title: discovery set 75

description:
D15.1239.19.M
Gene expression data from embryonic stem cells without Hdh


title: Wild-type Repl2

status: Public on May 03 2013

type: RNA

city: Parkville

first: Moshe

last: Olshansky

state: Victoria

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter & Eliza Hall Institute of Medical Research

description: SAMPLE 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was background corrected, quantile normalised and log2 transformed (with shift = 16) using neqc function from limma package (v.3.14.4) in R /Bioconductor (v.2.15.2).

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Wild-type DbNP366-specific CD8+ T cells

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

extract_protocol: RNA was extracted using a Qiagen RNeasy Mini Kit followed by DNase treatment. Quality control was performed with Agilent Bioanalyser.

tag: strain background

value: B6.SJL-Ptprca Pepcb/BoyJ

tag: genotype/variation

value: Wild-type

tag: tissue

value: Spleen

tag: cell type

value: Db-NP366 specific CD8+ T cells


title: Id2-GFPhigh Repl3

description: SAMPLE 6

source_name: Purified Id2-GFPhigh DbNP366-specific CD8+ T cells

extract_protocol: RNA was extracted using a Qiagen RNeasy Mini Kit followed by DNase treatment . Quality control was performed with Agilent Bioanalyser.

tag: levels of gfp

value: high


title: MM901 formate-excess(380 mM sodium formate) P-excess(0.8 mM K2HPO4) N-excess(NH4Cl) rep2

city: Seoul

first: Sung Ho

last: Yoon

address: 120 Neungdong-ro, Gwangjin-gu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Konkuk University

description: Technical replicate 2 of 2

hyb_protocol: 7.5 µg of labeled sample RNA and 7.5 µg of labeled reference RNA were fragmented in total 250 µl mixture (50 µl of 10X blocking agent, 10 µl of 25X fragmentation buffer, H2O) at 60°C for 30 min, then put it on ice for 1 min. 250 µl of fragmentation mix and 250 µl of GE hybridization buffer HI-RPM were mixed and spinned for 1 min at RT at 13,000 rpm, and put on ice. 490 µl of the hybridization mix was applied to the slide in chamber, and put in a hybridization oven at 65°C for 17 hrs. After hybridization, the slide was washed sequentially in GE wash buffer 1 (twice) and 2.

scan_protocol: The arrays were scanned by Microarray Scanner (Agilent Technologies, Santa Clara, CA).

data_processing: Signal intensities and local backgrounds were determined by Feature Extraction software (Agilent Technologies). Cy3 and Cy5 intensities were normalized by scaling so that the 75th percentile in the Cy3 and Cy5 channels were equal.

organism: Methanococcus maripaludis S2

source_name: ss HighFormate noH2 HighP HighN

label_protocol: 1.5 µg of total RNA were directly labeled with 1.5 µl of Kreatech  dye (Cy3 or Cy5) at 95°C for 5 min, then put it on ice. The solutions were purified by KREApure column.

extract_protocol: Total RNAs were extracted using mirVana miRNA isolation kit (Applied Biosystems, Austin, TX) following manufacturer’s instructions.

tag: strain

tag: treatment

source_name: bulk from a mid-log phase culture(OD660=0.804)


title: discovery set 66

city: Boston

first: Jong-Min

last: Lee

state: MA

department: CHGR

country: USA

institute: MGH

description:
D06.21092.66.M
Gene expression data from embryonic stem cells without Hdh

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: gcRMA

label: biotin

organism: Homo sapiens

source_name: Human lymphoblastoid cell line

label_protocol: Affymetrix protocol

growth_protocol: Standard growth condition for human lymphoblastoid cell lines

extract_protocol: Trizol extraction and Qiagen Rneasy mini coulmn clean up

tag: gender

value: male

tag: htt cag repeat length (longer allele)

tag: batch

value: D


title: discovery set 72

description:
D12.1242.34.F
Gene expression data from embryonic stem cells without Hdh

value: female


title: Id2-GFPhigh Repl1

description: SAMPLE 4


title: discovery set 78

description:
D18.1089.58.M
Gene expression data from embryonic stem cells without Hdh


title: Id2-GFPint Repl1

description: SAMPLE 1

source_name: Purified Id2-GFPintermediate DbNP366-specific CD8+ T cells

value: intermediate (int)


title: discovery set 73

description:
D13.19330.60.F
Gene expression data from embryonic stem cells without Hdh


title: discovery set 65

description:
D05.1210.18.F
Gene expression data from embryonic stem cells without Hdh


title: discovery set 74

description:
D14.19323.69.M
Gene expression data from embryonic stem cells without Hdh


title: Id2-GFPint Repl2

description: SAMPLE 2


title: Id2-GFPint Repl3

description: SAMPLE 3


title: discovery set 71

description:
D11.19321.41.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 70

description:
D10.19165.57.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 67

description:
D07.21243.36.F
Gene expression data from embryonic stem cells without Hdh


title: discovery set 69

description:
D09.21613.56.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 63

description:
D02.1188.46.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 68

description:
D08.21526.34.M
Gene expression data from embryonic stem cells without Hdh


title: MM901 formate-excess(380 mM sodium formate) N-limiting(2 mM NH4Cl) rep2

description: Technical replicate 2 of 2

source_name: ss HighFormate noH2 LowN


title: MM901 formate-excess(380 mM sodium formate) P-excess(0.8 mM K2HPO4) N-excess(NH4Cl) rep1

description: Technical replicate 1 of 2


title: discovery set 62

description:
D01.1120.24.F
Gene expression data from embryonic stem cells without Hdh


title: discovery set 64

description:
D03.1154.48.M
Gene expression data from embryonic stem cells without Hdh


title: MM901 formate-excess(380 mM sodium formate) N-limiting(2 mM NH4Cl) rep1

description: Technical replicate 1 of 2


title: human PCa osteolytic bone metastasis 08-020HH1

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

hyb_protocol: Hybridizations to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2505B (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software was used to grid, extract, and normalize data.

label_protocol: amplified amino-allyl cDNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl cDNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

extract_protocol: Total RNA was purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by one round of mRNA amplification with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: osteolytic bone metastasis from PCa patient


title: discovery set 55

description:
C17.25496.48.M
Gene expression data from embryonic stem cells without Hdh

value: C


title: Wild-type Repl1

description: SAMPLE 1


title: MM901 formate-excess(380 mM sodium formate) P-limiting(0.08 mM K2HPO4) rep1

description: Technical replicate 1 of 2

source_name: ss HighFormate noH2 LowP


title: discovery set 58

description:
C20.15503.19.F
Gene expression data from embryonic stem cells without Hdh


title: human PCa osteolytic bone metastasis 05-214BB2


title: human PCa osteolytic bone metastasis 07-050EE1


title: MM901 formate-excess(380 mM sodium formate) P-limiting(0.08 mM K2HPO4) rep2

description: Technical replicate 2 of 2


title: discovery set 61

description:
C23.10442.18.F
Gene expression data from embryonic stem cells without Hdh


title: MM901 formate-limiting(200 mM sodium formate) rep2

description: Technical replicate 2 of 2

source_name: ss LowFormate noH2

value: formate-limiting(200 mM sodium formate)


title: discovery set 59

description:
C21.11239.54.M
Gene expression data from embryonic stem cells without Hdh


title: human PCa osteolytic bone metastasis 06-047QQ1


title: discovery set 56

description:
C18.25360.20.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 60

description:
C22.21453.46.F
Gene expression data from embryonic stem cells without Hdh


title: Control3 vs. Treatment3 at 72hr [mRNA]

first: Ji-Hoon

last: Cho

address: 401 Terry Avenue North

institute: Institute for Systems Biology

description: Control3 vs. Treatment3 at 72hr

hyb_protocol: Labeled samples were hybridized to Agilent Whole Mouse Genome Microarray as described in the manufacturer's protocol.

scan_protocol: After hybridization, the slides were washed and scanned with a scanner from Agilent (Santa Clara, CA).

data_processing: Scanned data was processed using Agilent Feature Extraction

source_name: Control mouse 3

label_protocol: Total RNAs from liver were isolated with a miRNeasy column (Qiagen, Valencia, CA), and both Cy3 and Cy5-labeled samples were prepared with two color labeling kits (Agilent Technologies, Santa Clara, CA), then hybridized at 65°C for 17 h.

extract_protocol: Liver samples were collected from different time points after mice had been exposed to acetaminophen.  Total RNA from liver was extracted with the miRNeasy kit (Qiagen, Germantown, MD), as described.  The quality and quantity of the RNA were evaluated with Agilent 2100 Bioanalyzer (Santa Clara, CA) and NanoDrop 1000 spectrophotometer

treatment_protocol: To study the global changes of transcriptome in the liver after acetaminophen overdose.  Eight week old female C57BL/6 mice were fasted for 24 hours prior to a single intraperitoneal injection of 350mg/kg of acetaminophen in phosphate buffer saline (PBS) (treatment group) or PBS (control group). The mice were euthanized at different time points post exposure; plasma and tissue samples were collected for pathological examination and biochemical analyses.

tag: group

value: Control

tag: agent

tag: time point

source_name: Treatment mouse 3

value: Treatment

value: 350mg/kg of acetaminophen


title: discovery set 57

description:
C19.11299.24.F
Gene expression data from embryonic stem cells without Hdh


title: Control3 vs. Treatment3 at 8hr [mRNA]

description: Control3 vs. Treatment3 at 8hr


title: Control3 vs. Treatment3 at 3hr [mRNA]

description: Control3 vs. Treatment3 at 3hr


title: human PCa osteolytic bone metastasis 01-087QQ1


title: human PCa osteolytic bone metastasis 05-144EE1


title: human PCa osteolytic bone metastasis 05-144HH1


title: D55 sample1 rep1

city: San Francisco

first: Cory

middle: R

last: Nicholas

state: CA

address: 35 Medical center way

department: Neurology

institute: UCSF

hyb_protocol: Performed by Southern California Genotyping Consortium

data_processing: Generated using Illumina Genome Studio Gene Expression Module Software

source_name: Differentiated

growth_protocol: hESCs were differentiated along a 55-day time course using the B27+5factor method in Neurobasal media supplemented with B27-vitaminA and including: BMPRIA-Fc, SB431542, DKK1, Y27632, and Purmorphamine

extract_protocol: RNAeasy Kit

treatment_protocol: NKX2.1-GFP+ cells were isolated by FACS sorting purification

value: hESC-derived MGE


title: human PCa osteoblastic bone metastasis 07-050XX1

value: osteoblastic bone metastasis from PCa patient


title: Control3 vs. Treatment3 at 24hr [mRNA]

description: Control3 vs. Treatment3 at 24hr


title: Control1 vs. Treatment3 at 48hr [mRNA]

description: Control1 vs. Treatment3 at 48hr

source_name: Control mouse 1


title: D35 sample1 rep1

scan_protocol: Performed by Southern California Genotyping Consortium


title: human PCa osteoblastic bone metastasis 07-042EE1


title: discovery set 52

description:
C14.4128.81.M
Gene expression data from embryonic stem cells without Hdh


title: human PCa osteoblastic bone metastasis 07-044KK5


title: discovery set 53

description:
C15.9810.21.F
Gene expression data from embryonic stem cells without Hdh


title: D35 sample1 rep2

label_protocol: Performed by Southern California Genotyping Consortium


title: human PCa osteoblastic bone metastasis 02-142II


title: MM901 formate-limiting(200 mM sodium formate) rep1

description: Technical replicate 1 of 2


title: discovery set 51

description:
C13.6469.64.F
Gene expression data from embryonic stem cells without Hdh


title: Control2 vs. Treatment1 at 48hr [mRNA]

description: Control2 vs. Treatment1 at 48hr

source_name: Control mouse 2

source_name: Treatment mouse 1


title: D20 sample1 rep1


title: discovery set 54

description:
C16.5560.17.F
Gene expression data from embryonic stem cells without Hdh


title: human PCa osteoblastic bone metastasis 01-087MM


title: Control2 vs. Treatment1 at 3hr [mRNA]

description: Control2 vs. Treatment1 at 3hr


title: human PCa osteoblastic bone metastasis 01-181AA


title: discovery set 50

description:
C12.23547.26.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 49

description:
C11.1820.43.F
Gene expression data from embryonic stem cells without Hdh


title: Control2 vs. Treatment2 at 8hr [mRNA]

description: Control2 vs. Treatment2 at 8hr

source_name: Treatment mouse 2


title: discovery set 48

description:
C10.131.73.F
Gene expression data from embryonic stem cells without Hdh


title: D0 sample1 rep4

source_name: Undifferentiated


title: D0 sample1 rep2


title: Control3 vs. Treatment3 at 72hr [miRNA]

description: Control3 vs. Treatment3 at 72hr

hyb_protocol: Labeled samples were hybridized to Exiqon 5th generation miRCURY LNA microRNA array according to the manufacturer's protocol.

data_processing: Scanned data was processed using AnalyzerDG software. Cy3 and Cy5 (high energy scanned) intensities were normalized using LOWESS

label_protocol: Total RNAs from liver were labeled with Hy3 and Hy5 dye with labeling kits from Exiqon then hybridized at 56°C for 16 h.


title: Control3 vs. Treatment3 at 8hr [miRNA]

description: Control3 vs. Treatment3 at 8hr


title: D20 sample3 rep1


title: D0 sample1 rep3


title: discovery set 46

description:
C08.170.75.M
Gene expression data from embryonic stem cells without Hdh


title: human PCa osteoblastic bone metastasis 00-140FF


title: D20 sample2 rep1


title: D0 sample1 rep1


title: Control2 vs. Treatment1 at 72hr [mRNA]

description: Control2 vs. Treatment1 at 72hr


title: discovery set 47

description:
C09.2773.22.M
Gene expression data from embryonic stem cells without Hdh


title: Control3 vs. Treatment3 at 3hr [miRNA]

description: Control3 vs. Treatment3 at 3hr


title: discovery set 44

description:
C06.11321.42.F
Gene expression data from embryonic stem cells without Hdh


title: Immature MDDC_SB203580 24h_ replicate 3

city: Madrid

first: Angel

middle: L

last: Corbí

state: Madrid

address: Ramiro de Maeztu 9

department: Molecular Microbiology and Infection Biology

country: Spain

institute: Consejo Superior de Investigaciones Científicas

description: SB 24h DC7

hyb_protocol: 1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven  (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays. Images provided by the scanner were analyzed using Feature Extraction software (Agilent Technologies).

data_processing: Data files from Feature Extraction were imported into GeneSpring® GX software version 9.0. (Agilent Technologies). Quantile normalization was performed and expression values (log2 transformed) were obtained for each probe

source_name: SB203580 treated immature MDDC 24h replicate 3

label_protocol: For each sample, we have generated cyanine 3-labeled cRNA from one microgram of total RNA, using the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color. Briefly, total RNA is reverse-transcribed using T7-oligo (dT) primer; after first and second strand cDNA synthesis, cRNA is synthesized from the double-stranded cDNA using T7 RNA polymerase, which simultaneously incorporates cyanine 3.

growth_protocol: Human peripheral blood monocytes were were cultured for 5 days in RPMI 10% FCS containing GM-CSF and IL-4 to generate immature monocyte-derived dendritic cells (MDDC). For MDDC maturation, LPS was added to the culture for 4, 10 or 24hours.

extract_protocol: Total RNA from each condition was extracted and purified using the All prep DNA/RNA/protein mini kit (Qiagen).Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.

treatment_protocol: Immature MDDC were exposed to MEK inhibitor, U0126, or p38MAPK inhibitor, SB203580 for 1 hour and a final dose of GM-CSF and IL-4, and LPS in the case of mature MDDC, were added to the culture. Cells were collected for analysis after 4, 10 or 24 hours.

tag: healthy donor

tag: time


title: Control2 vs. Treatment2 at 8hr [miRNA]

description: Control2 vs. Treatment2 at 8hr


title: Immature MDDC_U0126 24h_ replicate 1

description: UO 24h DC4

source_name: U0126 treated immature MDDC  24h replicate 1

value: immature monocyte-derived dendritic cells (MDDC)


title: Immature MDDC_U0126 24h_ replicate 2

description: UO 24h DC5

source_name: U0126 treated immature MDDC  24h replicate 2


title: Immature MDDC_SB203580 24h_ replicate 1

description: SB 24h DC4

source_name: SB203580 treated immature MDDC 24h replicate 1


title: Immature MDDC_SB203580 24h_ replicate 2

description: SB 24h DC5

source_name: SB203580 treated immature MDDC 24h replicate 2


title: discovery set 45

description:
C07.11359.56.M
Gene expression data from embryonic stem cells without Hdh

source_name: Human lymphoblastoid cell line


title: Control2 vs. Treatment1 at 24hr [mRNA]

description: Control2 vs. Treatment1 at 24hr


title: Control2 vs. Treatment1 at 48hr [miRNA]

description: Control2 vs. Treatment1 at 48hr


title: Control2 vs. Treatment1 at 72hr [miRNA]

description: Control2 vs. Treatment1 at 72hr


title: Control3 vs. Treatment3 at 24hr [miRNA]

description: Control3 vs. Treatment3 at 24hr


title: Control2 vs. Treatment1 at 3hr [miRNA]

description: Control2 vs. Treatment1 at 3hr


title: Immature MDDC_DMSO 24h_ replicate 3_duplicate

description: DMSO 24h DC7 bis

source_name: DMSO treated immature MDDC 24h replicate 3 duplicate

value: vehicle


title: Immature MDDC_DMSO 24h_ replicate 2_duplicate

description: DMSO 24h DC5 bis

source_name: DMSO treated immature MDDC 24h replicate 2 duplicate


title: Immature MDDC_DMSO 24h_ replicate 1_duplicate

description: DMSO 24h DC4 bis

source_name: DMSO treated immature MDDC 24h replicate 1 duplicate


title: discovery set 42

description:
C04.4220.42.F
Gene expression data from embryonic stem cells without Hdh


title: discovery set 43

description:
C05.10438.29.F
Gene expression data from embryonic stem cells without Hdh


title: discovery set 41

description:
C03.9473.31.F
Gene expression data from embryonic stem cells without Hdh


title: discovery set 40

description:
C02.15485.15.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 39

description:
C01.2723.33.F
Gene expression data from embryonic stem cells without Hdh


title: Control2 vs. Treatment1 at 24hr [miRNA]

description: Control2 vs. Treatment1 at 24hr


title: Immature MDDC_DMSO 24h_ replicate 3

description: DMSO 24h DC7

source_name: DMSO treated immature MDDC 24h replicate 2


title: Immature MDDC_DMSO 24h_ replicate 2

description: DMSO 24h DC5


title: discovery set 35

description:
B19.2745.47.F.Y25
Gene expression data from embryonic stem cells without Hdh

value: B


title: Immature MDDC_SB203580 10h_ replicate 2

description: SB 10h DC5

source_name: SB203580 treated immature MDDC 10h replicate 2


title: Immature MDDC_DMSO 24h_ replicate 1

description: DMSO 24h DC4

source_name: DMSO treated immature MDDC 24h replicate 1


title: Immature MDDC_SB203580 10h_ replicate 1

description: SB 10h DC4

source_name: SB203580 treated immature MDDC 10h replicate 1


title: Intercaruncular_Non-pregnant_NA_9813

type: genomic

city: Auckland

first: Caroline

middle: Gwendolyn

last: Walker

state: Outside the US or Canada

address: 3A symonds st

department: University of Auckland

country: New Zealand

institute: DairyNZ Ltd

hyb_protocol: All of the labeled IP DNA (~ 3-4 µg) and 4 µg of labeled Input DNA were hybridized onto the 400K custom designed Agilent microarray (2 x 400K array format, AMADID and Part no. are 027994 and G4820A respectively.) for 40 hours at 65°C.  Microarray was washed using aCGH wash buffer 1 and 2 for five minutes and 1 minute respectively.

scan_protocol: Hybridized arrays were scanned at 2μm resolution on an Agilent Technologies Scanner G2505C. Data extraction from Images was done using Feature Extraction software v 10.5.1.1 of Agilent.

data_processing: Normalization of the data was done using the centralization method (Centralization adds or subtracts a constant value from each log ratio measurement. This recenters the log ratio values, and makes sure that the zero- point reflects the most common ploidy state). Methylation states were obtained using the BATMAN Algorithm. BATMAN is a visualization and report analysis that determines the absolute methylation level for CpG dinucleotides contained within DNA fragments queried by probes across the microarray. The algorithm begins with a calibration step, which uses a regression to fit a trend between local CpG density and either probe logratios, or Z- scores (Methylation Status Detection Algorithm). This was followed by a modeling step, which used the calibration results to construct the conditional probability of the log- ratios (or Z- scores) given the methylation state. A sampling step occurs to generate a large number of possible methylation states. Bayesian methodology is used to invert the conditional probability and summarize the methylation state per probe. Finally, a methylation call step fits a distribution to the scores on a per- chromosome basis.  Methylation Status Detection Algorithm  The methylation status detection algorithm is designed for two-color assays, where the green (Cy3) channel is comprised of input DNA, and the red (Cy5) channel is comprised of the affinity-enriched DNA. As a result of constraints imposed on the array design, the probes that target genomic regions with varying CG content do not share a uniform melting temperature (Tm), which can result in compression of the log-ratios. The methylation detection algorithm allows normalizing the log- ratios for each probe, based on its Tm, and returns the methylation status of a probe. The algorithm first bins the probes by their melting temperature. For each bin, it applies Gaussian fits using one of three models. It fits the probe log- ratios to Gaussians, using a local searching algorithm called random hill climbing. Z-Scores and p-values derived from the Gaussian data give probabilities and confidence values for methylated and unmethylated probe populations. The algorithm then calculates a methylation logOdds, which gives the relative probability that a probe is more likely, methylated than unmethylated.

molecule: genomic DNA

organism: Bos taurus

label_protocol: Input DNA was labeled with Cy3 and IP DNA with Cy5 using Agilent's Genomic DNA labeling kit (Cat. no. 5190-0453). Labeled samples were cleaned and concentrated using Microcon YM-30 columns( Millipore Cat. no. 42410)

extract_protocol: DNA was extracted from endometrial tissue using a Qiagen DNAeasy blood and tissue kit (QIAGEN catalogue# 69506). DNA quantity was determined by spectrophotometry using a Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE). Genomic DNA integrity was assessed by running it on a 0.8% Agarose Gel. Genomic DNA purity was assessed by the NanoDrop® ND-1000 UV-Vis Spectrophotometer (Nanodrop technologies, Rockland, USA). Genomic DNA with OD260/OD280>1.8 and OD260/OD230 ≥ 1.3 was used for microarray experiments. We considered DNA to be good quality when a single clear band was seen when run against a reference genomic DNA sample.

treatment_protocol: All Animals had estrous cycles syncronised with 12 animals receiving grade 1 embryo transfers at day 7 of the reproductive cycle, animals were then slaughtered at day 17 of the reproductive cycle and endometrial tissue samples obtained.

value: Intercaruncular

tag: phenotype

value: sub-fertile

tag: breed

value: Holstein-Friesian

tag: pregnancy status

value: Non-pregnant

tag: fraction

value: Input DNA

value: Affinity enriched DNA


title: discovery set 37

description:
B21.1749.49.M.O43
Gene expression data from embryonic stem cells without Hdh

value: male


title: discovery set 38

description:
B22.3382.41.F.O64
Gene expression data from embryonic stem cells without Hdh

value: female


title: Sinus tissue_infected_visible severe clinical symptoms_rep1

city: Bloemfontein

first: Charlotte

last: Boucher

state: Free State

address: Nelson Mandela Drive

department: Microbial, Biochemical and Food Biotechnology

country: South Africa

institute: University of the Free State

description: Infected with A.paragallinarum until severe symtomps were visible

hyb_protocol: Cyanine-3-CTP, 1.65ug per sample was fragmentd and prepared for One-Color based hybridization using the Gene Expression Hybridization Kit, Agilent Technologies. cRNA samples were hybridized at 65˚C for 17 hrs on separate Agilent Chicken V2 4x44K Gene Expression Microarrays. The microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies) and the design file 026441_D_F_20130125.xml.

data_processing: The software tools Feature Extraction 10.7.3.1, GeneSpring GX 12.5 (both Agilent Technologies) and Spotfire Decision Site 9.1.2 (TIBCO) were used for quality control, statistical analysis, Gene Ontology annotation and visualization. The Gene Expression Data Analysis tool of the PANTHER database, release 8.0 was applied for enrichment analysis.

organism: Gallus gallus

source_name: Sinus tissue, infected bird, visible severe clinical symptoms

label_protocol: 100 ng total RNA per sample was introduced into an RT-IVT reaction. Prior to RT-IVT, the total RNA samples were spiked with in-vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In-Mix, Agilent Technologies), which served as the internal labeling control for linearity, sensitivity and accuracy. The spiked total RNA was reverse transcribed into cDNA and then converted into labeled RNA by in-vitro transcription incorporating Cyanine-3-CTP, this was done using the Low Input Quick-Amp labeling Kit One-Color, Agilent Technologies.

extract_protocol: Total RNA was isolated using Rneasy Fibrous Tissue Mini Kit (Qiagen) follwong manufacturer's instructions, without modifications. The principle of this kit is a silica membrane-based purification of total RNA. The RNA was treated to an on-column DNAse digestion (Qiagen), following manufacturer's protocol. The final volume of the eluate was 40ul

treatment_protocol: Tissue exiced from sinus area of infected and non-infected birds at age 21 weeks. Tissue was submerged in RNALater (SIGMA), stored at -80˚C, until processed.

tag: tissue

value: Sinus tissue

tag: age

value: 21 weeks

value: male /cocks


title: Sinus tissue_infected_visible severe clinical symptoms_rep2


title: discovery set 34

description:
B18.1524.53.M.Y16
Gene expression data from embryonic stem cells without Hdh


title: Sinus tissue_infected_visible moderate clinical symptoms_rep2

description: Infected with A.paragallinarum until moderate symptoms were visible

source_name: Sinus tissue, infected bird, visible moderate clinical symptoms


title: Intercaruncular_Non-pregnant_NA_2970


title: Sinus tissue_infected_visible moderate clinical symptoms_rep1


title: discovery set 36

description:
B20.20708.45.F.O50
Gene expression data from embryonic stem cells without Hdh


title: Immature MDDC_SB203580 10h_ replicate 3

description: SB 10h DC7

source_name: SB203580 treated immature MDDC 10h replicate 3

tag: cell type


title: Immature MDDC_U0126 10h_ replicate 3

description: UO 10h DC7

source_name: U0126 treated immature MDDC 10h replicate 3


title: Sinus tissue_infected_visible mild clinical symptoms_rep2

description: Infected with A.paragallinarum until mild symptoms were visible

source_name: Sinus tissue, infected bird, visible mild clinical symptoms


title: Intercaruncular_Non-pregnant_NA_9778

tag: strain


title: Intercaruncular_Non-pregnant_NA_3811


title: discovery set 33

description:
B17.3181.61.F.Y24
Gene expression data from embryonic stem cells without Hdh


title: Immature MDDC_U0126 10h_ replicate 2

description: UO 10h DC5

source_name: U0126 treated immature MDDC 10h replicate 2


title: discovery set 32

description:
B14.1632.48.M.Y31
Gene expression data from embryonic stem cells without Hdh


title: Control1 vs. Treatment3 at 48hr [miRNA]

description: Control1 vs. Treatment3 at 48hr

source_name: Control mouse 1

value: Control

source_name: Treatment mouse 3

value: Treatment

value: 350mg/kg of acetaminophen


title: Intercaruncular_Non-pregnant_NZ_9960

value: NZ

value: fertile


title: Immature MDDC_U0126 10h_ replicate 1

description: UO 10h DC4

source_name: U0126 treated immature MDDC 10h replicate 1

value: immature monocyte-derived dendritic cells (MDDC)


title: Sinus tissue_infected_visible mild clinical symptoms_rep1


title: discovery set 30

description:
B12.17300.51.F.Y25
Gene expression data from embryonic stem cells without Hdh

source_name: Human lymphoblastoid cell line

value: B


title: Intercaruncular_Non-pregnant_NA_9786

value: Intercaruncular

value: sub-fertile


title: discovery set 31

description:
B13.19728.42.F.O57
Gene expression data from embryonic stem cells without Hdh


title: Immature MDDC_DMSO 10h_ replicate 2_duplicate

description: DMSO 10h DC5 bis

source_name: DMSO treated immature MDDC 10h replicate 2 duplicate

value: vehicle


title: Sinus tissue_control_rep2

description: Control: uninfected

source_name: Sinus tissue, healthy bird


title: Sinus tissue_control_rep1

description: Control: uninfected


title: Immature MDDC_DMSO 10h_ replicate 3_duplicate

description: DMSO 10h DC7 bis

source_name: DMSO treated immature MDDC 10h replicate 3 duplicate


title: Immature MDDC_DMSO 10h_ replicate 1_duplicate

description: DMSO 10h DC4 bis

source_name: DMSO treated immature MDDC 10h replicate 1 duplicate


title: I-Thy 130

city: Pisa

first: Iacopo

last: Petrini

address: Via Roma 67

country: Italy

institute: Pisa University

description:
Thymic epithelial tumor FFPE
Platform GPL4093 is based on NCBI Build 35, and Platform GPL10123 is based on NCBI Build 36.

hyb_protocol: According to ULS labeling kit protocol version 3 November 2008

data_processing:
Data were extracted and normalized using the linear method by Feature Extraction v10.5 (Agilent).
Copy number call thresholds were defined: high gain +0.8, gain +0.3, loss -0.3 and big loss -0.8
Data were further Centralized.  For complete details, please see readme.txt supplementary file on the Series record.  Centralized data files are available as Sample supplementary files.

source_name: Thymic epithelial tumor FFPE

label_protocol: The labeling procedure was conducted using the Genomic DNA Enzymatic Labeling Kit (Agilent) for 7 samples and using the Genomic DNA ULS labeling kit (Agilent) for the remaining 52 samples

growth_protocol: All cell lines were cultured in RPMI 1640 containing 200 mM L-Glutamine (Gibco, Invitrogen, Grand Island, NY), 50 U/mL penicillin, 50 U/mL streptomycin (Invitrogen) and 10% heat-inactivated calf serum (Invitrogen) and grown in a 37 oC incubator with humidified 5% CO2 atmosphere. Media was supplemented with 25nM Hepes for T1889 and T1682.

extract_protocol: FFPE tumor specimens were assessed for quality and adequacy of fixation and storage. A Hematoxylin & Eosin stained slide was prepared for each sample. A pathologist verified the presence of tumor tissue and marked the areas with more than 80% cancer cells on the paraffin blocks. Five cores of tissue were punched from the marked area on FFPE blocks using a 0.6-mm tissue microarray needle, to a depth of approximately 1 mm. The DNA was extracted using DNeasy kit (Qiagen, Inc., Valencia, CA) according to Genomic DNA ULS labeling kit protocol (Agilent Technologies, Inc., Palo Alto, CA)

value: Thymic epithelial tumor FFPE

tag: who histotype

value: F

tag: labeling kit

value: ULS labeling kit

source_name: Promega Genomic DNA

tag: sex

value: Male


title: discovery set 28

description:
B09.4884.44.M.Y37
Gene expression data from embryonic stem cells without Hdh

tag: gender

value: male

tag: htt cag repeat length (longer allele)

tag: batch


title: discovery set 29

description:
B11.2628.36.M.Y42
Gene expression data from embryonic stem cells without Hdh


title: Immature MDDC_DMSO 10h_ replicate 3

description: DMSO 10h DC7

source_name: DMSO treated immature MDDC 10h replicate 2

tag: agent


title: I-Thy 109

scan_protocol: According to ULS labeling kit protocol version 3 November 2008

value: M


title: discovery set 27

description:
B08.2627.41.M.Y42
Gene expression data from embryonic stem cells without Hdh


title: Intercaruncular_Non-pregnant_NZ_1950

value: Holstein-Friesian

value: Non-pregnant

value: Input DNA

value: Affinity enriched DNA


title: Intercaruncular_Pregnant_NA_9921

value: Pregnant


title: Intercaruncular_Non-pregnant_NZ_2952

value: NZ

value: fertile


title: I-Thy 102

value: A

value: enzymatic labeling kit


title: Intercaruncular_Non-pregnant_NZ_3972

value: Intercaruncular


title: Intercaruncular_Non-pregnant_NZ_1940


title: Immature MDDC_DMSO 10h_ replicate 2

description: DMSO 10h DC5

tag: healthy donor

value: immature monocyte-derived dendritic cells (MDDC)

value: vehicle


title: discovery set 26

description:
B07.18756.92.F.O12
Gene expression data from embryonic stem cells without Hdh

value: female

value: B


title: Immature MDDC_DMSO 10h_ replicate 1

description: DMSO 10h DC4

source_name: DMSO treated immature MDDC 10h replicate 1

tag: time


title: I-Thy 097

value: Thymic epithelial tumor FFPE

value: AB

value: F

value: Male


title: Intercaruncular_Pregnant_NA_3807

tag: phenotype

value: sub-fertile

value: Holstein-Friesian


title: discovery set 24

description:
B05.4852.43.F.Y25
Gene expression data from embryonic stem cells without Hdh


title: Immature MDDC_SB203580 4h_ replicate 3

description: SB 4h DC7

source_name: SB203580 treated immature MDDC 4h replicate 3


title: I-Thy 086A

value: M

value: ULS labeling kit


title: Immature MDDC_SB203580 4h_ replicate 2

description: SB 4h DC5

source_name: SB203580 treated immature MDDC 4h replicate 2


title: Immature MDDC_SB203580 4h_ replicate 1

description: SB 4h DC4

source_name: SB203580 treated immature MDDC 4h replicate 1


title: I-Thy 103


title: discovery set 23

description:
B04.4883.47.F.Y27
Gene expression data from embryonic stem cells without Hdh


title: Intercaruncular_Pregnant_NA_3803

tag: breed

value: Pregnant

value: Input DNA

value: Affinity enriched DNA


title: Intercaruncular_Pregnant_NA_3805

tag: pregnancy status


title: Intercaruncular_Pregnant_NA_9790

tag: fraction


title: Intercaruncular_Pregnant_NA_977

tag: tissue


title: Immature MDDC_U0126 4h_ replicate 2

description: UO 4h DC5

source_name: U0126 treated immature MDDC 4h replicate 2


title: Immature MDDC_U0126 4h_ replicate 3

description: UO 4h DC7

source_name: U0126 treated immature MDDC 4h replicate 3


title: Intercaruncular_Pregnant_NZ_926

value: NZ

value: fertile


title: discovery set 19

description:
A19.1714.53.M
Gene expression data from embryonic stem cells without Hdh

value: male

value: A


title: discovery set 18

description:
A18.21145.31.F
Gene expression data from embryonic stem cells without Hdh

value: female


title: discovery set 21

description:
B02.1730.47.F.O45
Gene expression data from embryonic stem cells without Hdh

value: B


title: discovery set 22

description:
B03.4606.71.M.O29
Gene expression data from embryonic stem cells without Hdh


title: discovery set 20

description:
B01.334.41.M.O62
Gene expression data from embryonic stem cells without Hdh


title: I-Thy 046

value: Thymic epithelial tumor FFPE

tag: age


title: Immature MDDC_U0126 4h_ replicate 1

description: UO 4h DC4

source_name: U0126 treated immature MDDC 4h replicate 1

tag: cell type

value: immature monocyte-derived dendritic cells (MDDC)


title: Immature MDDC_DMSO 4h_ replicate 3_duplicate

description: DMSO 4h DC7 bis

source_name: DMSO treated immature MDDC 4h replicate 3 duplicate

value: vehicle


title: Intercaruncular_Pregnant_NZ_3956

value: Intercaruncular

tag: strain


title: I-Thy 083A

tag: who histotype

value: F

value: enzymatic labeling kit

value: Male


title: I-Thy 054B

value: M

tag: labeling kit

value: ULS labeling kit


title: I-Thy 064

tag: sex


title: I-Thy 032

value: AB

tag: gender


title: discovery set 25

description:
B06.8138.39.F.O67
Gene expression data from embryonic stem cells without Hdh

tag: htt cag repeat length (longer allele)


title: I-Thy 078


title: Intercaruncular_Pregnant_NZ_1943

value: Holstein-Friesian

value: Pregnant

value: Input DNA

value: Affinity enriched DNA


title: discovery set 17

description:
A17.7356.17.M
Gene expression data from embryonic stem cells without Hdh

value: male

tag: batch

value: A


title: I-Thy 030


title: Intercaruncular_Pregnant_NZ_932

value: NZ

value: fertile


title: discovery set 16

description:
A16.1729.82.F
Gene expression data from embryonic stem cells without Hdh

value: female


title: Intercaruncular_Pregnant_NZ_3957


title: I-Thy 027

value: Thymic epithelial tumor FFPE


title: Immature MDDC_DMSO 4h_ replicate 2

description: DMSO 4h DC5

source_name: DMSO treated immature MDDC 4h replicate 2

value: immature monocyte-derived dendritic cells (MDDC)

tag: agent

value: vehicle


title: Intercaruncular_Pregnant_NZ_9246

value: Intercaruncular


title: discovery set 14

description:
A14.21519.24.M
Gene expression data from embryonic stem cells without Hdh

source_name: Human lymphoblastoid cell line


title: discovery set 15

description:
A15.13257.43.M
Gene expression data from embryonic stem cells without Hdh


title: I-Thy 024

description:
Thymic epithelial tumor FFPE
Platform GPL4093 is based on NCBI Build 35, and Platform GPL10123 is based on NCBI Build 36.

value: Male


title: Immature MDDC_DMSO 4h_ replicate 1

description: DMSO 4h DC4

source_name: DMSO treated immature MDDC 4h replicate 1

tag: healthy donor


title: Immature MDDC_DMSO 4h_ replicate 3

description: DMSO 4h DC7

tag: time


title: I-Thy 026

value: F


title: discovery set 12

description:
A12.21565.38.F
Gene expression data from embryonic stem cells without Hdh


title: Null Control  water stress 2

city: Lincoln

first: Harkamal

last: Walia

state: NE

address: Agronomy and Horticulture

institute: University of Nebraska

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: RMA normalization of raw data (CEL files)

organism: Triticum aestivum

source_name: Null Control  water stress

label_protocol: Standard Affymetrix IVT protocol

growth_protocol: Wheat seeds were germinated and cultured in sand under well watered and low water conditions.

extract_protocol: Trizol total RNA extraction protocol was used for these experiments

treatment_protocol: 18 day old seedlings were harvsted after daily watering for well watered plants and watering every second day for water stress treatment. Root tissue was sampled for RNA.

value: root tissue

tag: development stage

value: 18 day old seedlings


title: Caruncular_Non-pregnant_NZ_1950

value: Caruncular

tag: phenotype

tag: breed

value: Holstein-Friesian

value: Non-pregnant


title: discovery set 13

description:
A13.301.43.F
Gene expression data from embryonic stem cells without Hdh


title: I-Thy 020

value: ULS labeling kit


title: Null Control water stress 1

source_name: Null Control water stress


title: I-Thy 004

value: M

value: enzymatic labeling kit


title: Immature MDDC_DMSO 4h_ replicate 2_duplicate

description: DMSO 4h DC5 bis

source_name: DMSO treated immature MDDC 4h replicate 2 duplicate


title: Caruncular_Non-pregnant_NA_9786

value: sub-fertile

tag: pregnancy status

tag: fraction

value: Input DNA

value: Affinity enriched DNA


title: Caruncular_Non-pregnant_NA_9778

tag: tissue


title: xpa-1_rep4

city: Solna

first: Jessica

middle: Margareta

last: Lindvall

address: Tomtebodavägen 23A

department: NBIS

country: Sweden

institute: SciLifeLab. Stockholm University

description: Untreated mixed stage xpa-1 strain

hyb_protocol: Hybridization protocol according to manufacturers instruction (Affymetrix)

scan_protocol: Scan protocol according to manufacturers instruction (Affymetrix)

data_processing: Pre-processing using the software Expression Console (Affymetrix). Processing algorithm: Global Median, following Background correction (PM-GCBG) and the summarization method of Plier.

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans xpa-1 mutant

label_protocol: biotin using Genechip 3' IVT Express kit (Affymetrix)

growth_protocol: Mixed stage C. elegans strains were cultured at 20◦C on solid NGM agar plates on HT115(DE3) E. coli as a food source for 3-4 days. For each replicate worms from 10-20 9-cm NGM plates were collected using sucrose floatation. Starved plates were discarded.

extract_protocol: Nematodes were disrupted using Mini-Beadbeater (BioSpec Products) in TRIZOL (Invitrogen) and total RNA was extracted according to manufacturer's instructions

treatment_protocol: Untreated

tag: genotype


title: I-Thy 007

source_name: Thymic epithelial tumor FFPE

value: Thymic epithelial tumor FFPE

value: C

tag: age

source_name: Promega Genomic DNA


title: Caruncular_Non-pregnant_NA_3811

tag: strain


title: Caruncular_Non-pregnant_NA_2970


title: xpa-1_rep5

description: Untreated mixed stage xpa-1 strain


title: Pavon-TL water stress 2

source_name: Pavon-TL water stress


title: discovery set 11

description:
A11.10928.20.F
Gene expression data from embryonic stem cells without Hdh

value: female

value: A


title: Pavon-TL water stress 1


title: discovery set 9

description:
A09.13402.47.F
Gene expression data from embryonic stem cells without Hdh


title: xpa-1_rep3

description: Untreated mixed stage xpa-1 strain


title: Caruncular_Non-pregnant_NZ_2952

value: NZ

value: fertile


title: Caruncular_Non-pregnant_NZ_9960


title: discovery set 8

description:
A08.21521.36.M
Gene expression data from embryonic stem cells without Hdh

value: male


title: Caruncular_Non-pregnant_NZ_1940


title: Pavon76 water stress 2

source_name: Pavon76 water stress

value: root tissue

value: 18 day old seedlings


title: discovery set 10

description:
A10.10438.29.F
Gene expression data from embryonic stem cells without Hdh


title: xpa-1_rep1

description: Untreated mixed stage xpa-1 strain


title: N2_rep5

description: Untreated mixed stage N2 strain

source_name: Caenorhabditis elegans wild type

value: Bristol N2


title: discovery set 7

description:
A07.21250.34.M
Gene expression data from embryonic stem cells without Hdh


title: Pavon76 water stress 1


title: Caruncular_Pregnant_NA_9921

value: Caruncular

value: Holstein-Friesian

value: Pregnant


title: N2_rep4

description: Untreated mixed stage N2 strain


title: discovery set 6

description:
A06.4606.71.M
Gene expression data from embryonic stem cells without Hdh


title: discovery set 5

description:
A05.15213.42.M
Gene expression data from embryonic stem cells without Hdh


title: Null Control  well water 2

source_name: Null Control  well water


title: Pavon-TL well water 2

source_name: Pavon-TL well water


title: Null Control well water 1

source_name: Null Control well water


title: discovery set 4

description:
A04.21273.38.F
Gene expression data from embryonic stem cells without Hdh


title: Immature MDDC_DMSO 4h_ replicate 1_duplicate

description: DMSO 4h DC4 bis

source_name: DMSO treated immature MDDC 4h replicate 1 duplicate

tag: cell type

value: immature monocyte-derived dendritic cells (MDDC)

value: vehicle


title: Caruncular_Pregnant_NA_3803

value: sub-fertile

value: Input DNA


title: Pavon-TL well water 1


title: N2_rep2

description: Untreated mixed stage N2 strain


title: N2_rep1

description: Untreated mixed stage N2 strain


title: Caruncular_Pregnant_NA_977

value: Affinity enriched DNA


title: discovery set 2

description:
A02.19217.35.F
Gene expression data from embryonic stem cells without Hdh


title: discovery set 1

description:
A01.3227.82.M
Gene expression data from embryonic stem cells without Hdh


title: Control Day 3, Sample.69

status: Public on May 02 2013

city: Ottawa

first: Andrew

last: Williams

state: ON

address: 50 Columbine

country: Canada

institute: Health Canada

hyb_protocol: Agilent Mouse G4852A Microarrays (containing approximately 44,000 probes) were hybridized with 300 ng Cy5-labelled heart RNA and 300 ng Cy3-labelled Universal Mouse Reference RNA (Stratagene, CA, USA), used as a common reference on all arrays. Arrays were incubated for 17 hours at 65 ºC in Agilent hybridization solution and washed according to manufacturer’s instructions.

scan_protocol: Arrays were scanned on an Agilent G2505B scanner. Data were acquired using Agilent Feature Extraction software version 10.7.3.1.

data_processing: The log2 of the ratio (sample(Cy5)/reference(Cy3)), using the median signal intensities, were normalized using lowess using the transform.madata function in the maanova library in R.

source_name: Heart tissue, control, day 3

label_protocol: Individual 200 ng aliquots of RNA from each sample were amplified and labelled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent, (5184-3523)).

extract_protocol: RNA was isolated using the TRIzol reagent (Invitrogen Canada Inc., Burlington, ON, Canada), and further purified using RNeasy Mini Kits (Qiagen Inc., Mississauga, ON, Canada). RNA was quantified using a UV spectrophotometer, and quality was confirmed using the Agilent 2100 Bioanalyzer and RNA 6000 NanoLab Chip Kit (Agilent Technologies Canada Inc., Mississauga, ON, Canada).

treatment_protocol: Female C57BL/6 mice (Taconic, Denmark) were acquired at 5-6 weeks of age and given food (Altromin no 1324; Christian Petersen, Denmark) and water ad libitum. Printex 90 was suspended by sonication in 0.9% NaCl MilliQ water containing 10% v/v acellular bronchial alveolar lavage fluid from C57BL/6 mice. A 40 µl suspension was instilled followed by 150 μl air.

value: heart

tag: treatment

value: vehicle control

tag: dose

value: 0 ug

tag: time point

value: day 3

tag: sampleID

source_name: Universal Mouse Reference RNA

extract_protocol: Material was purchased as total RNA (Universal Mouse Reference RNA) from Stratagene (CA, USA).

tag: sample type

value: reference


title: discovery set 3

description:
A03.115.17.M
Gene expression data from embryonic stem cells without Hdh

source_name: Human lymphoblastoid cell line

tag: gender

value: male

tag: htt cag repeat length (longer allele)

tag: batch

value: A


title: Control Day 1, Sample.71

source_name: Heart tissue, control, day 1

value: female

value: day 1


title: Control Day 28, Sample.70

source_name: Heart tissue, control, day 28

value: day 28


title: High Dose Day 28, Sample.67

source_name: Heart tissue, high-dose Printex 90, day 28

value: Printex 90 carbon black nanoparticles


title: Caruncular_Pregnant_NA_3805

value: Caruncular

tag: phenotype

value: Holstein-Friesian

value: Pregnant


title: High Dose Day 3, Sample.66

source_name: Heart tissue, high-dose Printex 90, day 3


title: xpa-1_rep2

description: Untreated mixed stage xpa-1 strain

source_name: Caenorhabditis elegans xpa-1 mutant


title: Caruncular_Non-pregnant_NZ_3972

value: NZ

value: fertile

tag: breed

value: Non-pregnant


title: N2_rep3

description: Untreated mixed stage N2 strain

value: Bristol N2


title: Control Day 3, Sample.54

value: heart

value: vehicle control


title: High Dose Day 1, Sample.65

source_name: Heart tissue, high-dose Printex 90, day 1


title: Control Day 1, Sample.53

value: 0 ug


title: Pavon76 well water 2

source_name: Pavon76 well water

value: root tissue

tag: development stage

value: 18 day old seedlings


title: High Dose Day 28, Sample.52

value: reference


title: Caruncular_Non-pregnant_NA_9813

value: sub-fertile

tag: pregnancy status

tag: fraction

value: Input DNA

value: Affinity enriched DNA


title: Caruncular_Pregnant_NZ_9246

tag: tissue


title: Caruncular_Pregnant_NA_9790


title: Caruncular_Pregnant_NZ_932


title: Control Day 28, Sample.49

value: female

value: day 28


title: Caruncular_Pregnant_NA_3807

value: Caruncular

value: Holstein-Friesian


title: High Dose Day 3, Sample.48

value: Printex 90 carbon black nanoparticles

value: day 3


title: High Dose Day 1, Sample.44

value: day 1


title: Pavon76 well water 1


title: Caruncular_Pregnant_NZ_926

value: NZ

value: fertile

value: Pregnant


title: Caruncular_Pregnant_NZ_3957


title: High Dose Day 3, Sample.36

value: heart


title: Control Day 3, Sample.33

value: vehicle control

value: 0 ug


title: Control Day 1, Sample.41

value: reference


title: Control Day 3, Sample.45


title: High Dose Day 28, Sample.40


title: High Dose Day 1, Sample.32


title: Control Day 28, Sample.55


title: Control Day 28, Sample.37


title: Caruncular_Pregnant_NZ_1943


title: High Dose Day 3, Sample.26


title: High Dose Day 28, Sample.27


title: Control Day 3, Sample.14


title: Control Day 1, Sample.13


title: High Dose Day 1, Sample.16


title: Control Day 1, Sample.29


title: High Dose Day 1, Sample.25


title: Caruncular_Pregnant_NZ_3956


title: High Dose Day 28, Sample.12


title: High Dose Day 3, Sample.8


title: Control Day 28, Sample.9


title: Control Day 28, Sample.39

extract_protocol: Total RNA was extracted using the mirVana Isolation kit (Ambion, Canada).


title: High Dose Day 1, Sample.38


title: High Dose Day 1, Sample.4


title: Control Day 28, Sample.15


title: Control Day 1, Sample.1


title: Control Day 3, Sample.40


title: High Dose Day 3, Sample.37


title: Control Day 1, Sample.36


title: Control Day 1, Sample.34


title: Control Day 1, Sample.28


title: High Dose Day 28, Sample.29


title: Control Day 28, Sample.22


title: High Dose Day 28, Sample.35


title: Control Day 3, Sample.26


title: Control Day 3, Sample.23


title: High Dose Day 3, Sample.16


title: Control Day 28, Sample.25


title: Control Day 28, Sample.24


title: High Dose Day 28, Sample.27


title: High Dose Day 28, Sample.14


title: Control Day 3, Sample.32


title: Control Day 3, Sample.15


title: High Dose Day 3, Sample.30


title: High Dose Day 28, Sample.18


title: High Dose Day 1, Sample.31


title: Control Day 3, Sample.9


title: Control Day 28, Sample.12


title: alive, burned skin tissue B1

city: chongqing

first: li

middle: mu

last: han

address: gaotanyuan street

country: China

institute: Southwest Hospital, Third Military Medical University

description: miRNA microarrays were applied at postburn day 7

hyb_protocol: The samples were hybridized on a hybridization station following the scheme you outlined in the sample submission.

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing: The intensity of green signal is calculated after background subtraction and replicated spots on the same slide have been averaged by getting a median intensity. We use Median Normalization Method to obtain "Normalized Data". Normalized Data=(Foreground-Background)/Median; the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction. We also show the scatter plot comes with Correlation R-value in the Correlation & Scatter Plot.

source_name: burned skin tissue

label_protocol: After having passed RNA measurement on the Nanodrop instrument, the samples are labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.11.0).

growth_protocol: C57BL/6 mice were bred in specific pathogen-free conditions and received humane care. All animal experiments were approved by the Animal Care and Use Committee of ourUniversity and were carried out in compliance with the ‘Guide for the Care and Use of Laboratory Animals’ published by the National Institutes of Health.

extract_protocol: Total RNA are harvested using TRIzol (Invitrogen) and RNeasy mini kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: Round aluminum templates heated to 100°C and applied for 8 s to the moistened and depilated dorsal skin produced a circular spot of 1.5 cm diameter on the mice

tag: Sex

value: male

tag: tissue-type

value: burned skin


title: High Dose Day 3, Sample.21

tag: strain


title: High Dose Day 1, Sample.10

tag: treatment


title: Control Day 1, Sample.17

tag: dose


title: High Dose Day 1, Sample.20

tag: time point


title: alive, normal skin tissue N1

source_name: normal skin tissue

value: normal skin


title: Control Day 1, Sample.7

value: female

tag: sampleID


title: High Dose Day 3, Sample.13

tag: sample type


title: Control Day 3, Sample.5

tag: gender


title: Control Day 1, Sample.11


title: High Dose Day 1, Sample.3


title: wildtype whole animal, biological rep2

city: Nashville

first: William

middle: Clay

last: Spencer

state: TN

address: 465 21st Ave S

department: Cell & Developmental Biology

institute: Vanderbilt University

hyb_protocol: Following fragmentation, 5 ug of cDNA was hybridized for 16 hr at 45C on GeneChip C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Genechips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Data were background-adjusted and normalized using Robust Multiarray Analysis (RMA, R/Bioconductor). Custom gene-level annotation was provided by a custom chip definition file (CDF) derived from Wormbase version 200 (WS200) (see Spencer, et al. 2011).

source_name: Caenorhabditis elegans larvae at L2/L3 stage

label_protocol: Samples were amplified and labeled using NuGEN WT-Pico amplification and FL-Ovation cDNA Biotin Module V2 kits following the manufacturer's protocol.

growth_protocol: Animals were grown at 25C on 150 mm 8P plates inoculated with the E. coli strain Na22

extract_protocol:
The reference sample RNA was isolated from    whole animal lysates as described (Roy, et al., 2002). Total RNA was    isolated from whole animals as described (Roy, et al. 2002) . Total RNA was    isolated by mixing 250 [image: micro]l of the animal lysate with 1 ml of    trizol, and then mixing 250 [image: micro]l of chloroform. After letting    the mixture stand for 10 min, it was spun in a microfuge at 12,000 *g* for    15 min at 4  C, and then the supernatant was extracted with chloroform. RNA    was precipitated by adding 600 [image: micro]l of isopropanol, incubating    at room temperature for 10 min and then centrifuging in a microfuge for    20 min at 12,000 *g* at 4  C. The RNA pellet was rinsed twice with 1 ml of    70% ethanol.
poly(A) RNA was isolated from wildtype and mec-3(e1338) PVD/OLL sensory neurons as described (Von Stetina, et al. 2006).

value: whole animal

tag: developmental stage

tag: genotype


title: Control Day 28, Sample.2

value: day 28


title: mec-3(e1338) whole animal, biological rep2


title: Control Day 28, Sample.39, miRNA

hyb_protocol: Hybridisations were performed in Agilent SureHyb chambers for 20 hours at 55C and washed according to manufacturer's instructions.

scan_protocol: Arrays were scanned at a resolution of 5 mm using an Agilent G2505B scanner.

data_processing: The log2 of median signal intensites were cyclic lowess normalized using R software and the technical replicates were averaged using the median.

label_protocol: Total RNA samples were labelled using the Agilent miRNA Complete Labelling and Hybridisation Kit (Agilent Tech, Mississauga, ON, Canada).

extract_protocol: Total RNA enriched with small RNA was extracted using the mirVana Isolation kit (Ambion, Canada).


title: mec-3(e1338) whole animal, biological rep1


title: Control Day 3, Sample.40, miRNA


title: High Dose Day 1, Sample.38, miRNA


title: wildtype whole animal, biological rep1


title: High Dose Day 3, Sample.37, miRNA


title: High Dose Day 28, Sample.6


title: wildtype PVD/OLL, biological rep1

molecule: polyA RNA

extract_protocol:
poly(A)-enriched RNA was isolated from PVD    neurons as described (Roy, et al. 2002) . RNA was isolated by mixing    250 [image:    micro]l of the immunoprecipitation supernatant with 1 ml of trizol, and    then mixing 250 [image: micro]l of chloroform. After letting the mixture    stand for 10 min, it was spun in a microfuge at 12,000 *g* for 15 min at    4  C, and then the supernatant was extracted with chloroform. RNA was    precipitated by adding 600 [image: micro]l of isopropanol, incubating at    room temperature for 10 min and then centrifuging in a microfuge for 20 min    at 12,000 *g* at 4  C. The RNA pellet was rinsed twice with 1 ml of 70%    ethanol.
poly(A) RNA was isolated from wildtype and mec-3(e1338) PVD/OLL sensory neurons as described (Von Stetina, et al. 2006).

value: PVD/OLL sensory neurons


title: mec-3(e1338) PVD/OLL, biological rep1


title: High Dose Day 3, Sample.1

value: Printex 90 carbon black nanoparticles


title: mec-3(e1338) PVD/OLL, biological rep2


title: High Dose Day 1, Sample.5


title: mec-3(e1338) PVD/OLL, biological rep3


title: wildtype PVD/OLL, biological rep3


title: wildtype PVD/OLL, biological rep2


title: High Dose Day 28, Sample.35, miRNA


title: Control Day 1, Sample.36, miRNA


title: Control Day 3, Sample.34, miRNA

value: day 3


title: IN1760 siPD treated, Biological replicate2

city: Wolverhampton

first: Farjana

middle: B

last: Rowther

address: Wulfruna Street

department: BRAIN TUMOUR RESEARCH LAB

country: United Kingdom

institute: University of Wolverhampton

description: gene expression data from siPD treated IN1760 cells

hyb_protocol: Hybridised on to the Human Genome U133 Plus 2.0 oligonucleotide array. The arrays were washed and stained using the GeneChip Fluidics Station 450

scan_protocol: scanned with the GeneChip Scanner 3000 7G according to manufacturers’ standard protocols

data_processing: Raw microarray data from Affymetrix CEL files for each of the biological replicates of siNT and siPD in IN1472 and IN1760 were initially normalised using the MAS5 (Affymetrix Microarray Suite, version 5.0) algorithm. The raw intensity values were further assessed by the Robust Multi-array Analysis (RMA) as implemented in R/Bioconductor [Irizarry et al, 2003]. The RMA intensity in log2 scale was generated for each probe set and the perfect-match (PM) intensities per probe set were background-corrected, quantile-normalised and signal intensities for each probe set were summarised using median signal intensity to fit linear model (GeneSpring GX 12). Array background, Q values, and mean intensities were within acceptable ranges for all arrays

source_name: PDE1C siRNA treated for 10 days

label_protocol: 1 µg total RNA was reverse transcribed using the MessageAmp™ II-Biotin Enhanced Kit according to the manufacturer's instructions

growth_protocol: short-term cell cultures were prepared from approximately 10mg of adult GBM biopsy tissue and maintained in Hams F10 nutrient mix containing 10% foetal calf serum in a 37C non-CO2 incubator

extract_protocol: Total RNA was extracted using RNeasy Mini Kit  according to the manufacturers’ instructions.

treatment_protocol: ON-TARGETplus SMARTpool siRNA targeting human PDE1C were employed to deplete the transcript levels of PDE1C. In addition, these cultures were transfected in parallel with ON-TARGETplus non-targeting siRNA pool. Cells were seeded at 40-50% confluency and incubated for 48 hours before commencing siRNA transfections. Cells were transfected twice; first at day1 and secondly at day 6. At the end of day 10, cells were collected.

tag: cell culture

value: grade VI GBM short term cultures


title: IN1472 siPD treated, Biological replicate3

description: gene expression data from siPD treated IN1472 cells


title: IN1760 siNT treated, Biological replicate1

description: gene expression data from siNT treated IN1760 cells

source_name: non-targeting siRNA treated for 10 days


title: IN1760 siPD treated, Biological replicate1


title: IN1760 siNT treated, Biological replicate3


title: IN1760 siNT treated, Biological replicate2


title: High Dose Day 1, Sample.33, miRNA

value: day 1


title: High Dose Day 1, Sample.31, miRNA


title: Control Day 3, Sample.32, miRNA


title: High Dose Day 3, Sample.30, miRNA


title: High Dose Day 1, Sample.26, miRNA


title: Control Day 1, Sample.28, miRNA


title: High Dose Day 3, Sample.27, miRNA


title: High Dose Day 28, Sample.29, miRNA


title: Control Day 28, Sample.24, miRNA


title: Control Day 3, Sample.23, miRNA


title: High Dose Day 1, Sample.20, miRNA


title: Control Day 28, Sample.22, miRNA


title: High Dose Day 28, Sample.19, miRNA


title: IN1472 siPD treated, Biological replicate1


title: IN1472 siNT treated, Biological replicate3

description: gene expression data from siNT treated IN1472 cells


title: High Dose Day 28, Sample.18, miRNA


title: IN1472 siNT treated, Biological replicate2


title: IN1472 siPD treated, Biological replicate2


title: minor non-tumor8

city: Kanazawa

first: Yuji

last: Hodo

address: 13-1 Takara-Machi

country: Japan

institute: Kanazawa University Graduate School of Medical Sciences

description:
LC-MI8
Gene expression data from resected non-tumor liver tissue

hyb_protocol: The biotin-labeled cDNA was suspended in hybridization cocktail (NuGen), and used for the hybridization. Affymetrix Human 133 Plus 2.0 microarray chip (Affymetrix, Santa Clara, CA, USA) containing 54,675 gene transcripts was used for the analysis. Hybridization (45°C for 16hrs at 60 rpm), washing and staining (using Fluidics Station) were performed according to the standard protocol (Affymetrix).

scan_protocol: The probe array was scanned by GeneChip® Scanner 3000(Affymetrix).

data_processing: Hybridized data files (CEL) were obtained with the GeneChip® Operating Software 1.4 (GCOS) (Affymetrix).The intensity of each gene chip was normalized by one patient using GeneChip® Operating Software 1.4 (GCOS) and further processed by using R 2.13.0(http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) software.Raw CEL file data were normalized using the MAS 5.0 algorithm as implemented in the affy package. Normalized data were log2 transformed.

source_name: resected non-tumor liver tissue

label_protocol: Aliquots of total RNA (50 ng) isolated from the liver biopsy specimens were subjected to amplification with the WT-OvationTM Pico RNA Amplification System (NuGen, San Carlos, CA, USA) as recommended by the manufacturer (http://www.nugeninc.com/).5 microgram of resultant cDNA was used for fragmentation and biotin labeling using the FL-OvationTM cDNA Biotin Module V2 (NuGen) as recommended by the manufacturer.

extract_protocol: Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Valencia, CA)

value: resected non-tumor liver tissue

value: minor [rs8099917 TG/GG]


title: Control Day 1, Sample.17, miRNA

value: heart


title: minor non-tumor7

description:
LC-MI7
Gene expression data from resected non-tumor liver tissue


title: High Dose Day 3, Sample.16, miRNA


title: Control Day 3, Sample.15, miRNA

value: vehicle control


title: minor non-tumor4

description:
LC-MI4
Gene expression data from resected non-tumor liver tissue


title: minor non-tumor9

description:
LC-MI9
Gene expression data from resected non-tumor liver tissue


title: minor non-tumor10

description:
LC-MI10
Gene expression data from resected non-tumor liver tissue


title: minor non-tumor6

description:
LC-MI6
Gene expression data from resected non-tumor liver tissue


title: minor non-tumor5

description:
LC-MI5
Gene expression data from resected non-tumor liver tissue


title: IN1472 siNT treated, Biological replicate1


title: minor non-tumor1

description:
LC-MI1
Gene expression data from resected non-tumor liver tissue


title: minor non-tumor2

description:
LC-MI2
Gene expression data from resected non-tumor liver tissue


title: High Dose Day 3, Sample.13, miRNA


title: minor non-tumor3

description:
LC-MI3
Gene expression data from resected non-tumor liver tissue


title: minor HCC9

description:
HC-MI9
Gene expression data from resected liver tumor

source_name: resected liver tumor

value: resected liver tumor


title: minor HCC8

description:
HC-MI8
Gene expression data from resected liver tumor


title: minor HCC10

description:
HC-MI10
Gene expression data from resected liver tumor


title: High Dose Day 28, Sample.14, miRNA


title: Control Day 1, Sample.11, miRNA

value: 0 ug


title: High Dose Day 1, Sample.10, miRNA


title: minor HCC5

description:
HC-MI5
Gene expression data from resected liver tumor


title: minor HCC6

description:
HC-MI6
Gene expression data from resected liver tumor


title: Control Day 3, Sample.9, miRNA

source_name: Heart tissue, control, day 3


title: minor HCC4

description:
HC-MI4
Gene expression data from resected liver tumor


title: minor HCC7

description:
HC-MI7
Gene expression data from resected liver tumor


title: minor HCC3

description:
HC-MI3
Gene expression data from resected liver tumor


title: Control Day 28, Sample.12, miRNA


title: minor HCC1

description:
HC-MI1
Gene expression data from resected liver tumor


title: 250ng 16S rRNA gene amplicon of faecal sample LO+A1

type: other

city: Clermont-Ferrand

first: william

last: tottey

address: 28 place Henry Dunant

country: France

institute: EA-CIDAM 4678

description:
LO+A1
raw data file: LO3_Cy3_And_LO+A1_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.

hyb_protocol: For microarray hybridization, 250ng of each labelled faecal sample were used. Hybridization was performed following the Agilent OligoaCGH hybridization protocol (Agilent Technologies, Palo Alto, CA) at 65°C for 24h.

scan_protocol: slides were scanned at a 3-µm resolution using a Surescan microarray scanner (Agilent Technologies, Palo Alto, CA).

data_processing: Pixel intensities were extracted using the 'Feature Extraction' software (Agilent Technologies, Palo Alto, CA). No normalization step was performed and the retained intensity value for each probe was the ratio between the spot’s median intensity signals and the median of background signals.

molecule: other

organism: Rattus norvegicus

source_name: linseed oil + aleurone (A+LO) treated

label_protocol: For each sample, the purified 16S rRNA gene PCR products (1 µg) were labelled with either Cy3 or Cy5 using the Genomic DNA ULS labelling Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

growth_protocol: Faecal samples were collected by the Laboratoire Cœur et Nutrition, TIMC-IMAG CNRS UMR 5525, Université Joseph Fourier, Grenoble, France

extract_protocol: Total DNA was extracted from 25 rat faecal samples using Qiagen’s DNA Stool Kit (Qiagen, West Sussex, UK). 10ng of sample was then used for PCR amplification. 16S rRNA genes were amplified using universal primers 27F (AGAGTTTGATCMTGGCTCAG) and 1492R (TACGGYTACCTTGTTACGACT). PCR reactions were performed in a 50µl volume, using DreamTaq DNA polymerase (Fermentas, St. Leon-Rot, Germany). The PCR reaction consisted of an initial denaturation step at 95°C for 5min followed by 35 cycles of denaturation at 95°C for 30 s, annealing at 58°C for 40 s and elongation at 72°C for 2 min. A final extension step was performed at 72°C for 5 min. PCR product size was verified by electrophoresis with 1% (w/v) agarose gel and were purified using the MinElute PCR Purification Kit (Qiagen Ltd., UK) following manufacturer’s instructions and stored at -20°C.

tag: strain source

value: Wistar

tag: characteristics

value: fed with  :linseed oil + aleurone (A+LO) for 12 wks

value: faecal sample

tag: molcule subtype

value: 16S rRNA gene amplicon


title: 250ng 16S rRNA gene amplicon of faecal sample LO+A2

description:
LO+A2
raw data file: LO4_Cy3_And_LO+A3_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: major non-tumor8

description:
LC-MA8
Gene expression data from resected non-tumor liver tissue

value: major [rs8099917 TT]


title: 250ng 16S rRNA gene amplicon of faecal sample LO+A11

description:
LO+A11
raw data file: LO+A11_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: 250ng 16S rRNA gene amplicon of faecal sample LO+A4

description:
LO+A4
raw data file: LO8_Cy3_And_LO+A5_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: 250ng 16S rRNA gene amplicon of faecal sample LO+A5

description:
LO+A5
raw data file: LO9_Cy3_And_LO+A2_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: 250ng 16S rRNA gene amplicon of faecal sample LO+A9

description:
LO+A9
raw data file: LO11_Cy3_And_LO+A9_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: major non-tumor9

description:
LC-MA9
Gene expression data from resected non-tumor liver tissue


title: 250ng 16S rRNA gene amplicon of faecal sample LO11

description:
LO11
raw data file: LO11_Cy3_And_LO+A9_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.

source_name: linseed oil (LO) treated

value: fed with  :linseed oil (LO) for 12 wks


title: 250ng 16S rRNA gene amplicon of faecal sample LO+A3

description:
LO+A3
raw data file: LO6_Cy3_And_LO+A4_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: major non-tumor5

description:
LC-MA5
Gene expression data from resected non-tumor liver tissue


title: major non-tumor10

description:
LC-MA10
Gene expression data from resected non-tumor liver tissue


title: 250ng 16S rRNA gene amplicon of faecal sample LO9

description:
LO9
raw data file: LO9_Cy3_And_LO+A2_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: 250ng 16S rRNA gene amplicon of faecal sample LO8

description:
LO8
raw data file: LO8_Cy3_And_LO+A5_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: 250ng 16S rRNA gene amplicon of faecal sample LO6

description:
LO6
raw data file: LO6_Cy3_And_LO+A4_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: 250ng 16S rRNA gene amplicon of faecal sample LO4

description:
LO4
raw data file: LO4_Cy3_And_LO+A3_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: major non-tumor7

description:
LC-MA7
Gene expression data from resected non-tumor liver tissue


title: minor HCC2

description:
HC-MI2
Gene expression data from resected liver tumor


title: major non-tumor2

description:
LC-MA2
Gene expression data from resected non-tumor liver tissue


title: 250ng 16S rRNA gene amplicon of faecal sample LO3

description:
LO3
raw data file: LO3_Cy3_And_LO+A1_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: major HCC8

description:
HC-MA8
Gene expression data from resected liver tumor


title: major HCC9

description:
HC-MA9
Gene expression data from resected liver tumor


title: major non-tumor4

description:
LC-MA4
Gene expression data from resected non-tumor liver tissue


title: major non-tumor6

description:
LC-MA6
Gene expression data from resected non-tumor liver tissue


title: major non-tumor1

description:
LC-MA1
Gene expression data from resected non-tumor liver tissue


title: major HCC10

description:
HC-MA10
Gene expression data from resected liver tumor


title: 250ng 16S rRNA gene amplicon of faecal sample PO+A6

description:
PO+A6
raw data file: PO6_Cy3_And_PO+A6_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.

source_name: control oil + aleurone (A+PO) treated

value: fed with  :control oil + aleurone (A+PO) for 12 wks


title: 250ng 16S rRNA gene amplicon of faecal sample PO+A5

description:
PO+A5
raw data file: PO5_Cy3_And_PO+A5_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: 250ng 16S rRNA gene amplicon of faecal sample PO+A3

description:
PO+A3
raw data file: PO3_Cy3_And_PO+A3_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: 250ng 16S rRNA gene amplicon of faecal sample PO+A1

description:
PO+A1
raw data file: PO1_Cy3_And_PO+A1_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: 250ng 16S rRNA gene amplicon of faecal sample PO+A2

description:
PO+A2
raw data file: PO2_Cy3_And_PO+A2_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: 250ng 16S rRNA gene amplicon of faecal sample PO6

description:
PO6
raw data file: PO6_Cy3_And_PO+A6_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.

source_name: iso-energetic control oil (PO) treated

value: fed with  :iso-energetic control oil (PO) for 12 wks


title: major HCC6

description:
HC-MA6
Gene expression data from resected liver tumor


title: major HCC7

description:
HC-MA7
Gene expression data from resected liver tumor


title: 250ng 16S rRNA gene amplicon of faecal sample PO5

description:
PO5
raw data file: PO5_Cy3_And_PO+A5_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: major HCC2

description:
HC-MA2
Gene expression data from resected liver tumor


title: major HCC5

description:
HC-MA5
Gene expression data from resected liver tumor


title: major HCC4

description:
HC-MA4
Gene expression data from resected liver tumor


title: 250ng 16S rRNA gene amplicon of faecal sample PO+A4

description:
PO+A4
raw data file: PO4_Cy3_And_PO+A4_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: major non-tumor3

description:
LC-MA3
Gene expression data from resected non-tumor liver tissue


title: 250ng 16S rRNA gene amplicon of faecal sample PO4

description:
PO4
raw data file: PO4_Cy3_And_PO+A4_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: IN1760 siPD treated, Biological replicate3

description: gene expression data from siPD treated IN1760 cells


title: 250ng 16S rRNA gene amplicon of faecal sample PO1

description:
PO1
raw data file: PO1_Cy3_And_PO+A1_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: LNCaP + ELK1-shRNA rep 1

city: Toledo

first: Robert

middle: J

last: Trumbly

state: OH

address: 3000 Arlington Avenue

department: Biochemistry and Cancer Biology

institute: University of Toledo

description: Gene expression data from LNCaP cells treated with vehicle and ELK1 shRNA

hyb_protocol: The cRNA was fragmented to 35-200 bases length using Affymetrix protocols and hybridized to HG U133 Plus 2.0 array set at 45ºC for 16 hours in an Affymetrix GeneChip® Hybridization Oven 640.

scan_protocol: Each GeneChip was then washed and stained with Streptavidin–Phycoerythrin conjugate (SAPE; Invitrogen Corp.) using an Affymetrix Fluidics Station 450 and scanned on a Affymetrix GeneChip scanner.

data_processing: Scanned image files were analyzed using the Gene Chip Operating System Version 1.4 software, and standard thresholding and filtering operations were used.   The data was normalized using house keeping genes. Normalization assumes that for a subset of genes (i.e., housekeeping genes) the ratio of measured expression averaged over the set should be one.

source_name: LNCaP cells treated with vehicle and ELK1-shRNA

label_protocol: Isolated total RNA was processed as recommended by Affymetrix, Inc. (Santa Clara, CA). In brief, cDNA was synthesized from the total RNA using the Super-Script Double Stranded cDNA Synthesis kit and T7 Oligo (dT) primers. Using the double stranded cDNA as template, biotin labeled cRNA was generated by in vitro transcription (MEGAscript Labeling Kit) reaction.

growth_protocol: Cells were routinely cultured at 37°C and in 5% CO2 in RPMI 1640 medium supplemented with FBS (10%), penicillin (100units/mL), streptomycin (100 mg/mL), L-glutamine (2mM), and sodium pyruvate (1mM). For hormone depletion, cells were grown in phenol-red free RPMI-1640 with 10% charcoal stripped FBS, penicillin (100 units/ml)/streptomycin (100 µg/ml)/L-glutamine (2mM) mix for 48 h before the experiments.,

extract_protocol: Total RNA was prepared using the RNeasy Mini kit (Qiagen).

treatment_protocol: LNCaP cells were infected with ELK1 shRNA lentivirus or non-target control lentivirus, and  grown in hormone-free media to deplete androgen. 96h after infection the cells were cells were grown for 48 h with either vehicle or R1881 (1nM) and harvested to obtain total RNA.

value: treated with vehicle and ELK1-shRNA

tag: cell line

value: LNCaP


title: 250ng 16S rRNA gene amplicon of faecal sample PO3

description:
PO3
raw data file: PO3_Cy3_And_PO+A3_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: LNCaP + ELK1-shRNA rep 2


title: LNCaP + ELK1-shRNA + R1881 rep 1

description: Gene expression data from LNCaP cells treated withR1881 and ELK1 shRNA

source_name: LNCaP cells treated with R1881 and ELK1-shRNA

value: treated with R1881 and ELK1-shRNA


title: LNCaP + ELK1-shRNA + R1881 rep 2


title: LNCaP + R1881 rep 2

description: Gene expression data from LNCaP cells treated with R1881 and control shRNA

value: treated with R1881 and control shRNA


title: LNCaP + vehicle rep 2

description: Gene expression data from LNCaP cells treated with vehicle and control shRNA

value: treated with vehicle and control shRNA


title: 250ng 16S rRNA gene amplicon of faecal sample PO2

description:
PO2
raw data file: PO2_Cy3_And_PO+A2_Cy5.txt
16S rRNA gene amplified from gDNA extracted from faecal samples of treated rats.


title: LNCaP + R1881 rep 1

source_name: LNCaP cells treated with R1881 and control shRNA


title: TW01 cells, induced LRIG1 expression for 48 hrs

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

description: TW01-LG1/a cells with LRIG1 induced expression for 48 hrs.

hyb_protocol: Samples were hybridized using GeneChip® Hybridization, Wash and Stain Kit (Affymetrix). The washing and staining steps were carried out using the GeneChip Fluidics station FS 450. All experiments were performed according to the manufacture's instruction.

scan_protocol: Slides were scanned with the Affymetrix Gene Chip scanner 3,000 7 G system

data_processing:
Data were processed using GeneSpring software. Preprocessing the data by setting the intensity of the control sample (TW01_LRIG1_0hr) as baseline for each sample analyzed. Gene level expression were summarized from the corrected intensities and then quantile normalized.
HuGene-1_0-st-v1_na31_hg19

label_protocol: 100 ng of total RNA were subjected to microarray analysis for each sample. cDNA was prepared and fragmentated using WT cDNA Synthesis Kit (Affymetrix), followed by biotinylation using WT Terminal Labeling Kit (Affymetrix). All experiments were performed according to the manufacture's instruction.

growth_protocol: LRIG1 stable transfectant, TW01-LG1/a, was cultured in medium with or without doxycycline (DOX) for turn off or turn on LRIG1 expression, respectively.

extract_protocol: Cellular RNA were harvested using RNeasy kit (Qiagen) according to the manufacturer's instruction.

tag: transgene

value: minus Dox

tag: time


title: placental trophoblast_HLAG+_rep3

city: Columbia

first: Laura

middle: Clamon

last: Schulz

state: MO

address: 1 Hospital Dr.

department: Obstetrics, Gynecology and Women's Health

institute: University of Missouri

description: HLAG placental 3

hyb_protocol: Purified cRNA (1 µg) was fragmented to uniform size and applied to Agilent 4x44K v2 microarrays (Design ID 026655, Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 h on a rotating incubator and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).  Values are normalized to 75th percentile intensity for each array (=1).

source_name: placenta, 8-12 week LMP

label_protocol: First and second strand cDNA was prepared from the total RNA samples.  cRNA target was prepared from the DNA template and verified on the Bioanalyzer.

growth_protocol: Human ES H1 (NIH code WA01) was maintained on irradiated mouse embryonic fibroblast (MEF) cells in 80% DMEM/F12 supplemented with 20% KnockOut serum replacement, 1 mM L-glutamine/0.1 mM 2-mercaptoethanol/1% nonessential amino acids (Life Technologies) and 4 ng/ml FGF2 . Placentas were collected from women undergoing surgery at 8-12 weeks of gestation by LMP (last menstrual period) due to fetal demise at University of Missouri Women‘s and Children’s Hospital. Trophoblast were isolated by mincing villous tissue and then incubating in dissociation solution (4.2mM MgSO4, 0.25 % trypsin, 100 kU/ml DNase I inDPBS) for 30 min at 37C. Cells were passed through a 100 µm cell filter, washed in Medium 199 and layered on a 40%/25% Percoll gradient. The TB layer was collected at the interface then washed and resuspended in PBS/ 0.5%BSA/ 2mM EDTA (PBS/BSA/EDTA).

extract_protocol: Both placental cells and BMP4-treated hESC were incubated with an anti-HLA-G antibody, conjugated to phycoerythrin (PE) and an anti-TACSTD2 (TROP2) antibody, conjugated to biotin for 10 min at 4C. Cells were washed in PBS/BSA/EDTA (x 3), then incubated in a 1:5 dilution of anti-PE antibody -conjugated to magnetic beads (Miltenyi Biotec, Auburn CA) at 4C for 10 min to tag HLA-G+ cells..  Cells were then separated into HLA-G+ and – fractions by using MS columns and a MimiMACS Separator held by a Multistand (Miltenyi) to capture magnetic beads. HLA-G- cells that passed through the columns were incubated in a 1:5 dilution of streptavidin -conjugated magnetic beads (R&D Systems) at 4C for 10 min to tag HLAGHLA-G-/TACSTD2+ cells. A second MS column was used to collect the bead-bound (HLA-G-/TACSTD2+) cells.  Total RNA was obtained using Ribopure (Ambion).

treatment_protocol: hESC were cultured in irradiated MEF-conditioned medium supplemented with either 4ng/ml FGF2 or 10 ng/ml BMP4 (R&D Systems) under a standard gas atmosphere of humidified air/5% CO2 at 37°C.

tag: cell source

value: primary human placenta from fetal demise

tag: cell surface marker

value: HLAG


title: D. alaskensis str. G20 in sulfate-limited monoculture (chemostat dilution rate 0.047h-1), C24

city: Berkeley

first: Jennifer

middle: V

last: Kuehl

state: California

address: 1 Cyclotron Road

department: Physical Biosciences

institute: Lawrence Berkeley National Laboratory

description: Monoculture C24E

hyb_protocol: Standard NimbleGen protocol.

scan_protocol: Standard NimbleGen protocol.

data_processing: Quantile normalized the probe intensities to match the G20 monoculture sample and averaged the log2 values for each gene and set the median log2 expression level in each sample to zero.

label: Alexa Fluor 555

organism: Oleidesulfovibrio alaskensis G20

source_name: Desulfovibrio alaskensis str. G20 in sulfate-limited monoculture (chemostat dilution rate 0.047h-1)

label_protocol: Prepared first-strand labeled cDNA with SuperScript Plus Indirect cDNA Labeling Module (Invitrogen).

growth_protocol: We collected expression data for 2 growth conditions: syntrophic or respiratory growth of Desulfovibrio alaskensis str. G20 on lactate. Desulfovibrio alaskensis str. G20 was grown in monoculture under sulfate-limited conditions and in syntrophic coculture with the methanogen Methanococcus maripaludis or Methanospirillum hungatei in chemostats at constant dilution rate of 0.027h-1. The basal salt solution of the media is described in Walker et. al. (2009) and contained 30 mM sodium DL-lactate or sodium pyruvate, resazurin as redox indicator, and 10 mM Na2SO4 (chemostat monoculture media). The media were prepared in bioreactor glass vessels (2 liters) and medium reservoir bottles (10 liters) anoxically under a N2-CO2 (80:20, v/ v) gas atmosphere according to Widdel and Bak (1992). The media were buffered using 1.1 mM KH2PO4 and 30 mM NaHCO3. Nonchelated trace element mixture 1 and selenite-tungstate solution as well as vitamin mixture, riboflavin, vitamin B1 and B12 solutions and [1M] Na2S solution (79) were added aseptically in 1 ml aliquots per liter of medium. All stock solutions were prepared under anoxic conditions. After preparation, the bioreactor and medium reservoir bottles were connected to a N2-CO2 (90:10, v/ v) gas mixture tank. Cells were harvested from triplicate mono- and coculture chemostat runs after at least 3 volume turnovers at steady state in the chemostat at constant dilution rate of 0.027h-1, giving a total of six coculture and three monoculture gene expression data sets.

extract_protocol: Isolated total RNA with RNeasy mini kit (Qiagen).

treatment_protocol: Varying growth conditions: syntrophic growth at different growth rates and with different methanogenic partner on substrate lactate (relative to respiratory growth conditions).

tag: carbon source

value: lactate (30 mM)

tag: electron acceptor

value: sulfate (10 mM)

tag: stressor

tag: culture type

value: monoculture

tag: growth phase

value: growth rate 0.047h-1 (chemostat growth)


title: major HCC1

description:
HC-MA1
Gene expression data from resected liver tumor

tag: tissue

value: resected liver tumor


title: placental trophoblast_HLAG-/TROP2+_rep3

description: TROP2 placental 3

value: TROP2 (TACSTD2)


title: D. alaskensis str. G20 in sulfate-limited monoculture (chemostat dilution rate 0.047h-1), C19

description: Monoculture C19E


title: D. alaskensis str. G20 in syntrophic coculture with Methanococcus maripaludis (chemostat dilution rate 0.027h-1), C34rep

description: Coculture C34_G20+MM_rep

source_name: Desulfovibrio alaskensis str. G20 in syntrophic coculture with Methanococcus maripaludis (chemostat dilution rate 0.027h-1)

value: growth rate 0.027h-1 (chemostat growth)


title: TW01 cells, induced LRIG1 expression for 36 hrs

description: TW01-LG1/a cells with LRIG1 induced expression for 36 hrs.

tag: treatment


title: cPLA2a-/- macrophages_stimulated with candida albicans_2

city: Denver

first: Christina

last: Leslie

address: 1400 Jackson street

institute: National Jewish Health

hyb_protocol: Fragmentation followed by hybridization was performed (Agilent Gene Expression Hybridization Kit)  on Agilent Whole Mouse Genome kit 4x44 microarray slides at 65ºC for 16 hr.

scan_protocol: Slides were washed according to the Agilent Quick Amp Labeling Kit protocol and scanned immediately on an Agilent G2505B scanner.

data_processing: The scanned images were analyzed in Genespring GX 11.5 (Agilent technologies). The microarray results were log base 2 transformed and data normalization was applied using the 75% percentile shift method to adjust for experimental variability.  Boxplots of resulting expression were examined for consistency and all quality control metrics were within acceptable ranges.

source_name: Resident peritoneal macrophages from cPLA2a-/-, stimulated with candida albicans for 3 hours

label_protocol: Agilent Quick Amp Labeling kit was used to generate Cy3 labeled RNA. Yields of 3.7-6.8 mg were obtained with specific activities of 7.5-9.4 pmol/mg.

growth_protocol: Resident peritoneal macrophages were isolated from  cPLA2+/+ and -/- mice. After 2 hours of adhesion, cells were washed and incubated overnight.

extract_protocol: RNA was extracted using  Rneasy mini kit from Qiagen. Template RNA quality was assessed with the Agilent Bioanalyzer 2100 and an Agilent Nano RNA 6000 kit per the Agilent protocol.  RNA quality ranged from a RNA Integrity Number (RIN) of 8.1 to 10.

treatment_protocol: Macrophages were washed and incubated for 3 hours with and without candida albicans (m.o.i. 2).

tag: gender

value: female

tag: strain

value: Balb/c

tag: age

value: 8-12 weeks

value: Resident peritoneal macrophages


title: LNCaP + vehicle rep 1

source_name: LNCaP cells treated with vehicle and control shRNA

value: LNCaP


title: cPLA2a-/- macrophages_stimulated with candida albicans_3


title: D. alaskensis str. G20 in sulfate-limited monoculture (chemostat dilution rate 0.027h-1), C39

description: Monoculture C39_G20

source_name: Desulfovibrio alaskensis str. G20 in sulfate-limited monoculture (chemostat dilution rate 0.027h-1)


title: H1N1 PI 0 day

city: Seoul

first: Hyun Jik

last: Kim

address: 101 Daehak-ro, Jongno-gu

department: Department of otorhinolaryngology

institute: Seoul National University

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: nasal mucosa, mock infected

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

growth_protocol: Passage-2 NHNE cells (1 x 10^5 cells/culture) were seeded in 0.5 ml of culture medium on Transwell-clear culture inserts (24.5-mm, 0.45-µm pore size) and we cultured these specimens using a system designed for normal human nasal epithelial cells.

extract_protocol: Total RNA was isolated from normal human nasal epithelial cells infected with WSN/33 (H1N1) at day two using TRIzol. cDNA was synthesized from 3 μg of RNA with random hexamer primers using Moloney murine leukemia virus reverse transcriptase.

treatment_protocol: Normal human nasal epithelial cells were either mock-infected (PBS) or inoculated with IAV (WSN/33, H1N1) at a multiplicity of infection (MOI) of 1.

tag: cell type

value: nasal epithelial cells

value: mock infection


title: cPLA2a-/- macrophages_stimulated with candida albicans_1


title: D. alaskensis str. G20 in sulfate-limited monoculture (chemostat dilution rate 0.027h-1), C38

description: Monoculture C38_G20


title: TW01 cells, induced LRIG1 expression for 24 hrs

description: TW01-LG1/a cells with LRIG1 induced expression for 24 hrs.

value: minus Dox


title: placental trophoblast_HLAG+_rep2

description: HLAG placental 2

value: primary human placenta from fetal demise


title: H1N1 PI 2 day

source_name: nasal mucosa, IAV infected

value: influenza A virus (WSN/33, H1N1) infection for 2 days


title: D. alaskensis str. G20 in sulfate-limited monoculture (chemostat dilution rate 0.027h-1), C37

description: Monoculture C37_G20

value: lactate (30 mM)


title: placental trophoblast_HLAG-/TROP2+_rep1

description: TROP2 placental 1


title: placental trophoblast_HLAG-/TROP2+_rep2

description: TROP2 placental 2


title: cPLA2a-/- macrophages_unstimulated_3

source_name: Resident peritoneal macrophages from cPLA2a-/-, unstimulated


title: cPLA2a-/- macrophages_unstimulated_1


title: TW01 cells, induced LRIG1 expression for 12 hrs

description: TW01-LG1/a cells with LRIG1 induced expression for 12 hrs.


title: placental trophoblast_HLAG+_rep1

description: HLAG placental 1

value: HLAG


title: TW01 cells, no ectopic LRIG1 expression

description: TW01-LG1/a cells without ectopic expressed LRIG1

value: control

value: baseline


title: TW01 cells, induced LRIG1 expression for 6 hrs

description: TW01-LG1/a cells with LRIG1 induced expression for 6 hrs.

value: 6 h


title: cPLA2a+/+ macrophages_stimulated with candida albicans_2

source_name: Resident peritoneal macrophages from cPLA2a+/+, stimulated with candida albicans for 3 hours


title: cPLA2a-/- macrophages_unstimulated_2


title: D. alaskensis str. G20 in syntrophic coculture with Methanospirillum hungatei (chemostat dilution rate 0.027h-1), C30

description: Coculture C30_G20+MH

source_name: Desulfovibrio alaskensis str. G20 in syntrophic coculture with Methanospirillum hungatei (chemostat dilution rate 0.027h-1)


title: hESC_BMP4treated_HLAG+_rep3

description: HLAG hESC 3

source_name: embryonic stem cells

value: human embryonic stem cells

tag: treated with

value: 10 ng/ml BMP4 for 5 days


title: hESC_BMP4treated_HLAG-/TROP2+_rep2

description: TROP2 hESC 2

value: TROP2 (TACSTD2)


title: cPLA2a+/+ macrophages_stimulated with candida albicans_3

value: female

value: Balb/c


title: D. alaskensis str. G20 in syntrophic coculture with Methanospirillum hungatei (chemostat dilution rate 0.027h-1), C28

description: Coculture C28_G20+MH

value: growth rate 0.027h-1 (chemostat growth)


title: cortex-BAF170cKO-2

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

hyb_protocol: Illumina Direct Hybridization Assay  (performed by Cambridge Genomic Services, Cambridge, UK, certified Illumina provider)

scan_protocol: Illumina protocol using Illumina BeadArray Scanner  (performed by Cambridge Genomic Services, Cambridge, UK, certified Illumina provider).

data_processing:
Raw data was processed using Ilumina GenomeStudio software (performed by Cambridge Genomic Services, Cambridge, UK, certified Illumina provider). Probes passing a detection p-value threshold of 0.01 in at least one sample were selected using the R package lumi (Du et al., Bioinformatics 2008). The data were then transformed using variance stabilisation (Lin et al., Nucleic Acids Research 2008) and quantile normalised.
Values are variance-stabalised and quantile-normalised expression measures computed using the R package lumi (Du et al., Bioinformatics 2008; Lin et al., Nucleic Acids Research 2008). Only detected values are shown.

source_name: cortex from single E12.5 mouse embryo_conditional BAF170 knock out

label_protocol: Nugen ovation system (performed by Cambridge Genomic Services, Cambridge, UK, certified Illumina provider).

growth_protocol: BAF170fl and Emx1Cre mice were maintained on a C57BL6/J background. Animals were handled in accordance with the German Animal Protection Law and with the permission of the Bezirksregierung Braunschweig.

extract_protocol: 2.3-2.4ug of total RNA per sample was extracted using a Qiagen RNAeasy kit.

tag: strain background

tag: genotype/variation

value: BAF170fl/fl;Emx1Cre/+; conditional BAF170 knock out

value: cortex from single mouse embryo

tag: developmental stage


title: cPLA2a+/+ macrophages_stimulated with candida albicans_1

value: 8-12 weeks

value: Resident peritoneal macrophages


title: cortex-BAF170cKO-3


title: D. alaskensis str. G20 in syntrophic coculture with Methanospirillum hungatei (chemostat dilution rate 0.027h-1), C33

description: Coculture C33_G20+MH


title: D. alaskensis str. G20 in syntrophic coculture with Methanococcus maripaludis (chemostat dilution rate 0.027h-1), C34

description: Coculture C34_G20+MM


title: hESC_BMP4treated_HLAG+_rep2

description: HLAG hESC 2

tag: cell source


title: hESC_BMP4treated_HLAG-/TROP2+_rep3

description: TROP2 hESC 3

tag: cell surface marker


title: cortex-wildtype-3

source_name: cortex from single E12.5 mouse embryo_wildtype with floxed BAF170 allele

value: BAF170fl/fl; wild type with floxed BAF170 allele


title: cortex-BAF170cKO-1


title: cPLA2a+/+ macrophages_unstimulated_3

source_name: Resident peritoneal macrophages from cPLA2a+/+, unstimulated


title: D. alaskensis str. G20 in syntrophic coculture with Methanococcus maripaludis (chemostat dilution rate 0.027h-1), C32

description: Coculture C32_G20+MM

tag: carbon source


title: cortex-wildtype-2


title: cPLA2a+/+ macrophages_unstimulated_2


title: hESC_BMP4treated_HLAG+_rep1

description: HLAG hESC 1


title: cortex-wildtype-1


title: hESC_undifferentiated

description: Ctrl hESC 0

value: 4 ng/ml FGF2 for 5 days


title: cPLA2a+/+ macrophages_unstimulated_1