: HDQP1_T1_A


title: HCC38_T1_C


title: HCC70_T2_B


title: HCC3153_T2_A


title: HCC70_T1_B


title: HDQP1_T0_A


title: HCC3153_T2_B


title: HCC38_T1_B


title: HCC38_T2_A


title: HCC38_T1_A


title: HCC38_T2_C


title: HCC3153_T1_C


title: HCC2688_T2_A


title: HCC2688_T2_C


title: HCC2688_T2_B


title: HCC3153_T1_A


title: HCC3153_T0_B


title: HCC3153_T0_A


title: HCC2688_T0_A


title: HCC2688_T1_B


title: HCC3153_T2_C


title: HCC3153_T1_B


title: HCC2218_T2_B


title: HCC2688_T1_C


title: HCC2688_T1_A


title: HCC2218_T2_A


title: HCC2218_T1_A


title: HCC2218_T1_B


title: HCC2218_T0_B


title: HCC2218_T0_A


title: HCC2218_T1_C


title: HCC2185_T1_B


title: HCC2185_T1_C


title: HCC2185_T2_A


title: HCC2185_T2_C


title: HCC202_T2_A


title: HCC2185_T0_B


title: HCC2185_T2_B


title: HCC1954_T2_B


title: HCC2185_T0_A


title: HCC1954_T2_C


title: HCC202_T1_C


title: HCC202_T0_A


title: HCC2185_T1_A


title: HCC202_T1_B


title: HCC1954_T2_A


title: HCC202_T1_A


title: HCC202_T2_B


title: HCC202_T2_C


title: HCC1954_T1_A


title: HCC1954_T1_B


title: HCC1937_T2_A


title: HCC202_T0_B


title: HCC1937_T1_C


title: HCC1937_T2_C


title: HCC1937_T2_B


title: HCC1937_T1_B


title: HCC1937_T1_A


title: HCC1954_T1_C


title: HCC1806_T2_B


title: HCC1806_T1_C


title: HCC1806_T1_A


title: HCC1806_T2_A


title: HCC1806_T0_C


title: HCC1937_T0_B


title: HCC1937_T0_A


title: HCC1806_T1_B


title: HCC1599_T2_A


title: HCC1806_T2_C


title: HCC1806_T0_A


title: HCC1599_T2_B


title: HCC1599_T1_C


title: HCC1599_T1_B


title: HCC1599_T1_A


title: HCC1599_T0_B


title: HCC1806_T0_B


title: HCC1569_T2_B


title: HCC1569_T1_B


title: HCC1569_T2_A


title: HCC1569_T0_B


title: HCC1569_T0_A


title: HCC1569_T1_A


title: HCC1599_T0_A


title: HCC1569_T1_C


title: HCC1500_T2_C


title: HCC1500_T2_A


title: HCC1500_T2_B


title: HCC1500_T0_C


title: HCC1428_T1_A


title: HCC1428_T1_C


title: HCC1569_T2_C


title: HCC1428_T0_C


title: HCC1428_T1_B


title: HCC1500_T0_B


title: HCC1500_T0_A


title: HCC1500_T1_B


title: HCC1500_T1_C


title: HCC1500_T1_A


title: HCC1419_T2_A


title: HCC1428_T0_A


title: HCC1419_T1_C


title: HCC1419_T0_B


title: HCC1395_T2_A


title: HCC1419_T1_A


title: HCC1419_T0_A


title: JejunumWholeTissue_16d_lineY_pool22

city: Wageningen

first: Dirkjan

last: Schokker

address: Droevendaalsesteeg 1

department: Wageningen Livestock Research

country: Netherlands

institute: Wageningen UR

hyb_protocol: The input was 10 ng of total RNA and 600 ng of labelled cRNA was used for hybridization on the eight pack array (Agilent 049577 chicken array). Hybridization was performed as described in the One-Color Microarray-Based Gene Expression analyzis Low input Quick Amp Labelling protocol from Agilent in the hybridization oven (G2545A hybridization Oven Agilent Technologies). The hybridization temperature was 65°C with rotation speed 10 rpm for 17 hours. After 17 hours the arrays were washed as described in the One-Color Microarray-Based Gene Expression analyzis Low input Quick Amp Labelling protocol from Agilent.

scan_protocol: The arrays were scanned using the DNA microarray scanner with Surescan high resolution Technology from Agilent Technologies. Agilent Scan Control with resolution of 5 µm, 16 bits and PMT of 100%. Feature extraction was performed using protocol 10.7.3.1 (v10.7) for 1 colour gene expression.

data_processing: The data were analyzed by using R (v3.0.2) by executing different packages, including LIMMA (GENTLEMAN et al. 2005) and arrayQualityMetrics (KAUFFMANN et al. 2009). The data were read in and background corrected (method=normexp and offset=1) with functions from the R package LIMMA (GENTLEMAN et al. 2005) from Bioconductor (GENTLEMAN et al. 2004). Quantile normalization of the data was done between arrays. The duplicate probes mapping to the same gene were averaged (‘avereps’) and subsequently the lower percentile of probes were removed in a three-step procedure, 1) get the highest of the dark spots to get a base value, 2) multiply by 1.1, and 3) the gene/probe must be expressed in each of the samples in the experimental condition.

organism: Gallus gallus

label_protocol: Labelling of RNA was done as recommended by Agilent Technologies using the One-Color Microarray-Based Gene Expression analyzis Low input Quick Amp Labelling.

extract_protocol: Total RNA was extracted from 50 to 100 mg jejunum tissue. All samples were homogenized using the TisuPrep Homogenizer Omni TP TH220P) in TRizol reagent (Life Technologies) as recommended by the manufacturer with minor modifications. The homogenized tissue samples were dissolved in 5 ml of TRizol reagent. After centrifugation the supernatant was transferred to a fresh tube. Subsequently a phase separation with chloroform was performed as described by the manufacturer Life Technologies. The RNA was precipitated and dissolved and quantified by absorbance measurements at 260 nm. Quality Control was performed using the Agilent Bioanalyzer.

treatment_protocol: Two divergent chicken lines were compared, namely line X and line Y

value: jejunum

tag: line

value: Y

tag: age

value: 16 days


title: HCC1395_T2_C


title: HCC1395_T1_C


title: HCC1419_T1_B


title: HCC1428_T0_B


title: HCC1419_T2_B


title: JejunumWholeTissue_16d_lineY_pool24


title: HCC1395_T2_B


title: JejunumWholeTissue_16d_lineY_pool19


title: HCC1395_T0_C


title: JejunumWholeTissue_16d_lineY_pool20


title: JejunumWholeTissue_4d_lineY_pool16

value: 4 days


title: JejunumWholeTissue_4d_lineY_pool15


title: HCC1187_T2_B


title: JejunumWholeTissue_4d_lineY_pool13


title: HCC1395_T0_A


title: HCC1187_T2_A


title: HCC1419_T2_C


title: HCC1395_T1_B


title: JejunumWholeTissue_16d_lineY_pool18


title: JejunumWholeTissue_16d_lineY_pool21


title: HCC1395_T1_A


title: HCC1187_T1_C


title: HCC1395_T0_B


title: HCC1419_T0_C


title: JejunumWholeTissue_4d_lineY_pool11


title: HCC1187_T0_C


title: JejunumWholeTissue_4d_lineY_pool10


title: JejunumWholeTissue_16d_lineY_pool23


title: HCC1187_T2_C


title: HCC1187_T0_B


title: HCC1187_T0_A


title: JejunumWholeTissue_4d_lineY_pool8

value: 0 days


title: HCC1187_T1_A


title: JejunumWholeTissue_4d_lineY_pool12


title: JejunumWholeTissue_4d_lineY_pool7


title: JejunumWholeTissue_4d_lineY_pool9


title: HCC2218_T2_C


title: JejunumWholeTissue_4d_lineY_pool6


title: HCC1143_T1_A


title: JejunumWholeTissue_4d_lineY_pool2


title: JejunumWholeTissue_4d_lineY_pool5


title: HCC1143_T1_B


title: HCC1143_T2_C


title: JejunumWholeTissue_4d_lineY_pool4


title: JejunumWholeTissue_16d_lineX_pool22

value: X


title: JejunumWholeTissue_4d_lineY_pool3


title: JejunumWholeTissue_16d_lineX_pool24


title: JejunumWholeTissue_16d_lineX_pool20


title: HCC1143_T2_A


title: HCC1008_T1_C


title: HCC1143_T0_B


title: HCC1008_T2_A


title: JejunumWholeTissue_16d_lineX_pool23


title: HCC1143_T0_A


title: HCC1008_T2_C


title: HCC1008_T2_B


title: HCC1143_T2_B


title: HCC1143_T1_C


title: JejunumWholeTissue_16d_lineX_pool19


title: HCC1008_T1_B


title: JejunumWholeTissue_16d_lineX_pool18


title: HCC1008_T1_A


title: JejunumWholeTissue_16d_lineX_pool21


title: JejunumWholeTissue_4d_lineX_pool13


title: JejunumWholeTissue_16d_lineX_pool17


title: JejunumWholeTissue_4d_lineX_pool16


title: HBL100_T2_C


title: HCC1008_T0_B


title: JejunumWholeTissue_4d_lineX_pool14


title: HBL100_T1_B


title: JejunumWholeTissue_4d_lineX_pool15


title: JejunumWholeTissue_4d_lineX_pool12


title: HBL100_T0_B


title: HBL100_T2_A


title: HCC1008_T0_A


title: HBL100_T1_A


title: JejunumWholeTissue_0d_lineX_pool8


title: JejunumWholeTissue_4d_lineX_pool9


title: JejunumWholeTissue_0d_lineX_pool5


title: HBL100_T1_C


title: EVSAT_T2_C

value: EVSAT


title: JejunumWholeTissue_4d_lineX_pool11


title: HBL100_T2_B


title: EVSAT_T2_B


title: JejunumWholeTissue_0d_lineX_pool6


title: JejunumWholeTissue_0d_lineX_pool7


title: HBL100_T0_A


title: JejunumWholeTissue_4d_lineX_pool10


title: EVSAT_T2_A


title: JejunumWholeTissue_0d_lineX_pool4


title: JejunumWholeTissue_16d_lineY_pool17


title: EVSAT_T1_C


title: EFM19_T1_C


title: EVSAT_T1_B


title: JejunumWholeTissue_0d_lineX_pool2


title: JejunumWholeTissue_0d_lineX_pool3


title: EFM192A_T2_C


title: EFM19_T1_A


title: EFM19_T1_B


title: EFM192A_T2_A


title: EVSAT_T0_A


title: EFM19_T2_B


title: EVSAT_T1_A


title: EFM192A_T1_C


title: EFM192A_T2_B


title: EFM19_T2_A


title: EFM19_T2_C


title: DU4475_T2_C


title: DU4475_T2_A


title: EFM192A_T1_A


title: EFM192A_T0_A


title: EVSAT_T0_B


title: DU4475_T1_B


title: DU4475_T1_C


title: DU4475_T0_B


title: EFM192A_T0_B


title: EFM192A_T1_B


title: DU4475_T1_A


title: CAMA1_T2_C


title: DU4475_T2_B


title: CAMA1_T2_A


title: CAMA1_T2_B


title: DU4475_T0_A


title: CAMA1_T0_C


title: CAL851_T2_C


title: CAMA1_T0_B


title: CAL851_T2_B


title: CAMA1_T0_A


title: African green monkeys Blood exposed to Y.pestis Exposed72 hr 6386T 72hr rep2

city: Silver Spring

first: Aarti

last: Gautam

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

description: The causal relationship between disease progression and molecular perturbation is crucial to understand in order to develop a next generation therapeutic strategy

hyb_protocol: RNA was hybridized and scanned, and microarray images were visualized and normalized using Feature Extraction (Agilent Technologies, CA); resulting data was analyzed using GeneSpring software (Agilent Technologies, CA).

data_processing:
Agilent Feature Extraction software
TimeClust was used for carrying out Self Organization Map (SOM) for initial filtering (simplification) and Bayesian Clustering to construct GoI-TimeUp and GoI-TimeDown (Figure S3A).  Here, GoI-TimeUp consists of the genes showing a gradual trend of up-regulation during the time course, while GoI-TimeDown consists of the genes showing a gradual trend of down-regulation during the time course.

organism: Chlorocebus aethiops

label_protocol: The Agilent Quick Amp Labeling Kit (Agilent Technologies, CA) was used to label BioChain Monkey universal reference RNA (BioChain Institute, Inc., Newark, CA) with Cy3 and RNA (Cy5) from either control or exposed samples for comparison

growth_protocol: Y. pestis CO92 strain cultures were grown overnight at 28°C in shaker flasks containing Brain Heart Infusion broth (Becton, Dickinson and Company (BD), East Rutherford, NJ), then diluted directly from the broth to the correct dosage based on spectrophotometric optical density readings (OD600).  The suspensions were prepared immediately prior to administration and kept on ice

extract_protocol: From each animal venous blood was collected twice from femoral vein (Figure S1).  During each draw, samples were collected into Vacutainer® CPT (BD, Baltimore, MD) tubes and PAXgene tubes (Qiagen, Inc., Germantown, MD). An aliquot of whole blood was plated on a Congo red agar plate, incubated at 28oC for 72 h before counting the colonies.  The result is shown in Figure 1.

treatment_protocol: Each of the fasted and anesthetized animals was placed in dorsal recumbency in the plethysmography box, inserting its head through the dental dam head port into the head-only exposure apparatus contained within a Class 3 biosafety cabinet.  The bacteria were nebulized using a low-flow 6-jet Bio Aerosol Nebulizing Generator (BANG, CH Technologies, Inc., Westwood, NJ) with an exposure time of between 5 to 15 m.  The aerosol particle stream was delivered at a flow volume of 12 lpm to each anesthetized monkey which was allowed to breathe freely.   Real-time plethysmography (Skornick Plethysmography, CH Technologies, Inc., NJ) was used to measure tidal, minute and accumulated inhaled volumes during exposure to ensure correct aerosol dose.

tag: sample type

value: universal reference RNA

source_name: Y. pestis

value: aerosolized Y. pestis CO92 strain

value: Blood samples

tag: time


title: African green monkeys Blood exposed to Y.pestis Exposed 32 hr 6606T 32hr

scan_protocol: RNA was hybridized and scanned, and microarray images were visualized and normalized using Feature Extraction (Agilent Technologies, CA);


title: African green monkeys Blood exposed to Y.pestis Exposed 12 hr 6506T 12hr


title: CAL851_T1_C


title: African green monkeys Blood exposed to Y.pestis control 6472C

source_name: Chlorocebus aethiops_blood_Control

value: Control


title: CCR5-

city: Cleveland

first: David

last: Askew

state: OH

address: 2103 Cornell Road

department: Pediatrics

institute: CWRU

hyb_protocol: Overnight (16hrs) in an Affymetrix Genechip Hybridization Oven 640 at 45oC, with rotation (60rpm).

scan_protocol: GCS3000 system

data_processing: cel files were converted into expression values (log base 2) using robust multichip analysis algorithm feature of expression console.

source_name: CCR5- OTI T cells

label_protocol: Affymetrix WT plus protocol

growth_protocol: OT1 T cells were freshly isolated from mouse spleens and lymph nodes while CpG ODN-activated LNs were isolated from CCR5ko mice.

extract_protocol: High purity total RNA was isolated from each sorted population using the TRIZOL and Qiagen RNEasy kit protocol and submitted for microarray analysis using the Affymetrix Mouse Gene ST1.0 array chip

treatment_protocol: Draining lymph nodes collected 72h after injecting CpG into CCR5ko mice were teased in media in 96-well plates and freshly isolated OT-1 T cells were added for 6h at 37oC. After incubation, cells were recovered, stained for surface CCR5 and FACS-sorted into CCR5+ (Hua2) and CCR5- (Hua1) populations.

value: naïve T cells

tag: strain

value: OT-I

tag: fraction


title: CAMA1_T1_B


title: African green monkeys Blood exposed to Y.pestis control 6560C


title: CCR5+

source_name: CCR5+ OTI T cells


title: CAL851_T1_A


title: African green monkeys Blood exposed to Y.pestis Exposed24 hr 6528T 24hr


title: African green monkeys Blood exposed to Y.pestis Exposed72 hr 6386T 72hr rep1


title: African green monkeys Blood exposed to Y.pestis Exposed24 hr 6472T 24hr


title: African green monkeys Blood exposed to Y.pestis control 5507C


title: African green monkeys Blood exposed to Y.pestis Exposed 42 hr 5507T 42hr


title: CAMA1_T1_A


title: CAL851_T2_A


title: African green monkeys Blood exposed to Y.pestis control 6606C


title: CAL851_T1_B


title: African green monkeys Blood exposed to Y.pestis control 6628C


title: CAMA1_T1_C


title: CAL851_T0_B


title: African green monkeys Blood exposed to Y.pestis control 6645C


title: African green monkeys Blood exposed to Y.pestis control 6573C


title: CAL851_T0_A


title: African green monkeys Blood exposed to Y.pestis Exposed24 hr 6645T 24hr


title: African green monkeys Blood exposed to Y.pestis Treated IO35T


title: African green monkeys Blood exposed to Y.pestis Exposed 18 hr 5771T 18hr


title: CAL51_T2_B


title: African green monkeys Blood exposed to Y.pestis control IO35C


title: CAL51_T2_C


title: African green monkeys Blood exposed to Y.pestis control 6528C


title: CAL51_T1_C


title: African green monkeys Blood exposed to Y.pestis Exposed 18 hr 6432T 18hr


title: African green monkeys Blood exposed to Y.pestis Exposed 45 min NI207 45min

source_name: Blood_exposure_45 min

value: 45 min


title: African green monkeys Blood exposed to Y.pestis Exposed 32 hr 3286T 32hr


title: African green monkeys Blood exposed to Y.pestis Exposed24 hr 6628T 24hr


title: African green monkeys Blood exposed to Y.pestis Exposed 18 hr 5596T 18hr


title: African green monkeys Blood exposed to Y.pestis control 6513C


title: CAL51_T1_A


title: CAL51_T2_A


title: African green monkeys Blood exposed to Y.pestis control 3286C


title: African green monkeys Blood exposed to Y.pestis Exposed 42 hr 6513T 42hr


title: African green monkeys Blood exposed to Y.pestis Exposed 6 hr NI207T 6hr


title: CAL51_T0_A


title: African green monkeys Blood exposed to Y.pestis Exposed 45 min 3286 45 min


title: African green monkeys Blood exposed to Y.pestis control 5596C


title: African green monkeys Blood exposed to Y.pestis control 6409C


title: African green monkeys Blood exposed to Y.pestis control NI207C


title: CAL51_T1_B


title: CAL51_T0_B


title: African green monkeys Blood exposed to Y.pestis Exposed 9hr 6409T 9hr


title: CAL148_T2_C


title: African green monkeys Blood exposed to Y.pestis Exposed 12 hr 6614T 12hr


title: African green monkeys Blood exposed to Y.pestis Exposed 72 hr 6386T 72hr


title: CAL148_T2_B


title: African green monkeys Blood exposed to Y.pestis Exposed 6 hr 6627T 6hr


title: African green monkeys Blood exposed to Y.pestis control 6627C


title: African green monkeys Blood exposed to Y.pestis control 6607C


title: CAL148_T1_C


title: African green monkeys Blood exposed to Y.pestis Exposed 12 hr 6607T 12hr


title: African green monkeys Blood exposed to Y.pestis Exposed 9hr 6436T 9hr


title: African green monkeys Blood exposed to Y.pestis control 6386C


title: CAL148_T1_A


title: African green monkeys Blood exposed to Y.pestis control IO79T Control


title: African green monkeys Blood exposed to Y.pestis control 6432C


title: African green monkeys Blood exposed to Y.pestis control 6613C


title: African green monkeys Blood exposed to Y.pestis control IO79C control


title: African green monkeys Blood exposed to Y.pestis Exposed 6 hr 6307T 6hr


title: African green monkeys Blood exposed to Y.pestis Exposed 42 hr 5096T 42 hr


title: African green monkeys Blood exposed to Y.pestis control 6307C


title: African green monkeys Blood exposed to Y.pestis control 5096C


title: CAL120_T2_C


title: African green monkeys Blood exposed to Y.pestis control 5771C


title: CAL148_T1_B


title: African green monkeys Blood exposed to Y.pestis control 6436C


title: CAL148_T2_A


title: African green monkeys Blood exposed to Y.pestis Exposed 32 hr 6573T 32 hr


title: African green monkeys Blood exposed to Y.pestis control 6614C


title: CAL120_T2_B


title: CAL148_T0_A


title: CAL120_T2_A


title: CAL148_T0_B


title: African green monkeys Blood exposed to Y.pestis Exposed 45 min 3274 45 min


title: CAL120_T1_B


title: CAL120_T1_A


title: African green monkeys Blood exposed to Y.pestis control 3274C


title: African green monkeys Blood exposed to Y.pestis Exposed 12 hr 3274T 12hr


title: CAL120_T1_C


title: African green monkeys Blood exposed to Y.pestis Exposed 9hr 5021T 9hr.


title: African green monkeys Blood exposed to Y.pestis control T855T Control


title: African green monkeys Blood exposed to Y.pestis control T855C control


title: African green monkeys Blood exposed to Y.pestis Exposed 45 min 5021 45min


title: BT549_T2_C


title: CAL120_T0_A


title: eightHr_Ca_PMA_2

source_name: Jurkat T cells

growth_protocol: Jurkat T cells were cultured at 0.3-0.5 million cells/mL in RPMI 1640 medium (BioWhittaker, Walkersville, MD) supplemented with 10% heat inactivated fetal bovine serum (Hyclone, Thermoscientific, Logan, Utah), 2 mM Lglutamine, penicillin (50 U/ml), and streptomycin (50 U/ml).

extract_protocol: RNA was extracted using the Qiagen RNeasy Plus kit

treatment_protocol: Jurkat T cells (3 million cells per sample at 10 million/mL) were stimulated with PMA (200nM) or PMA (200nM) and Ionomycin (1uM) in a solution containing 145mM NaCl, 4.5mM KCl, 1mM MgCl2, 10mM glucose, 10mM HEPES, 2mM glutamine, and 2% fetal bovine serum (Hyclone, ThermoScientific, Logan, Utah) with either 0mM Ca2+ and 0.25mM EGTA or 2mM Ca2+ at 37C for 1, 4, or 8 hours.

tag: stimulation

value: calcium + PMA

tag: timepoint post-stimulation

value: 8 hour

tag: calcium concentration


title: eightHr_Ca_PMA_Iono_2

value: calcium + PMA + Ionomycin


title: BT549_T2_A


title: African green monkeys Blood exposed to Y.pestis control 5021C


title: fourHr_PMA_Iono_2

value: PMA + Ionomycin

value: 4 hour


title: eightHr_Ca_PMA_Iono_1


title: eightHr_Ca_PMA_1


title: fourHr_Ca_PMA_2


title: fourHr_Ca_PMA_Iono_2


title: BT549_T2_B


title: fourHr_PMA_Iono_1


title: fourHr_Ca_PMA_Iono_1


title: oneHr_PMA_Iono_2

value: 1 hour


title: BT549_T1_B


title: eightHr_PMA_Iono_1


title: BT549_T1_C


title: oneHr_PMA_Iono_1


title: untreated_2

value: untreated


title: untreated_1


title: oneHr_Ca_PMA_Iono_2


title: oneHr_Ca_PMA_1


title: BT549_T0_C


title: oneHr_Ca_PMA_Iono_1


title: fourHr_Ca_PMA_1


title: BT549_T1_A


title: BT549_T0_B


title: oneHr_Ca_PMA_2


title: BT474_T0_B


title: BT474_T1_C


title: BT474_T1_A


title: BT474_T0_C


title: BT483_T2_C


title: BT483_T1_A


title: BT483_T0_B


title: BT474_T2_A


title: BT474_T0_A


title: BT483_T1_C


title: BT483_T1_B


title: SA_melanoma_day60_1

source_name: melanoma

growth_protocol: Whole melanomas were recovered at day 20, 38, or 60 post-tamoxifen administration

extract_protocol: Tumor samples were dissected from mice after humane euthanasia and processed directly for RNA extraction using the Qiagen miRNeasy kit

treatment_protocol: Topical administration of 4-hydroxytamoxifen (4-HT) of BrafCA; Tyr::CreER; Ifnar1-/- or BrafCA; Tyr::CreER; Ifnar1+/+ mice was performed by preparing 25–50 mg/ml (65–130 mM) solution of 4-HT (70% Z-isomer, Sigma) in dimethylsulphoxide and applying enough solution to wet the right ear, right flank and tail with a small paint brush on postnatal days 2, 3 and 4.

tag: strain of mouse

value: BrafCA, Tyr::CreER, Ptenlox/lox, Ifnar1SA


title: SA_melanoma_day60_2

tag: genotype


title: BT474_T1_B


title: BT474_T2_C


title: BT483_T2_A


title: SA_melanoma_day38_2


title: SA_melanoma_day20_2


title: WT_melanoma_day38_1

value: BrafCA, Tyr::CreER, Ptenlox/lox, Ifnar1+/+


title: BT20_T2_A


title: BT20_T2_B


title: SA_melanoma_day20_1


title: SA_melanoma_day38_1


title: BT20_T1_B


title: WT_melanoma_day38_2


title: BT549_T0_A


title: BT483_T0_A


title: BT20_T2_C


title: BT20_T1_C


title: BT483_T2_B


title: BT20_T1_A


title: NILDOG1, rep2

first: Leónie

last: Bentsink

institute: Wageningen University

description: NILDOG1 -2

hyb_protocol: The GeneChip (#900720) HWS kit was used for hybridisation, washing and staining of the cartridges.

scan_protocol: Scanning of the arrays was performed using the Affymetrix 3000G scanner.

data_processing: The GeneChip data were analyzed using the R statistical programming environment and Bioconductor packages. The data were normalized using the RMA algorithm. The P values were adjusted for multiple testing with the Benjamini and Hochberg method to control for false positives.

organism: Arabidopsis thaliana

source_name: NILDOG1-Cvi dry seeds

label_protocol: RNA was processed and cRNA synthesized according to the 3’ GeneChips OneCycle kit.

growth_protocol: For the transcriptome analyses, Ler, NILDOG1 and the dog1-1 were grown in a randomized complete block design with three replicates. Each replicate consisted of a bulk of eight plants. The precise growth conditions used were described by (El-Lithy et al., Genetics, 2006).

extract_protocol: Total RNA was prepared from dry seeds using RNAqueous columns with Plant RNA isolation aid (Ambion) according to the manufacturer’s protocol. The RNA was further purified through precipitations with isopropanol and a high-salt precipitation solution containing 0.24 M sodium citrate and 0.16 M sodium chloride and subsequently with 2 M lithium chloride. RNA was qualitatively assessed and quantified using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip kit (Agilent) and NanoDrop1000 spectrometry (NanoDrop Technologies).

treatment_protocol: RNA was extracted from freshly harvested, dry seeds of three biological replicates of each genotype.

tag: genetic background

value: Landsberg erecta

tag: genotype/variation

value: DELAY Of GERMINATION 1 NIL (NILDOG1-Cvi)

tag: dog1 expression level

value: strong

tag: tissue

value: mature freshly harvested dry seeds

tag: plant stage

value: end of seed maturation


title: BT20_T0_C

tag: cell line

tag: time point


title: BT20_T0_A


title: dog1-1, rep3

description: dog1-1 -3

source_name: dog1-1 mutant dry seeds

value: delay of germination 1 (dog1-1) mutant

value: absent


title: NILDOG1, rep3

description: NILDOG1 -3


title: AU565_T2_B


title: dog1-1, rep2

description: dog1-1 -2


title: AU565_T1_B


title: NILDOG1, rep1

description: NILDOG1 -1


title: AU565_T2_A


title: C. elegans N2 supplemented with C13ISO L1 hatched on food-free NGM plate, rep 1

city: Boulder

first: Marina

last: Kniazeva

address: Porter Biosciences Bldg

institute: HHMI/UC Boulder

description:
Sample name: N2_OP50C13_NGM_1
gene expression level analysis with dChip

hyb_protocol: Samples were hybridized with C. elegans GeneChip (Affymetrix) and scanned at the Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data was validated and correctedusing Affymetrix software and normalized and modelled using dChip (DNA Chip Analyzer), https://sites.google.com/site/dchipsoft/.

organism: Caenorhabditis elegans

source_name: N2 L1 unfed C13ISO supplemented

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: elo-5(gk208) and N2 control animals were grown from eggs for one generation on NGM plates spotted with 300µl OP50 overnight liquid culture supplemented with 1mM C17ISO in DMSO at 20°C. Gravid adults were washed off the plates with M9 and bleached. Eggs were plated on OP50/NGM plates supplemented with 1mM of either C13ISO or C17ISO and maintained at 20°C to obtain gravid adults. Adults were washed off the plates and bleached, and eggs were then plated on food-free NGM or OP50/NGM plates at 20°C.

extract_protocol: RNA isolation with Trizol and Qiagen’s RNAse Easy Kit, according to the manufacturers’ protocols

treatment_protocol: Twenty-four hours later, L1s from food-free plates were collected

tag: supplement

value: C13ISO supplemented

tag: developmental stage

value: L1 larva

value: whole worm


title: BT20_T0_B


title: C. elegans N2 supplemented with C13ISO L1 hatched on food-free NGM plate, rep 2

description:
Sample name: N2_OP50C13_NGM_2
gene expression level analysis with dChip


title: Ler, rep3

description: Ler -3

source_name: WT Ler dry seeds

value: wild type

value: low


title: Ler, rep1

description: Ler -1


title: C. elegans elo-5 supplemented with C17ISO L1 hatched on food-free NGM plate, rep 1

description:
Sample name: elo5_OP50C17_NGM_1
gene expression level analysis with dChip

source_name: elo-5 L1 larvae unfed C17ISO supplemented

value: C17ISO supplemented


title: AU565_T2_C


title: AU565_T1_A


title: C. elegans elo-5 supplemented with C17ISO L1 hatched on food-free NGM plate, rep 2

description:
Sample name: elo5_OP50C17_NGM_2
gene expression level analysis with dChip


title: 600MPE_T2_C


title: CAL120_T0_B


title: dog1-1, rep1

description: dog1-1 -1


title: Ler, rep2

description: Ler -2


title: AU565_T1_C


title: Arabidopsis tetraploid Col GCP_rep2

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

institute: Kyushu University

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 1.65 μg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Arabidopsis Genome Oligo Microarrays 4x44K V4 using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.

source_name: Arabidopsis tetraploid Col, guard cell protoplasts, replicate 2

label_protocol: For the linear T7-based amplification step, 100 ng of each total RNA sample was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Plants were grown on solid MS medium for 18 days in a growth chamber [constant white light of 80 μmol m-2 s-1 at 22°C and 60% relative humidity (RH)], and then transplanted into vermiculite pots supplemented with mineral nutrients.

extract_protocol: Total RNA was isolated from guard cell protoplasts by using RNAiso Plus (Takara Bio Inc.).

treatment_protocol: Guard cell protoplasts were isolated from mature rosette reaves of  four-week-old plants.

tag: ecotype

value: Col

value: guard cell protoplast

tag: ploidy level

value: tetraploid


title: Arabidopsis tetraploid Col GCP_rep1

source_name: Arabidopsis tetraploid Col, guard cell protoplasts, replicate 1


title: Arabidopsis tetraploid Col GCP_rep3

source_name: Arabidopsis tetraploid Col, guard cell protoplasts, replicate 3


title: AU565_T0_B


title: gonad_celecoxib_96h_rep5

city: Costa Mesa

first: Alvine

middle: C

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

institute: Southern California Coastal Water Research Project

description: Gene expression profiling after 96 hours exposure

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 8 pmol Cy3/ug cRNA) was fragmented using the Agilent Gene Expression Hybridization kit and hybridized onto  custom-designed fathead minnow (15K oligonulceotide) arrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed using the following Agilent solutions: GE Wash Buffer 1 for 1 min, GE Wash buffer 2 kept at 37°C for 1 min, and Stabilization and Drying solution for 30 sec.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_10and Grid: 019597_D_F_20080305) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Pimephales promelas

source_name: FHM female gonad, celecoxib, 96h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the One-Color Quick Amp labeling kit (Agilent) according to the manufacturer's instructions.  Cy3 dye incorporation and cRNA yield were measured with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using RNeasy Mini RNA purification kit (Qiagen) following the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Sexually mature fish were subjected to 4 treatments (100 µg/L indomethacin, 200 µg/L ibuprofen, 20 µg/L celecoxib, and water control) for 96 hours.

value: gonad

tag: Stage

value: sexually mature female

tag: gender

value: female


title: C. elegans elo-5 C17ISO-deficient supplemented with C13ISO L1 hatched on food-free NGM plate, rep 2

description:
Sample name: elo5_OP50C13_NGM_2
gene expression level analysis with dChip

source_name: elo-5 L1 larvae unfed C17ISO deficient C13ISO supplemented

value: C17ISO deficient C13ISO supplemented


title: gonad_celecoxib_96h_rep7


title: gonad_celecoxib_96h_rep4


title: gonad_celecoxib_96h_rep3


title: C. elegans elo-5 C17ISO-deficient supplemented with C13ISO L1 hatched on food-free NGM plate, rep 1

description:
Sample name: elo5_OP50C13_NGM_1
gene expression level analysis with dChip


title: 600MPE_T0_B

source_name: breast cancer cell line


title: Arabidopsis Me-0 GCP_rep4

source_name: Arabidopsis Me-0, guard cell protoplasts, replicate 4


title: Arabidopsis Me-0 GCP_rep1

source_name: Arabidopsis Me-0, guard cell protoplasts, replicate 1


title: 600MPE_T2_B


title: LOD-rem_8

city: Maebashi

first: Shigeo

last: Miyata

address: 3-39-22 Showa-machi

institute: Gunma University Graduate School of Medicine

hyb_protocol: For each hybridization, 600 ng of Cy3-labeled cRNA was fragmented and hybridized at 65°C for 17 h to the Agilent SurePrint G3 Human GE 8×60K v2 Microarray (Design ID: 039494).

scan_protocol: After washing, the microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: The intensity values of each scanned feature were quantified using Agilent feature extraction software version 10.7.3.1, which performs background subtractions. The normalization was performed using Agilent GeneSpring GX version 11.0.2 (per chip: normalization to the 75th percentile shift; per gene: none). The probes that were declared as “present” in all the assayed samples and that displayed a raw intensity value above 50 in at least 2 samples were used for the following statistical analyses.

source_name: leukocytes

label_protocol: Total RNA was amplified and labeled with Cyanine 3 (Cy3) using a one-color Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. Briefly, 100 ng of total RNA was reverse-transcribed to obtain double-stranded cDNA using a poly dT-T7 promoter primer. The primer, template RNA, and quality-control transcripts of known concentrations and quality were first denatured at 65°C for 10 min and then incubated for 2 h at 40°C with 5× first-strand buffer, 0.1 M dithiotreitol, 10 mM dNTP mix, and AffinityScript RNase Block Mix. The AffinityScript enzyme was then inactivated at 70°C for 15 min. The cDNA products were used as templates for in vitro transcription to generate fluorescent cRNA. The cDNA products were mixed with a transcription master mix in the presence of T7 RNA polymerase and Cy3-labeled CTP and then incubated at 40°C for 2 h. The labeled cRNAs were purified using Qiagen’s RNeasy mini spin columns and eluted using 30 µl of nuclease-free water. After cRNA was amplified and labeled, the cRNA quantity and cyanine incorporation were determined using a NanoDrop ND-1000 spectrophotometer and an Agilent Bioanalyzer.

extract_protocol: The total RNA was extracted using the QIAmp RNA Blood Mini Kit (QIAGEN K.K., Tokyo, Japan) according to the manufacturer’s instructions. The eluted samples were processed with the standard method of ethanol precipitation, and the RNA pellet was dissolved in RNase-free water. The RNA quantity and quality were assessed using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA) and an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) as recommended.

treatment_protocol: The blood samples were obtained between 9:00 and 12:00, and then heparinized.

value: Male

tag: diagnosis

value: Major depressive disorder

tag: state

value: Remission

tag: age


title: 600MPE_T1_B


title: Arabidopsis Me-0 GCP_rep2

source_name: Arabidopsis Me-0, guard cell protoplasts, replicate 2


title: 184B5_T2_C


title: Arabidopsis Me-0 GCP_rep3

source_name: Arabidopsis Me-0, guard cell protoplasts, replicate 3


title: AU565_T0_A


title: gonad_celecoxib_96h_rep1


title: LOD-rem_10


title: LOD-rem_7

value: Female


title: LOD-rem_9


title: 600MPE_T1_C


title: 600MPE_T0_A


title: 600MPE_T1_A


title: 600MPE_T2_A


title: 184B5_T2_B


title: gonad_celecoxib_96h_rep2


title: gonad_celecoxib_96h_rep6


title: BT474_T2_B


title: gonad_indomethacin_96h_rep8

source_name: FHM female gonad, indomethacin, 96h


title: LOD-rem_6


title: LOD-rem_5


title: LOD-rem_4


title: 184B5_T1_C


title: LOD-rem_3


title: LOD-rem_2


title: gonad_indomethacin_96h_rep5


title: gonad_indomethacin_96h_rep2


title: gonad_indomethacin_96h_rep6


title: 184B5_T2_A


title: 184B5_T1_B


title: LOD-dep_10

value: Depression


title: gonad_indomethacin_96h_rep4


title: gonad_indomethacin_96h_rep7


title: LOD-dep_6


title: gonad_indomethacin_96h_rep1


title: 184A1_T2_B


title: LOD-dep_9


title: 184A1_T2_C


title: 184B5_T0_A


title: LOD-rem_1


title: LOD-dep_8


title: 184B5_T1_A


title: LOD-dep_7


title: 184A1_T2_A


title: 184B5_T0_B


title: gonad_indomethacin_96h_rep3


title: gonad_ibuprofen_96h_rep8

source_name: FHM female gonad, ibuprofen, 96h


title: gonad_ibuprofen_96h_rep7


title: gonad_ibuprofen_96h_rep6


title: 184A1_T1_C


title: LOD-dep_5


title: LOD-dep_4


title: gonad_ibuprofen_96h_rep5


title: 184A1_T0_B


title: gonad_ibuprofen_96h_rep4


title: 184A1_T1_B


title: gonad_ibuprofen_96h_rep3


title: gonad_control_96h_rep8

source_name: FHM female gonad, control water, 96h


title: gonad_control_96h_rep7


title: PMPs derived from apoptosis platelets miRNA_rep5

city: shanghai

first: Meiling

last: tang

state: shanghai

address: 536 Chang Le RD, Jiang An district, Shanghai, 200040, China

department: Gynecology

country: China

description:
miRNA expression in PMPs
3（-）344427

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x Agilent fragmentation buffer and 10x Agient blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 25ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-046065 Mouse miRNA Microarray V19.0 8x60K(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were maintained.

source_name: PMPs derived from apoptosis platelets,replicate 5

label_protocol: 0.1ug total RNA were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP（Cy3）using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions,then followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer  version 3.2.1.

extract_protocol: total RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions

treatment_protocol: The platelets were derived from citrated blood of healthy human donors under an Institutional Review Board-approved protocol.  Platelets were isolated after centrifugation of blood (1200r for 30 min at 21℃), then the supernatant (platelet-rich plasma) was centrifuged at 2000r for 30 min at 21℃, and the pellet containing platelets was resuspended in RPMI-1640 medium (HyClone, Logan, UT). Platelets were counted (Clinical Laboratory, Shanghai First Maternity and Infant Hospital, Shanghai) and adjusted to a density of 150 × 106 cells/mL before supplement with 1.5% ACD(sigma ) and stimulated with thrombin (1.0 u/mL; Takeda Austria) for 1 h. PMPs were in the supernatant after centrifugation at 4000r for 10 min at 4℃,then the supernatants were centrifuged at 50,000 × g for 60 min at 4 °C. The pellets containing MPs were resuspended in RPMI-1640 medium and quantified by BCA method.

value: whole blood


title: gonad_ibuprofen_96h_rep1


title: LOD-dep_3


title: 184A1_T1_A


title: PMPs derived from apoptosis platelets miRNA_rep4

institute: Shanghai First Maternity and Infant Hospital

description:
miRNA expression in PMPs
1（-）406317

source_name: PMPs derived from apoptosis platelets,replicate 4


title: HC_12

value: Healthy


title: LOD-dep_1


title: gonad_ibuprofen_96h_rep2


title: gonad_control_96h_rep6


title: HC_10


title: PMPs derived from apoptosis platelets miRNA_rep3

description:
miRNA expression in PMPs
2（-）

source_name: PMPs derived from apoptosis platelets,replicate 3


title: HC_9


title: PMPs derived from apoptosis platelets miRNA_rep2

description:
miRNA expression in PMPs
2014.09.24-

source_name: PMPs derived from apoptosis platelets,replicate 2


title: 184A1_T0_A


title: HC_7


title: gonad_control_96h_rep3


title: HC_6


title: LOD-dep_2


title: gonad_control_96h_rep5


title: gonad_control_96h_rep4


title: HC_11


title: HC_8


title: PMPs derived from thrombin stimulating platelets miRNA_rep5

description:
miRNA expression in PMPs
3（+）344427

source_name: PMPs derived from thrombin stimulating platelets,replicate 5


title: PMPs derived from apoptosis platelets miRNA_rep1

description:
miRNA expression in PMPs
-

source_name: PMPs derived from apoptosis platelets,replicate 1


title: gonad_control_96h_rep1


title: HC_2


title: gonad_control_96h_rep2


title: PMPs derived from thrombin stimulating platelets miRNA_rep3

description:
miRNA expression in PMPs
1（+）406317

source_name: PMPs derived from thrombin stimulating platelets,replicate 3


title: HC_3


title: HC_5


title: PMPs derived from thrombin stimulating platelets miRNA_rep1

description:
miRNA expression in PMPs
+

source_name: PMPs derived from thrombin stimulating platelets,replicate 1


title: PMPs derived from thrombin stimulating platelets miRNA_rep4

description:
miRNA expression in PMPs
2014.09.24+

source_name: PMPs derived from thrombin stimulating platelets,replicate 4


title: PMPs derived from thrombin stimulating platelets miRNA_rep2

description:
miRNA expression in PMPs
2（+）

source_name: PMPs derived from thrombin stimulating platelets,replicate 2


title: HC_1


title: Tim-3 KD rep1

city: Beijing

first: Gencheng

last: HAN

address: 27 Taiping Road, Haidian District

department: Department of Immunology

institute: Beijing Institute of Basic Medical Sciences

description: microRNA data from RAW264.7 cell line

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

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000

data_processing: The data were analyzed with GeneChip Operating Software (GCOS)

source_name: RAW264.7_Tim-3 KD

label_protocol: FlashTag Biotin RNA Labeling Kits (Affymetrix) were used to label RNA

growth_protocol: RAW264.7 cell was stably transfected with Tim-3 siRNA(SI)  or negative control(NC) and were analyzed for microRNA expression

extract_protocol: Extraction of total RNA using Trizol reagent was performed according to the manufacturer's instructions (Invitrogen, Carlsbad, CA, USA)

treatment_protocol: RAW264.7 cells stably transfected with Tim-3 siRNA(SI)  or negative control(NC) and were used to collect microRNA without any other treatment

tag: cell type

value: macrophage cell line


title: V12RAS VGP versus control 2

status: Public on Jan 13 2016

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

institute: Leiden University

hyb_protocol: The dual colour hybridization of the microarray chips was performed at the company Service XS  (Leiden, The Netherlands) using the standard Agilent protocol.

scan_protocol: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. The arrays were scanned twice with 10% PMT and 100% PMT laser power.

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.0 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. The Agilent Feature Extraction files contain the final log ratio data. The algorithms that were used to normalize the feature signal and calculate the log ratios are described in the Reference Guide for Agilent Feature Extraction Software v9.5. The standard settings as described for the GE2-v5_95 protocol in the Reference Guide were used. In order to calculate the normalized signal, the Rank Consistency Probes method was used and the Linear&LOWESSDyeNormFactor (= DyeNormalSignal/(BGSubSignal x LinearDyeNormFactor) was calculated as described on page 231 of the Reference Guide. The dye normalized signal was calculated as follows (page 232): DyeNormSignal = BGSubSignal x DyeNormFactor. The log10 ratio was subsequently calculated as follows (page 232): LogRatio = Log(rProcessedSignal/gProcessedSignal), where rProcessedSignal and gProcessedSignal are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The surrogate values are calculated and used as the lowest limit of detection to replace the dye normalized signal when either the mean feature signal is less than the background signal or not significant when compared to the background signal, or when the mean signal is less than its background standard deviation (page 226).

organism: Danio rerio

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dye (GE Healthcare) and column purified.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org).

extract_protocol: For RNA isolation, three pools of 10 caudal fins or 6 tumours within caudal fins were  snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Transgenic zebrafish expressing V600EBRAF or G12VHRAS in the melanocyte lineage have been previously described (Michailidou et al., 2009). Zebrafish husbandry and experimental studies conducted at the University of Manchester were performed in compliance with the Animals (Scientific Procedures) Act 1986 under a Home Office approved Project licence.

value: wild type fish

value: Caudal fins

source_name: D. rerio_V12RAS VGP

value: V12RAS transgenic fish with melanoma of the VGP type


title: V600EBRAF versus control 3

source_name: D. rerio_V600EBRAF

value: transgenic V600EBRAF fish


title: V12RAS RGP versus control 3

source_name: D. rerio_V12RAS RGP

value: V12RAS transgenic fish with melanoma of the RGP type


title: Tim-3 KD rep2

description: microRNA data from RAW264.7 cell line


title: V12RAS RGP versus control 2


title: HC_4

source_name: leukocytes


title: V12RAS VGP versus control 3


title: NC rep1

description: microRNA data from RAW264.7 cell line

source_name: RAW264.7_negative control


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 42 days - rep2

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007, 3/18/2008; V. riparia on 3/26/2007, 3/24/2008) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (4/25/2007, 4/23/08) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h). Five days after this (4/30/2007, 4/28/2008) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued. SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems). After 42 days of additional LD or SD, buds were harvested from nodes 3 to 12 (from shoot base), immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction. Three replications (5 vines/replication) were harvested between 05/07-06/07. After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. (May still include original submitter created erros/discrepancies)

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

organism: Vitis riparia

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 42 days)

label_protocol: Affy-Eukaryotic Target Preparation

growth_protocol: Growth Description:  Three to four shoots were trained vertically on spur pruned greenhouse grown vines. Vines were watered two times daily at 8:30 am and 3:00 pm.  Environmental Conditions:  Vines were grown in greenhouse at 44N latitude with 15h day using supplemental lighting (Na halide lamps) to maintain 600 micro mole m-2s-1.

extract_protocol: Modified Pine Buffer RNA Extraction Procedure

tag: germplasm name

value: Vitis riparia PI588259

tag: organism part

value: second order axillary bud

tag: development stage

value: paradormancy

value: 31 days after bud break

tag: growth media

value: peat/perlite/soil


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 42 days - rep1


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 28 days - rep1

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007, 3/18/2008; V. riparia on 3/26/2007, 3/24/2008) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (4/25/2007, 4/23/08) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h). Five days after this (4/30/2007, 4/28/2008) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued. SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems). After 28 days of additional LD or SD, buds were harvested from nodes 3 to 12 (from shoot base), immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction. Three replications (5 vines/replication) were harvested between 05/07-06/07. After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. (May still include original submitter created erros/discrepancies)

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 28 days)


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 42 days - rep3


title: V12RAS VGP versus control 1

tag: genotype/variation

tag: tissue


title: V12RAS RGP versus control 1


title: V600EBRAF versus control 2


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 21 days - rep2

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007, 3/18/2008; V. riparia on 3/26/2007, 3/24/2008) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (4/25/2007, 4/23/08) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h). Five days after this (4/30/2007, 4/28/2008) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued. SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems). After 21 days of additional LD or SD, buds were harvested from nodes 3 to 12 (from shoot base), immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction. Three replications (5 vines/replication) were harvested between 05/07-06/07. After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. (May still include original submitter created erros/discrepancies)

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 21 days)


title: V600EBRAF versus control 1


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 28 days - rep3


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 21 days - rep1


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 28 days - rep2


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 21 days - rep3


title: NC rep2

description: microRNA data from RAW264.7 cell line

tag: cell line


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 7 days - rep2

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007, 3/18/2008; V. riparia on 3/26/2007, 3/24/2008) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (4/25/2007, 4/23/08) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h). Five days after this (4/30/2007, 4/28/2008) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued. SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems). After 7 days of additional LD or SD, buds were harvested from nodes 3 to 12 (from shoot base), immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction. Three replications (5 vines/replication) were harvested between 05/07-06/07. After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. (May still include original submitter created erros/discrepancies)

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 7 days)


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 7 days - rep3


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 14 days - rep1

description: Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval on 3/19/2007, 3/18/2008; V. riparia on 3/26/2007, 3/24/2008) and grown under a LD (15 h) at 25/20 + 3C day/night temperatures (D/N). When vines reached 12-15 nodes (4/25/2007, 4/23/08) they were randomized into two replicated treatment groups, long photoperiod (LD, 15h) or short photoperiod (SD,13h). Five days after this (4/30/2007, 4/28/2008) the SD (13h, 25/20C) photoperiod treatment was started and LD (15h 25/20C) treatment continued. SD treatment was imposed with automated photoperiod system (VRE Greenhouse Systems). After 14 days of additional LD or SD, buds were harvested from nodes 3 to 12 (from shoot base), immediately frozen in liquid nitrogen, and placed at -80C for future RNA, protein, and metabolite extraction. Three replications (5 vines/replication) were harvested between 05/07-06/07. After bud harvests, the pruned vines were returned to LD and monitored for bud endodormancy. The endodormant vines were identified after 28 days and moved to cold storage. The nondormant vines were allowed to grow again and induced into dormancy at a later date. (May still include original submitter created erros/discrepancies)

source_name: second order axillary bud (genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 14 days)


title: genotype: V. riparia (VR, PI588259) - year: 2 - photoperiod: 13 h - time: 7 days - rep1