title: PAXgene whole blood, sepsis_survivor, Day_1, ID=47

description:
5445295006_G
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=47


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=42

status: Public on Feb 04 2014

type: RNA

city: Kingswood

first: Grant

last: Parnell

state: NSW

address: Nepean Hospital

department: Nepean Clinical School

country: Australia

institute: University of Sydney

description:
5445295021_L
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

hyb_protocol: Hybridization protocol as per the Illumina Whole-Genome Gene Expression Direct Hybridization Experienced User Guide.

scan_protocol: Scanned using default parameters on Illumina BeadArray Reader.

data_processing: Data pre-processed in GenomeStudio. A detection p value of <0.005 was required in at least 1 sample for probe to be retained. Probes which passed this filter were uploaded into BRB-ArrayTools.

molecule: total RNA

organism: Homo sapiens

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=42

label_protocol: cRNA prepared using Ambion Illumina TotalPrep RNA Amplification Kit.

extract_protocol: RNA was extracted using PAXgene blood RNA kit v2 (PreAnalytix).

tag: tissue

value: whole blood

tag: disease status

value: sepsis survivor

tag: gender

value: M

tag: age (years)

tag: severity (apacheii)

tag: neutrophil proportion

tag: site of infection

value: lung


title: Human gut microbiome from healthy individuals with alcohol abuse CD11

type: genomic

city: Norman

first: Qichao

last: Tu

state: OK

address: 101 David L Boren Blvd

country: USA

institute: University of Oklahoma

hyb_protocol: DNA was suspended in hybridization buffer and then kept at 65°C until hybridization. Hybridizations were performed at 42°C for 10 h using a Tecan HS4800 Pro hybridization station

scan_protocol: Arrays were scanned with a ScanArray 500 microarray scanner  at 633 nm using a laser power of 90% and a photomultiplier tube (PMT) gain of 75%.

data_processing: Signal intensity were normalized by CORS universal standard probes (Liang et. al 2010 AEM), probes with SNR<2 are removed, normalized signal intensities was calculated for further statistical analysis. We used minimal signal intensity of 1000 and SNR (Signal to Noise Ratio) cutoff of 2 for positive callings of the presence of a gene.

molecule: genomic DNA

organism: human metagenome

label_protocol: DNA was labeled with the fluorescent dye Cy5 (GE Healthcare) by random priming

extract_protocol: For oral microbiome sampling, bacteria were separated from the paper-points by vortexing. The paper points were discarded and community DNA was extracted using the QIAamp TM DNA micro Kit (QIAGEN Sciences, Maryland, USA) following the manufacturer’s instructions and adding a lysozyme (3 mg/mL, 1.5 h) treatment step. For gut microbiome sampling, all fecal samples were immediately frozen on collection and stored at -70℃ before analysis. A frozen aliquot (200 mg) of each fecal sample was added to a 2.0-ml screwcap vial containing 300 mg glass beads of 0.1 mm diameter (Sigma, St. Louis, MO, USA), and kept on ice until the addition of 1.4-ml ASL buffer from the QIAamp DNA Stool Mini Kit (Qiagen, Valencia, CA, USA). Samples were immediately subjected to beadbeating (45 s, speed 6.5) using a FastPrep machine (Bio 101, Morgan Irvine, CA, USA), prior to the initial incubation for heat and chemical lysis at 95 ℃ for 5 minutes. Subsequent steps of DNA extraction followed the QIAamp kit protocol for pathogen detection.

tag: source


title: Hypo+ 2

city: ottawa

first: hongyan

last: dong

address: 50 colombine Dr.

country: Canada

institute: health canada

hyb_protocol: Biotin-labeled cRNA was purified using the GeneChip cleanup module prior to fragmenting to a size of 35-200 bases by incubating at 94 °C for 35 min in fragmentation buffer.  Fragmented cRNA was hybridized to the arrays for 16 hours at 45 °C .

scan_protocol: After hybridization, arrays were washed using an Affymetrix fluidics station and stained with streptavidin-phycoerythrin (10 mg/ml, Molecular Probes). Washed arrays were scanned on an Affymetrix GeneChip scanner 3000.  Scanned output files were visually inspected for hybridization artifacts.

data_processing:
MAS 5.0
contents of CHP files: Algorithm: ExpressionStat 5.0
All pre-processing of the data was conducted using the R package. The data were normalized by robust multi-array average (RMA) using the ReadAffy function in the Affy R library (Irizarry RA et al., 2003). The Fs statistic (Cui X et al., 2005), a shrinkage estimator, was used for the gene-specific variance components, and the associated p-values (unadjusted p) for all the statistical tests were estimated using the permutation method (30,000 permutations with residual shuffling). These p-values were then adjusted for multiple comparisons using the false discovery rate (FDR) approach (Benjamini Y et al., 2001). The least squares mean (Goodnight JH HW, 1978; Searle SR SF, Milliken GA, 1980), a function of the model parameters, was used to estimate the fold-change for each pairwise comparison of interest (control versus each of the three treatment groups: hyper, hypo, and hypo+).

label: biotin

organism: Mus musculus

source_name: mouse fetal cerebral cortex on GD16 treated with PTU for 3 days and injected with thyroid hormone 12 hours before sacrifice

label_protocol: The Yale Center for the Neuroscience Microarray Consortium carried out the Affymetrix microarray analysis using The GeneChip Rat Genome 230 2.0 Array.  Preparation of labeled cRNA for hybridization onto Affymetrix GeneChips followed the recommended Affymetrix protocol.  Briefly, double stranded cDNA was synthesized from 1 to 5 ug of total RNA by using a Superscript Choice System (Invitrogen), with an HPLC-purified oligo (dT) 24 primer containing a T7 RNA polymerase promoter sequence at the 5’-end (Proligo LLC. Boulder, CO). The second cDNA strand was synthesized by using E. Coli DNA polymerase I, RNase H and DNA ligase.  Labeled cRNA was generated from cDNA by in vitro transcription using a GeneChip IVT labeling kit (Affymetrix Inc.) following the manufacturer’s instructions and incorporating biotinylated synthetic analog as pseudouridine reagent, a reaction mediated by MEGAscript T7 RNA Polymerase.

extract_protocol: Dams were killed by exposure to CO2. Fetuses were dissected from the uterine horn and embryonic membranes then frozen on pulverized dry ice. Tissue samples were taken from the fetuses to determine sex using PCR for SRY (Yang J and RT Zoeller, 2002). Fetal cerebral cortices were removed from each mouse and used for microarray and RT-PCR analysis. Total RNA was extracted from half cortices of individual female fetuses using RNeasy Lipid tissue Mini kits (Qiagen, Germantown, MD) according to the manufacturer's instructions.  The quality of total RNA was evaluated by A260/A280 ratio (found to be at least 1.8 for each sample) and by electrophoresis on the Agilent Bioanalyzer.

treatment_protocol: Timed-pregnant C57BL/6 mice (n=20; Harlan, Indianapolis, IN) arrived on gestational day (GD) 11 and were housed individually in plastic cages under a 12:12 light cycle (0600 h–1800 h) with food available ad libitum. Mice were divided randomly into one of 4 groups (control, hypo, hypo+ and hyper; 5 per group) . Mice in the control and hyper groups were provided with fresh drinking water containing 2% sucrose from GD 13 to GD 16 until sacrifice. Mice in hypo and hypo+ were provided with fresh drinking water daily containing 1% Perchlorate (Per) and 0.025% Methimazole (MMI) supplemented with 2% sucrose (to mask bitterness) from GD 13 to sacrifice on GD 16. Twelve hours prior to sacrifice on GD 16 all mice received a single subcutaneous injection. Control and hypo mice received vehicle (0.9% saline in 100 µl volume); the hypo+ group received 25.0 µg/100g body weight thyroxine (T4) with 2.5 µg/100g body weight T3 to restore a physiological level of TH; the hyper group received 100.0 µg/100g body weight T4 with 10.0 µg/100g body weight T3 to model hyperthyroidism.

tag: strain

tag: treatment

value: provided with fresh drinking water daily containing 1% Perchlorate (Per) and 0.025% Methimazole (MMI) supplemented with 2% sucrose (to mask bitterness) from GD 13 to sacrifice on GD 16 +  25.0 µg/100g body weight thyroxine (T4) with 2.5 µg/100g body weight T3 to restore a physiological level of TH

value: Fetal cerebral cortex

tag: genotype

value: wild type

tag: age

value: gestational day 16


title: Hypo 1

source_name: mouse fetal cerebral cortex on GD16 treated with PTU for 3 days

value: provided with fresh drinking water daily containing 1% Perchlorate (Per) and 0.025% Methimazole (MMI) supplemented with 2% sucrose (to mask bitterness) from GD 13 to sacrifice on GD 16 + vehicle


title: Whole transcriptome analysis of INA6 cells using TileShuffle (permanently cultured in presence of IL-6 )

city: Leipzig

first: Kristin

last: Reiche

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells have been permanently cultured in IL-6. Intensities were processed with TileShuffle.

hyb_protocol: Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.

scan_protocol: Affymetrix Human Tiling 1.0 array were proceed using the GCS3000 7G system according to manufacturer's protocol.

data_processing: Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using the corresponding BPMAP files. Intensities of perfect match (PM) probes were processed with TileShuffle (Otto C, Reiche K, Hackermüller J. "Detection of differentially expressed segments in tiling array data". Bioinformatics. 2012 Jun 1;28(11):1471-9. Epub 2012 Apr 6.) using a window size of 200, the arithmetic mean trimmed by maximal and minimal value as scoring function, four GC content bins, 10000 permutations, and a q-value threshold of 0.05. In order to estimate the significance of a window score we repeatedly permute all probe intensities across the array while interchanging only those that belong to the same sequence-specific affinity bin, recompute the window scores, and compare them with the original ones. By counting the number of permuted windows with higher score, we estimate empirical p-values of windows, and report q-values adjusted according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995.).

source_name: Human multiple myeloma cells (INA6) permanently cultured in presence of IL-6

label_protocol: 10µg RNA were analyzed on Affymetrix Human Tiling 1.0 array set according to the manufacturer's protocol.

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

tag: cell line

tag: tumor

value: multiple myeloma


title: Hypo 3


title: Control 5

source_name: mouse fetal cerebral cortex on GD16

value: provided with fresh drinking water containing 2% sucrose from GD 13 to GD 16 until sacrifice + vehicle


title: Control 4


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 withdrawal)

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours

value: IL-6 has been withdrawn for 13 hours


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=40

description:
5125398047_A
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=40

value: F

value: UT


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 restimulation)

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: Hypo 2


title: Whole transcriptome analysis of HFF cells using TileShuffle (G2 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G2 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G2 phase of mitotic cell cycle

value: HFF

tag: phase


title: Whole transcriptome analysis of HFF cells using TileShuffle (S phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in S phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in S phase of mitotic cell cycle

value: S


title: Human gut microbiome from healthy individuals with alcohol abuse CD2


title: Human gut microbiome from healthy individuals with alcohol abuse CD6


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=41

description:
5125398047_H
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=41


title: Human gut microbiome from healthy individuals with alcohol abuse CD8


title: Human gut microbiome from healthy individuals with alcohol abuse CD3


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G1 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle


title: Human gut microbiome from healthy individuals with alcohol abuse CD10


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=39

description:
5125398047_C
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=39


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G0 phase of mitotic cell cycle


title: P53_ind_chipB_TileShuffle

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct P53 on Affymetrix Human Tiling 1.0 array set after induction of P53 expression. Intensities were processed with TileShuffle.

source_name: Colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53

tag: cell type

value: colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=37

description:
5125398041_J
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=37

value: whole blood


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=35

description:
4674281015_B
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=35

value: sepsis survivor


title: Control 2


title: Human gut microbiome from healthy individuals with alcohol abuse CD1


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=38

description:
4717421101_J
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=38

value: M


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=36

description:
4717421101_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=36

value: Other


title: Human gut microbiome from healthy individuals with alcohol abuse CD4


title: Control 1


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=34

description:
4674281015_E
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=34


title: Human gut microbiome from healthy individuals with alcohol abuse CD9


title: P53_nor_chipB_TileShuffle

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct P53 on Affymetrix Human Tiling 1.0 array set. Intensities were processed with TileShuffle.

source_name: Colorectal carcinoma cells with defunct P53 (D53wt cells)

value: colorectal carcinoma cells with defunct P53 (D53wt cells)


title: Control 3

source_name: mouse fetal cerebral cortex on GD16

value: Fetal cerebral cortex


title: Whole transcriptome analysis of INA6 cells using TileShuffle (permanently cultured in presence of IL-6 )

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells have been permanently cultured in IL-6. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) permanently cultured in presence of IL-6


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=32

description:
4481649065_I
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=32


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 withdrawal)

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours


title: Human gut microbiome from alcoholic cirrhosis patients AB12


title: Human gut microbiome from alcoholic cirrhosis patients AB11


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=31

description:
4481649092_A
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=31

value: lung


title: PAXgene whole blood, sepsis_survivor, Day_2, ID=30

description:
4674281008_A
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 2, ID=30

value: blood


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 restimulation)

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


value: permanently cultured in presence of IL-6


title: Whole transcriptome analysis of HFF cells using TileShuffle (G2 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G2 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G2 phase of mitotic cell cycle


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=30

description:
4674281008_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=30


title: Human gut microbiome from alcoholic cirrhosis patients AB9


title: Human gut microbiome from alcoholic cirrhosis patients AB10


title: Whole transcriptome analysis of HFF cells using TileShuffle (S phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in S phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in S phase of mitotic cell cycle


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=33

description:
4674281014_G
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=33


title: Human gut microbiome from alcoholic cirrhosis patients AB7


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G1 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle


value: multiple myeloma

value: restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: NH-02_RV_mRNA

type: SRA

city: Berlin

first: Silke

last: Sperling

state: Berlin

address: Lindenberger Weg 80

department: Cardiovascular Genetics

institute: Experimental and Clinical Research Center (ECRC), Charité / MDC for Molecular Medicine

description: mRNA-Seq.

library_source: transcriptomic

data_processing:
Sequencing reads were extracted from the image files using the open source Firecrest and Bustard applications (Illumina Genome Analyzer pipeline 1.3.2, 1.4.0 and 1.5.0). mRNA reads were mapped to the human reference genome (NCBI v36.1; hg18) using RazerS allowing at most 10 equally-best hits and two mismatches (no InDels) per read. Multimatched reads were proportionately assigned to each of their mapping locations using MuMRescueLite software with a window size of 200 bp. Reads were assigned to genes and transcripts if their mapped location is inside of exon boundaries as defined by ENSEMBL (v54)5. To further assign unmapped reads, a gene-wise splice junction sequence library was produced from pairwise connection of exon sequences corresponding to all known 5' to 3' splice junctions (supported by the analysis of aligned EST and cDNA sequences). For transcripts, the read counts were adjusted using the proportion estimation (POEM) method in the Solas package. Read count normalization for mRNAs (genes and transcripts) was performed using the RNA composition adjustment by trimmed mean of M-values (TMM) and quantile-to-quantile count adjustment implemented in the edgeR package.

Processed data files are linked to the Series record as supplementary files.

source_name: right ventricle from normal human heart

extract_protocol: Total RNA was isolated from human heart samples using TRIzol reagent. Messenger RNAs were isolated from total RNA and prepared for sequencing using Illumina Kit RS-100-0801 according to the manufacturer's protocol (Preparing Samples for Sequencing of mRNA Sept 2008). The sequencing libraries were generated using a non-strand-specific library construction method.

value: heart, right ventricle

tag: disease state

value: healthy


title: Human gut microbiome from alcoholic cirrhosis patients AB6


title: Human gut microbiome from alcoholic cirrhosis patients AB4


title: PAXgene whole blood, sepsis_survivor, Day_1, ID=29

description:
4481649065_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_survivor, Day 1, ID=29

tag: tissue

value: F


title: PAXgene whole blood, sepsis_nonsurvivor, Day_5, ID=23

description:
4717421101_C
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 5, ID=23

tag: disease status

value: sepsis nonsurvivor


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G0 phase of mitotic cell cycle

value: HFF


title: PAXgene whole blood, sepsis_nonsurvivor, Day_5, ID=24

description:
4717421050_J
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 5, ID=24

tag: gender


title: Human gut microbiome from alcoholic cirrhosis patients AB8


title: Human gut microbiome from alcoholic cirrhosis patients AB5


title: PAXgene whole blood, sepsis_nonsurvivor, Day_5, ID=19

description:
4674281008_K
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 5, ID=19

tag: age (years)


title: Whole transcriptome analysis of HFF cells using TileShuffle (G2 phase)


title: Human gut microbiome from alcoholic cirrhosis patients AB3


title: P53_ind_chipC_TileShuffle

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct P53 on Affymetrix Human Tiling 1.0 array set after induction of P53 expression. Intensities were processed with TileShuffle.

source_name: Colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53

value: colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53


value: S


title: P53_nor_chipC_TileShuffle

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct P53 on Affymetrix Human Tiling 1.0 array set. Intensities were processed with TileShuffle.

source_name: Colorectal carcinoma cells with defunct P53 (D53wt cells)


title: 61

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: 11F11, 5850 College Street

department: Pathology

institute: Dalhousie University

description: puromycin selected polyclonal cells

hyb_protocol: Purified cRNA samples were fragmented and hybridized to an Agilent SurePrint G3 8x60K Gene Expression microarray v2 slide

scan_protocol: scanned at 5uM resolution with an Agilent G2565CA High Resolution Scanner

data_processing: Data was processed with Agilent’s Feature Extraction software version 11.0.1.1 using the protocol GE1_1100_Jul11 and 8x60K grid file 039494_D_F_20120628. Samples were normalized using the percentile shift algorithm with no baseline transformation.

source_name: MDA-MB-468 ALDH1A3 shRNA1 cells

label_protocol: 400ng of the RNA samples spiked with RNA spike in controls were converted to cDNA and in vitro transcribed for amplification and incorporation of labelled CTP (cRNA).

growth_protocol: Stable transfectants were maintained in DMEM supplemented with 10% FBS and 0.25ug/mL puromycin.

extract_protocol: RNA extracted with TRIzol and Purelink RNA kit

value: breast cancer


title: SMP

description: puromycin selected polyclonal cells

source_name: MDA-MB-468 shRNA scramble control cells


title: Whole transcriptome analysis of INA6 cells using TileShuffle (permanently cultured in presence of IL-6 )

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells have been permanently cultured in IL-6. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) permanently cultured in presence of IL-6


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 withdrawal)

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours

value: IL-6 has been withdrawn for 13 hours


title: 1A3

description: puromycin selected polyclonal cells

source_name: MDA-MB-231 ALDH1A3 overexpression cells


title: P53_ind_chipN_TileShuffle


title: Human gut microbiome from alcoholic cirrhosis patients AB2


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 restimulation)

source_name: Human multiple myeloma cells (INA6) restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: MSCV

description: puromycin selected polyclonal cells

source_name: MDA-MB-231 vector control cells


title: P53_nor_chipN_TileShuffle


title: PAXgene whole blood, sepsis_nonsurvivor, Day_4, ID=21

description:
4717421101_H
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 4, ID=21

value: whole blood

tag: severity (apacheii)

value: UT


title: PAXgene whole blood, sepsis_nonsurvivor, Day_4, ID=20

description:
4674281009_L
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 4, ID=20

value: M

tag: neutrophil proportion

value: Other


title: PAXgene whole blood, sepsis_nonsurvivor, Day_4, ID=19

description:
4674281008_E
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 4, ID=19

tag: site of infection

value: lung


description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G2 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G2 phase of mitotic cell cycle


title: Human gut microbiome from alcoholic cirrhosis patients AB1

tag: source


title: Whole transcriptome analysis of HFF cells using TileShuffle (S phase)

source_name: Human foreskin fibroblasts (HFF) in S phase of mitotic cell cycle


title: PAXgene whole blood, sepsis_nonsurvivor, Day_4, ID=24

description:
4717421050_I
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 4, ID=24

value: blood


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)

source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle


title: PAXgene whole blood, sepsis_nonsurvivor, Day_4, ID=23

description:
4717421050_L
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 4, ID=23


title: PAXgene whole blood, sepsis_nonsurvivor, Day_3, ID=27

description:
5445295006_H
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 3, ID=27


title: PAXgene whole blood, sepsis_nonsurvivor, Day_3, ID=26

description:
5125398046_G
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 3, ID=26


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)

source_name: Human foreskin fibroblasts (HFF) in G0 phase of mitotic cell cycle


title: P53_ind_chipA_TileShuffle

source_name: Colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53


title: PAXgene whole blood, sepsis_nonsurvivor, Day_3, ID=24

description:
4717421050_H
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 3, ID=24


title: PAXgene whole blood, sepsis_nonsurvivor, Day_3, ID=19

description:
4481649065_J
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 3, ID=19


title: PAXgene whole blood, sepsis_nonsurvivor, Day_3, ID=23

description:
4717421050_K
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 3, ID=23


title: Whole transcriptome analysis of INA6 cells using TileShuffle (permanently cultured in presence of IL-6 )

source_name: Human multiple myeloma cells (INA6) permanently cultured in presence of IL-6

value: multiple myeloma


title: PAXgene whole blood, sepsis_nonsurvivor, Day_3, ID=21

description:
4717421101_G
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 3, ID=21


title: PAXgene whole blood, sepsis_nonsurvivor, Day_2, ID=26

description:
5125398046_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 2, ID=26


title: PAXgene whole blood, sepsis_nonsurvivor, Day_2, ID=23

description:
4717421005_L
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 2, ID=23


title: P53_nor_chipA_TileShuffle

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct P53 on Affymetrix Human Tiling 1.0 array set. Intensities were processed with TileShuffle.

source_name: Colorectal carcinoma cells with defunct P53 (D53wt cells)

value: colorectal carcinoma cells with defunct P53 (D53wt cells)


title: PAXgene whole blood, sepsis_nonsurvivor, Day_2, ID=27

description:
5445295006_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 2, ID=27


title: PAXgene whole blood, sepsis_nonsurvivor, Day_2, ID=24

description:
4717421050_G
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 2, ID=24


title: PAXgene whole blood, sepsis_nonsurvivor, Day_3, ID=22

description:
4674281009_E
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 3, ID=22


title: Teratoma Replicate 1

city: Jerusalem

first: Deborah

last: Nejman

address: Ein Kerem

country: Israel

institute: Hebrew University

hyb_protocol: The labeled Input and Bound DNAs were combined and hybridized for 60 h at 67°C in 15% deionized formamide to a CpG island microarray using the Agilent aCGH hybridization buffer and protocol.

scan_protocol: Arrays were washed according to the Agilent aCGH protocol, immediately scanned on an Agilent microarray scanner and processed using Agilent Feature extraction software version 9.5.

data_processing: Probe log ratio signals were Loess normalized and transformed into Z-scores according to their Tm.

label_protocol: The Input and Bound DNAs were labeled using the Agilent Technologies Genomic Labeling kit Plus according to the manufacturer’s instructions. Briefly, 300ng of each sample was labeled with Cyanine-3 or Cyanine-5 dUTP and purified using microcon YM 30 columns.

extract_protocol: Human (10µg) DNA was sonicated to an average fragment size of 300–1000 bp, precipitated with  400 mM NaCl, 2 volumes of ethanol and 1 µl glycogen. 1.5 µg were set aside as the Input fraction. DNA was denatured and anti-5-methylcytidine  monoclonal antibody (10 µl for 5 µg) was added and incubated on a rotator at 4°C overnight. 40 µl Dynabeads (Sheep anti-Mouse IgG) were prewashed  with 0.1% BSA/PBS and added to the DNA. The DNA was then washed 3 times and Ab-bound DNA resuspended and extracted with proteinase K,  phenol-chloroform and ethanol precipitation.

value: Teratoma

tag: sample type

value: input

value: bound

tag: antibody

tag: antibody manufacturer

value: Diagenode

tag: antibody catalog #


title: PAXgene whole blood, sepsis_nonsurvivor, Day_2, ID=22

description:
4674281009_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 2, ID=22

value: sepsis nonsurvivor


title: P53_nor_chipG_TileShuffle


title: PAXgene whole blood, sepsis_nonsurvivor, Day_2, ID=21

description:
4674281014_A
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 2, ID=21

value: F


title: Retinoic Acid treated Human embryonic stem cells CSES2 Replicate 1

source_name: human ES cells - CSES2 treated with Retinoic Acid_INPUT

tag: cell line

source_name: human ES cells - CSES2 treated with Retinoic Acid_BOUND


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 restimulation)

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours

tag: tumor

tag: treatment


title: PAXgene whole blood, sepsis_nonsurvivor, Day_2, ID=19

description:
4674281009_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 2, ID=19


title: Human embryonic stem cells CSES2 Replicate 1

source_name: human ES cells - CSES2_INPUT

tag: cell type

value: human ES cells - CSES2

source_name: human ES cells - CSES2_BOUND


title: Human embryoid bodies from CSES2 Replicate 1

source_name: CSES2 - Embryoid Bodies_INPUT

value: CSES2 - Embryoid Bodies

source_name: CSES2 - Embryoid Bodies_BOUND


title: P53_ind_chipG_TileShuffle

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct P53 on Affymetrix Human Tiling 1.0 array set after induction of P53 expression. Intensities were processed with TileShuffle.

source_name: Colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53

value: colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 withdrawal)

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours

value: IL-6 has been withdrawn for 13 hours


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G1 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle

value: HFF

tag: phase


title: Whole transcriptome analysis of HFF cells using TileShuffle (G2 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G2 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G2 phase of mitotic cell cycle


title: Whole transcriptome analysis of HFF cells using TileShuffle (S phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in S phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in S phase of mitotic cell cycle

value: S


title: PAXgene whole blood, sepsis_nonsurvivor, Day_1, ID=28

description:
5445295027_L
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 1, ID=28

tag: tissue

value: whole blood


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G0 phase of mitotic cell cycle


title: Colon Fetal Replicate 1

source_name: Fetal Colon_INPUT

value: Fetal Colon

value: Male

tag: age

value: 26 weeks

source_name: Fetal Colon_BOUND


title: Human embryonic stem cells CSES2 Replicate 2


title: P53_ind_chipL_TileShuffle


title: PAXgene whole blood, sepsis_nonsurvivor, Day_1, ID=27

description:
5445295025_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 1, ID=27

tag: disease status

tag: gender

value: lung


title: Atrophy, corpus 22C

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description: replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Human stomach

label_protocol: cRNA amplification and biotin labeling from 500 ng of total RNA were performed using Illumina® TotalPrep RNA amplification kit (Ambion, Inc., Austin, TX)

extract_protocol: The tissue was disrupted using a glass mortar and pestle and added to a QIAshredder column (Qiagen, Hilden, Germany) before RNA extraction to ensure proper lysis of the tissue. Total RNA was extracted using the RNEasy Mini Kit (Qiagen).

treatment_protocol: Biopsies from the antrum and corpus mucosa were obtained during endoscopy and stored at -70 °C

tag: disease state

value: atrophy

tag: stomach region

value: corpus

value: stomach


title: P53_nor_chipL_TileShuffle

source_name: Colorectal carcinoma cells with defunct P53 (D53wt cells)

value: colorectal carcinoma cells with defunct P53 (D53wt cells)


title: Atrophy, corpus 48C

description: replicate 6


title: Helicobacter pylori non-infected, antrum 35A

description: replicate 1

value: non-infected

value: antrum


title: Helicobacter pylori non-infected, corpus 35C

description: replicate 2


title: Atrophy, corpus 44C

description: replicate 6


title: Atrophy, antrum 48A

description: replicate 5


title: PAXgene whole blood, sepsis_nonsurvivor, Day_1, ID=26

description:
5125398046_E
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 1, ID=26

value: sepsis nonsurvivor

value: M

tag: age (years)

tag: severity (apacheii)

tag: neutrophil proportion

tag: site of infection

value: blood


title: Colon Fetal Replicate 2

value: 29 weeks

tag: sample type

value: input

value: bound

tag: antibody

tag: antibody manufacturer

value: Diagenode


title: Atrophy, antrum 44A

description: replicate 5


title: Whole transcriptome analysis of INA6 cells using TileShuffle (permanently cultured in presence of IL-6 )

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells have been permanently cultured in IL-6. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) permanently cultured in presence of IL-6

tag: cell line

tag: tumor

value: multiple myeloma


title: PAXgene whole blood, sepsis_nonsurvivor, Day_1, ID=22

description:
4674281008_D
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 1, ID=22

value: whole blood


title: Helicobacter pylori infected, corpus 8C

description: replicate 4

value: infected


title: PAXgene whole blood, sepsis_nonsurvivor, Day_1, ID=23

description:
4717421005_K
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 1, ID=23

value: F

value: lung


title: PAXgene whole blood, sepsis_nonsurvivor, Day_1, ID=24

description:
4717421050_F
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 1, ID=24


tag: treatment

value: IL-6 has been withdrawn for 13 hours


title: Helicobacter pylori infected, corpus 9C

description: replicate 4

value: corpus

value: stomach


title: Atrophy, antrum 22A

description: replicate 5

value: atrophy


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 restimulation)

source_name: Human multiple myeloma cells (INA6) restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


value: HFF

tag: phase


title: PAXgene whole blood, sepsis_nonsurvivor, Day_1, ID=21

description:
4674281014_B
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 1, ID=21

tag: tissue

value: sepsis nonsurvivor

value: UT


value: S


title: Helicobacter pylori infected, antrum 30A

description: replicate 3

value: antrum


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)

source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle


title: Muscle Fetal Replicate 2

source_name: Fetal Skeletal Muscle_INPUT

value: Fetal Skeletal Muscle

value: Male

tag: age

value: 29 weeks

value: input

source_name: Fetal Skeletal Muscle_BOUND

tag: antibody catalog #


title: PAXgene whole blood, Control, Day_1, ID=16

description:
4950679036_G
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=16

value: whole blood

tag: disease status

value: healthy

tag: gender


title: PAXgene whole blood, Control, Day_1, ID=15

description:
4950679036_E
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=15

value: F


title: Helicobacter pylori infected, antrum 8A

description: replicate 3

tag: disease state

value: infected

tag: stomach region


title: PAXgene whole blood, Control, Day_1, ID=17

description:
4950679036_I
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=17

tag: age (years)

tag: severity (apacheii)


title: P53_ind_chipE_TileShuffle

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct P53 on Affymetrix Human Tiling 1.0 array set after induction of P53 expression. Intensities were processed with TileShuffle.

source_name: Colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53

tag: cell type

value: colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53


title: PAXgene whole blood, sepsis_nonsurvivor, Day_1, ID=25

description:
5125398047_G
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 1, ID=25

value: M

tag: neutrophil proportion

tag: site of infection

value: lung


title: Muscle Fetal Replicate 3

value: 24 weeks

tag: sample type

value: bound

tag: antibody

tag: antibody manufacturer

value: Diagenode


title: Helicobacter pylori infected, antrum 9A

description: replicate 3

source_name: Human stomach

value: stomach


title: Liver Fetal Replicate 3

source_name: Fetal Liver_INPUT

value: Fetal Liver

value: 26 weeks

source_name: Fetal Liver_BOUND


title: PAXgene whole blood, sepsis_nonsurvivor, Day_1, ID=19

description:
4674281009_C
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, sepsis_nonsurvivor, Day 1, ID=19

value: sepsis nonsurvivor


title: PAXgene whole blood, Control, Day_1, ID=14

description:
4950679036_C
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=14


title: Helicobacter pylori non-infected, antrum 23A

description: replicate 1

value: non-infected

value: antrum


title: Helicobacter pylori non-infected, antrum 49A

description: replicate 1


title: Helicobacter pylori infected, corpus 30C

description: replicate 4

value: corpus


title: Helicobacter pylori non-infected, corpus 23C

description: replicate 2


title: Helicobacter pylori non-infected, corpus 49C

description: replicate 2


title: Muscle Fetal Replicate 1

value: Fetal Skeletal Muscle

value: Male

value: 29 weeks

value: input


title: Liver Fetal Replicate 2


title: P53_nor_chipE_TileShuffle

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct P53 on Affymetrix Human Tiling 1.0 array set. Intensities were processed with TileShuffle.

source_name: Colorectal carcinoma cells with defunct P53 (D53wt cells)

value: colorectal carcinoma cells with defunct P53 (D53wt cells)


title: Liver Fetal Replicate 1


title: Brain Fetal Replicate 1

source_name: Fetal Brain_INPUT

value: Fetal Brain

value: Female

value: 28 weeks

source_name: Fetal Brain_BOUND


title: Brain Fetal Replicate 2

value: 37 weeks

value: bound


title: PAXgene whole blood, Control, Day_1, ID=12

description:
4950679034_K
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=12

value: whole blood

value: healthy

value: F


title: PAXgene whole blood, Control, Day_1, ID=9

description:
4950679034_E
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=9

value: M


title: PAXgene whole blood, Control, Day_1, ID=8

description:
4950679034_C
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=8


title: KH092-7AS vs KH092-7SD rep 4

city: Montreal

first: Maria

middle: Luz

last: Jaramillo

state: Quebec

address: 6100 Royalmount Ave

institute: National Research Council of Canada

description: resistant KHO92-7AS ascites cell line vs resistant KHO92-7SD solid tumor derived cell line replicate #4

hyb_protocol: Probes were denatured for 5 min at 95°C.The slides were hybridized with labeled cDNAs overnight at 65°C in Agilent Hyb buffer with yeast tRNA (Invitrogen) and salmon sperm DNA (Invitrogen) in a microslides box hybridization chamber. Slides were washed 2 times in 1 X SSC-0.1% SDS at 42°C and at once each at room temperature in 1X SSC and 0.1XSSC. Slides were dried by centrifugation.

scan_protocol: Microarrays were scanned at 5 microns per pixel in a ScanArray Gx microarray scanner (Perkin Elmer).

data_processing: Signal intensity was quantified with Imagene (BioDiscovery) and final Lowess normalization and inspection of the data was done with the GeneSpring package GX v.7.3 (Agilent Technologies).

source_name: resistant KHO92-7AS ascites cell line

label_protocol: Labeled cDNA was synthesized from 25ug of total RNA with Superscript III (Invitrogen) in the presence of Cyanine 3-dCTP or Cyanine 5-dCTP (Perkin-Elmer Life Sciences) and oligo (dT) primer.

growth_protocol: cell lines were grown in RPMI 1640 (Hyclone) supplemented with 5% fetal bovine serum in a humidified atmosphere at 37°C in 5% CO2.

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

treatment_protocol: resistant cell lines were derived from tumors evaluated for resistance to long term  treatment in vivo with 1 mg/Kg topotecan and 150 mg/Kg pazopanib

value: ovarian

tag: cell line

value: resistant KHO92-7AS ascites cell line

value: resistant solid tumor 7SD cell line


title: PAXgene whole blood, Control, Day_1, ID=10

description:
4950679034_G
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=10


title: PAXgene whole blood, Control, Day_1, ID=11

description:
4950679034_I
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=11


title: KH092-7AS vs KH092-7SD rep 2

description: resistant KHO92-7AS ascites cell line vs resistant KHO92-7SD solid tumor derived cell line replicate #2


title: PAXgene whole blood, Control, Day_1, ID=5

description:
4950679008_I
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=5


title: 5-D2-DOXO 2

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing: The data were normalised using quantile normalisation with Genome Studio software 2011.1

source_name: Bulk of MCA205 sarcoma

label_protocol: standard Illumina protocol

growth_protocol: ex vivo isolation, no in vitro stimulation

extract_protocol: Trizol

tag: genotype

value: WT

tag: treatment

value: Doxorubucin

tag: time

value: 2 days

value: Bulk of MCA205 sarcoma

tag: genetic background


title: PAXgene whole blood, Control, Day_1, ID=4

description:
4950679008_G
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=4

tag: tissue

tag: disease status


title: PAXgene whole blood, Control, Day_1, ID=6

description:
4950679008_K
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=6

tag: gender


title: 3-D2-PBS 3

treatment_protocol: ex vivo isolation, no in vitro stimulation

value: PBS


title: 7-D7-PBS 1

value: 7 days


title: 23-D10-DOXO R2

value: 10 days

tag: response

value: responder


title: KH092-7AS vs KH092-7SD rep 3

description: resistant KHO92-7AS ascites cell line vs resistant KHO92-7SD solid tumor derived cell line replicate #3


title: KH092-7AS vs KH092-7SD rep 1

description: resistant KHO92-7AS ascites cell line vs resistant KHO92-7SD solid tumor derived cell line replicate #1


title: 2-D2-PBS 2


title: 13-D7-DOXO R 1


title: PAXgene whole blood, Control, Day_1, ID=7

description:
4950679034_A
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=7

tag: age (years)


title: SKOV3-13 vs KH092-7AS rep 2

description: resistant KHO92-7AS ascites cell line replicate # 2 vs sensitive SKOV3-13

source_name: sensitive SKOV3-13

value: sensitive SKOV-13 cell line


title: SKOV3-13 vs KH092-7AS rep 4

description: resistant KHO92-7AS ascites cell line replicate # 4 vs sensitive SKOV3-13


title: SKOV3-13 vs KH092-7SD rep 4

description: resistant KHO92-7SD solid tumor derived cell line replicate # 4 vs sensitive SKOV3-13


title: SKOV3-13 vs KH092-7AS rep 1

description: resistant KHO92-7AS ascites cell line replicate # 1 vs sensitive SKOV3-13


title: 10-D7-DOXO NR 1

value: non-responder


title: SKOV3-13 vs KH092-7AS rep 3

description: resistant KHO92-7AS ascites cell line replicate # 3 vs sensitive SKOV3-13


title: 9-D7-PBS 3


title: PAXgene whole blood, Control, Day_1, ID=2

description:
4950679008_C
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=2

value: whole blood

tag: severity (apacheii)


title: PAXgene whole blood, Control, Day_1, ID=3

description:
4950679008_E
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=3

value: healthy


title: PAXgene whole blood, Control, Day_1, ID=1

description:
4950679008_A
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=1

value: F


title: 8-D7-PBS 2


title: SKOV3-13 vs KH092-7SD rep 2

description: resistant KHO92-7SD solid tumor derived cell line replicate # 2 vs sensitive SKOV3-13

tag: cell type


title: SKOV3-13 vs KH092-7SD rep 1

description: resistant KHO92-7SD solid tumor derived cell line replicate # 1 vs sensitive SKOV3-13


title: adult female on HFD in normoxia, rep3

city: LA JOLLA

first: Erilynn

last: Heinrichsen

state: CA

address: 9500 Gilman Dr, MC0735

institute: UC-San Diego

description: Adult female Drosophila, after 1 week on high-fat diet (with 20% weight: volume coconut oil) in normoxia

hyb_protocol: All samples were labeled, hyb'd and scanned by the GeneChip Microarray Core at UCSD following Affymetrix specifications.

data_processing: The raw data were normalized using Bioconductor Affy software (www.bioconductor.org/packages/2.0/bioc/html/affy.html) with the MAS5 algorithm, followed by analysis of the normalized data for each array spot with VAMPIRE microarray suite.  A spot was considered differentially expressed between two samples when the threshold of false discovery rate (fdr) was smaller than 0.05. Significance limits were set at changes of 1.5-fold (for up-regulated genes) and 0.67-fold (for down-regulated genes).

organism: Drosophila melanogaster

source_name: Adult female Drosophila, high-fat diet in normoxia

growth_protocol: w1118 flies eclosed in 25 degree incubator and then were kept at room temperature.

extract_protocol: Trizol extraction of total RNA was followed by RNA cleanup using RNeasy kit, according to the manufacturer's instructions.

treatment_protocol: At day 3-5, flies were put on their specific food and oxygen condition for one week.

value: whole body

value: female

tag: age

value: adult, d10-12


title: 12-D7-DOXO NR 3


title: Smad3/TGF-B2

city: Madison

first: Xudong

middle: daniel

last: Shi

state: WI

address: 1111 Highland Ave

department: Surgery

institute: University of Wisconsin

hyb_protocol: Labeled cDNA was hybridized to rat Genechip (Rat Gene 1.0 ST Array) overnight in the AFX HybOven480 (Santa Clara, CA), and then post-processed on the Fluidics450 station.

scan_protocol: The microarray slides were scanned on a G7 scanner (Affirmatrix, Santa Clara, CA).

data_processing: Data were extracted using the Affymetrix console software (Affymetrix, Santa Clara, CA).

organism: Rattus norvegicus

source_name: male adult vascular smooth muscle cells

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

growth_protocol: Vascular SMCs were used at passages 5 to 6 for all experiments and were maintained in DMEM supplemented with 10% fetal bovine solution (FBS) at 37 °C with 5% CO2.

treatment_protocol: Adenovirus infected smooth muscle cells were serum starved for 16 h and Then treated with TGf-B for 24 h.

value: smooth muscle cells

value: wild type

value: adult


title: adult female on HFD in normoxia, rep2

scan_protocol: All samples were labeled, hyb'd and scanned by the GeneChip Microarray Core at UCSD following Affymetrix specifications.


title: 1-D2-PBS 1

value: WT

value: 2 days


title: GFP3

description: GFP control

value: GFP control


title: Smad3/TGF-B3


title: Smad3/TGF-B1


title: SKOV3-13 vs KH092-7SD rep 3

description: resistant KHO92-7SD solid tumor derived cell line replicate # 3 vs sensitive SKOV3-13

value: ovarian

value: resistant solid tumor 7SD cell line


title: 11-D7-DOXO NR 2

value: Doxorubucin

value: 7 days

value: Bulk of MCA205 sarcoma


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 withdrawal)

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours

tag: tumor

value: multiple myeloma

value: IL-6 has been withdrawn for 13 hours


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 restimulation)

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: GFP2

description: GFP control


title: GFP1

description: GFP control


title: Whole transcriptome analysis of HFF cells using TileShuffle (G2 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G2 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G2 phase of mitotic cell cycle

value: HFF

tag: phase


title: PAXgene whole blood, Control, Day_1, ID=18

description:
4950679036_K
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=18

value: whole blood

value: healthy

value: M

tag: neutrophil proportion

tag: site of infection


title: 22-D10-DOXO R1

value: 10 days

value: responder


title: adult female on RD in normoxia, rep2

description: Adult female Drosophila, after 1 week on regular diet (Jazz-Mix food) in normoxia

source_name: Adult female Drosophila, regular diet in normoxia

label_protocol: All samples were labeled, hyb'd and scanned by the GeneChip Microarray Core at UCSD following Affymetrix specifications.

value: whole body

value: female

value: adult, d10-12


title: adult female on RD in normoxia, rep1


title: Gα12QL-Huh7, Rep3

city: Seoul

first: Sang Geon

last: Kim

state: Seoul

address: San56-1, Sillim-dong, Kwanak-gu

department: College of Pharmacy

country: South Korea

institute: Seoul National University

hyb_protocol: Each sample was placed on an Agilent human miRNA V14 and covered with an Agilent 8-plex Gasket chamber (Agilent Technologies, CA). Slides were then hybridized for 20 hr at 55ºC using an Agilent hybridization system (Agilent Technologies, CA)

scan_protocol: Hybridized slides were scanned with an Agilent 2505C scanner (Agilent Technologies, CA).

data_processing: Scanned images were analyzed with Feature Extraction v10.7.5.1 (Agilent Technologies, CA) and GeneSpring GX v11.0.2 software (Agilent Technologies, CA)

source_name: Hepatocellular carcinoma cell line

label_protocol: the total RNA sample (100 ng) containing miRNA was labeled with Cyanine 3-pGp (Cy3) using the Agilent miRNA Complete Labeling and Hyb Kit (microRNA Microarray system protocol v.1.5, Agilent Technologies, CA)

growth_protocol: Cells were cultured in RPMI medium 1640 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: RNA was prepared using the mirVana microRNA isolation kit (Ambion, Austin, TX) according to manufacturer’s protocol.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Huh7 hepatoma cells were transfected with pCMV or the plasmid encoding for activated mutant of Gα12 (Gα12QL). Stable transfectants were selected by incubating the cells in culture medium containing Geneticin for 3 weeks.  For experiments, the cells were grown to 70-80% confluency, and were deprived of serum for 24 h.

tag: cell line

value: hepatocellular carcinoma

tag: genotype/variation


title: adult female on RD in normoxia, rep3

tag: genotype


title: adult female on HFD in normoxia, rep1


title: 15-D7-DOXO R 3

value: WT

tag: treatment

tag: time


title: Whole transcriptome analysis of HFF cells using TileShuffle (S phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in S phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in S phase of mitotic cell cycle

value: S


title: Gα12QL-Huh7, Rep2


title: Whole transcriptome analysis of INA6 cells using TileShuffle (permanently cultured in presence of IL-6 )

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells have been permanently cultured in IL-6. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) permanently cultured in presence of IL-6


title: 14-D7-DOXO R 2

source_name: Bulk of MCA205 sarcoma

value: Doxorubucin

tag: tissue

tag: genetic background


title: 4-D2-DOXO 1

value: 2 days


title: doxorubicin_6 hours_rep3 (gene-level)

city: ORSAY

first: Martin

last: Dutertre

address: Rue Henri Becquerel

country: France

institute: INSERM

description:
MCF17 treated by doxorubicin for 6 hours
MCF7_DOXO_n3

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). Transfer 200ul of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Analyses were obtained using the Affymetrix Power Tools software ; core probesets, and antigenomic probes for background correction. The plier-gcbg-sketch algorithm was used to determine gene-level expression data and the RMA-sketch algorithm for the exon-level expression data.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps (for gene-level analyses)

source_name: MCF7 cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: MCF7 cells were maintained in DMEM with 10% fetal bovine serum in a CO2 humidified chamber at 37 °C

extract_protocol: Total RNA was isolated using Trizol total RNA isolation reagent (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: Cells were treated with doxorubicin (2 µg/ml) or 0.1% DMSO as a control.

tag: tumor stage

value: ER+ breast cancer cell line

tag: agent

value: doxorubicin


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G0 phase of mitotic cell cycle


title: Gα12QL-Huh7, Rep4


title: P53_ind_chipI_TileShuffle

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct P53 on Affymetrix Human Tiling 1.0 array set after induction of P53 expression. Intensities were processed with TileShuffle.

source_name: Colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53

value: colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53


title: Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G1 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle

value: HFF


title: Gα12QL-Huh7, Rep1


title: WT-Huh7, Rep4

value: wild-type


title: control_6 hours_rep3 (gene-level)

description:
MCF17 treated by DMSO for 6 hours
MCF7_CTRL_n3

value: control


title: P53_nor_chipI_TileShuffle

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct P53 on Affymetrix Human Tiling 1.0 array set. Intensities were processed with TileShuffle.

source_name: Colorectal carcinoma cells with defunct P53 (D53wt cells)

value: colorectal carcinoma cells with defunct P53 (D53wt cells)


title: WT-Huh7, Rep2


value: multiple myeloma

value: permanently cultured in presence of IL-6


value: IL-6 has been withdrawn for 13 hours


value: restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: WT-Huh7, Rep3


title: doxorubicin_6 hours_rep1 (gene-level)

description:
MCF17 treated by doxorubicin for 6 hours
MCF7_DOXO_n1


title: WT-Huh7, Rep1


title: control_6 hours_rep2 (gene-level)

description:
MCF17 treated by DMSO for 6 hours
MCF7_CTRL_n2


title: PAXgene whole blood, Control, Day_1, ID=13

description:
4950679036_A
"Day 1" refers to the first 24 hrs of ICU admission for the sepsis_survivor and sepsis_nonsurvivor groups, and the day of the first sample collection in healthy controls.

source_name: PAXgene whole blood, Control, Day 1, ID=13

value: whole blood

tag: disease status

value: healthy

tag: gender

value: M

tag: age (years)


value: S


title: doxorubicin_6 hours_rep2 (gene-level)

description:
MCF17 treated by doxorubicin for 6 hours
MCF7_DOXO_n2


title: P53_nor_chipJ_TileShuffle

tag: cell type


title: P53_ind_chipJ_TileShuffle


title: control_6 hours_rep1 (gene-level)

description:
MCF17 treated by DMSO for 6 hours
MCF7_CTRL_n1


title: LLC_E25

city: Carrières sur Seine

first: Damien

last: VALOUR

state: Île-de-France

address: 34, rue Victor HUGO (Bât D)

department: PHASE

institute: INRA

description: Syntax of the sample names: EmbryoName, EnergyStatus of the mother. Where the energy status is either GH, ELC, LLC. Annotations = Energy balance. Experimental variables: Energy Status = Growing heifers (GH) having a positive energy balance, Early lactating cows (ELC) having a negative energy balance, Late lactating cows (LLC) having a null energy balance. Additional data: Holstein cows. Flushed D18 conceptuses. Animals were managed in accordance with the European Community Directive, 86-609-EC and under the license of French Institute of Agronomical Research (INRA-UCEA).

hyb_protocol: Prior to hybridization, microarrays were prehybridized for 30 min at 50°C in a filtered solution of 1% BSA, 3.5X SSC, 0.1% SDS and rinsed twice at room temperature in ultrapure water for 5 min with orbital agitation. They were dried using compressed air. Each microarray was co-hybridized with two fluorescently labelled (Cy3 and Cy5) cDNA samples according to the experimental design (reference design). An evaluated amount of 500 ng of each labelled cDNA was fragmented for 30 min at 60°C in 1X fragmentation buffer (Agilent Technologies). KREAblock is a background blocker and was added as 1/4th of the final volume of 200µL (adjusted with ultra-pure water). Hybridisation were performed on the ICE platform (previously, PICT Gem, Jouy en Josas, http://www4.jouy.inra.fr/gabi_eng/Our-resources/ICE-Integrated-Microgenomics-platform). Then, fragmented labelled cDNA samples were diluted in 200µL of Agilent hybridization buffer 2X and hybridized on the 22K bovine oligo-array for 20 h at 60°C in a rotating hybridization oven (Agilent Technologies). After hybridization, microarrays were washed at room temperature with orbital agitation successively twice for 5 min in a 2X SSC-0.1% SDS solution, once for 5 min in a 0.5X SSC-0.1% SDS solution and three times for 5 min in a 0.2X SSC solution. They were finally dried using compressed air.

scan_protocol: Scanner: Agilent G2505B Microarray Scanner System. Raw data set: Feature extraction with GenePix Pro 6.1.0.4 software. GenePix software was used to extract data at the CRB GADIE of Jouy-en-Josas (http://crb-gadie.inra.fr/)

data_processing: Intensity = Signal Median. Normalization = Signal Median were normalized using the Limma functions in R: - NormalizeWithinArrays (log2, loess transformations) - NormalizeBetweenArrays (Aquantile transformation) - Flags = -50

organism: Bos taurus

source_name: Extra-embryonic tissues (EET), Late lactating cows (LLC) having a null energy balance

label_protocol: The amplified RNA were labelled with the ULSTM aRNA Labelling Kit. Briefly, 2µg of amplified RNA were directly labelled with 2µL of Cy(3-5)-ULS. Amplified RNA and Cy-ULS were mixed with 2µL of 10x labelling solution to obtain a 1x labelling solution mixture in a volume of 20µl (adjusted with ultra-pure water). The mixture was incubated at 85°C for 15 min and chilled on ice. Labelled targets were then purified on KREApure columns. Frequencies of dye incorporation (FOI, rate per thousand labelled nucleotides) and cDNA concentrations were estimated for both dyes by measuring the absorbance at 260 nm, 550 nm and 650 nm on a Nanodrop spectrophotometer (Thermo Scientific). The following ratios were calculated: FOI per 1000 bases (Cy3) = 58.5 * Abs550/Abs260, FOI per 1000 bases (Cy5) = 35.1 * Abs650/Abs260.

extract_protocol: Total RNA from extra-embryonic tissues (N=29) were isolated using Trizol (Invitrogen) and linear amplification was performed using MessageAmp aRNA kit (Ambion, Courtaboeuf, France), starting from 1 µg total RNA as in Degrelle et al. (2008).

treatment_protocol: D18 conceptuses were flushed, the embryonic tissues were dissected out and the Extra-embryonic tissues immediately snap-frozen.

tag: breed

value: Holstein

value: D18 conceptuses

source_name: Pool Placenta - 10 hours amplified RNA from a pool of Placenta.

extract_protocol: Total RNA from Placenta at different stages of pregnancy were isolated using Trizol (Invitrogen), pooled and linear amplification was performed using MessageAmp aRNA kit (Ambion, Courtaboeuf, France), starting from 1 µg total RNA as in Degrelle et al. (2008).

treatment_protocol: Placenta were dissected and tissues were immediately snap-frozen.

value: Pool Placenta Reference


title: ELC_E17

source_name: Extra-embryonic tissues (EET), Early lactating cows (ELC) having a negative energy balance


title: GH_E08

source_name: Extra-embryonic tissues (EET), Growing heifers (GH) having a positive energy balance


title: LLC_E21


title: ELC_E13


title: ELC_E12


title: 24-D10-DOXO R3

value: WT

value: Doxorubucin

value: 10 days

tag: response

value: responder

value: Bulk of MCA205 sarcoma


title: ELC_E27


title: ELC_E29


title: LLC_E26


value: HFF

tag: phase


title: GH_E03


title: Expression analysis of primary glioblastoma (WHO grade IV)F6

description: Expression analysis of primary glioblastoma patient samples (WHO grade IV).

hyb_protocol: nONCOchip 1.0 arrays were proceed using the Agilent Hybridization Kit, Agilent Hybrization-Chambers and an commercial Hyb-Oven according to the manufacturer's protocol (Agilent One-Color Quick Amp Labeling Kit).

scan_protocol: Arrays were scanned using a GenePix 4200 Scanner and the GenePix Pro 6.1 Software (Molecular Devices) with following settings: laser power: 2.32-2.43, PMT: 400, resolution: 5µm, Focus: 1µm, Lines to Average: 2, Wavelength: 532nm, Filter: Standard Green.

data_processing: The data were analyzed with R (version 2.14.2) and BioConductor. Expression levels were quantile normalized and a linear model was fitted using the R package limma in order to identify differentially expressed probes. Reliable variance estimations were obtained by empirical Bayes moderated t-statistics. False discovery rate was controlled by Benjamini-Hochberg adjustment.

source_name: Patient samples of primary glioblastoma (WHO grade IV)

label_protocol: 1µg RNA were analyzed on nONCOchip 1.0 array according to the manufacturer's protocol (Agilent One-Color Quick Amp Labeling kit protocol) with the adaptation of using an N6 − T 7 primer instead of a polyT-T7 primer.

tag: disease state

value: astrocytoma

tag: who grade

value: IV


title: GH_E07


title: Expression analysis of primary glioblastoma (WHO grade IV)I9


title: T24 DDP exp 2

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

country: Netherlands

institute: Erasmus University Medical Center

hyb_protocol: Labeled RNA were hybridized to Custom Exiqon LNA probes for 16 hours at 60°C, subsequently washed and scanned

scan_protocol: After hybridization, samples were scanned using the ScanArray Express HT (Tecan). Image generation and feature extraction were performed using Imagene 6.0.

data_processing: The raw microRNA data, median signal minus median background, were normalized using quantile normalization. Obvious outliers were removed and human miRNAs were selected with an average expression above background. Duplicate spots on the array were averaged. For each cell line, the average expression of 2-3 experiments was calculated and paired Significant Analysis of Micro-arrays (SAM)(MeV; v4.4) was used to identify miRNAs that were differentially expressed in cisplatin resistant cells.

source_name: T24 DDP 10

label_protocol: 1ug of total RNA was labeled using the Createch Cy3 label kit (Createch).

growth_protocol: Cell lines were cultured in RPMI1640 Glutamax, supplemented with 10% FBS and Penicillin/Streptomycin. The cells were cultured at 37 0C, 5% CO2 in a humidified incubator

extract_protocol: Total RNA was isolated using RNA Bee (BioConnect, the Netherlands) according to the manufacturer’s instructions. All samples passed RNA quality control using Nanodrop 2000. MicroRNA profiling was performed as previously described (Pothof et al. 2009).

tag: cell line

value: T24 DDP10


title: T24 DDP exp 1


title: Expression analysis of astrocytoma patient samples of WHO grade IIIV22

description: Expression analysis of astrocytoma patient samples of WHO grade III.

source_name: Patient samples of astrocytoma of WHO grade III

value: III


title: Expression analysis of primary glioblastoma (WHO grade IV)G7


title: T24 exp 2


title: ELC_E22


title: LLC_E18


title: Expression analysis of astrocytoma patient samples of WHO grade IX24

description: Expression analysis of astrocytoma patient samples of WHO grade I.

source_name: Patient samples of astrocytoma of WHO grade I

value: I


description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G2 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G2 phase of mitotic cell cycle


title: LLC_E24


title: ELC_E14


title: P53_ind_chipH_TileShuffle

value: colorectal carcinoma cells (D53wt cells) stably transfected with tetracycline responsive wild type P53


title: Expression analysis of primary glioblastoma (WHO grade IV)Y25


title: Expression analysis of astrocytoma patient samples of WHO grade IIIO15


title: Expression analysis of astrocytoma patient samples of WHO grade IU21


title: Expression analysis of astrocytoma patient samples of WHO grade IIIH8


title: LLC_E30


title: T24 exp 1


title: P53_nor_chipH_TileShuffle

value: colorectal carcinoma cells with defunct P53 (D53wt cells)


description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells have been permanently cultured in IL-6. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) permanently cultured in presence of IL-6

tag: tumor

value: multiple myeloma


title: HCT8 DDP exp 2

source_name: HCT8 DDP

value: HCT8 DDP


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 withdrawal)

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. IL-6 has been withdrawn for 13 hours which initiates apoptosis. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) after IL-6 has been withdrawn for 13 hours

tag: treatment

value: IL-6 has been withdrawn for 13 hours


title: Expression analysis of astrocytoma patient samples of WHO grade IQ17


title: Whole transcriptome analysis of INA6 cells using TileShuffle (IL-6 restimulation)

description: Whole transcriptome expression analysis of INA6 cells on Affymetrix Human Tiling 1.0 array set. Cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours. Intensities were processed with TileShuffle.

source_name: Human multiple myeloma cells (INA6) restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: HCT8 DDP exp 1


title: HCT8 exp 2


title: Whole transcriptome analysis of HFF cells using TileShuffle (G2 phase)


title: HCT8 exp 1


title: GH_E10

value: Holstein

value: D18 conceptuses

value: Pool Placenta Reference


title: GH_E05


title: ELC_E31


title: A2780 DDP exp 3

source_name: A2780 DDP

value: A2780 DDP


title: Expression analysis of astrocytoma patient samples of WHO grade IN14


title: GH_E01


source_name: Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle


title: Whole transcriptome analysis of HFF cells using TileShuffle (S phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in S phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in S phase of mitotic cell cycle

value: S


title: Expression analysis of astrocytoma patient samples of WHO grade IIIJ10


title: A2780 DDP exp 2


title: A2780 DDP exp 1


title: Whole transcriptome analysis of HFF cells using TileShuffle (G0 phase)

description: Whole transcriptome expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.

source_name: Human foreskin fibroblasts (HFF) in G0 phase of mitotic cell cycle


title: LLC_E32

source_name: Extra-embryonic tissues (EET), Late lactating cows (LLC) having a null energy balance


title: colorectal carcinoma cells with induced TP53, biological replicate 1

description: Expression analysis of custom probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway. In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe sets 014850. Colorectal carcinoma cells with induced TP53.

scan_protocol: Arrays were scanned using a GenePix 4200 Scanner and the GenePix Pro 6.1 Software (Molecular Devices) with following settings: laser power: 100%, PMT: 300/400, resolution: 5µm, Focus: 0µm, Lines to Average: 2, Wavelength: 532nm, Filter: Standard Green.

data_processing: The data were analyzed with R (version 2.9.0) and BioConductor (version 2.4). Expression levels were normalized (quantile normalization) and a linear model was fitted using the R package limma in order to identify differentially expressed probes. Reliable variance estimations were obtained by empirical Bayes moderated t-statistics. False discovery rate was controlled by Benjamini-Hochberg adjustment.

label_protocol: 1µg RNA were analyzed on nONCOchip 1.0 array according to the manufacturer's protocol (Agilent One-Color Quick Amp Labeling kit protokoll).

value: colorectal carcinoma cells

value: TP53 induced


title: LLC_E16

source_name: Pool Placenta - 10 hours amplified RNA from a pool of Placenta.


title: LLC_E15


title: A2780 exp 3


title: P53_nor_chipK_TileShuffle

description: Whole transcriptome expression analysis of colorectal carcinoma cells with defunct P53 on Affymetrix Human Tiling 1.0 array set. Intensities were processed with TileShuffle.

source_name: Colorectal carcinoma cells with defunct P53 (D53wt cells)


title: colorectal carcinoma cells with defunct TP53, biological replicate 2

description: Expression analysis of custom probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway. In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe sets 014850. Colorectal carcinoma cells with defunct TP53.

value: TP53 defunct


title: A2780 exp 2


title: colorectal carcinoma cells with defunct TP53, biological replicate 3

source_name: Colorectal carcinoma cells with defunct TP53


title: ELC_E20

source_name: Extra-embryonic tissues (EET), Early lactating cows (ELC) having a negative energy balance


title: A2780 exp 1


title: ELC_E28


title: colorectal carcinoma cells with induced TP53, biological replicate 3

source_name: Colorectal carcinoma cells with induced TP53


title: INA6 cells restimulated with IL-6 for 1 hour, biological replicate 3

description: Expression analysis of custom probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway. In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe sets 014850. INA6 cells were restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours.


title: INA6 cells with 13 hours of IL-6 withdrawal, biological replicate 2

description: Expression analysis of custom probes for genomic regions that have been found to be differentially expressed (i) throughout cell cycle progression, (ii) in response to the anti-proliferative and pro-apoptotic p53 pathway, and (iii) the anti-apoptotic and pro-proliferative STAT-3 pathway. In addition, the Agilent custom array (244K) interrogates probes for genomic regions predicted to contain a conserved secondary structure identified by RNAz (Washietl et al. "Fast and reliable prediction of noncoding RNAs." Proc Natl Acad Sci USA. 102:2454-9, 2005.) or Evofold (Pedersen et al. "Identification and classification of conserved RNA secondary structures in the human genome." PLoS Comput Biol. 2:e33, 2006.), as well as known non-coding RNAs from public databases, and the Agilent mRNA probe sets 014850. INA6 cells after 13 hours of IL-6 withdrawal.

value: after IL-6 has been withdrawn for 13 hours


title: GH_E09

source_name: Extra-embryonic tissues (EET), Growing heifers (GH) having a positive energy balance


title: T47D_expression_rep1

city: Barcelona

first: Albert

last: Jordan

address: Baldiri Reixac 4

department: Molecular Genomics

country: Spain

institute: IBMB-CSIC

description: T47D-MTVL cell line under basal growth conditions, biological replicate 1

hyb_protocol: Hybridization mix was laid onto each sector of subarray gasket slide and sandwiched against a 8 x 65K format oligonucleotide microarray (Human v1 Sureprint G3 Human GE 8x60k Microarray, Agilent design ID 028004) inside a hybridization chamber which wqs hybridized overnight at 65ºC in a rotisserie oven rotating at 10 rpm for a total of 17 hours. Subsequently array chambers were disassembled submerged in Agilent Gene Expression Buffer 1 and washed 1 minute in another dish with the same solution with a magnetic stirrer at 200 rpm at room temperature, followed by 1 minute in gilent Gene Expression Buffer 2 with a magnetic stirrer at 200 rpm at 37ºC and immediate withdrawal from the solution and air drying.

scan_protocol: Fluorescent signal was captured into TIF images with an Agilent scanner using recommended settings (20 bit, 5 um resolution, 100% PMT and 100% laser power) with Scan Control software (Agilent).

data_processing: Signal intensities were extracted into a tabulated text file using Feature Extraction software (Agilent) using the appropriate array configuration and annotation files. The normalized log2intensities were obtained using quantile method with normexp background correction the Bioconductor Limma package in R.

source_name: breast cancer cell T47D-MTVL (breast cancer cell line carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter)

label_protocol: For each sample 100 ng of total RNA mixed with 2 ul of 1:10000 Agilent One Color Spike Mix were reversed transcribed into cDNA with a T7 promoter and the cDNA was in vitro transcribed into cRNA in the presence of Cy3-CTP using the Low input quick Amp kit (Agilent). Labelled samples were purified using RNeasy mini spin columns (Qagen) and yield and specific activity wwere assessed by spectrophotometry (Nanodrop) and confirmed to be within specifications (>825 ng and >6 pmol Cy3/ug cRNA). 600 ng of cRNA were preblocked and fragmented in Agilent fragmentation buffer and mixed with  Agilent GEx Hybridization mix.

growth_protocol: T47D-MTVL (RPMI 1640 medium + 10%FBS, 1% glutamine, 1% penicillin/streptomycin)

extract_protocol: Total RNA was extracted using High Pure RNA isolation kit (Roche) according to the manufacturer's instructions. cDNA was obtained from 100 ng of total RNA using SuperScript VILO cDNA synthesis (Invitrogen). High RNA integrity was assessed by Bioanalyzer nano 6000 assay with RIN numbers 9.5 fopr T47D_r1 and 9.2 for T47D_r2

value: female

value: breast cancer ductal carcinoma


title: ELC_E23


title: INA6 cells restimulated with IL-6 for 1 hour, biological replicate 1

value: restimulated with IL-6 for 1 hour after IL-6 has been withdrawn for 13 hours


title: GH_E02


title: INA6 cells with 13 hours of IL-6 withdrawal, biological replicate 1


title: T47D_expression_rep2

description: T47D-MTVL cell line under basal growth conditions, biological replicate 2


title: INA6 cells restimulated with IL-6 for 1 hour, biological replicate 2


title: Naive Rep 3

status: Public on Feb 03 2014

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

institute: QIMR Berghofer Medical Research Insitute

hyb_protocol: Labelled cRNA was hybridized to MouseRef-8 v2.0 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.

data_processing: Data were extracted in GenomeStudio (Illumina) using default analysis settings and no normalization method.  Resulting data were imported into GeneSpring GX v12.5 (Agilent Technologies, Santa Clara, CA, USA).  Expression values were normalized using quantile normalization with default settings.

source_name: CD4+GFP+ nTreg from B6.FoxP3-GFP mice

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA).

extract_protocol: RNA was extracted using Qiagen RNeasy mini kit as per manufacturer’s instructions, then DNase treated and purified.  RNA concentration was determined using the NanoDrop 2000 (Thermo Scientific, Wilmington, DE, USA).

value: Saline

tag: strain


title: Naive Rep 4

scan_protocol: Labelled cRNA was hybridized to MouseRef-8 v2.0 BeadChip Arrays (Illumina Inc, San Diego, CA, USA), and then washed and scanned according to standard Illumina protocols.