title: Control vs RD5

city: Ulsan

first: Sook-Kyoung

last: Heo

address: 877 Bangeojinsunhwan-doro

department: Biomedical Research Center

country: South Korea

institute: University of Ulsan College of Medicine

description: Whole Human Genome Microarray 4x44K v2 (Probe Name version)

hyb_protocol: The fragmented cRNA was resuspended with 2× hybridization buffer and directly pipetted onto the microarray, which was placed in the Hybridization Chamber (Agilent Technologies, Inc.). By incubating the hybridization chamber at 42°C for 16 hours with mild agitation, competitive hybridization reactions occurred between labeled targets and probes on the microarray. To eliminate the non-specific binding, hybridized microarrays were washed with Agilent’s Gene Expression Wash Buffer Kit. Finally, microarrays were spin-dried and stored in dark conditions until scanned.

scan_protocol: Scanned images were analyzed using the Feature Extraction program (Agilent Technologies, Inc.).

data_processing: All data manipulations, the selection of genes exhibiting fold-changes, and statistical t-tests were performed using GeneSpring 7.3.1 (Agilent Technologies, Inc.). All numerical data were normalized by intensity-dependent normalization (locally weighted scatterplot smoothing, LOWESS), where the ratio was reduced to the residual of the Lowess fit of the intensity vs. ratio curve using GeneSpring 7.3.1.

source_name: Human acute acute myeloid leukemic cells RD5 treated

label_protocol: During transcription-amplification, cRNA samples were labeled with Cy3-CTP and Cy5-CTP, respectively. Amplified and labeled cRNA was purified and quantified using an ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE, USA) to check labeling efficiency, followed by fragmentation of cRNA by adding 10× blocking agent and 25× fragmentation buffer and incubating at 60°C for 30 min

growth_protocol: Kasumi-1 cells were incubated with 0 and 5 µM radotinib for 48 h, and were analyzed using a 44K oligo-microarray (Agilent Technologies, Inc., Palo Alto, CA, USA)

extract_protocol: For RNA samples, the synthesis of target cRNA probes and hybridization were performed using Agilent’s Low RNA Input Linear Amplification Kit PLUS according to the manufacturer’s instructions. Briefly, 1 μg of total RNA for each sample and T7 promoter primer mix were mixed and incubated at 65°C for 10 min. cDNA master mix (5× first-strand buffer, 0.1 M DTT, 10 mM dNTP mix, RNase-Out, and MMLV-RT) was prepared and added to RNA and the primer mixture. The samples were incubated at 40°C for 2 h for reverse-transcription and double-strand cDNA (dsDNA) synthesis and terminated by incubation at 65°C for 15 min. The transcription master mix was prepared following the manufacturer’s protocol (4× Transcription buffer, 0.1 M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP), added to the dsDNA reaction mixture, and incubated at 40°C for 2 h for transcription of dsDNA.

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

value: Kasumi-1 (CRL-2724)

tag: time

value: day 2 (48hr)

source_name: control


title: dGEN1a_c

status: Public on Sep 11 2015

type: genomic

city: Evry

first: Daniel

last: Stockholm

address: 1bis rue de l'Internationale

department: R&D

country: France

institute: Genethon - EPHE

description:
CD34+ Transduced sample c with vector dGEN1a
Vector Type: dGEN
Production System: Tri UC
Initial Name: aADN.9
Chip Name: ab

hyb_protocol: Hybridisation to Illumina Infinium Human Methylation450k Beadchip used standard Illumina protocol.

scan_protocol: Beachips were scanned using an iScan

data_processing: Normalized Raw beta values exported from GenomeStudio software were imported into R and analyzed with our homemade scripts. Probes on chromosomes X and Y were removed. Probes with a detection P-value > 0.01 exceeding 5% of the samples were also filtered out.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: CD34+ purified cells from mobilized peripheral blood cells #6 treated with dGEN

label_protocol: From each sample 500ng genomic DNA was bisulfite treated using EZ DNA methylation kit.

growth_protocol: 1x106 cells of CD34+ purified cells were pre-activated overnight at 37C° in X-VIVO culture medium, supplemented with antibiotics and cytokines  (Flt3-ligand (300 ng/ml), stem cell factor (300 ng/ml), trombopoietin (100 ng/ml) and IL3 (20ng/ml)).

extract_protocol: Genomic DNA was prepared using Nucleospin TissuXS kit (Nacherey Nagel).

treatment_protocol: Transduction was performed in the presence of 4ug/ml genomic DNA (Sigma) with 5x107 IG/ml (infectious genome) LV. A 2nd round of transduction was performed in the same conditions 6h later. Transduction reaction was stopped 24h after the beginning of the first round of transfection and cells were collected.

tag: tissue type

value: cord blood

tag: cell type


title: Transgenic fish 6, skin

type: RNA

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Following One-Color Microarray-Based Gene Expression Analysis protocol Version 6.6 (Agilent p/n G4140-90040), 1650 ng of labeled cRNA was hybridized with the Zeno Custom Gene Expression Microarray

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565C) according to the manufacturer’s protocol Metric Set GE1_QCMT_ Oct12.

data_processing: Data were extracted using Agilent Feature Extraction Software 11.5.1.1 following the Agilent protocol GE1_1050_Oct12, grid template 044138_D_F_20121017 and the QC

molecule: total RNA

organism: Danio rerio

source_name: Skin of transgenic fish

label_protocol: 150 ng of total RNA were used to produce Cyanine 3-CTP-labeled cRNA using the Low Input Quick Amp Labelling Kit, One-Color (Agilent p/n 5190-2305) according to the manufacturer’s instructions.

growth_protocol: Twenty ASIP1 (5 males + 5 females) and wildtype (5 males + 5 females) zebrafish were placed in 6-liter tanks and acclimated during 30 days prior to sampling to minimize physiological differences.

extract_protocol: RNA was extracted with Tri-Reargent (Sigma) following manufacturer protocol and treated with DNAse (Promega). Subsequently, RNA total were quantified by spectrometry (NanoDrop ND1000) and quality confirmed by RNA 6000 Nano Bioanalyzer (Agilent Technologies) assay

treatment_protocol: The sampling day, animals were sacrificed and the brain + pituitary dissected under the stereo microscope, placed in trizol and stored at -80C until RNA extraction.

tag: tissue

value: skin

tag: genotype/variation

value: transgenic


title: Ctrl5_b

description:
CD34+ Untransduced sample 5_b
Vector Type: None
Production System: None
Initial Name: cPAPb
Chip Name: c

source_name: CD34+ purified cells from mobilized peripheral blood cells #11 untreated


title: Transgenic fish 5, skin


title: Transgenic fish 6, brain

source_name: Brain of transgenic fish

value: brain


title: ES-CM-siErbB4-2

city: Tainan

first: Desy

middle: S

last: Lee

address: University Road

country: Taiwan

institute: NCKU

description: Gene expression after transfected with si-Scr

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 4*44K v2 Microarrays (G4846A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) at 535 nm for Cy3.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep0 and Grid: 026655_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.
GeneSpring GX v12.6 (Agilent Technologies) was used to analyze the expression profiles obtained after microarray hybridization. The feature extraction files from all the samples were uploaded to GeneSpring.  Follow by Percentile Shift Normalization.

organism: Mus musculus

source_name: embryonic stem cells-derived cardiomyocytes treated with si-ErbB5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mouse embryonic stem cells-derived cardiomyocytes were cultured in DMEM-LG+2%FBS. The cultures were incubated for 6 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA were extracted using RNEasy Plus Mini Kit with DNAse treatment

treatment_protocol: The cells were transfected with siScr or siErbB4 for 48 hours using Pepmute transfection agent

tag: cell line

tag: transfection


title: Transgenic fish 5, brain


title: Ctrl3_c

description:
CD34+ Untransduced sample 3_c
Vector Type: None
Production System: None
Initial Name: fPAP_c
Chip Name: f

source_name: CD34+ purified cells from mobilized peripheral blood cells #9 untreated


title: Ctrl3_b

description:
CD34+ Untransduced sample 3_b
Vector Type: None
Production System: None
Initial Name: fPAP_b
Chip Name: f

source_name: CD34+ purified cells from mobilized peripheral blood cells #8 untreated


title: dENV3_b

description:
CD34+ Transduced sample b with vector dENV3
Vector Type: dENV
Production System: Quadri UC
Initial Name: fENV3_b
Chip Name: f

source_name: CD34+ purified cells from mobilized peripheral blood cells #8 treated with dENV


title: Ctrl5_a

description:
CD34+ Untransduced sample 5_a
Vector Type: None
Production System: None
Initial Name: cPAPa
Chip Name: c

source_name: CD34+ purified cells from mobilized peripheral blood cells #10 untreated


title: Ctrl4_b

description:
CD34+ Untransduced sample 4_b
Vector Type: None
Production System: None
Initial Name: aPAP.5
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #5 untreated


title: Transgenic fish 1, brain


title: Transgenic fish 2 skin


title: Ctrl4_a

description:
CD34+ Untransduced sample 4_a
Vector Type: None
Production System: None
Initial Name: aPAP.4
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #4 untreated


title: Ctrl3_a

description:
CD34+ Untransduced sample 3_a
Vector Type: None
Production System: None
Initial Name: fPAP_a
Chip Name: f

source_name: CD34+ purified cells from mobilized peripheral blood cells #7 untreated


title: Ctrl2_b

description:
CD34+ Untransduced sample 2_b
Vector Type: None
Production System: None
Initial Name: b2PAP.14
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #2 untreated


title: Transgenic fish 4, skin


title: Transgenic fish 4, brain


title: Control fish 8, brain

source_name: Brain of control fish

value: control


title: Transgenic fish 2, brain


title: ES-CM-siErbB4-1

source_name: embryonic stem cells-derived cardiomyocytes treated with si-ErbB4


title: Ctrl2_c

description:
CD34+ Untransduced sample 2_c
Vector Type: None
Production System: None
Initial Name: b2PAP.15
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #3 untreated


title: Transgenic fish 1 skin


title: dENV1a_b

description:
CD34+ Transduced sample b with vector dENV1
Vector Type: dENV
Production System: Tri UC
Initial Name: aEnv.17
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #5 treated with dENV


title: Ctrl5_c

description:
CD34+ Untransduced sample 5_c
Vector Type: None
Production System: None
Initial Name: cPAPc
Chip Name: c

source_name: CD34+ purified cells from mobilized peripheral blood cells #12 untreated


title: Control fish 5, skin

source_name: Skin of control fish


title: Ctrl1_b

description:
CD34+ Untransduced sample 1_b
Vector Type: None
Production System: None
Initial Name: b1PAP.5
Chip Name: ab


title: Ctrl4_c

description:
CD34+ Untransduced sample 4_c
Vector Type: None
Production System: None
Initial Name: aPAP.6
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #6 untreated


title: Ctrl1_a

description:
CD34+ Untransduced sample 1_a
Vector Type: None
Production System: None
Initial Name: b1PAP.4
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #1 untreated


title: Soy 4; 19-24 months post-menarche

city: Winston-Salem

first: Jeff

last: Chou

state: NC

address: Medical Center Blvd

country: USA

institute: Atrium Health Wake Forest Baptist

hyb_protocol: 10 ug biotinylated cRNA was hybridized to the Affymetrix Gene Atlas Rhesus Gene 1.1 ST WT Array Strips according to current Affymetrix protocols.

scan_protocol: The arrays were washed and scanned according to standard Affymetrix GeneAtlas instructions using the GeneAtlas scanner and software control(GeneAtlas Instrument Control (GAIC) v. 1.0.6.).

data_processing: Raw data (CEL files) were generated using Affymetrix AGCC software and quantile normalized by the RMA method. Log intensity distributions, pair-wise correlations and internal Affymetrix controls were examined to evaluate hybridization quality using Partek Genomics Suite software (Partek Inc.).

label: Biotin

organism: Macaca fascicularis

source_name: Soy; 19-24 months post-menarche

label_protocol: 250 ng total RNA was amplified and labeled according to the Affymetrix GeneChip WT Terminal Labeling and Controls Kit protocol.

extract_protocol: Total RNA was isolated from frozen mammary tissue using Tri-Reagent (Molecular Research Center, Cincinnati, OH) and purified using RNeasy Mini Kit (Qiagen, Valencia, CA)

tag: diet

value: SOY

tag: age

value: 19-24 months post-menarche

tag: gender

value: F

value: breast biopsy


title: Ctrl2_a

description:
CD34+ Untransduced sample 2_a
Vector Type: None
Production System: None
Initial Name: b2PAP.13
Chip Name: ab


title: Soy 1; 19-24 months post-menarche


title: Soy 3; 19-24 months post-menarche


title: Control fish 4, skin


title: Control fish 7, skin


title: dENV2_a

description:
CD34+ Transduced sample a with vector dENV2
Vector Type: dENV
Production System: Quadri UC
Initial Name: fENV2_a
Chip Name: f

source_name: CD34+ purified cells from mobilized peripheral blood cells #7 treated with dENV


title: Control 4; 19-24 months post-menarche

source_name: Control; 19-24 months post-menarche

value: CONTROL


title: Control fish 4, brain


title: Ctrl1_c

description:
CD34+ Untransduced sample 1_c
Vector Type: None
Production System: None
Initial Name: b1PAP.6
Chip Name: ab


title: dENV1a_a

description:
CD34+ Transduced sample a with vector dENV1
Vector Type: dENV
Production System: Tri UC
Initial Name: aEnv.16
Chip Name: ab

source_name: CD34+ purified cells from mobilized peripheral blood cells #4 treated with dENV


title: Control 3; 19-24 months post-menarche


title: Control fish 7, brain


title: Control fish 2 skin


title: Control fish 3, brain


title: Control 2; 19-24 months post-menarche


title: Control 1; 19-24 months post-menarche


title: Control fish 5, brain


title: Control fish 2, brain


title: ES-CM-siScr-2

description: Gene expression after transfected with si-Scr

source_name: embryonic stem cells-derived cardiomyocytes treated with si-Scramble

value: siRNA-Scramble


title: Control fish 3, skin


title: Soy 3; 7-12 months post-menarche

source_name: Soy; 7-12 months post-menarche

value: 7-12 months post-menarche


title: Soy 2; 7-12 months post-menarche


title: Control_No_2

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: RMA normalization log2 transformed, using the oligo package of Bioconductor

label: Cy3 fluorescent label

organism: Macaca nemestrina

source_name: myometrium, lower uterus

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Rhesus Macaque Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: RNA was extracted from tissue samples using the Qiagen RNeasy kit, following the manufacturer's recommendations. Quality and quantity were assessed using an Agilent 2100 Bioanalyzer, and NanoDrop 8000 spectrophotometer, respectively.

value: female

tag: origin

value: lower uterus

value: myometrium

tag: treatment

value: Control

tag: labor

value: No


title: Soy 4; 7-12 months post-menarche


title: Control_No_4


title: Control 4; 7-12 months post-menarche

source_name: Control; 7-12 months post-menarche


title: Control 3; 7-12 months post-menarche


title: Soy 1; 7-12 months post-menarche


title: Stretch_Yes_2

value: Stretch

value: Yes


title: Stretch_Yes_3


title: Control_No_5


title: Control_No_1


title: Control 1; 7-12 months post-menarche


title: Soy 2; 19-24 months post-menarche


title: ES-CM-siScr-1


title: Control fish 8, skin

value: skin


title: Stretch_Yes_1


title: Drosha KO LSK in vitro 72hr 2

status: Public on Sep 10 2015

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent's Institute of Medical Research

hyb_protocol: Labeled, fragmented RNA hybridized to Agilent Mouse 8x 60K Array at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), according to manufacturers instructions.

scan_protocol: Arrays were scanned at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), following manufacturers instructions.

data_processing: Differential expression analysis of microarray data was performed using the Bioconductor R package limma (Smyth, 2004). Background intensities were corrected using the ‘normexp’ method (Ritchie et al., 2006). Intensities were normalised between arrays using quantile normalisation (Yang et al., 2002). The data was then fitted to a linear model and then tested for significance using an empirical Bayes method (Smyth, 2004).

source_name: Bone marrow haematopoietic stem cell enriched population (lineage marker- Sca1+ cKit+)

label_protocol: RNA was fragmented, biotin labeled at the Ramaciotti Centre for Gene Function Analysis at the University of New South Wales (UNSW, Sydney, NSW, Australia), according to manufacturers instructions.

growth_protocol: Sorted LSKs incubated in RPMI-HEPES supplemented with 10% FCS, 10 ng/mL murine IL-3 (Peprotech), 10 ng/mL murine IL-6 (Peprotech), 50 ng/mL murine stem cell factor (Peprotech) and 250 nM 4OH-tamoxifen (Sigma) for 72hours at 37oC, 5% CO2 in 96 well flat bottom plates. 50,000 LSKs were cultured per well in 50 µL. After 3 days the cells were harvested by vigorous washing with PBS. Cells for RNA examination were resuspended in TRI homogenate (Ambion, Grand Island, New York, USA).

extract_protocol: In order to extract and purify RNA from cells, chloroform (1:5 vol/vol) was added to cell suspensions in TRI homogenate (thawed on ice) before vigorously mixing.  This was allowed to settle for 15 minute at 4oC. Phases were then separated by centrifugation for 15 minutes at 4oC. An ethanol precipitation was then performed by adding carrier (glycoblue, Invitrogen) to the transferred aqueous phase prior to addition of two times volume of ethanol. The solution was then precipitated at -80oC for 25 minutes before centrifugation for 15 minutes at 4oC. The supernatant was discarded and the pellet washed in 70% ethanol. All supernatant was discarded following a final centrifugation step and the pellet resuspended in RNase-free water.

tag: strain

value: Drosha fl/fl Gt(ROSA)26Sor CreERT2

tag: genotype

value: drosha ko


title: Dicer KO LSK in vitro 72hr 3

value: Dicer fl/fl Gt(ROSA)26Sor CreERT2

value: dicer ko

value: Bone marrow haematopoietic stem cell enriched population (lineage marker- Sca1+ cKit+)


title: Dicer KO LSK in vitro 72hr 2


title: Control LSK in vitro 72hr 3

value: Gt(ROSA)26Sor CreERT2

value: control


title: WT in stationary phase, biological rep1

city: Oklahoma City

first: Jens

last: Kreth

address: 940 Stanton L. Young Blvd

department: Microbiology & Immunology

institute: University of Oklahoma Health Sciences Center

hyb_protocol: Following fragmentation, 2 μ of cDNA were hybridized for 16 hr at 47℃ on GeneChip S. pyogenes Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a laser scanner 7G (Affymetrix)

data_processing: Data were analyzed with Gene Chip Operating Software version 1.4 (GCOS 1.4) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Streptococcus pyogenes

source_name: S. pyogenes wild-type in stationary phase

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Cells were grown aerobically in C-medium (0.5% proteose peptone #3, 1.5% yeast extract, 10 mM K2SO4, 0.4 mM MgSO4, 17 mM NaCl)

extract_protocol: Cells were lysed using beat-beater. Extraction of total RNA was performed using TRIzol reagent (Invitrogen) according to the manufacturers protocol.

treatment_protocol: Cells were collected at the mid-exponential phase (OD600 = 0.3-0.35) or early stationary phase (one hour after the culture reached the maximum optical density).

tag: strain (m type)

value: wild type


title: Control LSK in vitro 72hr 2


title: ΔIG in mid-exponential phase, biological rep3

source_name: S. pyogenes ΔIG in mid-exponential phase

value: ΔIG


title: ΔIG in stationary phase, biological rep3

source_name: S. pyogenes ΔIG in stationary phase


title: ΔIG in mid-exponential phase, biological rep2


title: WT in stationary phase, biological rep2


title: Dicer KO LSK in vitro 72hr 1

value: female


title: ΔIG in stationary phase, biological rep2


title: Stretch_No_1

value: lower uterus


title: Drosha KO LSK in vitro 72hr 3


title: ΔIG in stationary phase, biological rep1


title: WT in stationary phase, biological rep3


title: WT in mid-exponential phase, biological rep3

source_name: S. pyogenes wild-type in mid-exponential phase


title: ΔIG in mid-exponential phase, biological rep1


title: WT in mid-exponential phase, biological rep2


title: WT in mid-exponential phase, biological rep1


title: Control LSK in vitro 72hr 1


title: MEF ST1 KO mST2 4h, rep2

city: Poznań

first: Hans

last: Bluyssen

address: Umultowska 89

department: Department of Human Molecular Genetics

country: Poland

institute: Faculty of Biology, University of Adam Mickiewicz

description:
8491191007_G
Replicate 2
MEFs are described in PMID 19272190.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data were background subtracted and quantile normalised in GenomeStudio (Illumina).

source_name: MEF, ST1 KO mST2, IFNalpha, 4h

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

growth_protocol: Mouse Embryonic Fibroblast (MEF) and Mouse Embryonic Fibroblast STAT1 KO mouse STAT2 stable cells (MEF ST1 KO mST2) were kept in DMEM 4.5g Glucose/L with 10% FBS and Pen-Strep. Cells were split when they reached 80%-90%.

extract_protocol: RNA was isolated using GeneMATRIX Universal RNA Purification Kit (EurX). Quality control was performed with Agilent Bioanalyser.

treatment_protocol: In vitro growing cells were starved overnight in DMEM 4.5g Glucose/L with 2% FBS and Pen-Strep afterwards mouse IFNα (Millipore) has been added in 200U/ml for: 0h, 4h, 8h, 24h.

value: mouse embryonic fibroblasts (MEFs)

value: STAT1 KO - hSTAT2 stable

value: IFNalpha

tag: treatment duration


title: MEF ST1 KO mST2 24h, rep1

description:
8491191007_B
Replicate 1
MEFs are described in PMID 19272190.

source_name: MEF, ST1 KO mST2, IFNalpha, 24h


title: MEF ST1 KO mST2 8h, rep2

description:
8491191069_H
Replicate 2
MEFs are described in PMID 19272190.

source_name: MEF, ST1 KO mST2, IFNalpha, 8h


title: MEF ST1 KO mST2 24h, rep2

description:
8491191069_E
Replicate 2
MEFs are described in PMID 19272190.


title: MEF ST1 KO mST2 0h, rep1

description:
8491191007_D
Replicate 1
MEFs are described in PMID 19272190.

source_name: MEF, ST1 KO mST2, IFNalpha, 0h


title: MEF ST1 KO mST2 0h, rep2

description:
8491191007_E
Replicate 2
MEFs are described in PMID 19272190.


title: MEF ST1 KO mST2 4h, rep1

description:
8491191069_F
Replicate 1
MEFs are described in PMID 19272190.


title: Control_No_3

value: myometrium

value: Control

value: No


title: MEF WT 0h, rep2

description:
8491191007_H
Replicate 2
MEFs are described in PMID 19272190.

source_name: MEF, WT, IFNalpha, 0h


title: MEF WT 4h, rep1

description:
8491191069_A
Replicate 1
MEFs are described in PMID 19272190.

source_name: MEF, WT, IFNalpha, 4h


title: MEF WT 4h, rep2

description:
8491191007_C
Replicate 2
MEFs are described in PMID 19272190.


title: MEF WT 0h, rep1

description:
8491191069_D
Replicate 1
MEFs are described in PMID 19272190.


title: MEF WT 8h, rep1

description:
8491191007_A
Replicate 1
MEFs are described in PMID 19272190.

source_name: MEF, WT, IFNalpha, 8h


title: Relapse_Patient_5694_week2

city: London

first: Jackie

last: Cliff

address: Keppel Street

department: Immunology and Infection

country: United Kingdom

institute: London School of Hygiene & Tropical Medicine

hyb_protocol: Fragmented and biotinylated cDNA was hybridised to Human U133 Plus 2.0 Affymetrix GeneChips at 45C, 60 rpm for 18 hours. GeneChips were washed and stained with an Affymetrix GeneChip Fluidics station 450, protocol EukGE-WS2v4_450.

scan_protocol: Affymetrix GeneChip Scanner 3000.

data_processing: GC-RMA summarised and baseline normalised to median of all arrays using GeneSpring GX11.5

label: NuGEN Ovation® Whole Blood Solution

molecule: polyA RNA

source_name: M. tuberculosis-stimulated diluted blood

label_protocol: 500pg mRNA processed using NuGEN Ovation® Whole Blood Solution

growth_protocol: human blood, 1ml, diluted 10-fold and cultured with M. tuberculosis H37Rv for 6 days. Supernatant removed and cells lysed in 10ml RNA/DNA Stabilization reagent (Roche Applied Science)

extract_protocol: mRNA Isolation Kit for Blood/Bone Marrow (Roche Applied Science) and Turbo DNA-free™ treatment (Ambion: Applied Biosystems)

treatment_protocol: Tuberculosis patients, samples taken at beginning and after 2 or 4 weeks of conventional combination therapy (2HRZE/4HR)

tag: treatment outcome

value: Week 2

tag: timepoint

value: Relapse


title: Relapse_Patient_5527_week4

value: Week 4


title: Relapse_Patient_5413_week4


title: MEF WT 24h, rep1

description:
8491191069_G
Replicate 1
MEFs are described in PMID 19272190.

source_name: MEF, WT, IFNalpha, 24h

tag: cell type


title: MEF WT 24h, rep2

description:
8491191007_F
Replicate 2
MEFs are described in PMID 19272190.


title: Stretch_No_2

tag: tissue

value: Stretch


title: Drosha KO LSK in vitro 72hr 1

value: Drosha fl/fl Gt(ROSA)26Sor CreERT2

value: drosha ko

value: Bone marrow haematopoietic stem cell enriched population (lineage marker- Sca1+ cKit+)


title: Relapse_Patient_5527_diagnosis

value: Diagnosis


title: Relapse_Patient_5694_diagnosis


title: Relapse_Patient_5694_week4


title: hST2-U3C 24h_rep 1

description:
SAMPLE 22
6898333051_E
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were background subtracted and quantile normalised in GenomeStudio (Illumina)

source_name: hST2-U3C 24h

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

growth_protocol: 2fTGH and hST2-U3C cells were keept in DMEM 4,5g Glucose/L with 10% FBS and Pen-Strep. Cells were splited when they reached 80% - 90%.

treatment_protocol: In vitro grwoing cells were starved over night in DMEM 4,5g Glucose/L with 2% FBS and Pen-Strep afterwards human IFNα (Millipore) has been added in 200U/ml for: 0h, 4h, 8h, 24h

tag: genotype/variation

tag: agent

value: IFNα

tag: time


title: hST2-U3C 24h_rep 2

description:
SAMPLE 23
6898333051_C
replicate 2

tag: cell line


title: MEF WT 8h, rep2

description:
8491191069_C
Replicate 2
MEFs are described in PMID 19272190.

value: wild type


title: MEF ST1 KO mST2 8h, rep1

description:
8491191069_B
Replicate 1
MEFs are described in PMID 19272190.


title: hST2-U3C 24h_rep 3

description:
SAMPLE 24
6898333051_J
replicate 3


title: Relapse_Patient_5527_week2


title: Relapse_Patient_5413_diagnosis


title: Relapse_Patient_5413_week2


title: hST2-U3C 8h_rep 3

description:
SAMPLE 21
6898333051_I
replicate 3

source_name: hST2-U3C 8h


title: hST2-U3C 8h_rep 2

description:
SAMPLE 20
6898333051_H
replicate 2


title: hST2-U3C 8h_rep 1

description:
SAMPLE 19
6898333051_B
replicate 1


title: Relapse_Patient_5410_diagnosis


title: Relapse_Patient_5410_week2


title: Relapse_Patient_5386_week4


title: hST2-U3C 4h_rep 3

description:
SAMPLE 18
6898333051_F
replicate 3

source_name: hST2-U3C 4h


title: Relapse_Patient_5410_week4


title: hST2-U3C 4h_rep 2

description:
SAMPLE 17
6898333051_D
replicate 2


title: Relapse_Patient_5386_week2


title: hST2-U3C 4h_rep 1

description:
SAMPLE 16
6898333051_K
replicate 1


title: 2fTGH 24h_rep 2

description:
SAMPLE 11
6898333065_F
replicate 2

source_name: 2fTGH 24h

value: Wild type


title: Relapse_Patient_5296_week2


title: Crowding 2

city: Cartagena

first: Marcos

last: Egea-Cortines

address: Edificio I+D+i Plaza del Hospital s/n

department: Instituto de Biotecnología Vegetal

country: Spain

institute: Universidad Politécnica de Cartagena

hyb_protocol: Nimblegen hybridization kit

scan_protocol: Genespring  12.5

data_processing: Data was subject to summarization by computing the geometric mean of duplicate probe intensity values. Data was then log base 2 transformed and normalized. Normalization accross arrays was done using Genespring default values: Percentile shift075% (after log transformation, for each array,  the selected percentile is calculated and subtracted from values for that array down the column, thus shifting the distribution for each array to be more similar). Finally baseline transformation to median for all samples accross columns of a row was performed. The resulting data gave a fold change and a significant up or down regulation based on a 2-fold cut-off with P-values <0.005.

organism: Antirrhinum majus

source_name: Plants grown under crowding conditions (10 plant per pot)

label_protocol: Standard Cy3 Nimblegen

growth_protocol: Plants were grown under greenhouse conditions in 1.2 liter pots. They contained a mixture of perlite:vermiculite:coconout fiber:bedding compost of 1:0.5:1:2 in volume. They were watered when required.

extract_protocol: RNAeasy- Macherei & Nagel

tag: line

tag: growth condition

value: 10 plants per pot (crowded conditions)

value: Inflorescence meristem


title: Control 2; 7-12 months post-menarche

source_name: Control; 7-12 months post-menarche

tag: diet

value: CONTROL

tag: age

value: 7-12 months post-menarche

tag: gender

value: F

value: breast biopsy


title: hST2-U3C 0h_rep 3

description:
SAMPLE 15
6898333051_L
replicate 3

source_name: hST2-U3C 0h

value: STAT1 KO - hSTAT2 stable

value: untreated


title: Relapse_Patient_5296_diagnosis

value: Relapse


title: Crowding 3


title: hST2-U3C 0h_rep 2

description:
SAMPLE 14
6898333051_G
replicate 2


title: 2fTGH 24h_rep 3

description:
SAMPLE 12
6898333065_B
replicate 3


title: 2fTGH 24h_rep 1

description:
SAMPLE 10
6898333065_E
replicate 1


title: Relapse_Patient_5292_week4

value: Week 4


title: hST2-U3C 0h_rep 1

description:
SAMPLE 13
6898333051_A
replicate 1


title: Relapse_Patient_5296_week4


title: Relapse_Patient_5386_diagnosis


title: Control 2

source_name: Plants grown under normal conditions (1 plant per pot)

value: single plant per pot (control)


title: 2fTGH 8h_rep 3

description:
SAMPLE 9
6898333065_C
replicate 3

source_name: 2fTGH 8h


title: Relapse_Patient_5292_diagnosis


title: Control 1


title: 2fTGH 8h_rep 2

description:
SAMPLE 8
6898333065_A
replicate 2


title: Relapse_Patient_5015_week4


title: Crowding 1


title: 2fTGH 8h_rep 1

description:
SAMPLE 7
6898333065_K
replicate 1


title: Relapse_Patient_5292_week2

value: Week 2


title: Relapse_Patient_5015_week2


title: 2fTGH 4h_rep 2

description:
SAMPLE 5
6898333065_J
replicate 2

source_name: 2fTGH 4h


title: Relapse_Patient_5015_diagnosis


title: Ferret Lung Tissue - Day 6 post-A/California/07/2009 (H1N1) infection - Replicate #3

city: Toronto

first: Stephane

middle: G

last: Paquette

state: Ontario

address: 101 College Street

department: Experimental Therapeutics

country: Canada

institute: University Health Network

description:
Gene expression data from adult ferret lung collected at day 6 post-infection with A/California/07/2009 (H1N1)
LG-D6-3

hyb_protocol: Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45C on GeneChip Canine Genome 2.0 Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with PLIER using Expression Console Version 1.1 (Affymetrix) default analysis settings.

organism: Mustela putorius furo

source_name: Ferret_A/California/07/2009 (H1N1)_day6

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Prior to infection experiment, ferrets were housed in an on-site specific pathogen free (SPF) facility.

extract_protocol: Tissues were homogenized in TRIzol immediately following collection at stored at -80C. Total RNA was extracted as per manufacturer's instructions.

treatment_protocol: Ferrets were infected intranasally with 10^5 EID50 A/California/07/2009 (H1N1). At days 3, or 6 post-infection, ferrets were euthanized and lungs were collected for immediate RNA extraction (described below).  Lungs of uninfected ferrets were also collected in a similar manner.

tag: virus strain

value: A/California/07/2009 (H1N1)

value: Lung


title: Ferret Lung Tissue - Day 6 post-A/California/07/2009 (H1N1) infection - Replicate #2

description:
Gene expression data from adult ferret lung collected at day 6 post-infection with A/California/07/2009 (H1N1)
LG-D6-2


title: Ferret Lung Tissue - Day 6 post-A/California/07/2009 (H1N1) infection - Replicate #1

description:
Gene expression data from adult ferret lung collected at day 6 post-infection with A/California/07/2009 (H1N1)
LG-D6-1


title: 2fTGH 4h_rep 1

description:
SAMPLE 4
6898333065_L
replicate 1

value: IFNα


title: 2fTGH 4h_rep 3

description:
SAMPLE 6
6898333065_H
replicate 3


title: 2fTGH 0h_rep 2

description:
SAMPLE 2
6898333065_D
replicate 2

source_name: 2fTGH 0h


title: Ferret Lung Tissue - Day 3 post-A/California/07/2009 (H1N1) infection - Replicate #3

description:
Gene expression data from adult ferret lung collected at day 3 post-infection with A/California/07/2009 (H1N1)
LG-D3-3

source_name: Ferret_A/California/07/2009 (H1N1)_day3


title: Ferret Lung Tissue - Day 3 post-A/California/07/2009 (H1N1) infection - Replicate #2

description:
Gene expression data from adult ferret lung collected at day 3 post-infection with A/California/07/2009 (H1N1)
LG-D3-2


title: Relapse_Patient_4546_diagnosis


title: Relapse_Patient_4570_week4


title: Ferret Mammary Gland Tissue - Day 7 post-kit A/California/07/2009 (H1N1) infection - Replicate #2

description:
Gene expression data from ferret mammary gland of nursing mother collected at day 7 post-kit infection with A/California/07/2009 (H1N1)
MG-D7-2

source_name: Ferret_A/California/07/2009 (H1N1)_day7

treatment_protocol: Kits housed in litters with their nursing mother were infected intranasally with 105 EID50 A/California/07/2009 (H1N1). At days 3, 4, 6, or 7 post-kit infection, mother ferrets were euthanized and mammary glands were collected for immediate RNA extraction (described below).  Mammary glands from nursing mothers of uninfected kits were also collected in a similar manner.

value: Mammary Gland


title: 2fTGH 0h_rep 1

description:
SAMPLE 1
6898333065_G
replicate 1

value: Wild type


title: Ferret Lung Tissue - Baseline (no infection) - Replicate #1

description:
Gene expression data from adult ferret lung (no virus exposure)
LG-Base-1

value: None; Uninfected


title: Ferret Mammary Gland Tissue - Day 4 post-kit A/California/07/2009 (H1N1) infection - Replicate #2

description:
Gene expression data from ferret mammary gland of nursing mother collected at day 4 post-kit infection with A/California/07/2009 (H1N1)
MG-D4-2

source_name: Ferret_A/California/07/2009 (H1N1)_day4


title: Cured_Patient_5760_week4

source_name: M. tuberculosis-stimulated diluted blood

value: Cured


title: Ferret Lung Tissue - Day 3 post-A/California/07/2009 (H1N1) infection - Replicate #1

description:
Gene expression data from adult ferret lung collected at day 3 post-infection with A/California/07/2009 (H1N1)
LG-D3-1


title: Ferret Mammary Gland Tissue - Day 7 post-kit A/California/07/2009 (H1N1) infection - Replicate #1

description:
Gene expression data from ferret mammary gland of nursing mother collected at day 7 post-kit infection with A/California/07/2009 (H1N1)
MG-D7-1


title: Ferret Mammary Gland Tissue - Day 6 post-kit A/California/07/2009 (H1N1) infection - Replicate #1

description:
Gene expression data from ferret mammary gland of nursing mother collected at day 6 post-kit infection with A/California/07/2009 (H1N1)
MG-D6-1


title: 2fTGH 0h_rep 3

description:
SAMPLE 3
6898333065_I
replicate 3


title: Ferret Lung Tissue - Baseline (no infection) - Replicate #2

description:
Gene expression data from adult ferret lung (no virus exposure)
LG-Base-2


title: Ferret Mammary Gland Tissue - Day 4 post-kit A/California/07/2009 (H1N1) infection - Replicate #1

description:
Gene expression data from ferret mammary gland of nursing mother collected at day 4 post-kit infection with A/California/07/2009 (H1N1)
MG-D4-1


title: Cured_Patient_5760_week2


title: Ferret Mammary Gland Tissue - Baseline (no infection) - Replicate #3

description:
Gene expression data from ferret mammary gland of nursing mother (no virus exposure)
MG-Base-3


title: Cured_Patient_5760_diagnosis

value: Diagnosis


title: Ferret Mammary Gland Tissue - Baseline (no infection) - Replicate #2

description:
Gene expression data from ferret mammary gland of nursing mother (no virus exposure)
MG-Base-2


title: Relapse_Patient_4570_diagnosis


title: Ferret Lung Tissue - Baseline (no infection) - Replicate #3

description:
Gene expression data from adult ferret lung (no virus exposure)
LG-Base-3


title: Ferret Mammary Gland Tissue - Day 3 post-kit A/California/07/2009 (H1N1) infection - Replicate #1

description:
Gene expression data from ferret mammary gland of nursing mother collected at day 3 post-kit infection with A/California/07/2009 (H1N1)
MG-D3-1


title: Ferret Mammary Gland Tissue - Baseline (no infection) - Replicate #1

description:
Gene expression data from ferret mammary gland of nursing mother (no virus exposure)
MG-Base-1


title: Cured_Patient_5754_week4


title: CIT_Biopsy_28

city: Bronx

first: Pilib

last: Ó Broin

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

description:
Sample name: 295
Gene expression data from CIT biopsy sample

hyb_protocol: Total RNA samples hybridized to the Affymetrix Hugene 1.0 st chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip 3000 7G scanner, software AGCC v2.0

data_processing: Probe intensities were extracted from Affymetrix CEL files, normalized and summarized at the transcript cluster level using the Robust Multiarray Average method from the R/Bioconductor (http://bioconductor.org) oligo package. Array quality control was performed to remove arrays that significantly differed in initial overall probe intensity. Expression values were analyzed on the log base 2 scale. Significance testing was performed by fitting gene-wise linear models using the limma Bioconductor package, and genes were ranked for differential expression using Benjamini & Hochberg adjusted p-values and log-posterior odds of differential expression. Gene set analysis was performed using the limma romer method. Gene set used were taken from the Molecular Signatures Database (MSigDB) Pathogenesis Based Transcripts (PBT; http://transplants.med.ualberta.ca/Nephlab/data/gene_lists.html) gene sets from the University of Alberta, Edmonton. Analysis for changes in gene expression of Gene Ontology (GO) categories was performed using the GOstats Bioconductor package to calculate Hypergeomtric p-values for over or under-representation of each GO term.

source_name: Cold Ischemia time < 20 hrs, Basiliximab

label_protocol: Labelled as per manufacturer's instruction in Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

extract_protocol: Biopsy cores were immediately placed into a vial containing 1ml of RNALater® (Ambion, Catalog Number AM7023), stored at -20°C for 24 hours and then transferred to -70°C until RNA isolation.  Renal tissue content in all cores was verified using a dissecting microscope and non-renal tissue was removed. Total RNA was isolated using the QIAGEN RNeasy Mini Kit (Catalog Number 74104, Qiagen, USA) and QIAGEN PAXgene Blood RNA Kit (Catalog Number 762164, Qiagen, Valencia, CA) for biopsy and blood samples respectively.

tag: treatment

value: CIT less than 20 hours

value: Basiliximab

value: post transplant biopsy


title: CIT_Biopsy_27

description:
Sample name: 290
Gene expression data from CIT biopsy sample


title: Cured_Patient_5754_diagnosis


title: CIT_Biopsy_25

description:
Sample name: 203
Gene expression data from CIT biopsy sample

source_name: Cold Ischemia time < 20 hrs, Rabbit antithymocyte globulin

value: Rabbit antithymocyte globulin


title: Cured_Patient_5754_week2


title: CIT_Biopsy_23

description:
Sample name: 96
Gene expression data from CIT biopsy sample


title: Cured_Patient_5709_week2


title: Cured_Patient_5709_diagnosis


title: Cured_Patient_5655_week4


title: CIT_Biopsy_21

description:
Sample name: 34
Gene expression data from CIT biopsy sample


title: CIT_Biopsy_18

description:
Sample name: 334
Gene expression data from CIT biopsy sample

source_name: Cold Ischemia time > 20 hrs, Basiliximab

value: CIT greater than 20 hours


title: CIT_Biopsy_17

description:
Sample name: 330
Gene expression data from CIT biopsy sample


title: CIT_Biopsy_24

description:
Sample name: 104
Gene expression data from CIT biopsy sample


title: CIT_Biopsy_22

description:
Sample name: 90
Gene expression data from CIT biopsy sample


title: Du-Ksi_pool6

city: Bochum

first: Henrik

last: Rudolf

address: Universitätsstr. 150

department: Medical computer science, Biometry and Epidemiology

country: Germany

institute: Ruhr-Universität Bochum

hyb_protocol: The fragmented cRNA was hybridized overnight (45°C) to the Affymetrix GeneChip MOE 430A mouse expression arrays. Each sample pool was hybridized to two arrays to reduce the technical variation. Arrays were then washed using the GeneChip Fluidics Station (Affymetrix) according to the manufacturer’s protocol and stained by R-Phycoerythrin Streptavidin (Molecular Probes). This was followed by an antibody amplification procedure using a biotinylated anti-streptavidin antibody (Vector laboratories) and goat IgG (Sigma).

scan_protocol: Scanning was carried out with 3µm resolution, 488nm excitation and 570nm emission wavelengths employing the GeneArray Scanner 2500 (Hewlett Packard)

data_processing: For calculation of normalized signal intensities GC-RMA procedure was used.

source_name: Ovary

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

growth_protocol: Mice were kept in Makrolon-cages of 30 x 12.5 x 12.5 cm with free access to pellet concentrate and water. The light regime was LD 12:12, the room temperature was standardized to 22.5 °C.

extract_protocol: Total RNA was prepared with the RNeasey Mini Kit with simultaneous removal of genomic DNA with RNAse free DNAse (Qiagen)

treatment_protocol: Line FL1 was selected for an index trait, combining litter size (LS0) and litter weight (LW0) at birth in primiparous females (Index (I) = 1.6 x LS0 + LW0)) to generation 130

tag: Stage

value: metestrous


title: Du-Ksi_pool6a


title: Cured_Patient_5709_week4

value: Week 4


title: CIT_Biopsy_15

description:
Sample name: 309
Gene expression data from CIT biopsy sample


title: CIT_Biopsy_16

description:
Sample name: 322
Gene expression data from CIT biopsy sample


title: Cured_Patient_5655_diagnosis


title: Du-Ksi_pool5a


title: CIT_Biopsy_26

description:
Sample name: 274
Gene expression data from CIT biopsy sample


title: CIT_Biopsy_20

description:
Sample name: 15
Gene expression data from CIT biopsy sample


title: Cured_Patient_5600_week4


title: CIT_Biopsy_13

description:
Sample name: 306
Gene expression data from CIT biopsy sample

source_name: Cold Ischemia time > 20 hrs, Rabbit antithymocyte globulin


title: CIT_Biopsy_11

description:
Sample name: 289
Gene expression data from CIT biopsy sample


title: CIT_Biopsy_14

description:
Sample name: 307
Gene expression data from CIT biopsy sample


title: Cured_Patient_5655_week2


title: CIT_Biopsy_19

description:
Sample name: 11
Gene expression data from CIT biopsy sample


title: Du-Ksi_pool4a


title: CIT_Biopsy_10

description:
Sample name: 280
Gene expression data from CIT biopsy sample


title: Cured_Patient_5600_week2


title: CIT_Biopsy_12

description:
Sample name: 302
Gene expression data from CIT biopsy sample


title: CIT_Biopsy_8

description:
Sample name: 247
Gene expression data from CIT biopsy sample


title: CIT_Biopsy_6

description:
Sample name: 197
Gene expression data from CIT biopsy sample


title: Cured_Patient_5418_week4


title: CIT_Biopsy_7

description:
Sample name: 237
Gene expression data from CIT biopsy sample


title: Du-Ksi_pool3a


title: Du-Ksi_pool5


title: Cured_Patient_5418_week2


title: CIT_Biopsy_2

description:
Sample name: 99
Gene expression data from CIT biopsy sample


title: Cured_Patient_5600_diagnosis


title: CIT_Biopsy_5

description:
Sample name: 189
Gene expression data from CIT biopsy sample


title: Du-Ksi_pool3


title: CIT_Biopsy_9

description:
Sample name: 278
Gene expression data from CIT biopsy sample


title: CIT_Biopsy_3

description:
Sample name: 114
Gene expression data from CIT biopsy sample


title: CIT_Biopsy_1

description:
Sample name: 1
Gene expression data from CIT biopsy sample


title: Cured_Patient_5418_diagnosis


title: Du-Ksi_pool2a


title: Du-Ksi_pool2


title: Cured_Patient_5181_week2


title: SG_NSG salisphere transplant_rep3

city: Groningen

first: Sarah

last: Pringle

state: Groningen

address: Antonius Deusinglaan 1

department: Cell Biology

country: Netherlands

institute: University Medical Centrum Groningen

scan_protocol: Standard Illumina scanning  protocol, using iScan.

data_processing:
The data were normalized using data extraction with GenomeStudio Software and normalization in R version 3.0.1 neqc function of the BioConductor version 2.12 library limma 3.16.5 (Smyth, GK 2005)
Differential expression analysis was performed using eBayes function of the BioConductor library limma and an adjustment method BH (Benjamini Hochberg)  to exclude false positives, with a p value of 0.05. Assignment of probes upregulated at 1 week post-transplantation to biological pathways was performed using ENrichR online resources

organism:
Homo sapiens
Mus musculus

source_name: salivary gland

label_protocol: RNA was aplified using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: Prior to transplantation, NSG salispheres were maintained in our standard culture medium, as per Lombaert et al, 2008.

extract_protocol: SGs were harvested from mice and homogenized using a tissue processor. Total RNA was extracted using the Qiagen RNeasy  Mini Kit, according to manufacturers instructions.

treatment_protocol: NSG mice were locally irradiated in the neck region with 5Gy of X-rays, to induce clinically relevant hyposalivation.

tag: strain

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ

tag: Sex

value: Female

value: 14 weeks at sacrifice


title: Du-Ksi_pool4


title: Du-Ksi_pool1aw


title: SG_irradiated control_rep3 reanalysis


title: CIT_Biopsy_4

description:
Sample name: 132
Gene expression data from CIT biopsy sample


title: SG_irradiated control_rep2 reanalysis


title: Du-Ksi_pool1w


title: SG_NSG salisphere transplant_rep2


title: SG_NSG salisphere transplant_rep1


title: Du-Ksi26


title: SG_human salisphere transplant_rep3

growth_protocol: Prior to transplantation, human salispheres were maintained in our standard culture medium, as stated in materials and methods section of this paper.

extract_protocol: SGs were harvested from mice and homogenized using a tissue processor. Total RNA was extracted using the Qiagen Rneasy Mini Kit, according to manufacturers instructions.


title: Cured_Patient_5181_week4

tag: treatment outcome

tag: timepoint


title: SG_human salisphere transplant_rep2


title: Du-Ksi21


title: Cured_Patient_5122_week4


title: SG_irradiated control_rep1


title: SG_human salisphere transplant_rep1


title: Cured_Patient_5181_diagnosis


title: Cured_Patient_5122_week2

value: Week 2


title: Du-Ksi16


title: SG_irradiated control_rep1 reanalysis


title: Du-Ksi13w


title: colorectal cancer tissue 12

city: Peking

first: wang

middle: li

last: yong

state: Peking

address: No 10 xi tou tiao, you an gate

department: medical school

country: China

institute: Capital Medical University

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

source_name: colon

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

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

tag: tissue

value: cancerous


title: Cured_Patient_5118_week4


title: Du-Ksi18


title: SG_irradiated control_rep2


title: Cured_Patient_5122_diagnosis


title: SG_irradiated control_rep3


title: colorectal cancer tissue 11


title: Cured_Patient_5118_week2


title: colorectal cancer tissue 10


title: colorectal cancer tissue 8


title: Du-Ksi8


title: Du-K_pool5_aw


title: Du-Ksi4


title: Du-Ksi2w


title: Du-K_pool4_aw


title: Cured_Patient_5118_diagnosis


title: colorectal cancer tissue 6

value: paracancerous


title: Du-Ksi5


title: Du-Ksi1


title: Du-K_pool5w


title: Cured_Patient_5037_week4


title: colorectal cancer tissue 9


title: Du-K_pool6_a


title: Du-K_pool3new_a


title: Du-K_pool3new


title: Du-K_pool4w


title: Du-K_pool6


title: Blood_medium_r1

description: NuGEN Ovation® Whole Blood Solution

data_processing: GC-RMA summarised using GeneSpring GX11.5.  GC-RMA and baseline normalised to the medium control array provided on the Series record.

source_name: Diluted Blood

label_protocol: A total of 500pg mRNA (166.67 from each donor) was processed using NuGEN Ovation® Whole Blood Solution

growth_protocol: Human blood from BCG-vaccinated health donors (1ml) incubated for 6 days with/without live mycobacteria in L-glutamine-supplemented RPMI-1640 medium. Supernatant removed and cells lysed in 10ml RNA/DNA Stabilization reagent (Roche Applied Science). Samples from three donors were pooled after RNA extraction.

treatment_protocol: Blood was incubated alone, or with 5 x 10 [4] live mycobacteria, which is equivalent to a multiplicity of infection of 1 mycobacterium to 1 monocyte.

value: blood

tag: stimulus


title: colorectal cancer tissue 3


title: colorectal cancer tissue 2


title: colorectal cancer tissue 7


title: Cured_Patient_5037_week2


title: colorectal cancer tissue 5


title: Blood_M.tuberculosis_r1

description: NuGEN Ovation® Whole Blood Solution

source_name: Diluted Blood plus M. tuberculosis

value: M. tuberculosis (1:1 MOI)


title: colorectal cancer tissue 1


title: colorectal cancer tissue 4


title: Blood_BCG_r1

description: NuGEN Ovation® Whole Blood Solution

source_name: Diluted Blood plus BCG

value: M. bovis BCG (1:1 MOI)


title: Du-K_pool2


title: Du-K_pool1


title: Du-K_pool1aw


title: Cured_Patient_5037_diagnosis

value: Diagnosis

value: Cured


title: Du-K29


title: Du-K20w


title: Du-K17


title: Du-K26


title: Du-K_pool2a


title: Du-K19


title: Du-K27w


title: BDNF, IBET858_12h_1

status: Public on Sep 09 2015

city: New York

first: Josefa

middle: M

last: Sullivan

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: BDNF, IBET858_12h_1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with GeneSpring version 13.0 using Affymetrix default analysis settings and RMA summarization algorithm with quantile normalization. The baseline was transformed to the median of all samples and data was trimmed arbitrarily to exclude raw expression below 20

source_name: primary cortical neurons, BDNF, IBET858 - 12h

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: E18 primary cortical neurons were cultured and maintained for 1 week then treated as described

extract_protocol: Total RNA was isolated using Trizol LS as per the manufacturer's protocol

treatment_protocol: Cultures were treated with 50ng / ml BDNF and/or 1µM IBET858

tag: cell type

value: primary cortical neurons


title: Du-K6


title: Du-K13


title: BDNF_12h_2

source_name: primary cortical neurons, BDNF - 12h


title: BDNF, IBET858_12h_2

description: BDNF, IBET858_12h_2


title: H3_Q_IN

city: Dublin 2

first: Darren

middle: John

last: Fitzpatrick

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

hyb_protocol: 7.5 ug of amplified ChIP and input DNAs were hybridized to Affimetrix GeneChipR S. cerevisiae Tiling 1.0R Arrays according to Affymetrix specifications.

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing: A version of the Model-based Analysis of Tiling-arrays (MAT) adapted for use with the R programming language (rMAT) was used to normalise probe intensities (Droit et al., 2010). rMAT was applied to the immunoprecipitated and input sample arrays and MATscores were calculated from all probes using a 300bp sliding window.

organism: Saccharomyces cerevisiae

source_name: Q cells, S1, Cross-linked, sonicated, No antibody

label_protocol: The protocol used to amplify DNAs was adapted from {Bohlander, 1992 #146}, as modified by the DiRisi and Rando labs.

growth_protocol: All yeast cells (YCH406; MATa (hta1-htb1)∆::LEU2, (hta2-htb2)∆::TRP1, his3∆200 leu2∆1, ura3-52, trp1∆ RPB3-9Myc::hphNT1 <pSAB6 (HTA1-HTB1-URA3)> <pZS145 (HTA1-Flag-HTB1::HIS3)>) were cultured at 30oC in YPD + A medium (.04 mg/mL adenine and 50 mg/mL ampicillin) and grown to an OD600 of 0.8 – 1.0 for log phase samples.  Cells were grown through the diauxic shift into stationary phase and separated into quiescent and non-quiescent populations at 3, 5, 7 and 14 days after inoculation according to Allen et al., (2006). J. Cell Biol. 174. 89-100. 6.5 mL of cells were overlaid on a 10 mL PercollTM gradient after resuspension in 1/10 volume of 50 mM Tris-HCl, pH 7.5.   Quiescent and non-quiescent cell fractions were collected, and the quiescent cell fraction was further purified by centrifugation and collection on a fresh Percoll gradient.   Cells were washed in 5 volumes of Tris-HCl buffer, pelleted, and then treated with 1% formaldehyde for chromatin immunoprecipitation (as described in Fleming et al., (2008). Mol. Cell.).

extract_protocol: Cell pellets were thawed on ice and resuspended in 400 μl of ice-cold FA-lysis buffer (50 mM HEPES, pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate) with 1 x protease inhibitor (PI, Sigma) and 2 mM phenylmethylsulfonyl fluoride (PMSF, Sigma) and divided between two 1.5 ml tubes.  Cells were disrupted by vortexing (Vortex Genie 2 with a Turbomix adapter) in the presence of approximately 300 μl of 425 - 600 μM acid washed glass beads (Sigma) for 60 min at full speed at 4°C.  Following lysis, the bottom of the 1.5 ml tubes were pierced and placed in 15 ml centrifuge tubes to enable recovery of lysate.  The nested tubes were spun gently (1000 r.p.m, 2 min) and recovered lysate was transferred to fresh microcentrifuge tubes.  Lysates were pooled and made up to 1 ml with ice cold FA-lysis buffer (+ PI + PMSF).  The sample was sonicated manually using a Sanyo Soniprep 150 to yield an average DNA fragment size of 500 bp.  DNA fragment size was determined by agarose gel electrophoresis after each lysate preparation.  Sonication was achieved by applying 10 x 10 s pulses at amplitude 9 with alternating 1 min incubation on ice between pulses.  Following sonication, cell debris was pelleted by centrifugation (13,200 r.p.m, 30 min, 4°C).  Supernatant containing soluble, sheared chromatin was recovered and aliquots equivalent to a cell density of 5 (mid-log) or 7.5 (Q cells) OD600 units were stored at - 80°C until required. 1 mg of protein was added to FA lysis buffer to a total volume of 500 ul according to Fleming et al., 2008, Mol Cell.  The FA lysis buffer for anti-Myc ChIPs contained an additional 0.1% SDS. Lysates were incubated with the following antibodies overnight at 4oC: 2.5 ul anti-H3 (Millipore 05-724); 2.5-4 ul anti-H3K4me3 (Active Motif 39159); 8 ul anti-H3K36me3 pre-bound to 60 ul Protein A beads (Abcam ab9050); 2 ul anti-H3K79me3 (Abcam ab2621); and 2.5 ul anti-Myc (Millipore 05-724).  Immune complexes were collected with 60-80 ul of Protein A or Protein G beads that were prewashed and resuspended in FA lysis buffer. Immune complexes were eluted in 250 uL of 50mM Tris-HCl pH7.5, 10 mM EDTA, 1% SDS at 65o C for 20 minutes followed by 10 minutes nutation at room temperature.  Chromatin was sequentially digested with RNase A and pronase, and the cross-links were reversed by overnight incubation at 65oC.  DNA was extracted using a QiaQuick PCR Purification kit (Qiagen #28106).        For ChIP-chip analysis two independent experiments were performed in log phase and 7-day Q cells using antibodies against Rpb3-Myc, H3K4me3, H3K36me3, and H3K79me3 as described above.

treatment_protocol:
Q cells, S1, Cross-linked, sonicated (10 x 10s), No antibody
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.

tag: cell growth stage

value: Stationary Phase; Day 7

tag: antibody

value: No antibody


title: H3_Q_IP

source_name: Q cells, S1, Cross-linked, sonicated, Anti-H3

treatment_protocol:
Q cells, S1, Cross-linked, sonicated (10 x 10s), Anti-H3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: H3_Log_IN

source_name: Log cells, S1, Cross-linked, sonicated, No antibody

treatment_protocol:
Log cells, S1, Cross-linked, sonicated (10 x 10s), No antibody
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.

value: Log phase


title: H3K79me3_Q_IN_Replicate

source_name: Q cells, S2, Cross-linked, sonicated, No antibody

treatment_protocol:
Q cells, S2, Cross-linked, sonicated (10 x 10s), No antibody
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: Du-K7

value: metestrous


title: Du-K28w


title: BDNF, IBET858_12h_3

description: BDNF, IBET858_12h_3


title: BDNF_12h_1


title: IBET858_12h_2

source_name: primary cortical neurons, IBET858 - 12h


title: BDNF_12h_3


title: H3K79me3_Q_IP_Replicate

source_name: Q cells, S2, Cross-linked, sonicated, Anti-H3K79me3

treatment_protocol:
Q cells, S2, Cross-linked, sonicated (10 x 10s), Anti-H3K79me3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: IBET858_2h_3

source_name: primary cortical neurons, IBET858 - 2h


title: IBET858_12h_3


title: Control_12h_2

source_name: primary cortical neurons, DMSO - 12h


title: H3_Log_IP

source_name: Log cells, S1, Cross-linked, sonicated, Anti-H3

treatment_protocol:
Log cells, S1, Cross-linked, sonicated (10 x 10s), Anti-H3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: H3K79me3_Q_IN

treatment_protocol:
Q cells, S1, Cross-linked, sonicated (10 x 10s), Anti-H3K79me3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: H3K79me3_Q_IP

source_name: Q cells, S1, Cross-linked, sonicated, Anti-H3K79me3


title: BDNF, IBET858_2h_3

description: BDNF, IBET858_2h_3

source_name: primary cortical neurons, BDNF, IBET858 - 2h


title: Control_12h_3


title: BDNF, IBET858_2h_2

description: BDNF, IBET858_2h_2


title: H3K79me3_Log_IN_Replicate_2

source_name: Log cells, S3, Cross-linked, sonicated, No antibody

treatment_protocol:
Log cells, S3, Cross-linked, sonicated (10 x 10s), No antibody
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: H3K79me3_Log_IP_Replicate_2

source_name: Log cells, S3, Cross-linked, sonicated, Anti-H3K79me3

treatment_protocol:
Log cells, S3, Cross-linked, sonicated (10 x 10s), Anti-H3K79me3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: Control_12h_1


title: H3K79me3_Log_IP_Replicate

source_name: Log cells, S2, Cross-linked, sonicated, Anti-H3K79me3

treatment_protocol:
Log cells, S2, Cross-linked, sonicated (10 x 10s), Anti-H3K79me3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: H3K79me3_Log_IN_Replicate

source_name: Log cells, S2, Cross-linked, sonicated, No antibody

treatment_protocol:
Log cells, S2, Cross-linked, sonicated (10 x 10s), No antibody
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: IBET858_12h_1


title: primary osteoblasts at day 12 of differentiation

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

institute: University Medical Center Hamburg-Eppendorf

description: differentiated for 12 days

hyb_protocol: Hybridization was performed for 16 hr at 45°C. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Gene Chips were scanned suing the Affymetirx Gene Chip scanner 7G.

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software GCOS 1.4 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

source_name: murine calvarial cells

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix IVT labeling protocol from 5 µg total RNA.

growth_protocol: CD11b-negagtive calvarial cells were differentiated in the presence of ascorbic acid (50 µg/ml) and ß-glycerophosphate (10 mM) for 5 or 12 days.

extract_protocol: RNA was isolated using the RNAeasyMini kit (Qiagen).

treatment_protocol: No treatmenet was performed.

value: CD11b-negative cells

value: differentiated for 12 days


title: H3K79me3_Log_IP

source_name: Log cells, S1, Cross-linked, sonicated, Anti-H3K79me3

treatment_protocol:
Log cells, S1, Cross-linked, sonicated (10 x 10s), Anti-H3K79me3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: H3K79me3_Log_IN


title: BDNF_2h_1

source_name: primary cortical neurons, BDNF - 2h


title: Control_2h_2

source_name: primary cortical neurons, DMSO - 2h


title: H3K4me3_Q_IP_Replicate_2

source_name: Q cells, S3, Cross-linked, sonicated, Anti-H3K4me3

treatment_protocol:
Q cells, S3, Cross-linked, sonicated (10 x 10s), Anti-H3K4me3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: IBET858_2h_1


title: H3K4me3_Q_IN_Replicate

source_name: Q cells, S2, Cross-linked, sonicated, No antibody


title: H3K4me3_Q_IP_Replicate

source_name: Q cells, S2, Cross-linked, sonicated, Anti-H3K4me3

treatment_protocol:
Q cells, S2, Cross-linked, sonicated (10 x 10s), Anti-H3K4me3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: Control_2h_3


title: BDNF, IBET858_2h_1

description: BDNF, IBET858_2h_1


title: BDNF_2h_2


title: H3K4me3_Log_IN_Replicate


title: H3K4me3_Log_IP_Replicate_2

source_name: Log cells, S3, Cross-linked, sonicated, Anti-H3K4me3

treatment_protocol:
Log cells, S3, Cross-linked, sonicated (10 x 10s), Anti-H3K4me3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: H3K4me3_Log_IN_Replicate_2


title: H3K4me3_Q_IP

source_name: Q cells, S1, Cross-linked, sonicated, Anti-H3K4me3

treatment_protocol:
Q cells, S1, Cross-linked, sonicated (10 x 10s), Anti-H3K4me3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: H3K4me3_Q_IN

source_name: Q cells, S1, Cross-linked, sonicated, No antibody

treatment_protocol:
Q cells, S1, Cross-linked, sonicated (10 x 10s), No antibody
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: H3K4me3_Log_IN

source_name: Log cells, S1, Cross-linked, sonicated, No antibody


title: H3K4me3_Log_IP_Replicate

source_name: Log cells, S2, Cross-linked, sonicated, Anti-H3K4me3

treatment_protocol:
Log cells, S2, Cross-linked, sonicated (10 x 10s), Anti-H3K4me3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: BDNF_2h_3

treatment_protocol: Cultures were treated with 50ng / ml BDNF and/or 1µM IBET858


title: H3K4me3_Log_IP

source_name: Log cells, S1, Cross-linked, sonicated, Anti-H3K4me3

treatment_protocol:
Log cells, S1, Cross-linked, sonicated (10 x 10s), Anti-H3K4me3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: primary osteoblasts at day 5 of differentiation

description: differentiated for 5 days

value: differentiated for 5 days


title: H3K36me3_Q_IP_Replicate

source_name: Q cells, S2, Cross-linked, sonicated, Anti-H3K36me3

treatment_protocol:
Q cells, S2, Cross-linked, sonicated (10 x 10s), Anti-H3K36me3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: H3K4me3_Q_IN_Replicate_2

source_name: Q cells, S3, Cross-linked, sonicated, No antibody

treatment_protocol:
Q cells, S3, Cross-linked, sonicated (10 x 10s), No antibody
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: IBET858_2h_2

source_name: primary cortical neurons, IBET858 - 2h


title: Control_2h_1


title: H3K36me3_Q_IP

source_name: Q cells, S1, Cross-linked, sonicated, Anti-H3K36me3

treatment_protocol:
Q cells, S1, Cross-linked, sonicated (10 x 10s), Anti-H3K36me3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: H3K36me3_Log_IN_Replicate

source_name: Log cells, S2, Cross-linked, sonicated, No antibody


title: PolII_Q_IP_Replicate

source_name: Q cells, S2, Cross-linked, sonicated, Anti-Pol II

treatment_protocol:
Q cells, S2, Cross-linked, sonicated (10 x 10s), Anti-Pol II
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.

value: Anti-Pol II


title: PolII_Q_IN


title: H3K36me3_Log_IP

source_name: Log cells, S1, Cross-linked, sonicated, Anti-H3K36me3

treatment_protocol:
Log cells, S1, Cross-linked, sonicated (10 x 10s), Anti-H3K36me3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: PolII_Log_IN_Replicate


title: PolII_Q_IN_Replicate

treatment_protocol:
Q cells, S2, Cross-linked, sonicated (10 x 10s), No antibody
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: PolII_Log_IP_Replicate

source_name: Log cells, S2, Cross-linked, sonicated, Anti-Pol II

treatment_protocol:
Log cells, S2, Cross-linked, sonicated (10 x 10s), Anti-Pol II
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: sourceC_lineage3_ortet_1

city: St. Louis

first: Steve

middle: W.

last: smith

state: MO

address: 4041 Forest Park Ave

department: Bioinformatics

institute: Orion Genomics

description: This sample was not used in the analysis, therefore normalized data have not been presented.

hyb_protocol: Hybridizations were performed by Mogene (St. Louis, MO) following standard Nimblegen conditions.

scan_protocol: Arrays were scanned by Mogene (St. Louis, MO) on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Arrays were processed by Mogene (St. Louis, MO) using Nimblegen's standard protocol for custom Nimblescan data extraction.
For data processing, corrections on spatial non-uniformity of fluorescent signal intensities, done separately for the Cy3 and Cy5 dye channels, were made. Data were then normalized by background subtraction using negative control probes, followed by scaling. After normalization, median log signal of the control probes for each dye of each array is set to zero. MAD (median absolute deviation) log signal of all the probes on an array is a constant for a give treatment (untreated or DNA methylation depleted). DNA methylation was measured as the sample average (over the two pairs of dye-swapped technical replicates) of normalized log2 ratios of untreated over DNA methylation depleted. The raw data files are labeled with "UT" for untreated or "MD" for Methyl-depleted.

organism: Elaeis guineensis

source_name: UT (untreated) or MD (methyl-depleted)

label_protocol: For each fraction, 200 ng was used for cyanogen dye labeling (Cy3 or Cy5).  For each sample, four microarrays were hybridized in a duplicated dye swap design to differentially labeled untreated and DNA methylation depleted fractions.  Labeling was performed by MOgene (St. Louis, MO) following standard Nimblegen protocols.

extract_protocol: Genomic DNA was extracted from adult leaf tissue by standard methods.  Genomic DNA (60 µg) was mechanically sheared to 1-4 kb fragments by hydroshearing.  Sheared DNA was divided into four equal portions, two of which were digested with 10 units/µg McrBC (New England Biolabs) under manufacturer’s recommended conditions and the other two were mock treated without adding enzyme.  Following digestion, DNAs were treated with proteinase K (50mg/ml) for 1 hour at 50oC and then precipitated with EtOH under standard conditions.  Resuspended DNAs were resolved by agarose gel electrophoresis, and DNA in the 1-4 kb size range was excised from the gel and extracted.

tag: phenotype

value: Ortet

value: adult leaf


title: PolII_Log_IN

treatment_protocol:
Log cells, S1, Cross-linked, sonicated (10 x 10s), No antibody
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: H3K36me3_Log_IP_Replicate

source_name: Log cells, S2, Cross-linked, sonicated, Anti-H3K36me3

treatment_protocol:
Log cells, S2, Cross-linked, sonicated (10 x 10s), Anti-H3K36me3
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: H3K36me3_Log_IN


title: PolII_Log_IP

source_name: Log cells, S1, Cross-linked, sonicated, Anti-Pol II

treatment_protocol:
Log cells, S1, Cross-linked, sonicated (10 x 10s), Anti-Pol II
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: PolII_Q_IP

source_name: Q cells, S1, Cross-linked, sonicated, Anti-Pol II

treatment_protocol:
Q cells, S1, Cross-linked, sonicated (10 x 10s), Anti-Pol II
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: B4

first: Alice

last: Marmugi

address: Du cane Road

institute: Imperial College London

data_processing: Illumina's GenomeStudio® software

source_name: Pancreatic beta cells, SRI-tg10

label_protocol: Biotinylated cRNA were prepared using Illumina TotalPrep_96 RNA Amplidication kit

growth_protocol: Double transgenic mouse overexpressing Sorcin and Luciferase under a tetracycline inducible promoter and a tetracycline activated transactivator under the Rat Insulin Promoter

extract_protocol: Pancreatic islets of Langerhans were isolated by collagenase digestion following injection in the common bile duct and further separation from exocrine tissue by Histopaque density gradient. 12 total RNA samples from mouse origin extracted with Trizol reagent without DNase I treatment. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Glucose intolerance induced by high fat diet (60% fat) started at 4 week old. SRI-tg10 mice were fed a high fat diet and exposed to doxycycline (0.5 g/L) in drinking water for a duration of 4 weeks prior to tissue collection.

tag: mice no.

tag: tissue type

value: Mouse primary islets of Langerhans; pancreas

value: Male

value: 8 week old

tag: developmental stage

value: Adult


title: A4

tag: gender

tag: age


title: B5

source_name: Pancreatic beta cells, Control


title: B1


title: A5


title: B3


title: A1


title: A6


title: A2


title: B6


title: A3


title: Placenta_PD_infected_rep2

city: Montreal

first: Lisa

last: Starr

state: Quebec

address: 1001 Boul. Decarie

department: Child Health and Human Development

institute: McGill University Health Centre

description:
L.S. 4.6.2
Gene expression data from placentas of protein-deficient mice infected with H. bakeri.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 2.0 ST GeneChip. Arrays were washed and stained in the Affymetrix Fluidics Station 400 at McGill University and Génome Québec Innovation Centre.

scan_protocol: GeneChips were scanned using the GeneArray Scanner (Affymetrix, Santa Clara, CA) at McGill University and Génome Québec Innovation Centre.

data_processing: RMA normalization was performed using Expression Console; ANOVA statistical analysis was performed using FlexArray software version 1.6.1 (provided by McGill University and Génome Québec Innovation Centre, http://www.gqinnovationcenter.com/services/bioinformatics/flexarray/index.aspx?l=e).

source_name: Placenta of protein-deficient mouse infected with H. bakeri

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix) at McGill University and Génome Québec Innovation Centre.

growth_protocol: 8- to 9-week-old primiparous mice, timed pregnant mice were received on day 4 of pregnancy from Charles River Laboratories (Quebec, Canada) and housed individually in a temperature-controlled (22-25°C) room with a 14:10 h light:dark cycle.

extract_protocol: Extraction was performed using PureLink RNA extraction kit (Life Technologies, Carlsbad, CA) according to the manufacturer's instructions; samples from the last placenta from each uterine horn of each mouse was pooled; tissues were lysed using a mortar and pestle in the lysis buffer provided in the kit and homogenized using a column homogenizer (Life Technologies).

treatment_protocol: At day 5 of pregnancy, mice were divided into two diet groups receiving either PS (24% protein, TD.90017) or PD (6% protein, TD.90017) isocaloric diets (Harlan Teklad, Madison, WI) ad libitum and two infection groups [sham: 3 × 0 3rd stage larvae (L3); infected: 3 × 100 ± 3 L3] until necropsy on day 18 of pregnancy (total 14 days). Heligmosomoides bakeri infective L3 were obtained by fecal culture of stock parasites maintained in outbred CD-1 mice. Dams were infected with 100 L3 on days 5, 10 and 15 of pregnancy by oral gavage.

tag: strain/background

tag: diet group

value: protein deficient

tag: infection group

value: Heligmosomoides bakeri

value: placenta

value: day 18 of pregnancy


title: B2

tag: strain


title: Placenta_PD_infected_rep3

description:
L.S. 4.10.2
Gene expression data from placentas of protein-deficient mice infected with H. bakeri.


title: Pyayanosii_80_Mpa_rep3

city: Thuwal

first: Gregoire

last: Michoud

address: KAUST

country: Saudi Arabia

institute: KAUST

description:
Gene expression at 80 Mpa after 6 h in P. yayanosii
Y80_4

hyb_protocol: Hybridization was performed using 600 ng cRNA at 65 °C during 17 h per the manufacter instructions

scan_protocol: After the hybridization, the slides were washed and the microarrays were scanned using an Agilent G2505C scanner

data_processing: Feature extraction and image analysis software (Feature Extraction Software; Agilent Technologies) was used to locate and delineate every spot in the array, to integrate each spot’s intensity, using simple color Agilent protocol (GE1_1105_Oct12).

organism: Pyrococcus yayanosii

source_name: P. yayanosii_80 Mpa

label_protocol: Low Input Quick Amp WT Labeling Kit, One color (Agilent Technologies) was used to synthesize labeled cRNA from 50 ng of total RNA. cRNA were fragmented at 60 °C during 30 min in a specific buffer in order to obtain fragents between 50 and 200 nucleotides

extract_protocol: RNA was prepared using a method adapted from Voorhorst et al. (Voorhorst et al., 1995) and described in Vannier et al. (Vannier et al., 2015)

treatment_protocol: Cells were grown in Thermoccales Rich Medium at 98°C at different hydrostatic pressure and in anaerobic conditions

tag: pressure

value: 80 MPa

value: Whole cell


title: Placenta_PD_sham_rep2

description:
L.S. 3.12
Gene expression data from placentas of protein-deficient, sham-infected mice.

source_name: Placenta of protein-deficient, sham-infected mouse

value: sham


title: Placenta_PD_infected_rep1

description:
L.S. 4.4
Gene expression data from placentas of protein-deficient mice infected with H. bakeri.


title: Pyayanosii_80_Mpa_rep2

description:
Gene expression at 80 Mpa after 6 h in P. yayanosii
Y80_3


title: Placenta_PD_sham_rep1

description:
L.S. 3.7
Gene expression data from placentas of protein-deficient, sham-infected mice.


title: Placenta_PD_sham_rep3

description:
L.S. 3.13
Gene expression data from placentas of protein-deficient, sham-infected mice.


title: Placenta_PS_infected_rep3

description:
L.S. 2.14
Gene expression data from placentas of protein-sufficient mice infected with H. bakeri.

source_name: Placenta of protein-sufficient mouse infected with H. bakeri

value: protein sufficient


title: Placenta_PS_sham_rep3

description:
L.S. 1.7
Gene expression data from placentas of protein-sufficient, sham-infected mice, i.e. control.

source_name: Placenta of control mouse


title: Pyayanosii_80_Mpa_rep1

description:
Gene expression at 80 Mpa after 6 h in P. yayanosii
Y80_2


title: Placenta_PS_sham_rep2

description:
L.S. 1.5
Gene expression data from placentas of protein-sufficient, sham-infected mice, i.e. control.


title: Placenta_PS_infected_rep2

description:
L.S. 2.13
Gene expression data from placentas of protein-sufficient mice infected with H. bakeri.


title: Pyayanosii_52_Mpa_rep2

description:
Gene expression at 52 Mpa after 6 h in P. yayanosii
Y52_2

source_name: P. yayanosii_52 Mpa

value: 52 MPa


title: Pyayanosii_52_Mpa_rep1

description:
Gene expression at 52 Mpa after 6 h in P. yayanosii
Y52_1


title: Pyayanosii_52_Mpa_rep3

description:
Gene expression at 52 Mpa after 6 h in P. yayanosii
Y52_4


title: sourceB_lineage2_mantled_3_M

value: Mantled


title: Placenta_PS_infected_rep1

description:
L.S. 2.7
Gene expression data from placentas of protein-sufficient mice infected with H. bakeri.


title: H3K36me3_Q_IN_Replicate

source_name: Q cells, S2, Cross-linked, sonicated, No antibody

value: Stationary Phase; Day 7

value: No antibody


title: Pyayanosii_20_Mpa_rep3

description:
Gene expression at 20 Mpa after 6 h in P. yayanosii
Y20_3

source_name: P. yayanosii_20 Mpa

value: 20 MPa


title: Placenta_PS_sham_rep1

description:
L.S. 1.3
Gene expression data from placentas of protein-sufficient, sham-infected mice, i.e. control.


title: H3K36me3_Q_IN

source_name: Q cells, S1, Cross-linked, sonicated, No antibody

treatment_protocol:
Q cells, S1, Cross-linked, sonicated (10 x 10s), No antibody
30 OD units of log phase cells and 40-50 OD units of quiescent cells were fixed in 1% formaldehyde for 20 min, quenched with 125 mM glycine for 5 min, washed 2X in cold TBS, and quick-frozen on dry ice and stored at -80C.


title: Pyayanosii_20_Mpa_rep2

description:
Gene expression at 20 Mpa after 6 h in P. yayanosii
Y20_2


title: Pyayanosii_20_Mpa_rep1

description:
Gene expression at 20 Mpa after 6 h in P. yayanosii
Y20_1


title: sourceB_lineage2_mantled_2_M

value: adult leaf


title: Pfuriosus_45_Mpa_rep3

description:
Gene expression at 45 Mpa after 4 h in P. furiosus
F45_3

organism: Pyrococcus furiosus

source_name: P. furiosus_52 Mpa

value: 45 MPa


title: Pfuriosus_45_Mpa_rep2

description:
Gene expression at 45 Mpa after 4 h in P. furiosus
F45_2


title: Pfuriosus_45_Mpa_rep1

description:
Gene expression at 45 Mpa after 4 h in P. furiosus
F45_1


title: sourceB_lineage2_normal_4_N

description: There are intentionally only 6 raw data files associated with this sample. One of the four arrays for this sample failed QC. When this happens, as a compromise, we use one array twice in the two technical replicates for one way of labeling. In this way we keep dye-bias neutralized with the compromise that signals from one array are weighted twice as much as those from other arrays.

value: Normal


title: Pfuriosus_01_Mpa_rep2

description:
Gene expression at 0.1 Mpa after 4 h in P. furiosus
F0.1_2

source_name: P. furiosus_0.1 Mpa

value: 0.1 MPa


title: sourceB_lineage2_normal_3_N

source_name: UT (untreated) or MD (methyl-depleted)


title: Pfuriosus_01_Mpa_rep1

description:
Gene expression at 0.1 Mpa after 4 h in P. furiosus
F0.1_1


title: Pfuriosus_01_Mpa_rep3

description:
Gene expression at 0.1 Mpa after 4 h in P. furiosus
F0.1_3


title: sourceB_lineage2_normal_2_N


title: sourceB_lineage12_normal_5_N


title: sourceB_lineage2_mantled_1_M


title: sourceB_lineage2_normal_1_N


title: Biofilm_batch_13_6h

city: Nanjing

first: Dong

last: Liu

state: Jiangsu

address: No. 30, Puzhu South Road

department: National Engineering Research Center for Biotechnology, College of Biotechnology and Pharmaceutical Engineering

institute: Nanjing Tech University

description: Gene expression in batch13-grown C.acetobutylicum B3 biofilm cells

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US). After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Clostridium acetobutylicum

source_name: biofilm cells, batch 13, 6 h

label_protocol: Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany). Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Cultures of C. acetobutylicum B3 were grown in modified P2 medium containing 10 g/L glucose as the sole carbohydrate source for seed culture. Fermentation experiments were performed anaerobically in 2-L stainless steel columns containing 1.5 L of P2 medium (glucose 60 g/L; K2HPO4 0.5 g/L; KH2PO4 0.5 g/L; CH3COONH4 2.2 g/L; MgSO4•7H2O 0.2 g/L; MnSO4•H2O 0.01 g/L; NaCl 0.01 g/L; FeSO4•7H2O 0.01 g/L; p-aminobenzoic acid 1 mg/L; thiamine 1 mg/L; biotin 0.01 mg/L) at 37 °C with initial inoculum 10%(v/v).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: To collect the biofilm cells, a pieces of cotton towel was harvested from the fermentation broth and rinsed twice with PBS buffer (137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 2 mM KH2PO4, pH 7.40, 4°C) to remove contaminating planktonic cells. Then the cotton towel was submerged in 15-mL PBS buffer and vortexed vigorously to disperse adsorbed cells, after which the cotton towel was removed and the resulting suspension was centrifuged at 8,000 × g for 6 min at 4°C to pallet the biofilm cells. All the cells were frozen immediately using liquid nitrogen and then stored at -80 °C prior to RNA extraction.

tag: growth phase

value: biofilm mature


title: Biofilm_batch_13_12h

source_name: biofilm cells, batch 13, 12h

value: biofilm under adverse condition at the end of fermentation


title: sourceB_lineage12_mantled_1_M

tag: tissue


title: Biofilm_batch_13_15h

source_name: biofilm cells, batch 13, 15h


title: Biofilm_batch_13_17h

source_name: biofilm cells, batch 13, 17h


title: sourceB_lineage12_normal_1_N


title: sourceB_lineage12_normal_4_N


title: Biofilm_batch_9_6h

description: Gene expression in batch9-grown C.acetobutylicum B3 biofilm

source_name: biofilm cells, batch 9, 6 h


title: Sample_34

city: Seattle

first: Jamie

last: Guenthoer

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

scan_protocol: Standard Illumina hybridization protocol

data_processing: The raw array data were then exported to the R v3.0.3 statistical software Bioconductor lumi package for pre-processing, and the gene expression values were log2 transformed. Probes were identified to be low signal if the log2 expression values were below the median of negative controls for each sample. Probes with more than 1/3 low signal across samples were excluded. A median normalization was carried out. As the data were processed in batches, including the batch effect from FFPE vs. Frozen samples, the ComBat algorithm was used to remove the batch effect before combining data from different batches. Data were then subjected to shorth variance filtering to remove probes that have no or little variation across samples (9). In this filtering, probes with a standard deviation less than the mean of the standard deviations of arrays within the shorth interval were removed from further analysis. Of the starting 29,361 probes in the WG-DASL assay, after preprocessing there were 19,168 probes left for analysis.

source_name: Breast Tumor Tissue_7161-53 rep 1

label_protocol: cDNA generation and biotin labeling was performed using the Illumina Whole-Genome DASL HT assay according to manufacturer's recommended protocol.

extract_protocol: RNA was extracted from FFPE tissue sections using Qiagen FFPE RNeasy kit and from fresh or frozen tissue using Qiagen AllPrep DNA/RNA Mini Kit according to manufacturer's recommended protocols. RNA was further cleaned up with DnaseI treatment. RNA quantity and quality was assessed on a Nanodrop Spectrophotometer.

value: breast tumor

tag: specimen preparation

value: FFPE

tag: pre/post treatment

value: Pre

tag: dose cohort

value: Cohort E


title: Biofilm_batch_6_6h

description: Gene expression in betch6-grown C.acetobutylicum B3 biofilm

source_name: biofilm cells, batch 6, 6 h

value: biofilm growth


title: Sample_33

description: Due to high missing probe rate, sample dropped from final analysis and not included in normalized dataset

source_name: Breast Tumor Tissue_7161-50 rep 1

value: Cohort 9


title: Biofilm_batch_4_6h

description: Gene expression in batch4-grown C.acetobutylicum B3 biofilm

source_name: biofilm cells, batch 4, 6 h


title: sourceB_lineage12_normal_3_N


title: Sample_32

source_name: Breast Tumor Tissue_7161-18 rep 1

value: Frozen

value: Post

value: Cohort 4


title: Sample_31

source_name: Breast Tumor Tissue_7161-49 rep 1

value: pre


title: sourceB_lineage1_normal_5_N


title: sourceB_lineage12_normal_2_N


title: sourceB_lineage1_mantled_1_M

value: Mantled


title: Sample_30

source_name: Breast Tumor Tissue_7161-47 rep 1

value: Cohort 8


title: Heart-ISO-72hrs-rep3

type: protein

city: Beijing

first: Hao

last: LI

address: No. 49, Huayuan Bei Road, Haidian District

department: Institute of Vascular Medicine

institute: Peking University Third Hospital

hyb_protocol: Antibody arrays were used according to the manufacturer’s instructions. All sample measurements were performed in duplicate. The array glass slides were washed, incubated with a biotin-conjugated anti-cytokine mix for 2 hours, washed again, and developed for 2 hours with HRP-conjugated streptavidin.

scan_protocol: Expose to x-ray film and detect signal using film developer or detect signal directly from membrane using chemiluminescene imaging system.

data_processing: By comparing the signal intensities, relative expression levels of cytokines can be made. The intensities of signals can be quantified by densitometry. Positive control can be used to normalize the results from different membranes being compared.

molecule: protein

source_name: heart, ISO, 72hrs

label_protocol: Samples were labeled according to the manufacturer’s instructions

extract_protocol: Weigh out tissue and cut into cubes. Prepare protein extraction reagent containing inhibitors. Add ice-cold Protein Extraction Reagent containing protease inhibitors. Grind in a blender on low power using 30-second bursts until fully homogenized. Allow material to cool for 1 minute between bursts. Centrifuge the lysate at 14,000xg for 15 minutes and transfer the supernatant to a new tube for further analysis.

treatment_protocol: Mice were subcutaneous injected with a single dose of  isoproterenol (ISO, 5 mg/kg body weight) or vehicle saline (10 ml/kg body weight). Hearts were harvested and immediately frozen in liquid nitrogen.

value: 10 weeks old

tag: Sex

value: Male

value: Heart


title: Heart-ISO-72hrs-rep2


title: Heart-ISO-72hrs-rep1


title: sourceC_lineage6_normal_4_N

tag: phenotype

value: Normal

value: adult leaf


title: sourceB_lineage1_normal_2_N


title: Heart-ISO-24hrs-rep3

source_name: heart, ISO, 24hrs


title: Sample_29

source_name: Breast Tumor Tissue_7161-48 rep 1

value: breast tumor


title: sourceC_lineage6_normal_2_N


title: Sample_28

source_name: Breast Tumor Tissue_7161-41 rep 1

value: FFPE


title: sourceC_lineage6_normal_3_N

source_name: UT (untreated) or MD (methyl-depleted)


title: sourceB_lineage1_normal_3_N


title: sourceC_lineage6_mantled_2_MP


title: sourceC_lineage6_mantled_1_MP


title: sourceB_lineage1_normal_1_N


title: sourceC_lineage6_normal_1_N


title: Sample_27

source_name: Breast Tumor Tissue_7161-33 rep 1

value: Pre

value: Cohort 6


title: Heart-ISO-24hrs-rep2


title: Sample_26

source_name: Breast Tumor Tissue_7161-43 rep 1


title: sourceC_lineage6_mantled_3_MP


title: sourceC_lineage5_mantled_2_MP


title: sourceB_lineage1_normal_4_N


title: sourceC_lineage6_mantled_5_MP


title: sourceB_lineage1_mantled_2_M


title: Heart-ISO-24hrs-rep1


title: Heart-ISO-12hrs-rep3

source_name: heart, ISO, 12hrs


title: Sample_25

source_name: Breast Tumor Tissue_7161-40 rep 1

value: Cohort 7


title: Biofilm_batch_2_6h

description: Gene expression in batch2-grown C.acetobutylicum B3 biofilm

source_name: biofilm cells, batch 2, 6 h

value: biofilm growth


title: sourceC_lineage6_mantled_4_MP


title: Heart-ISO-12hrs-rep1


title: Heart-ISO-6hrs-rep3

source_name: heart, ISO, 6hrs


title: Sample_24

source_name: Breast Tumor Tissue_7161-38 rep 1


title: sourceC_lineage5_mantled_1_MP


title: Heart-ISO-12hrs-rep2


title: sourceC_lineage5_normal_5_N


title: Sample_23

source_name: Breast Tumor Tissue_7161-37 rep 1


title: Heart-ISO-6hrs-rep2


title: Heart-ISO-6hrs-rep1


title: Sample_21

source_name: Breast Tumor Tissue_7161-27 rep 1

value: Cohort 5


title: Sample_22

source_name: Breast Tumor Tissue_7161-34 rep 1


title: Heart-ISO-3hrs-rep3

source_name: heart, ISO, 3hrs


title: Sample_19

source_name: Breast Tumor Tissue_7161-45 rep 1

value: Frozen


title: Heart-ISO-3hrs-rep2


title: Sample_18

value: Fresh

value: Post


title: Sample_20

source_name: Breast Tumor Tissue_7161-23 rep 1


title: Sample_17

source_name: Breast Tumor Tissue_7161-28 rep 1


title: Heart-ISO-3hrs-rep1