title: Case 3636 blood mother cyto12 5659787018_R03C01


title: Case 8189 poc child cyto12b 6186408075_R05C01

status: Public on Jul 13 2015

type: genomic

city: San Carlos

first: Jennifer

last: Dikan

state: California

address: 201 Industrial Road, Suite 410

country: USA

institute: Natera

hyb_protocol: Illumunian infinium process

scan_protocol: Illumunian infinium process using iScan

data_processing:
All the raw data comes from illumina arrays. Illumina also post-processes the data using Bead Studio to create the b-allele-frequency number and log-r-ratio.  We use the b-allele-frequency in our analysis.
In some cases the post processing does not provide the b-allele-frequency numbers.  In those cases, we calculate radial and theta numbers for each snip.  The formulas are  radial = sqrt(chX^2+chY^2)  theta = arcsine(chY/radial)  This is done on per snip bases where chX and chY are the raw counts.  If both are 0, the output is not-a-number.
Series supplementary files contain raw X and Y signals only

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Unique barcodes are affixed to the sample and associated within an internal sample tracking system

extract_protocol: Qiagen Dneasy

treatment_protocol: Visual examination of the sample to determine if villi is present. Separation of villi from maternal tissue performed using scalple. Refrigeration if sample is not processed immediately

tag: sample id

tag: case id

tag: sample type

value: poc

tag: tissue

value: products of conception

tag: subject

value: child

tag: array type


title: Case 4062 blood mother cyto12 5979481025_R06C02

value: blood

value: mother


title: Case 5833 poc child cyto12 6192699016_R03C02


title: Case 4326 poc child cyto12 5979490076_R05C02


title: Case 5825 poc child cyto12 6192699016_R03C01


title: Case 4315 poc child cyto12 5979490076_R05C01


title: Case 5730 blood mother cyto12 6192701049_R01C02


title: Case 4625 poc child cyto12 5979481022_R06C01


title: Case 4790 blood mother cyto12 6042412027_R01C02


title: srp1-wt_srp2-wt_vs_srp1-16A_srp2_4A_replicate2

type: RNA

city: San Francisco

first: Jesse

middle: J

last: Lipp

state: CA

address: 600 16th Street

institute: UCSF

description: Biological replicate 2 of 2: srp1-wt_srp2-wt_vs_srp1-16A_srp2_4A

hyb_protocol: Samples were hybridized to Agilent custom 8 x 15K microarrays for 16 hrs at 60 ºC in the dark hybridization with rotation. Arrays were opened while submerged in Agilent Wash buffer I (Agilent) and transferred to a rack and washed in more Wash buffer I while stirring for 1 min. Arrays were then transferred to wash buffer II at 37 ºC for 1 min. Next, the arrays were transferred to acetonitrile for 1 min and finally Stabilization & Drying solution (Agilent) for 30 sec. The arrays were then immediately scanned in an ozone free chamber using a GenePix 4000B scanner (Molecular Devices).

scan_protocol: Scanning was carried out using Genepix software with 5 μM pixel size, 2 lines to average, and a focus position of 15. In order to get a balance between Cy5 and Cy3 fluorescent signals we varied the ratio of the PMT for each wavelength until they were approximately equal, usually between 400-600. Some spots on the array were then flagged due to over saturation or spotty hydration using GenePix pro 7 software and excluded from analysis.

data_processing: Raw data was normalized using loess as implemented in the R package limma.

molecule: total RNA

organism: Schizosaccharomyces pombe

source_name: log-phase cells

label_protocol: All of the cDNA from control samples was labeled with Cy3 dyes and all of the experimental samples with Cy5 dyes. Once samples were labeled experiments were continued without interruption and samples were exclusively kept in the dark. Appropriate Cy5 experimental and Cy3 control samples were combined.

growth_protocol: Yeast strains were grown in rich YES5 medium to mid-log phase (OD600 0.4-0.8) at 30 ºC unless otherwise noted.

extract_protocol: Cultures were collected by centrifugation and frozen at -80 ºC. Total RNA was isolated using hot phenol extraction as outlined previously. cDNA was synthesized using 500 U Superscript III (Invitrogen) for each reaction with 40 μg total RNA and 4 hr incubation at 42 ºC.

treatment_protocol: For prp2-1, yeast were grown at permissive 25 ºC to mid-log then shifted to 37C for 1 hr. For 3-BrB-PP1 treated kinase strains, prp4-wt and prp4-as strains were grown to mid-log phase, 10 μM of 3-BrB-PP1 was added for 1 hr. dsk1-wt and dsk1-as strains were treated with 10 μM 3-BrB-PP1 for 8 hrs and harvested at mid-log phase.

tag: genotype/variation

tag: treated with

tag: growth phase

value: log-phase cells


title: Case 4784 blood mother cyto12 6042412027_R01C01


title: srp2-wt_vs_srp2-4A_replicate1

description: Biological replicate 1 of 2: srp2-wt_vs_srp2-4A


title: prp2-wt_vs_prp2-4A_replicate2

description: Biological replicate 2 of 2: prp2-wt_vs_prp2-4A


title: Case 4131 blood mother cyto12 5979473091_R03C01


title: Case 5345 poc child cyto12 6086087059_R02C02


title: srp1-wt_srp2-wt_vs_srp1-16A_srp2_4A_replicate1

description: Biological replicate 1 of 2: srp1-wt_srp2-wt_vs_srp1-16A_srp2_4A


title: Case 5294 poc child cyto12 6086087059_R02C01


title: dsk1-wt_vs_dsk1-as_replicate3

description: Biological replicate 3 of 3: dsk1-wt_vs_dsk1-as

value: 10 µM 3-MB-PP1 for 8hrs


title: Case 12303 blood mother cyto12 5979481025_R06C01


title: Case 4276 blood mother cyto12 6042404034_R06C01


title: bpb1-wt_vs_bpb1-2A_replicate2

description: Biological replicate 2 of 2: bpb1-wt_vs_bpb1-2A


title: bpb1-wt_vs_bpb1-2A_replicate1

description: Biological replicate 1 of 2: bpb1-wt_vs_bpb1-2A


title: Case 3415 poc child cyto12 5901924081_R04C02


title: Case 2903 blood mother cyto12 5494812086_R02C02


title: dsk1-wt_vs_dsk1-as_replicate1

description: Biological replicate 1 of 3: dsk1-wt_vs_dsk1-as


title: Case 6795 blood mother cyto12 5979481082_R06C02


title: wt_vs_wt_replicate3

description: Biological replicate 3 of 3: wt_vs_wt

value: wt


title: dsk1-wt_vs_dsk1-as_replicate2

description: Biological replicate 2 of 3: dsk1-wt_vs_dsk1-as


title: lkh1-wt_vs_lkh1-as_replicate1

description: Biological replicate 1 of 2: lkh1-wt_vs_lkh1-as


title: prp2-wt_vs_prp2-4A_replicate1

description: Biological replicate 1 of 2: prp2-wt_vs_prp2-4A


title: Case 2270 poc child cyto12 5494812086_R02C01


title: Case 4619 poc child cyto12 5979481090_R05C01


title: Case 4643 poc child cyto12 5979481090_R05C02


title: lkh1-wt_vs_lkh1-as_replicate2

description: Biological replicate 2 of 2: lkh1-wt_vs_lkh1-as


title: wt_vs_wt_replicate2

description: Biological replicate 2 of 3: wt_vs_wt


title: wt_vs_wt_replicate1

description: Biological replicate 1 of 3: wt_vs_wt


title: Case 3347 poc child cyto12 5901924081_R04C01


title: Case 4549 blood mother cyto12 6042404139_R05C02


title: pDMR6:GFP GFP-positive cells Noks1 treated 7 days post-inoculation, biological rep1

city: Coventry

first: Miriam

last: Gifford

address: Gibbet Hill Road

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

description: NimbleGen gene expression array data for custom-design array based on the TAIR10 release of the Arabidopsis thaliana genome

hyb_protocol: Following fragmentation, 4 ug of cRNA was hybridized for 16 hr at 42oC on a NimbleGen hybridization unit.

scan_protocol: Slides were scanned using an MS 200 microarray scanner and associated NimbleGen software using only the 480 nm laser with gain calculated using the autogain feature of NimbleScan, based on a representative region of the slide (an area covering around half an array found to have average intensity based on a prescan at lower resolution), as per manufacturer’s instructions. Grids were aligned automatically to each microarray image and manually veriﬁed, ensuring reference spots in each corner and in the centre of the array were aligned to the grid and the alignment score minimised.

data_processing: Data were obtained using NimbleScan and normalised by robust multichip averaging (RMA) (quantile normalisation, taking into account outlier probes per gene) and summarised to gene level by median polish.

organism: Arabidopsis thaliana

source_name: GFP-positive (pathogen-local) from Noks1-treated (30,000-60,000 spores / ml) Arabidopsis plants, 7 days post-inoculation (14 days old)

label_protocol: RNA samples were amplified using Ovation Pico WTA System V2 kit (NuGEN Technologies Inc., San Carlos, CA, USA) as per the manufacturer’s ‘quick’ protocol. Post-ampliﬁcation puriﬁcation of cDNA was performed using the QIAquick PCR Puriﬁcation Kit (Qiagen) as manufacturer’s guidelines. RNA was labelled with the Cy3 dye according to NimbleGen protocols.

growth_protocol: Prior to treatment, plants were grown on soil for 7 days in a growth chamber (Weiss Technik, Veije, Denmark) at 20°C with 10 h of light. For the first 4 days seedlings were loosely covered in plastic film to retain moisture.

extract_protocol: FACS samples were collected in RLT lysis buffer (Qiagen) with 1 % (v:v) β-mercaptoethanol, then total RNA extracted using the Qiagen plant RNAeasy kit.

treatment_protocol: Hyaloperonospora arabidopsidis isolate Noks1 was sprayed onto 7-day-old seedlings at a concentration of 30,000-60,000 spores/ml according to Tome et al. (2014) Methods in molecular biology 1127:145-158. Inoculated plants and uninfected controls were then placed in water-tight propagator trays and incubated in a growth chamber (Weiss Technik, Vejle, Denmark) at 18°C with 10 h of light.

tag: organ and cell type

value: seedling leaves, pathogen-proximal cells

tag: organ

value: seedling leaves

tag: cell type

value: pathogen-proximal cells


title: pDMR6:GFP GFP-negative cells Noks1 treated 7 days post-inoculation, biological rep3

source_name: GFP-negative (pathogen-distal) from Noks1-treated (30,000-60,000 spores / ml) Arabidopsis plants, 7 days post-inoculation (14 days old)

value: seedling leaves, pathogen-distal cells

value: pathogen-distal cells


title: pDMR6:GFP GFP-positive cells Noks1 treated 7 days post-inoculation, biological rep2

source_name: GFP-positive (pathogen-local) from Noks1-treated (30,000-60,000 spores / ml) Arabidopsis plants, 7 days post-inoculation (42 days old)


title: Case 3225 blood mother cyto12 5494812045_R03C02


title: pDMR6:GFP GFP-negative cells Noks1 treated 7 days post-inoculation, biological rep2


title: pDMR6:GFP GFP-negative cells Uninfected 7 days post-inoculation, biological rep3

source_name: Cells from uninfected Arabidopsis plants, 14 days old


title: pDMR6:GFP GFP-positive cells Noks1 treated 7 days post-inoculation, biological rep3


title: pDMR6:GFP GFP-negative cells Uninfected 7 days post-inoculation, biological rep1


title: pDMR6:GFP GFP-negative cells Noks1 treated 7 days post-inoculation, biological rep1

source_name: GFP-negative (pathogen-distal) from Noks1-treated (30,000-60,000 spores / ml) Arabidopsis plants, 7 days post-inoculation (42 days old)


title: pDMR6:GFP GFP-negative cells Uninfected 7 days post-inoculation, biological rep2


title: pDMR6:GFP GFP-positive cells Noks1 treated 5 days post-inoculation, biological rep3

source_name: GFP-positive (pathogen-local) from Noks1-treated (30,000-60,000 spores / ml) Arabidopsis plants, 5 days post-inoculation (12 days old)


title: Case 2321 poc child cyto12 5497204006_R03C02


title: Case 3968 poc child cyto12 5979473069_R01C01


title: Case 2992 blood mother cyto12 5580649028_R03C01


title: pDMR6:GFP GFP-positive cells Noks1 treated 5 days post-inoculation, biological rep2


title: pDMR6:GFP GFP-positive cells Noks1 treated 5 days post-inoculation, biological rep1


title: Case 4525 poc child cyto12 6042404139_R05C01


title: Slide 347297

city: Groningen

first: Irfan

last: Manzoor

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description: Average ratio of inter slide replicates

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with Genpix software. Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP as previously described (15, 18, 49). Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of 0.5 mM Co over 0 mM Co in wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Streptococcus pneumoniae D39

source_name: F635 Mean

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences)

growth_protocol: Cells were grown to OD600 of 0.2 in CDM medium with and without 0.5 mM Co

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006; Shafeeq et al., 2011). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: co concentration

value: 0,5mM Co

tag: strain

source_name: F532 Mean

value: 0mM Co


title: Case 2297 poc child cyto12 5497204006_R03C01


title: Slide 347296

description: Average ratio of inter slide replicates


title: pDMR6:GFP GFP-negative cells Noks1 treated 5 days post-inoculation, biological rep3

source_name: GFP-negative (pathogen-distal) from Noks1-treated (30,000-60,000 spores / ml) Arabidopsis plants, 5 days post-inoculation (12 days old)


title: pDMR6:GFP GFP-negative cells Noks1 treated 5 days post-inoculation, biological rep2


title: DNA-PKcs knockdown, biological rep2

city: Philadelphia

first: Karen

last: Knudsen

state: Pennsylvania

institute: Thomas Jefferson University - Kimmel Cancer Center

hyb_protocol: 5ug cDNA in 220ul hybridization cocktail was hybridized on the Affymetrix Human Gene 2.0 ST Array in a GeneChip Hybridization Oven 645. Target denaturation was performed at 99C for 2 minutes, 45C for 5min, followed by hybridization for 18h.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneSpring 11.5 software with an Interative Plier16 summarazation algorithm, quantile normalization, baseline transformation of median of all samples, and filtering to remove low expression genes.
HuGene-2_0-st.pgf
HuGene-2_0-st.mps

label: biotin

source_name: C4-2 prostate cancer cells

label_protocol: 5ug cDNA was fragmanted and chemically labeled with biotin using the FL-Ovation cDNA biotin module (NuGen Technologies, Inc)

growth_protocol: C4-2 cells cultured in hormone proficient media

extract_protocol: Standard Trizol RNA extraction, followed by cDNA amplification using the Ovation Pico WTA-system V2 RNA amplification system (NuGen Technologies, Inc)

treatment_protocol: Cells were transfected with Control or PRKDC siRNA pools for 96 hours. Cells were seeded and control treated for 24 hours with 1uM NU7441 prior to harvest.

tag: treatment

value: transiently depleted of DNA-PKcs

tag: cell line


title: NU7441 treated, biological rep2

value: treated for 24hrs with 1uM NU7441


title: pDMR6:GFP GFP-negative cells Noks1 treated 5 days post-inoculation, biological rep1


title: DNA-PKcs knockdown, biological rep1


title: pDMR6:GFP GFP-negative cells Uninfected 5 days post-inoculation, biological rep2

source_name: Cells from uninfected Arabidopsis plants, 12 days old


title: NU7441 treated, biological rep1


title: pDMR6:GFP GFP-negative cells Uninfected 5 days post-inoculation, biological rep3


title: 30days root_rep2 (SP4-2)

status: Public on Jul 12 2015

city: Guangzhou

first: zhangying

last: wang

state: Guangdong

address: Jinying West 2nd Street 18#, Wushan Tianhe

department: Crops Research Institute

country: China

institute: Guangdong Academy of Agricultural Sciences

description: Sample roots were collected at 30days after transplanting, and this sample is the second biological replicate at 30days developmental stage.

hyb_protocol: Arrays were hybridized at 42 ◦C for 16 h using NimbleGen Hybridization System 12 and then washed three times.

scan_protocol: Hybridized microarray slides were scanned with Nimblegen MS 200 Microarray Scanner, and images were saved in Tagged Image File Format files (TIFF, .tif).

data_processing: The signal intensities of all spots on each image were quantified by using NimbleScan v2.5, and then further normalized using RAM (Robust Multi-Array Analysis)

organism: Ipomoea batatas

source_name: sweetpotato root at 30days after transplanting

label_protocol: RNA labeling was carried out using CapitalBio cRNA Amplification and Labeling Kit following the manufacturer’s protocols.

growth_protocol: The sweetpotato cultivar Guangshu 87, which is frequently used for genetic engineering, was employed in this present study. Stem cuts of sweetpotato were grown in the field.

extract_protocol: Total RNA was isolated using using the RNeasy® Mini Kit (Qiagen). RNA quality and quantity were determined using a NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies, Wilmington, DE) and verified for degradation using a 2100 Bioanalyser RNA Nanochip (Agilent, Palo Alto, CA).

treatment_protocol: Root samples at different developmental stages were collected from two independent biological replicates in the field and submerged into liquid nitrogen immediately. All samples were maintained in liquid nitrogen during transportation, and they were stored in an ultra-freezer (-80°C) until RNA extraction.

tag: cultivar

value: Guangshu 87

tag: developmental stage

value: root


title: 60days root_rep1 (SP5-1)

description: Sample roots were collected at 60days after transplanting, and this sample is the first biological replicate at 60days developmental stage.

source_name: sweetpotato root at 60days after transplanting


title: 90days root_rep1 (SP6-1)

description: Sample roots were collected at 90days after transplanting, and this sample is the first biological replicate at 90days developmental stage.

source_name: sweetpotato root at 90days after transplanting


title: 60days root_rep2 (SP5-2)

description: Sample roots were collected at 60days after transplanting, and this sample is the second biological replicate at 60days developmental stage.


title: 120days root_rep1 (SP7-1)

description: Sample roots were collected at 120days after transplanting, and this sample is the first biological replicate at 120days developmental stage.

source_name: sweetpotato root at 120days after transplanting


title: Control, biological rep1

value: DMSO treated control


title: 90days root_rep2 (SP6-2)

description: Sample roots were collected at 90days after transplanting, and this sample is the second biological replicate at 90days developmental stage.


title: 10days root_rep2 (SP1-2)

description: Sample roots were collected at 10days after transplanting, and this sample is the second biological replicate at 10days developmental stage.

source_name: sweetpotato root at 10days after transplanting


title: 120days root_rep2 (SP7-2)

description: Sample roots were collected at 120days after transplanting, and this sample is the second biological replicate at 120days developmental stage.


title: 15days root_rep1 (SP2-1)

description: Sample roots were collected at 15days after transplanting, and this sample is the first biological replicate at 15days developmental stage.

source_name: sweetpotato root at 15days after transplanting


title: 20days root_rep1 (SP3-1)

description: Sample roots were collected at 20days after transplanting, and this sample is the first biological replicate at 20days developmental stage.

source_name: sweetpotato root at 20days after transplanting


title: 15days root_rep2 (SP2-2)

description: Sample roots were collected at 15ays after transplanting, and this sample is the second biological replicate at 15days developmental stage.


title: 30days root_rep1 (SP4-1)

description: Sample roots were collected at 30days after transplanting, and this sample is the first biological replicate at 30 days developmental stage.


title: pDMR6:GFP GFP-negative cells Uninfected 5 days post-inoculation, biological rep1


title: 20days root_rep2 (SP3-2)

description: Sample roots were collected at 20days after transplanting, and this sample is the second biological replicate at 20days developmental stage.


title: THP1-Scr-3

city: Copenhagen

first: Kristian

last: Helin

address: Ole Maaløes vej 5

department: BRIC

country: Denmark

institute: Copenhagen University

description:
Negative control (Scrambled shRNA)
exp3_Scr

hyb_protocol: Hybridization samples were prepared using Gene Expression Hybridization Kit (Agilent) according to manufacturer's protocol.

scan_protocol: Slides were scanned on Agilent Microarray Scanner, Model number: G2600D  Serial number: SG12524268.

data_processing: All the data processing including background correction (backgroundCorrect with parameters: method=normexp;offset=50), normalization (normalizeBetweenArrays with parameters: method=quantile), filtering (a probe must be expressed in at least two samples of one group above the 95% quantile value of the negative controls), statistical analysis and plotting was done in R using the 'limma' package.

source_name: THP-1, shScr, replicate 3

label_protocol: Cy-3 labeled cRNA was prepared using Low Input Quick Amp Labeling Kit, One-Color (Agilent) according to manufacturer's protocol.

growth_protocol: THP-1 cells were grown in RPMI supplemented with 10% fetal bovine serum, penicillin and streptomycin.

extract_protocol: RNA was purified using RNeasy Plus RNA kit (Qiagen) and reverse transcribed using TaqMan Reverse Transcription Reagents (Applied Biosystems).

treatment_protocol: THP-1 cells were transduced with pLKO-puro vectors using retronectin (Takara) method and selected with 2 μg/ml puromycin (Sigma).

value: acute monocytic leukemia THP-1

value: Negative control


title: PFI.2

description: Gene expression data from MV4-11 cells treated with PFI-3

hyb_protocol: standard Affymetrix procedure

scan_protocol: standard Affymetrix procedure

data_processing: The raw data were analyzed in R and preprocessed using the RMA pipeline from package affy with default parameters ( Command example: rma.es <- rma(ReadAffy(filenames=dir(celfiles, full.names=TRUE))) ). Differential expression analysis was done with package limma using lmFit ( Command example, using suitable values for 'design' and 'contrasts.m': fit <- lmFit(rma.es, design); contr.fit <- contrasts.fit(fit, contrasts.m); contr.fit <- eBayes(contr.fit); contr.res <- decideTests(contr.fit) ). Individual contrasts can be deduced from the column header of the individual p-value columns in the processed data matrix file. The microarray and gene annotations were extracted from package hgu133plus2.db, version 3.0.0. All other post-processing including filtering, additional statistical analysis and plotting was also done in R.

label_protocol: standard Affymetrix procedure

growth_protocol: MV4-11 cells were grown in RPMI supplemented with 10% fetal bovine serum, penicillin and streptomycin

treatment_protocol: For shRNA expression MV4-11 cells were transduced with pLKO-puro lentiviral vectors and selected with 2 μg/ml puromycin (Sigma). PFI-3 treatment cells were grown with 10μM PFI-3 in the culture media for 6 days. As a negative control cells were grown with DMSO.

value: acute monocytic leukemia cell line MV4-11

tag: agent


title: Control, biological rep2


title: PFI.1


title: 10days root_rep1 (SP1-1)

description: Sample roots were collected at 10days after transplanting, and this sample is the first biological replicate at 10days developmental stage.


title: PFI.3


title: THP1-Scr-2

description:
Negative control (Scrambled shRNA)
exp2_Scr

source_name: THP-1, shScr, replicate 2


title: THP1-Scr-1

description:
Negative control (Scrambled shRNA)
exp1_Scr

source_name: THP-1, shScr, replicate 1


title: DMSO.3

description: Gene expression data from MV4-11 cells treated with DMSO

value: DMSO


title: THP1-8E6-3

description:
Gene expression after DPF2 knock-down
exp3_8E6

source_name: THP-1, shDPF2, replicate 3

value: DPF2 knockdown


title: DMSO.2


title: THP1-8E6-1

description:
Gene expression after DPF2 knock-down
exp1_8E6

source_name: THP-1, shDPF2, replicate 1


title: THP1-8E6-2

description:
Gene expression after DPF2 knock-down
exp2_8E6

source_name: THP-1, shDPF2, replicate 2


title: DMSO.1


title: KD.3

description: Gene expression data from MV4-11 cells transduced with shSMARCA4

value: SMARCA4 knockdown


title: THP1-4C3-2

description:
Gene expression after SMARCA4 knock-down
exp2_4C3

source_name: THP-1, shSMARCA4, replicate 2


title: THP1-4D1-2

description:
Gene expression after SMARCD2 knock-down
exp2_4D1

source_name: THP-1, shSMARCD2, replicate 2

value: SMARCD2 knockdown


title: THP1-4C3-3

description:
Gene expression after SMARCA4 knock-down
exp3_4C3

source_name: THP-1, shSMARCA4, replicate 3


title: KD.1


title: 72h P/K = C3 peptide 156-181/untreated

status: Public on Jul 11 2015

city: Hannover

first: Frank

last: Stahl

address: Callinstr. 3

department: Institut für Technische Chemie

country: Germany

institute: Universität Hannover

description:
Replicate arrays are technical replicates.
Run 2 was used as alignment control.

hyb_protocol: The differently labeled cDNAs (Fluorescein and Biotin) of both samples are hybridized (42°C, overnight) simultaneously in one experiment to the same array according to the slide manufacturer´s recommendations.

scan_protocol: The microarrays were scanned by the Axon 4000B scanner; image intensity data were extracted and analysed with GenePix® Pro 6.0 software.

data_processing: Data from different scans of Dye-swap experiment were extracted by GenePix Pro 6.0 software, normalized by the median of the background intensities and united. An outliertest has been applied in order to find outliers amongst the gene replicats. Subsequently, a t-test (1% and 5% probability of error) has been used in order to find regulated genes.

label: Biotin, Cy5

organism: Rattus norvegicus

source_name: transected rat sciatic nerve_C3 peptide 156-181

label_protocol: The indirect labeling by the tyramide-signal-amplification method was used to increase the Cy3/Cy5 signals of microarray detection. 6 µg of the total RNA were reverse transcribed and thereby the cDNA was labeled with Fluorescein-dCTP/ Biotin-dCTP.

growth_protocol: Isolated primary rat Schwann cells were cultivated on Poly-ornithin-Laminin coated 24-well plates.

extract_protocol: RNA-extraction was performed with the RNeasy Mini Kit (RNeasy MiniKit Qiagen, Santa Clarita, CA, USA) according to the manufacturer’s instruction.

treatment_protocol: Isolated primary rat neonatal SCs treated with 500 nm C3 or C3156-181-peptide compared to untreated cells. 72 h treatment

value: Sprague Dawley

value: sciatic nerve

value: Schwann cells

label: Fluorescein, Cy3

source_name: transected rat sciatic nerve_untreated

value: untreated


title: SCR.3

description: Gene expression data from MV4-11 cells transduced with shScr

value: control


title: SCR.2


title: 72h K/N = untreated/C3 bot

source_name: transected rat sciatic nerve_C3 bot

value: C3 bot 72h


title: THP1-4C3-1

description:
Gene expression after SMARCA4 knock-down
exp1_4C3

source_name: THP-1, shSMARCA4, replicate 1


title: 72h N/P = C3 bot/C3 peptide 156-181

value: C3bot 72h


title: 12h K/N = untreated/C3 bot

data_processing: Data from different scans of Dye-swap experiment were extracted by GenePix Pro 6.0 software, normalized by the median of the background intensities and united. An outlier test has been applied in order to find outliers amongst the gene replicates. Subsequently, a t-test (1% and 5% probability of error) has been used in order to find regulated genes.

treatment_protocol: Isolated primary rat neonatal SCs treated with 500 nm C3 or C3156-181-peptide compared to untreated cells. 12 h treatment

value: C3 bot 12h


title: SCR.1


title: THP1-4D1-1

description:
Gene expression after SMARCD2 knock-down
exp1_4D1

source_name: THP-1, shSMARCD2, replicate 1


title: 12h P/K = C3 peptide 156-181/untreated


title: 12h N/P  = C3 bot/C3 peptide 156-181


title: Pyometra sample 231

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

description: gene expression data from a uterus with pyometra

hyb_protocol: Performed using the Affymetrix  GeneChip® Hybridization, Wash and Stain Kit (P/N 900720) following manufacturer's instructions

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

data_processing:
The data were extracted using the Affymetrix® Genotyping Console™ software and normalized using quantile normalization and robust multi-array analysis (RMA) background correction
Filtering characteristics of fold-change -2.0 to 2.0 and a FDR at P<0.05 were used to identify the differentially expressed genes.

organism: Canis lupus familiaris

source_name: uterine disease

label_protocol: Performed using the Affymetrix GeneChip® WT Terminal Labeling Kit (P/N 900671) following manufacturer's instructions

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen Life Technologies Inc., Carlsbad, CA, USA) and the mRNA purified using the RNeasy MiniKit (Qiagen), according to the manufacturer’s recommendations

treatment_protocol: Not applicable

tag: gender

value: female

value: endometrium

tag: diagnosis

value: Pyometra


title: Pyometra sample 225

tag: tissue


title: Pyometra sample 228


title: Pyometra sample 229


title: Pyometra sample 217


title: Pyometra sample 218


title: Pyometra sample 214


title: Pyometra sample 207


title: Pyometra sample 213


title: Pyometra sample 205


title: Pyometra sample 222


title: Pyometra sample 186


title: Pyometra sample 199


title: Pyometra sample 100


title: Mucometra sample 216

description: gene expression data from a uterus with mucometra

value: Hemometra


title: Mucometra sample 220


title: Mucometra sample 219


title: Mucometra sample 227


title: Mucometra sample 191


title: Pyometra sample 198


title: Mucometra sample 210


title: Pyometra sample 185


title: Mucometra sample 200


title: Pyometra sample 206


title: Mucometra sample 215


title: Mucometra sample 188


title: Mucometra sample 182


title: Mucometra sample 174


title: Mucometra sample 172


title: Mucometra sample 91


title: Cystic endometrial hyperplasia sample 180

description: gene expression data from a uterus with cystic endometrial hyperplasia

value: Cystic endometrial hyperplasia (CEH)


title: Cystic endometrial hyperplasia sample 196


title: Mucometra sample 92


title: KD.2

value: acute monocytic leukemia cell line MV4-11


title: Mucometra sample 90


title: Cystic endometrial hyperplasia sample 226


title: Cystic endometrial hyperplasia sample 171


title: Cystic endometrial hyperplasia sample 162


title: Cystic endometrial hyperplasia sample 155


title: Cystic endometrial hyperplasia sample 208


title: Cystic endometrial hyperplasia sample 131


title: Cystic endometrial hyperplasia sample 133


title: Cystic endometrial hyperplasia sample 94


title: Cystic endometrial hyperplasia sample 13


title: Diestrus sample 170

description: gene expression data from a normal uterus (diestrus fase)

source_name: normal uterus

value: healthy


title: Cystic endometrial hyperplasia sample 81


title: Cystic endometrial hyperplasia sample 83


title: Cystic endometrial hyperplasia sample 127


title: Diestrus sample 148


title: Cystic endometrial hyperplasia sample 29


title: Diestrus sample 141


title: Diestrus sample 144


title: Diestrus sample 152


title: Diestrus sample 118


title: Diestrus sample 122


title: Diestrus sample 97


title: Diestrus sample 119


title: Diestrus sample 156


title: Diestrus sample 30


title: Diestrus sample 110


title: Diestrus sample 84


title: Diestrus sample 79


title: Diestrus sample 157


title: Diestrus sample 07


title: Diestrus sample 120


title: THP1-4D1-3

description:
Gene expression after SMARCD2 knock-down
exp3_4D1

source_name: THP-1, shSMARCD2, replicate 3

value: acute monocytic leukemia THP-1


title: Diestrus sample 25


title: Diestrus sample 06


title: deldosR_rep3

city: San Antonio

first: Deepak

last: Kaushal

state: TX

address: 8715 W Military Dr

department: HPI

institute: Texas Biomedical Research Institute

description: biological replicate 3 of 3

hyb_protocol: as in Mcgillivray A et al, JBC 2015

scan_protocol: as in Mcgillivray A et al, JBC 2015

data_processing: lowess norm

organism: Mycobacterium tuberculosis H37Rv

source_name: MtbdeldosR transcriptome from infected C3HeB/FeJ mice

label_protocol: as in Mcgillivray A et al, JBC 2015

growth_protocol: as in Mcgillivray A et al, JBC 2015

extract_protocol: as in Mcgillivray A et al, JBC 2015

treatment_protocol: as in Mcgillivray A et al, JBC 2015

tag: genotype

value: Mycobacterium tuberculosis H37Rv delta dosR

tag: host

value: C3HeB/FeJ mouse lung

source_name: MtbdeldosR transcriptome from in vitro cultures


title: deldosT rep1

description: biological replicate 1 of 3

source_name: MtbdeldosT transcriptome from infected C3HeB/FeJ mice

value: Mycobacterium tuberculosis H37Rv delta dosT

source_name: MtbdeldosT transcriptome from in vitro cultures


title: deldosT rep2

description: biological replicate 2 of 3


title: deldosT rep3

description: biological replicate 3 of 3


title: deldosS rep3

description: biological replicate 3 of 3

source_name: MtbdeldosS transcriptome from infected C3HeB/FeJ mice

value: Mycobacterium tuberculosis H37Rv delta dosS

source_name: MtbdeldosS transcriptome from in vitro cultures


title: deldosS rep2

description: biological replicate 2 of 3


title: MtbWTrep3

description: biological replicate 3 of 3

source_name: Mtb transcriptome from infected C3HeB/FeJ mice

value: Mycobacterium tuberculosis H37Rv

source_name: Mtb transcriptome from in vitro cultures


title: deldosS rep1

description: biological replicate 1 of 3


title: deldosR_rep2

description: biological replicate 2 of 3


title: deldosR_rep1

description: biological replicate 1 of 3


title: MtbWTrep2

description: biological replicate 2 of 3


title: MtbWTrep1

description: biological replicate 1 of 3


title: THP1 5 hours FRAX597 2ug per mL treatment

city: Bronx

first: Ashley

middle: M

last: Pandolfi

state: NY

address: 1300 Morris Park Chanin 606

department: Cell Biology

institute: Albert Einstein College of Medicine

description: Gene expression data from THP1 cells treated with FRAX-597 PAK1 inhibitor for 5 hours.

hyb_protocol: Labeled cRNA of each individual sample was hybridized to Affymetrix Human Gene 2.0ST microarrays (Affymetrix)

scan_protocol: Scanned by GeneChip Scanner 3000 7G system (Affymetrix) according to standard protocols.

data_processing: Affymetrix Expression Console Software and Transcriptome Analysis Console

source_name: THP1 acute myeloid leukemia cell line

label_protocol: RNA was labeled with the GeneChip WT terminal labeling kit (Affymetrix)

growth_protocol: THP-1 cells were purchased from ATCC and cultured according to ATCC recommendations (RPMI-1640 + 10%FCS + P/S). Cells were maintained in an incubator at 37°C and 5% CO2.

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

treatment_protocol: RNA was isolated from THP-1 cells after 5 hours of treatment with IPA-3 (6 ug/mL), FRAX-597 (2 ug/mL) or an equal volume of DMSO using Trizol Reagent (Invitrogen).

value: acute myeloid leukemia cell line


title: THP1 5 hours FRAX597 2ug per mL treatment replicate


title: THP1 5 hours IPA3 6ug per mL treatment replicate

description: Gene expression data from THP1 cells treated with IPA-3 PAK1 inhibitor for 5 hours.


title: THP1 5 hours DMSO treatment

description: Gene expression data from THP1 cells treated with DMSO for 5 hours.

value: DMSO


title: THP1 5 hours DMSO treatment replicate 4


title: THP1 5 hours DMSO treatment replicate 3


title: BMDM_INFg_Treatment_T630

status: Public on Jul 10 2015

city: Edinburgh

first: Nigel

last: Binns

address: The Chancellor's Building, 49 Little France Crescent

department: Division of Pathway Medicine

institute: The University of Edinburgh

hyb_protocol: Dual hybridisation (Cy3 and Cy5) to Agilent oligo microarrays.

scan_protocol: Arrays were scanned on an Agilent G2565AA scanner according to the Agilent G2565AA/G2565BA Microarray Scanner System Manual. Images were quantified using Agilent Feature Extraction Software (version 7.5).

data_processing: Basic processing of the microarray data set includes background correction, log2 transformation, subset normalisation and filtering, using the R limma package. Data quality and consistency was assessed at each stage. After background subtraction in each measurement channel, features resulting in negative expression levels were set to 1. All measurements were transformed to log base 2. Systematic variation between samples was corrected using a subset median normalisation step. For this, we identified 42 features (including duplications) that are positive control or housekeeping genes for the type of biological samples used. The median of these log2 scale features was calculated for 75 test and reference samples, respectively. For all samples, the normalisation constant to be added to each feature on an array was calculated as the difference between that individual array?s positive control probe median and a reference value which was calculated as the arithmetic mean of all 75 positive control probe medians. In order to minimise the number of genes with random expression spikes or invariant expression, we devised a method centered around detection thresholds through ROC analysis. A ROC analysis of a gold-standard set of 42 positive and 111 negative control probes is done separately for each of the 75 samples. A cut-off value for achieving sensitivity >= 80% is determined for each sample. The arithmetic mean of all 75 cut-off values then constitutes the desired detection threshold and is used to construct a binary filter matrix indicating if a gene is above or below that threshold. A gene is excluded from the data set if it does not exceed the detection threshold in 5 consecutive time points in any of the three biological conditions. Of the original 22393 features, 14819 remain.

organism: Mus musculus

source_name: Bone marrow-derived macrophages, INFg treated, 630 min

label_protocol: Agilent Low RNA Input: Agilent Low RNA Input HALF Fluorescent Linear Amplification. Synthesis of labelled cRNA from 50-500ng total RNA.

growth_protocol: 8x10^5 cells were plated out into 2 wells of a 6-well plate. Media - DMEM/F-12 + 10% FCS + 10% L929 + pen/strep. Media re-feed on day 3 and day 5.

extract_protocol: PAXgene RNA Extraction: extraction of total RNA from whole blood taken into PAXgene RNA tubes according to the manufacturer's instructions.

treatment_protocol: Day 7 - media taken off the two wells and new media added (mock infection) - DMEM/F-12 + 2% FCS + 10% L929 + pen/strep - for 1 hour (with shaking every 10 minutes). This mock infection media is taken off and the cells are washed three times in PBS. New media is added, with 10 units/ml interferon-gamma - DMEM/F-12 + 10% FCS + 10% L929 + pen/strep. The media is taken off at the sample timepoint and the cells are lysed in Trizol and stored at -80C.

value: BALB/c

value: male

tag: age

value: 10-12 weeks

value: adult

value: bone marrow

value: bone marrow-derived macrophages (BMDMs)

value: interferon-gamma (IFNg)

tag: time point

value: 630 min


title: BMDM_INFg_Treatment_T720

source_name: Bone marrow-derived macrophages, INFg treated, 720 min

value: 720 min


title: BMDM_INFg_Treatment_T690

source_name: Bone marrow-derived macrophages, INFg treated, 690 min

value: 690 min


title: BMDM_INFg_Treatment_T660

source_name: Bone marrow-derived macrophages, INFg treated, 660 min

value: 660 min


title: BMDM_INFg_Treatment_T600

source_name: Bone marrow-derived macrophages, INFg treated, 600 min

value: 600 min


title: THP1 5 hours IPA3 6ug per mL treatment


title: THP1 5 hours DMSO treatment replicate 2


title: Melanoma cell line Ma-Mel-13

city: Heidelberg

first: Rajiv

last: Kumar

address: Im Neuenheimer Feld 580

department: Division of Molecular Genetic Epidemiology

institute: German Cancer Research Center

hyb_protocol: RNA was converted into double stranded cDNA and cRNA and hybridized to each array according to the manufacturer's instructions.

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

data_processing: Image analysis was performed with the Affymetrix GeneChip Operating Software (GCOS) and for pair-wise comparisons of expression profiles. changes in expression. Marker analysis was performed using GeneCluster 2.0.

label: Biotin

source_name: Melanoma cell line Ma-Mel-13, derived from metastatic tumor

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen). Concentrations of  RNA were measured by UV spectrophotometry and the integrity of total RNA isolated from cell lines was determined on the Bioanalyzer 2100 System


title: BMDM_INFg_Treatment_T480

source_name: Bone marrow-derived macrophages, INFg treated, 480 min

value: 480 min


title: BMDM_INFg_Treatment_T420

source_name: Bone marrow-derived macrophages, INFg treated, 420 min

value: 420 min


title: BMDM_INFg_Treatment_T450

source_name: Bone marrow-derived macrophages, INFg treated, 450 min

value: 450 min


title: BMDM_INFg_Treatment_T510

source_name: Bone marrow-derived macrophages, INFg treated, 510 min

value: 510 min


title: BMDM_INFg_Treatment_T300

source_name: Bone marrow-derived macrophages, INFg treated, 300 min

value: 300 min


title: BMDM_INFg_Treatment_T210

source_name: Bone marrow-derived macrophages, INFg treated, 210 min

value: BALB/c

value: 210 min


title: BMDM_INFg_Treatment_T360

source_name: Bone marrow-derived macrophages, INFg treated, 360 min

value: male

value: 10-12 weeks

value: 360 min


title: BMDM_INFg_Treatment_T270

source_name: Bone marrow-derived macrophages, INFg treated, 270 min

value: adult

value: bone marrow

value: bone marrow-derived macrophages (BMDMs)

value: 270 min


title: BMDM_INFg_Treatment_T330

source_name: Bone marrow-derived macrophages, INFg treated, 330 min

value: interferon-gamma (IFNg)

value: 330 min


title: BMDM_INFg_Treatment_T570

source_name: Bone marrow-derived macrophages, INFg treated, 570 min

value: 570 min


title: BMDM_INFg_Treatment_T180

source_name: Bone marrow-derived macrophages, INFg treated, 180 min

value: 180 min


title: BMDM_INFg_Treatment_T240

source_name: Bone marrow-derived macrophages, INFg treated, 240 min

value: 240 min


title: BMDM_INFg_Treatment_T150

source_name: Bone marrow-derived macrophages, INFg treated, 150 min

value: 150 min


title: BMDM_INFg_Treatment_T120

source_name: Bone marrow-derived macrophages, INFg treated, 120 min

value: 120 min


title: BMDM_INFg_Treatment_T540

source_name: Bone marrow-derived macrophages, INFg treated, 540 min

value: 540 min


title: BMDM_INFg_Treatment_T90

source_name: Bone marrow-derived macrophages, INFg treated, 90 min

value: BALB/c

value: 90 min


title: BMDM_INFg_Treatment_T60

source_name: Bone marrow-derived macrophages, INFg treated, 60 min

value: male

value: 60 min


title: BMDM_MCMV(pSM3)_Infection_T720

scan_protocol: Scanned on an Agilent G2565AA scanner according to the Agilent G2565AA/G2565BA Microarray Scanner System Manual. Images were quantified using Agilent Feature Extraction Software (version 7.5).

data_processing: Basic processing of the microarray data set includes background correction, log2 transformation, subset normalisation and filtering, using the R limma package.  Data quality and consistency was assessed at each stage. After background subtraction in each measurement channel, features resulting in negative expression levels were set to 1. All measurements were transformed to log base 2. Systematic variation between samples was corrected using a subset median normalisation step. For this, we identified 42 features (including duplications) that are positive control or housekeeping genes for the type of biological samples used. The median of these log2 scale features was calculated for 75 test and reference samples, respectively. For all samples, the normalisation constant to be added to each feature on an array was calculated as the difference between that individual array?s positive control probe median and a reference value which was calculated as the arithmetic mean of all 75 positive control probe medians. In order to minimise the number of genes with random expression spikes or invariant expression, we devised a method centered around detection thresholds through ROC analysis. A ROC analysis of a gold-standard set of 42 positive and 111 negative control probes is done separately for each of the 75 samples. A cut-off value for achieving sensitivity >= 80% is determined for each sample. The arithmetic mean of all 75 cut-off values then constitutes the desired detection threshold and is used to construct a binary filter matrix indicating if a gene is above or below that threshold. A gene is excluded from the data set if it does not exceed the detection threshold in 5 consecutive time points in any of the three biological conditions. Of the original 22393 features, 14819 remain.

source_name: Bone marrow-derived macrophages, mCMV infected, 720 min

growth_protocol: 8x10^5 cells were plated out into 2 wells of a 6-well plate. Media - DMEM/F-12 + 10% FCS + 10% L929 + pen/strep. Media re-feed on day 3 and on day 5.

treatment_protocol: Day 7 - media taken off the two wells and new media added (infection) - DMEM/F-12 + 2% FCS+ 10% L929 + pen/strep, mCMV(pSM3) MOI of 1 - 0.5ml/well - for 1 hour (with shaking every 10 minutes). This infection media is taken off and the cells are washed three times in PBS. New media is added, mock interferon-gamma treatment - DMEM/F-12 + 10% FCS + 10% L929 + pen/strep. The media is taken off at the sample timepoint and the cells are lysed in Trizol and stored at -80C.

value: 10-12 weeks

value: murine cytomegalovirus (mCMV) infection

value: 720 min


title: BMDM_INFg_Treatment_T390

source_name: Bone marrow-derived macrophages, INFg treated, 390 min

value: adult

value: bone marrow

value: bone marrow-derived macrophages (BMDMs)

value: 390 min


title: BMDM_INFg_Treatment_T30

source_name: Bone marrow-derived macrophages, INFg treated, 30 min

value: interferon-gamma (IFNg)

value: 30 min


title: BMDM_INFg_Treatment_T0

source_name: Bone marrow-derived macrophages, INFg treated, 0 min

value: 0 min


title: BMDM_MCMV(pSM3)_Infection_T630

source_name: Bone marrow-derived macrophages, mCMV infected, 630 min

value: 630 min


title: BMDM_MCMV(pSM3)_Infection_T690

source_name: Bone marrow-derived macrophages, mCMV infected, 690 min

value: 690 min


title: tcf1-1 vs Wild type_22℃_R3

city: shijiazhuang

first: hongtao

last: Ji

state: hebei

address: 286 huaizhong rode

department: Centor for agricultural resources Research

institute: Institute of genetics and developmental biology,Chinese academy of sciences

description: compare gene expression profiles of control tissue

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy,the geometric mean  of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated.

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Arabidopsis seedls were germinated on MS medium containing 2% sucrose, pH 5.7 for 10 days and transferred to soil for three week growth.

extract_protocol: The rosetta of seedlings were were harvest, and total RNA was extracted with Trizol Reagent (Invitrogen) and ethanol precipitation.

treatment_protocol: Three-week-old tcf1-1 and wild-type plants grown in soil with cold-acclimation (4 °C for 7 days) and non-cold acclimation.

tag: genotype/variation

tag: temperature

value: leaves

source_name: Wild type_22℃

value: wild type


title: tcf1-1 vs Wild type_22℃_R2


title: tcf1-1 vs Wild type_4℃_R2

value: 4℃

source_name: Wild type_4℃


title: tcf1-1 vs Wild type_4℃_R1


title: tcf1-1 vs Wild type_4℃_R3


title: tcf1-1 vs Wild type_22℃_R1


title: Ec-pR VS Ec-1558 rep2

city: chongup

first: sun

middle: wook

last: Jeong

state: Chonbuk

address: Sinjeongdong 1266

department: Radiation biotechnology

country: South Korea

institute: Korea atomic energy research institute

description: Biological replicate 2 of 3, comparing control cells with dr1558 expressing cells

hyb_protocol: After fragmentation of Cy3- and Cy5-labeled cRNA, the cRNA was hybridized to the Escherichia coli K12 oligonucleotide 3X15 K microarray, which includes 4294 gene-specific probes (99.1% of all genes) (MYcroarray Inc., USA). The hybridizations were conducted at 57°C for 17 h in an Agilent Hybridization oven following the manufacturer’s instructions (Agilent Technologies, Inc.).

scan_protocol: The scans were performed using an Agilent DNA microarray Scanner (Agilent Technologies, Inc.) with Agilent Feature Extraction software 10.7 (Agilent Technologies, Inc.). The signal intensities were quantified using GeneSpring GX 7.3.1 software (Agilent Technologies, Inc.).

data_processing:
The genes were filtered by removing the flag-out genes in each experiment. The gene expression was normalized through LOWESS regression for 3 datasets obtained from 3 biological replicates.
The genes were considered differentially expressed when the logarithmic gene expression ratios had a 2-fold difference in the expression level. The significance of the data was determined using Student’s t test. P-values of less than 0.01 were considered significant.

organism: Escherichia coli

source_name: E. coli harboring pRadGro replicate 2

label_protocol: The extracted RNA was amplified and labeled using Agilent’s Low Input Quick Amp WT Labeling Kit (Agilent Technologies, Inc.) according to the manufacturer’s instructions. Briefly, 100 ng of total RNA was mixed with WT Primer Master Mix and incubated at 65°C for 10 m. Following the addition of cDNA Master Mix, the reaction mixture was incubated at 40°C for 2 h for reverse transcription and at 70°C for 10 m to stop the reaction. Transcription Master Mix was added to the reaction mixture, and the mixture was incubated at 40°C for 2 h to generate labeled cRNA probes (Cy3, Ec-pR and Cy5, Ec-1558).

growth_protocol: Cells grown aerobically to exponential phase (OD600 = 0.8) in LB media at 37C were harvested.

extract_protocol: Total RNA extracted using RiboEX reagent (GeneAll, Korea), treated with Dnase, and purified using the Rneasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.

treatment_protocol: Non-treatment

tag: strain information

value: E. coli harboring empty vector (pRADgro), used as a control strain

source_name: E. coli expressing dr1558 replicate 2

value: E. coli harboring pRADgro::dr1558


title: Ec-pR VS Ec-1558 rep1

description: Biological replicate 1 of 3, comparing control cells with dr1558 expressing cells

source_name: E. coli harboring pRadGro replicate 1

source_name: E. coli expressing dr1558 replicate 1


title: BMDM_MCMV(pSM3)_Infection_T600

source_name: Bone marrow-derived macrophages, mCMV infected, 600 min

value: BALB/c

value: male

value: 10-12 weeks

tag: cell type

value: 600 min


title: BMDM_MCMV(pSM3)_Infection_T570

source_name: Bone marrow-derived macrophages, mCMV infected, 570 min

tag: strain

value: adult

value: bone marrow

value: murine cytomegalovirus (mCMV) infection

value: 570 min


title: Cystic endometrial hyperplasia sample 175

source_name: uterine disease

value: female

value: endometrium

value: Cystic endometrial hyperplasia (CEH)


title: BMDM_MCMV(pSM3)_Infection_T510

source_name: Bone marrow-derived macrophages, mCMV infected, 510 min

value: bone marrow-derived macrophages (BMDMs)

tag: treatment

value: 510 min


title: BMDM_MCMV(pSM3)_Infection_T660

source_name: Bone marrow-derived macrophages, mCMV infected, 660 min

value: 660 min


title: BMDM_MCMV(pSM3)_Infection_T540

source_name: Bone marrow-derived macrophages, mCMV infected, 540 min

value: 540 min


title: HCC1806 @ 6 hours post treatment rep1

city: Los Angeles

first: Xinyu

last: Deng

address: 650 Charles E Young Dr.

department: Surgery

institute: University of California Los Angeles

description: Gene expression from HCC1806 cells treated w/ Docetaxel in DMSO

hyb_protocol: Human U133plus2.0 array hybridizations were performed by UCLA Clinical Microarray Core following standard Affymetrix GeneChip Expression Analysis protocol.

scan_protocol: The platform is Affymetrix microarray platform (scanner 7G. Fluidics station 450, Hyb oven 645).

data_processing: Subsequent raw data were analyzed using Partek Genomics Suite 6.4. We used RMA algorithm for data normalization using Affymetrix Expression Console.

source_name: HCC1806 with 6H Docetaxel treatment

label_protocol: With standard Affymtrix array labeling method

growth_protocol: HCC1806 cells were cultured with RPMI 1640 (Invitrogen) with 10% heat-inactivated Fetal Bovine Serum (Fisher Scientific, Pittsburgh, PA, USA), 100 units/mL penicillin, and 100 µg/mL streptomycin, at 37 ℃ in 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Life Technologies, NY, USA) followed by Qiagen column purification (Qiagen, Valencia, CA, USA).

treatment_protocol: Test group cells were treated with 6.4 uM docetaxel for 6 hours prior to RNA extraction. Control cells were treated with DMSO instead.

tag: cell line

value: mammary gland; breast

tag: disease

value: TNM stage IIB, grade 2, primary acantholytic squamous cell carcinoma


title: HCC1806 @ 6 hours post treatment rep2


title: untreated HCC1806 rep2

description: Gene expression from HCC1806 cells treated w/ DMSO control

source_name: HCC1806 negative control


title: BMDM_MCMV(pSM3)_Infection_T420

source_name: Bone marrow-derived macrophages, mCMV infected, 420 min

value: BALB/c

tag: developmental stage

value: 420 min


title: BMDM_MCMV(pSM3)_Infection_T450

source_name: Bone marrow-derived macrophages, mCMV infected, 450 min

value: male

value: 10-12 weeks

value: 450 min


title: untreated HCC1806 rep1


title: BMDM_MCMV(pSM3)_Infection_T480

source_name: Bone marrow-derived macrophages, mCMV infected, 480 min

value: adult

value: bone marrow

value: 480 min


title: Corrected Sample 3

city: Milwaukee

first: John

last: LaDisa

state: Wisconsin

address: 1637 West Wisconsin Ave

department: Biomedical Engineering

institute: Marquette University

description:
This sample displayed a different distribution of intensities compared to all other arrays and was therefore excluded from the analysis.
Gene expression at 32 wks  of age
4 mm aortic ring

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × blocking agent and 2.2 μl of 25 × fragmentation buffer, then heated at 60 °C for 30 min, and 55 μl 2 × GE buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (model G2505C).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software (Agilent Technologies). Probes for which at least 8 out of 12 samples had flags in Detected (“All Targets Value”) were then chosen for further data analysis.
Differentially expressed probes with statistical significance were identified through Volcano Plot filtering. Finally, hierarchical clustering was performed to show the distinguishable gene expression profiling among samples.

organism: Oryctolagus cuniculus

source_name: 4 mm aortic ring from thoracic aorta, 32wks, replicate 3

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Sample labeling and hybridization were performed using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

treatment_protocol: A 20 mmHg BP gradient was imposed using silk (permanent) or Vicryl (degradable) suture to mimic untreated CoA and surgically corrected CoA, respectively. Rabbits develop a pronounced stenosis and accompanying elevated BP as a stimulus for arterial remodeling within one week. Degradation of Vicryl suture in the corrected group restores aortic diameter close to normal, but with modest residual narrowing. Non-experimental rabbits were designated as a control group. This results in a statistically significant increase in mean, systolic and pulse BP proximal to the coarctation for CoA as compared to both control and corrected rabbits.

value: New Zealand white

value: aorta

value: 32 weeks


title: 7d-3

city: Hangzhou

first: Jialin

last: Chen

address: Yuhangtang Road

institute: Zhejiang University

description: Gene expression data from post-natal 7 day rat Achilles tendons

hyb_protocol: The fragmented aRNA was hybridized to Rat Genome 230 2.0 Array containing 30,000 transcripts. Hybridization was performed at 45oC with rotation for 16 h (AffymetrixGeneChip Hybridization Oven 640). The GeneChip arrays were washed and then stained (streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: The GeneChip arrays were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

source_name: Post-natal 7 day rat Achilles tendons

label_protocol: An aliquot of 200ng of total RNA was used to synthesize double-stranded cDNA, and then produce biotin-tagged aRNA using MessageAmp™ Premier RNA Amplification Kit. The resulting bio-tagged aRNA were fragmented to strands of 35-200 bases in length according to the protocols from Affymetrix.

growth_protocol: Achilles tendons at different development stages (post-natal 1 day and 7 days) were harvested

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: Tendons were isolated under the dissecting scope and placed on ice in the Trizol solution

value: post-natal 7d

value: Achilles tendons


title: 7d-1


title: Ec-pR VS Ec-1558 rep3

description: Biological replicate 3 of 3, comparing control cells with dr1558 expressing cells

source_name: E. coli harboring pRadGro replicate 3

value: E. coli harboring empty vector (pRADgro), used as a control strain

source_name: E. coli expressing dr1558 replicate 3

value: E. coli harboring pRADgro::dr1558


title: 7d-2


title: 1d-3

description: Gene expression data from post-natal 1 day rat Achilles tendons

source_name: Post-natal 1 day rat Achilles tendons

value: post-natal 1d


title: 1d-1


title: BMDM_MCMV(pSM3)_Infection_T360

source_name: Bone marrow-derived macrophages, mCMV infected, 360 min

value: bone marrow-derived macrophages (BMDMs)

value: murine cytomegalovirus (mCMV) infection

value: 360 min


title: Corrected Sample 4

description:
Gene expression at 32 wks  of age
4 mm aortic ring

source_name: 4 mm aortic ring from thoracic aorta, 32wks, replicate 4

value: male


title: TSPCs-56d

description: Gene expression data from post-natal 56 day tendon derived stem cells

hyb_protocol: The fragmented cRNA was hybridized to Rat Genome 230 2.0 Array containing 30,000 transcripts. Hybridization was performed at 45oC with rotation for 16 h (AffymetrixGeneChip Hybridization Oven 640). The GeneChip arrays were washed and then stained (streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: Achilles tendon stem/progenitor cells isolated from post-natal 56 day tendon tissue

label_protocol: An aliquot of 2 µg of total RNA was used to synthesize double-stranded cDNA, and then produce biotin-tagged cRNA using the MessageAmpTM II aRNA Amplification Kit. The resulting bio-tagged cRNA were fragmented to strands of 35-200 bases in length according to the protocols from Affymetrix.

growth_protocol: Cells were cultured in low glucose DMEM supplemented with 10% (v/v) fetal bovine serum  and 1% penicillin-streptomycin

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

treatment_protocol: Cells were placed on ice in the Trizol solution

tag: development stage

value: post-natal 56d


title: 1d-2


title: BMDM_MCMV(pSM3)_Infection_T330

source_name: Bone marrow-derived macrophages, mCMV infected, 330 min

value: BALB/c

tag: gender

value: 10-12 weeks

value: 330 min


title: Diestrus sample 21

source_name: normal uterus

value: female

value: endometrium

tag: diagnosis

value: healthy


title: Corrected Sample 2

source_name: 4 mm aortic ring from thoracic aorta, 32wks, replicate 2

value: New Zealand white

tag: tissue

value: aorta

value: 32 weeks


title: BMDM_MCMV(pSM3)_Infection_T390

source_name: Bone marrow-derived macrophages, mCMV infected, 390 min

value: adult

value: bone marrow

value: 390 min


title: BMDM_MCMV(pSM3)_Infection_T270

source_name: Bone marrow-derived macrophages, mCMV infected, 270 min

value: bone marrow-derived macrophages (BMDMs)

value: 270 min


title: TSPCs-1d

description: Gene expression data from post-natal 1 day tendon derived stem cells

source_name: Achilles tendon stem/progenitor cells isolated from post-natal 1 day tendon tissue

value: post-natal 1d


title: CoA Sample 3

value: male


title: Lrf deleted MEF, biological rep1

city: Shanghai

first: Xue-Song

last: Liu

address: 333 Haike Road

department: School of Life Science and Technology

institute: ShanghaiTech University

description: Lrf deleted 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse genome array.

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

data_processing:
The data were analyzed with Affymetrix Expression Console
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.4.1.46

source_name: Lrf deleted MEF

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

growth_protocol: MEFs were cultured in 37 degree, with 5% CO2

extract_protocol: Total RNA were extracted using the RNAeasy Mini Kit (Qiagen) and treated with RNase-free DNase set (Qiagen)

treatment_protocol: MEF were transduced with control or cre expresion retrovirus

tag: strain background

value: Mouse embryonic fibroblast (MEF)

value: Lrf deleted


title: M4_sus_0603_1 reanalysis

city: Seattle

first: Anne

last: Grosse-Wilde

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

hyb_protocol: 1.65 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 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarray 4x44K (G4112F) 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 compressed air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using the AgilentHD-GX-1-color scan setting for 4x44k arrays.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_D_F_20100115).
Normalized signal intensity: The normalization of the gene expression arrays was generated using the program ‘GeneData’, and was first a Central Tendency normalization, followed by relative normalization towards the average expression of adherent E and M clones.

source_name: HMLER

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 to 100 ng total RNA using Agilent’s Low Input Quick Amp One-Color Labeling Kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells that were normally cultured under adherent culture conditions (1:1 mixture DMEM:MEGM medium) were grown as mammospheres in DMEM:MEGM supplemented with 1% methylcellulose and B27 in ultra low adhesion plates for two to three weeks according to Dontu et al 2003. For replating mammospheres were directly plated into DMEM:MEGM medium in standard culture dishes.

extract_protocol: RNA was extracted using Trizol (Life Technologies) using the manufacturer's instructions. Ethanol-precipitated RNA was additionally purified using the RNeasy micro kit (Qiagen).

treatment_protocol: Replated mammospheres were allowed to adhere to dishes for either 6, 24, 96, and 240 hours, or when no time is indicated cells were harvested once they nearly reached confluency. RNA of replated (_re) cells was isolated by washing off non-adherent cells and mammospheres with PBS and by lysing adherent cells by addition of TRIzol (Life Technologies) directly to the dish.

tag: condition

value: mammosphere suspension culture

tag: clonality

value: single cell-derived clone


title: BMDM_MCMV(pSM3)_Infection_T210

source_name: Bone marrow-derived macrophages, mCMV infected, 210 min

value: BALB/c

tag: age

value: 10-12 weeks

value: murine cytomegalovirus (mCMV) infection

tag: time point

value: 210 min


title: TSPCs-7d

description: Gene expression data from post-natal 7 day tendon derived stem cells

source_name: Achilles tendon stem/progenitor cells isolated from post-natal 7 day tendon tissue

value: post-natal 7d


title: Corrected Sample 1

source_name: 4 mm aortic ring from thoracic aorta, 32wks, replicate 1

value: New Zealand white

value: aorta

value: 32 weeks


title: BMDM_MCMV(pSM3)_Infection_T300

source_name: Bone marrow-derived macrophages, mCMV infected, 300 min

value: adult

value: bone marrow

value: 300 min


title: CoA Sample 4


title: HP_sus_0603_2 reanalysis

value: parental cell line


title: Diestrus sample 82

description: gene expression data from a normal uterus (diestrus fase)

value: female

value: endometrium

value: healthy


title: M4_sus_0603_2 reanalysis

value: mammosphere suspension culture


title: BMDM_MCMV(pSM3)_Infection_T240

source_name: Bone marrow-derived macrophages, mCMV infected, 240 min

value: male

value: bone marrow-derived macrophages (BMDMs)

value: 240 min


title: CoA Sample 1


title: control MEF, biological rep1

description: control 1

source_name: control MEF

value: Mouse embryonic fibroblast (MEF)

tag: genotype/variation

value: empty vector control


title: CoA Sample 2


title: control MEF, biological rep2

description: control 2


title: BMDM_MCMV(pSM3)_Infection_T180

source_name: Bone marrow-derived macrophages, mCMV infected, 180 min

value: BALB/c

value: 10-12 weeks

value: murine cytomegalovirus (mCMV) infection

value: 180 min


title: Lrf deleted MEF, biological rep2

description: Lrf deleted 2

value: Lrf deleted


title: M4_adh_0210 reanalysis

value: adhesion culture

value: single cell-derived clone


title: M3_adh_2810 reanalysis


title: BMDM_MCMV(pSM3)_Infection_T150

source_name: Bone marrow-derived macrophages, mCMV infected, 150 min

value: adult

value: bone marrow

value: 150 min


title: Control Sample 4

source_name: 4 mm aortic ring from thoracic aorta, 32wks, replicate 4

value: New Zealand white

value: aorta

value: 32 weeks


title: HP_sus_0603_1 reanalysis

value: mammosphere suspension culture

value: parental cell line


title: BMDM_MCMV(pSM3)_Infection_T120

source_name: Bone marrow-derived macrophages, mCMV infected, 120 min

value: male

value: bone marrow-derived macrophages (BMDMs)

value: 120 min


title: M4_adh_0607 reanalysis


title: M3_adh reanalysis


title: M1_adh_0607 reanalysis


title: BMDM_MCMV(pSM3)_Infection_T90

source_name: Bone marrow-derived macrophages, mCMV infected, 90 min

value: BALB/c

value: 10-12 weeks

value: 90 min


title: M3_adh_2210 reanalysis


title: M1_adh_0210 reanalysis


title: BMDM_MCMV(pSM3)_Infection_T0

source_name: Bone marrow-derived macrophages, mCMV infected, 0 min

value: murine cytomegalovirus (mCMV) infection

value: 0 min


title: Control Sample 2

source_name: 4 mm aortic ring from thoracic aorta, 32wks, replicate 2


title: BMDM_MCMV(pSM3)_Infection_T30

source_name: Bone marrow-derived macrophages, mCMV infected, 30 min

value: 30 min


title: Control Sample 1


title: HP_adh_2210 reanalysis

value: adhesion culture


title: E4_adh_0607 reanalysis

value: single cell-derived clone


title: HP_adh_0629 reanalysis


title: HP_adh_0607sc reanalysis


title: E3_adh_0826 reanalysis


title: Control Sample 3

source_name: 4 mm aortic ring from thoracic aorta, 32wks, replicate 3


title: E5_adh_0607 reanalysis


title: E3_adh reanalysis


title: BMDM_MCMV(pSM3)_Infection_T60

source_name: Bone marrow-derived macrophages, mCMV infected, 60 min

value: adult

value: bone marrow

value: 60 min


title: E4_adh_0210 reanalysis

source_name: HMLER


title: HP_adh_0607c reanalysis


title: E3_adh_0629 reanalysis


title: M4_re_24hr_2

value: 24 hrs

value: M4 clone


title: M4_re_96hr_1

value: 96 hrs


title: mouse progenitors_DDB1 deficient_LSK sorted_rep2

city: Omaha

first: Shannon

last: buckley

state: Nebraska

address: 985805 Nebraska Medical Center

department: Genetics, Cell Biology, and Anatomy

institute: Unviversity of Nebraska Med Center

description: CKO 2

hyb_protocol: 15 mcg of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring 7.2 program. No further adjustments were made to the data in the table.

source_name: Lin-ckit+Sca1+ (LSK) sorted from fetal liver

label_protocol: 20 ng total RNA converted to cRNA using Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

extract_protocol: Rneasy (QIAGEN) according to manufacturer's protocol.

treatment_protocol: Feral livers were harvested at E16.5 and LSK cells were sorted by FACS.

value: fetal liver

value: DDB1 flox/flox, VavCre+


title: mouse progenitors_WT_LSK sorted_rep1

description: Control 1

value: DDB1 flox/flox, VavCre-


title: M4_re_96hr_2


title: HP_re_240hr_2

value: 240 hrs

value: parental HMLER, not clonal


title: M4_re_24hr_1


title: mouse progenitors_DDB1 deficient_LSK sorted_rep1

description: CKO 1


title: E5_adh_0210 reanalysis


title: mouse progenitors_WT_LSK sorted_rep2

description: Control 2


title: Rat bone marrow cells LIPUS day10-3

city: Nagoya

first: Daisuke

last: Yamaguchi

address: 2-11 Suemori-dori

country: Japan

institute: Aichi Gakuin University

description: Gene expression in response to LIPUS treatment on day10-3

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 5.5μl containing 25x Fragmentation buffer and 10x Blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 5.5μl of 2x Agilent GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4112A) 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).

scan_protocol: Slides were scanned immediately after washing on the DNA Microarray Scanner (Gene Pix 4000B) using one color scan setting for 4x44k array slides (Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Gene Pix Pro 6.1 (Molecular Devices) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Result files were imported into the analyzing GeneSpring GX software 11.0 (Agilent) for statistical analysis.

source_name: Rat bone marrow cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from100ng RNA using the One-ColorLow Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the guanidinium thiocyanate-phenol-chloroform extraction method (TRIzol, Invitrogen, USA) and purification columns (RNeasy, QIAGEN, USA), in accordance with the manufacturers’ instructions. DNase I treatment (TURBO DNA-free, Life Technologies, USA) was then applied to remove contaminating DNA. The concentration of the extracted RNA was measured using a spectrophotometer (ND-1000, Thermo Fisher Scientific, USA).

tag: Sex

value: male

value: LIPUS


title: HP_re_240hr_1


title: Rat bone marrow cells LIPUS day10-2

description: Gene expression in response to LIPUS treatment on day10-2


title: HP_re_6hr_2

value: 6 hrs


title: Rat bone marrow cells Control day10-1

description: Gene expression in response to without LIPUS treatment on day10-1


title: Rat bone marrow cells LIPUS day10-1

description: Gene expression in response to LIPUS treatment on day10-1


title: HP_re_96hr_1


title: HP_re_96hr_2


title: M4_re_240hr_2


title: Rat bone marrow cells Control day10-2

description: Gene expression in response to without LIPUS treatment on day10-2


title: HP_re_24hr_2


title: HP_re_8

value: until confluency


title: M2_re_3

value: M2 clone


title: M1_re_2

value: M1 clone


title: E4_re_1

value: E4 clone


title: Rat bone marrow cells Control day10-3

description: Gene expression in response to without LIPUS treatment on day10-3


title: HP_re_6hr_1


title: M4_re_240hr_1


title: HP_re_24hr_1


title: E5_re_2

value: E5 clone


title: HP_re_5


title: HP_re_6


title: M2_re_2


title: E4_re_2


title: HP_re_4


title: E5_re_1


title: HP_re_9


title: M2_re_5


title: M1_re_1


title: E3_re_2

value: E3 clone


title: HP_re_3


title: HP_re_7


title: M2_re_4


title: E3_re_1


title: M2_re_1


title: Cmah-null_cochlear 2

city: Seoul

first: Deug-Nam

last: Kwon

address: 1 hwayang-dong, Kwangjin-gu

institute: Konkuk University

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: cochlear from Cmah-null mouse

label_protocol: Biotinylated cRNA were prepared with Ambion's Illumina RNA Amplification kit for Illumina arrays

extract_protocol: Total RNA was extracted and purified from thecochlear tissues of WT and Cmah-null mice using RNeasy columns (Qiagen; Valencia, CA, USA) according to the manufacturer’s protocol.

value: Cmah-null

value: 12 months


title: Wild type_cochlear2

description: replicate 2

source_name: cochlear from control mouse

value: Wild type


title: Wild type_cochlear3

description: replicate 3


title: Rosette leaves treated with PIPL3 peptide for 3 hours compared to rosette leaves treated with mock peptide (replica 3)

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

description: Two color microarray. Biological replicas are dye-swapped between slides.

hyb_protocol: Hybridization was performed with the Gene Expression Hybridization Kit (Agilent p/n 5188-5242). 825 ng cRNA from both mock-treated plants and PIPL3 peptide-treated plants were used. The cRNA mixture was fragmented and hybridized on Arabidopsis (V4) Gene Expression Microarray 4x44K arrays in a rotary oven at 65°C in ~15 h. The slides were washed with Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325), Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326), acetonitrile (VWR International) and Stabilization and Drying Solution (Agilent Technologies) according to the manufacturer’s instructions.

scan_protocol: The slides were scanned at 5 µm resolution on an Agilent DNA microarray scanner (Agilent Technologies).

data_processing: Prior to the statistical analysis spots from control spikes, landmarks and genes with low expression (absent) were filtered out. The data were analysed using the limma package (Smyth, 2004) and the R statistical data analysis program package (R 2.10.1). No background subtraction was performed and data were normalized by the global loess normalization method. The Benjamini and Hochberg’s method to control the false discovery rate was used to identify differentially regulated genes (Benjamini and Hochberg, 1995). Genes with dye bias effects were removed and genes with an adjusted p-value less than 0.05 were regarded as significantly differentially expressed. The study is MIAME compliant.

source_name: PIPL3 peptide treatment of rosette leaves (3 hours), 2 week stage

label_protocol: Total RNA (~0.2 µg) was reverse transcribed, amplified and labelled using the Low Input Quick Amp Labeling Kit, two-color, (Agilent p/n 5190-2306) (Agilent Technologies, USA). cRNA from the mock and PIPL3-treated plants were alternately labelled with Cy3 or Cy5.

growth_protocol: Seeds of Col-0 ecotype were surface-sterilised and sown out on half-strength MS plates at a density of 20 seeds per Petri dish (14 cm diameter), and stratified for 3 days at 4°C. Plates were grown under a 16 h photoperiod (70 µmol m-2 s-1) at 22°C for two weeks.

extract_protocol: 100 mg frozen plant tissue each from four biological replicas were homogenised using TissueLyser II (Qiagen, Hilden, Germany) for 2 x 2 minutes at 25 Hz. Total RNA was extracted with the Spectrum Plant Total RNA kit (Sigma-Aldrich, Saint Louis, USA) as described by the supplier, but with lysis solution being added to the plant tissue between the two disruption cycles. An on-column DNase digestion was performed using the RNase-Free DNase Set (Qiagen, Hilden, Germany).

treatment_protocol: Seedlings were treated by spraying with an aqueous peptide solution (100 nM) supplemented with 0.02% silwet L-77 (Lehle Seeds, UK). Whole rosettes were collected 3h after treatment, snap-frozen in liquid nitrogen, and stored at -80°C.

tag: ecotype

source_name: Mock peptide treatment of rosette leaves (3 hours), 2 week stage


title: Wild type_cochlear1

description: replicate 1

tag: strain


title: Cmah-null_cochlear 1

description: replicate 1


title: diaphragm_PHIL_7dpi_rep2

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

description: replicate 2

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

source_name: whole mouse diaprhagm, PHIL, 7 days post-infection, Trichinella spiralis

label_protocol: Biotin labeled complementary RNA (cRNA) was made using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: Whole diaphragm was dissected from naïve or infected mice and stored in RNALater at -80c until ready for RNA extraction

extract_protocol: Total RNA was isolated using the Qiagen miRNeasy Kit

treatment_protocol: Tissue was homogenized in Qiazol reagent using a FastPrep-24 Sample Preparation System (MP Biomedicals) and RNA was isolated using the miRNeasy kit (Qiagen).

value: Whole diaphragm muscle

tag: genotype

value: PHIL

tag: treatment


title: diaphragm_PHIL_7dpi_rep1

description: replicate 1

value: 7 days post-infection, Trichinella spiralis


title: Rosette leaves treated with PIPL3 peptide for 3 hours compared to rosette leaves treated with mock peptide (replica 4)

value: Mock peptide treatment of rosette leaves (3 hours)

value: PIPL3 peptide treatment of rosette leaves (3 hours)


title: diaphragm_PHIL_naive_rep1

description: replicate 1

source_name: whole mouse diaphragm, PHIL, naïve

value: naïve


title: diaphragm_PHIL_7dpi_rep3

description: replicate 3


title: ara-c sensitive murine leukemia cells, Replicate 1

city: Suzhou

first: wenjun

last: zhao

state: Jiangsu

address: 199 Ren'ai Road

institute: Cyrus Tang Hematology Center

hyb_protocol: Phalanx Hybridization Protocol. http://www.phalanxbiotech.com/products/MOA.php

scan_protocol: Scanner Settings Using GenePix 4000B from Molecular Devices. Wavelength 635 nm 532 nm PMT: 630 V, 590 V. Minimum diameter(%): 80. Maximum diameter (%) :150 . CPI Threshold 100

data_processing: Data extraction using GenePix 4000B [90708] from Molecular Devices. GPR files were loaded into Rosetta Resolver® System (Rosetta Biosoftware) to process data analysis. The error due to random factors and systematic biases are estimated by an error model. the repeated probes within one chip are averaged.

source_name: AraC-sensitive Acute leukemia cell

label_protocol: 10 ug of quality RNA is needed for each labeling reaction. Target preparation was performed using an Eberwine-based amplification method with Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, AM1753) to generate amino-allyl antisense RNA(aa-aRNA). Labeled aRNA coupled with NHS-CyDye was prepared and purified prior to hybridization. Purified coupled aRNA was quantified using NanoDrop ND-1000; pass criteria for CyDye incorporation efficiency at > 10 dye molecular/1000nt.

growth_protocol: Myeloid leukemic cells were plated in high-glucose glutamine-containing Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 10% NCTC 109 medium, 10-5 M β-mercaptoethanol, 100 U of insulin, per ml, 1 mM sodium pyruvate, 1 mM oxalacetic acid, 0.1 mM nonessential amino acids, 10 mM N-2-hydroxyethylpiperazine-N9-2-ethanesulfonic acid (HEPES) buffer, and penicillin-streptomycin. Tumor cells were plated at 2.5×10^5 to 5×10^5 cells per ml and fed biweekly.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. RNA quantity and purity was assessed using NanoDrop ND-1000. Pass criteria for absorbance ratios are established at A260/A280 ≥ 1.8 and A260/A230 ≥ 1.5 indicating acceptable RNA purity. RIN values are ascertained using Agilent RNA 6000 Nano assay to determine RNA integrity.

treatment_protocol: a highly Ara-C resistant cell line, designated as B117HS, was derived from B117P by consecutive exposure to increasing concentrations of Ara-C. It took about 10 weeks to produce B117HS,the IC50 of B117HS to Ara-C was about ten times higher than that of B117P

value: bone marrow

tag: cell line

tag: cell type

value: Acute leukemia cell


title: diaphragm_PHIL_naive_rep2

description: replicate 2


title: Rosette leaves treated with PIPL3 peptide for 3 hours compared to rosette leaves treated with mock peptide (replica 2)


title: Cmah-null_cochlear 3

description: replicate 3


title: diaphragm_RAG_2dpi_rep3

description: replicate 3

source_name: whole mouse diaprhagm, RAG, 2 days post-infection, Trichinella spiralis

value: RAG


title: ara-c sensitive murine leukemia cells, Replicate 2


title: AraC resistant leukemia cells

description: R

source_name: AraC-resistant Acute leukemia cell

value: AraC-resistant Acute leukemia cell derived from B117P


title: diaphragm_RAG_7dpi_rep1

description: replicate 1

source_name: whole mouse diaprhagm, RAG, 7 days post-infection, Trichinella spiralis


title: diaphragm_PHIL_2dpi_rep1

description: replicate 1

source_name: whole mouse diaprhagm, PHIL, 2 days post-infection, Trichinella spiralis


title: thioacetamide treatment effect on wild-type mouse liver

city: Suita

first: Tomonori

last: Matsumoto

state: Osaka

address: 3-1 Yamadaoka

institute: Osaka University

hyb_protocol: 1.65microgram of cRNA was fragmented and hybridized to Agilent whole mouse genome oligo microarray

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

source_name: wild-type mouse

label_protocol: Sample labeling was done using Agilent’s Quick Amp Labeling Kit (5190-0442: Agilent) following manufacture’s instructions. Amplified cRNAs were quantified using the Agilent 2100 bioanalyzer and RNA 6000 Nano kit.

extract_protocol: Total RNA was extracted from mice liver tissues using RNeasy Mini Kit  (Qiagen, Valencia, CA).

value: wild-type

value: with thioacetamide

value: liver

tag: background strain


title: diaphragm_RAG_7dpi_rep2

description: replicate 2


title: thioacetamide treatment effect on AID transgenic mouse liver

source_name: AID transgenic mouse

value: AID transgenic


title: diaphragm_PHIL_2dpi_rep2

description: replicate 2

value: 2 days post-infection, Trichinella spiralis


title: Rosette leaves treated with PIPL3 peptide for 3 hours compared to rosette leaves treated with mock peptide (replica 1)


title: diaphragm_RAG_2dpi_rep2

description: replicate 2


title: diaphragm_RAG_7dpi_rep3

description: replicate 3


title: diaphragm_PHIL_2dpi_rep3

description: replicate 3


title: diaphragm_RAG_2dpi_rep1

description: replicate 1


title: MCF10A_MYC-ERVD_4-OHT_rep3

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

description: Biological replicate 3 of 3. MYC-ER V394D infected MCF10A cells, treated for 24h with 4-OHT.

hyb_protocol: Hybridization was performed as described in Agilent Two-Color Microarray-Based Gene Expression Analysis Protocol (Agilent publication number: G4140-90050)

scan_protocol: Slides were scanned using an Agilent DNA Microarray Scanner G2505C with scan software Agilent Scan Control Version A.8.1.3

data_processing: Agilent Feature Extraction Software Version 10.5.1.1 (FE Protocol GE2_105_Dec08). Data were background substracted and LOWESS normalized using R (2.15)/Bioconductor/Limma

source_name: MCF10A_MYC-ER V394D cells

label_protocol: Labeling was performed as described in Agilent Two-Color Microarray-Based Gene Expression Analysis Protocol (Quick Amp Labelling; Agilent publication number: G4140-90050)

growth_protocol: MCF10A cells were maintained in DMEM/F-12, supplemented with 5% horse serum, 100ug/ml EGF, 0.5ug/ml hydrocortisone, 10ug/ml insulin, 100ng/ml cholera toxin and 1% penicillin/streptomycin.

extract_protocol: Total RNA was extracted using Rneasy Kit (QIAGEN) with on-column DNAse digest according to the manufacturer's protocols.

treatment_protocol: MCF10A MYC-ER and MYC-ERVD cells were treated with 100nM 4-OHT or ethanol as a solvent control for 24h.

value: mammary gland / breast

source_name: mixed reference_pooled equal aliquot of every ch1 sample


title: MCF10A_MYC-ERVD_4-OHT_rep2

description: Biological replicate 2 of 3. MYC-ER V394D infected MCF10A cells, treated for 24h with 4-OHT.


title: diaphragm_WT_7dpi_rep3

description: replicate 3

source_name: whole mouse diaprhagm, WT, 7 days post-infection, Trichinella spiralis

value: WT


title: diaphragm_RAG_naive_rep1

description: replicate 1

source_name: whole mouse diaphragm, RAG, naïve

value: Whole diaphragm muscle


title: diaphragm_WT_7dpi_rep1

description: replicate 1


title: MCF10A_MYC-ERVD_4-OHT_rep1

description: Biological replicate 1 of 3. MYC-ER V394D infected MCF10A cells, treated for 24h with 4-OHT.


title: MCF10A_MYC-ERVD_control_rep2

description: Biological replicate 2 of 3. MYC-ER V394D infected MCF10A cells, treated for 24h with EtOH.


title: MCF10A_MYC-ERVD_control_rep1

description: Biological replicate 1 of 3. MYC-ER V394D infected MCF10A cells, treated for 24h with EtOH.


title: diaphragm_WT_2dpi_rep3

description: replicate 3

source_name: whole mouse diaprhagm, WT, 2 days post-infection, Trichinella spiralis


title: MCF10A_MYC-ER_4-OHT_rep1

description: Biological replicate 1 of 3. MYC-ER infected MCF10A cells, treated for 24h with 4-OHT.

source_name: MCF10A_MYC-ER cells


title: MCF10A_MYC-ER_4-OHT_rep2

description: Biological replicate 2 of 3. MYC-ER infected MCF10A cells, treated for 24h with 4-OHT.


title: diaphragm_RAG_naive_rep2

description: replicate 2


title: diaphragm_WT_2dpi_rep1

description: replicate 1


title: MCF10A_MYC-ER_4-OHT_rep3

description: Biological replicate 3 of 3. MYC-ER infected MCF10A cells, treated for 24h with 4-OHT.


title: diaphragm_WT_7dpi_rep2

description: replicate 2


title: diaphragm_WT_naive_rep2

description: replicate 2

source_name: whole mouse diaphragm, WT, naïve


title: MCF10A_MYC-ERVD_control_rep3

description: Biological replicate 3 of 3. MYC-ER V394D infected MCF10A cells, treated for 24h with EtOH.


title: MCF10A_MYC-ER_control_rep3

description: Biological replicate 3 of 3. MYC-ER infected MCF10A cells, treated for 24h with EtOH.


title: MCF10A_MYC-ER_control_rep2

description: Biological replicate 2 of 3. MYC-ER infected MCF10A cells, treated for 24h with EtOH.


title: diaphragm_WT_naive_rep1

description: replicate 1


title: diaphragm_WT_2dpi_rep2

description: replicate 2


title: Necromass 2

status: Public on Jul 09 2015

city: Bogota

first: Carlos

middle: Alexander

last: Ruiz Perez

state: CUNDINAMARCA

country: Colombia

institute: Corporacion CorpoGen

hyb_protocol: Samples were hybridized according to the protocol described previously (He et al 2010, Yan et al 2015) (Glomics (Norman, OK; USA).

scan_protocol: Samples were scanned according to the protocol described previously (He et al 2010, Yan et al 2015) (Glomics (Norman, OK; USA).

data_processing: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form;

organism: plant metagenome

source_name: Espeletia necromass

label_protocol: Samples were labelled according to the protocol described previously (He et al 2010, Yan et al 2015) (Glomics (Norman, OK; USA).

extract_protocol: Endophyte DNA was isolated following previously reported methodologies (Araujo et al 2002, Conn and Franco 2004, Miles et al 2012). Briefly, the plant tissue was surface-sterilized by washing with sterile H2O to remove dirt, placed in NAP buffer (124mM Na2HPO4.H2O) and vortexed for 1min to dislodge epiphytes. Leaves were then shaved to remove the pubescence on their surface, which facilitates the subsequent sterilization process (Miles et al 2012), washed with sterile H2O, submerged in 90% ethanol (60s), 5.25% sodium hypochlorite solution (6min), and 70% ethanol (30s), and finally rinsed with sterile distilled water. Sterilization was checked by taking an imprint of the leaf on Malt Extract Medium (Miles et al 2012) and incubating at 25ºC. 1g of the previously treated material was cut into 0.1-0.5mm sections, placed in a 1.5mL Eppendorf tube containing 1g of sterile 0.1mm-diameter glass beads and 1mL TE (10mM Tris, 10mM EDTA, pH 8.0) and homogenized in a mini-bead beater (BioSpec Products) for 5min. DNA was extracted using the PowerSoil DNA Isolation Kit (MOBIO Laboratories, Carlsbad, CA; USA), following the manufacturer’s instructions.   We obtained epiphyte DNA by first releasing bacteria from the surface of leaves by submerging 10-20g of healthy plant tissue in 100mL of Release buffer (0.1M Potassium Phosphate, 0.1% Glycerol, 0.15% Tween 80, pH 7.0), and vortexing for 7 minutes (Bodenhausen et al 2013, Izhaki et al 2013, Zhang et al 2010). The remaining bacteria were dislodged from the leaves with the help of a sterile swab and the buffer was then filtered through a 0.2µm-pore filter. DNA was extracted using the PowerSoil DNA Isolation Kit.  Combined epiphyte and endophyte DNA was extracted from root and necromass samples by cutting the tissue into 0.5-1cm fragments that were placed in 25mL of Release buffer in a 50mL tube and homogenized by vortexing for 10 minutes. The buffer was filtered through a 0.2µm-pore filter and the filters were used for DNA extraction using the PowerSoil DNA Isolation. All DNA extractions were quantified using Qubit® 2.0 Fluorometer (Life Technologies Corporation, Carlsbad, CA; USA). In total, we obtained six epiphyte and six endophyte DNA extractions, corresponding to the upper and mid tiers from three plant replicates, three DNA extractions for the necromass tier, one for each replicate, and two for the roots.

tag: host

value: Espeletia hartwegiana

tag: source

value: Necromass

tag: community

value: Total


title: MCF10A_MYC-ER_control_rep1

description: Biological replicate 1 of 3. MYC-ER infected MCF10A cells, treated for 24h with EtOH.

tag: tissue


title: Necromass 3


title: Necromass 1


title: Root 2

source_name: Espeletia roots

value: Roots


title: Young leaves - Endophyte 2

source_name: Espeletia leaves (Young)

value: Leaves

value: Endophyte


title: Young leaves - Endophyte 3


title: Young leaves - Epiphyte 2

value: Epiphyte


title: Root 1


title: Young leaves - Epiphyte 1


title: Young leaves - Epiphyte 3


title: Mature leaves - Epiphyte 3

source_name: Espeletia leaves (Mature)


title: CBD_LPS.2

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: CBD + LPS replicate 2

source_name: CBD + LPS replicate 2

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

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

value: BV-2 microglial cell line

tag: condition


title: Young leaves - Endophyte 1


title: Mature leaves - Epiphyte 2


title: LPS.5

description: LPS replicate 5

source_name: LPS replicate 5

value: LPS


title: Mature leaves - Endophyte 2


title: THC.4

description: THC replicate 4

source_name: THC replicate 4

value: THC


title: Cntr.4

description: Control replicate 4

source_name: Control replicate 4

value: Cntr


title: Mature leaves - Endophyte 1


title: LPS.6

description: LPS replicate 6

source_name: LPS replicate 6


title: Mature leaves - Endophyte 3


title: THC.3

description: THC replicate 3

source_name: THC replicate 3


title: Cntr.5

description: Control replicate 5

source_name: Control replicate 5


title: LPS.4

description: LPS replicate 4

source_name: LPS replicate 4


title: Cntr.6

description: Control replicate 6

source_name: Control replicate 6


title: CBD.1

description: CBD replicate 1

source_name: CBD replicate 1

value: CBD


title: THC_LPS.3

description: THC + LPS replicate 3

source_name: THC + LPS replicate 3


title: Cntr.3

description: Control replicate 3

source_name: Control replicate 3


title: CBD.2

description: CBD replicate 2

source_name: CBD replicate 2


title: CBD_LPS.1

description: CBD + LPS replicate 1

source_name: CBD + LPS replicate 1


title: THC_LPS.4

description: THC + LPS replicate 4

source_name: THC + LPS replicate 4


title: THC_LPS.2

description: THC + LPS replicate 2

source_name: THC + LPS replicate 2


title: THC_LPS.1

description: THC + LPS replicate 1

source_name: THC + LPS replicate 1


title: LPS.2

description: LPS replicate 2

source_name: LPS replicate 2


title: THC.1

description: THC replicate 1

source_name: THC replicate 1


title: LPS.3

description: LPS replicate 3

source_name: LPS replicate 3


title: LPS.1

description: LPS replicate 1

source_name: LPS replicate 1


title: Cntr.1

description: Control replicate 1

source_name: Control replicate 1


title: Cntr.2

description: Control replicate 2

source_name: Control replicate 2


title: THC.2

description: THC replicate 2

source_name: THC replicate 2