title: HRSRNAPilot-34

tag: hispanic


title: WT PAO1 biological rep3

status: Public on Nov 15 2015

type: RNA

city: Hanover

first: Deborah

middle: A

last: Hogan

state: NH

address: Vail Building Rm 208

department: Microbiology and Immunology

country: USA

institute: Geisel School of Medicine at Dartmouth

description: Pseudomonas aeruginosa grown as biofilms on ∆F508 cystic fibrosis bronchial epithelial cells (CFBEs)

hyb_protocol: cDNAs were hybridized to Affymetrix Pseudomonas GeneChips according to the manufacturer’s instructions with the GeneChip fluidics station 450 (Affymetrix).

scan_protocol: GeneChips were scanned with the GeneChip Scanner 3000 7G (Affymetrix) in the Dartmouth Genomics Shared Resource laboratory.

data_processing: The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings and processed using robust multi-array average.

label: Biotin

molecule: total RNA

organism: Pseudomonas aeruginosa

label_protocol: cDNAs were terminally labeled with biotin-ddUTP (Enzo Bio-Array terminal labeling kit, Affymetrix)

growth_protocol: P. aeruginosa were grown overnight at 37 degress C in LB prior to exposure to CFBE airway epithelial cells.

extract_protocol: Total RNA from CFBE cells and associated P. aeruginosa biofilms was isolated using the Qiagen RNA Easy extraction protocol. The MICROBExpress Bacterial mRNA Enrichment Kit (Life technologies) was used to deplete eukaryotic RNA from the samples.

treatment_protocol: P. aeruginosa were washed and resuspended at an OD600=0.5 in minimal essential media (MEM). Suspensions were applied to confluent CFBE cell monolayer grown in 24-well plastic dishes and incubated at 37 °C, 5% CO2 for 1 h. After 1 h planktonic cells were aspirated and fresh media was added. After an additional 90 min, planktonic cells were aspirated again, and the CFBE monolayer was washed x2 with PBS prior to recovery of cells for RNA extraction.

tag: strain

tag: genotype/variation

value: WT


title: HRSRNAPilot-32

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

hyb_protocol: Standard Illumina hybridization protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All available data are provided, with no additional filtering.

label: biotin

organism: Homo sapiens

source_name: Whole blood (PAXgene RNA)

label_protocol: Standard Illumina target synthesis for gene expression profiling (carried out UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted from primary peripheral blood samples (PAXgene RNA collection tubes) using a QIACube instrument.

tag: age (yrs)

tag: female

tag: black

tag: bmi

tag: diabcvdcastr

tag: smoke

tag: alcohol

tag: loneliness

tag: optimism

tag: pessimism

tag: anxiety

tag: cesd

tag: lifesatisfaction

tag: pa


title: HRSRNAPilot-35

tag: hispanic

value: missing


title: HRSRNAPilot-29


title: HRSRNAPilot-30


title: HRSRNAPilot-23


title: HRSRNAPilot-33


title: HRSRNAPilot-39


title: HRSRNAPilot-36


title: HRSRNAPilot-37


title: HRSRNAPilot-28


title: HRSRNAPilot-19


title: HRSRNAPilot-17


title: HRSRNAPilot-25


title: HRSRNAPilot-20


title: HRSRNAPilot-24


title: HRSRNAPilot-27


title: HRSRNAPilot-31


title: HRSRNAPilot-26


title: HRSRNAPilot-21


title: HRSRNAPilot-16


title: HRSRNAPilot-15


title: HRSRNAPilot-11


title: HRSRNAPilot-14


title: PBMC of SI female mouse #27

city: Rome

first: Luciano

last: Castiello

address: Viale Regina Elena 291

country: Italy

institute: Istituto Pasteur Italia - Fondazione Cenci Bolognetti

description: Gene expression of PBMC from female SI mouse #27

hyb_protocol: RNAs samples (n = 14) were hybridized on  Agilent mouse gene expression microarrays (G4852A)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20100804) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Quantile normalized data after filtering out for signal intensity (intensity <10), spot quality (flagged in Feature Extraction as Feature Non-uniform outliers) or presence across the data set (if present in less than 75% of the samples) were used. Replicate spots were averaged.

organism: Mus musculus

source_name: female SI 27

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice experiencing an hostile/adverse social environment during the third postnatal week and mice that were  social isolated during the third postnatal week underwent cocaine-seeking behavior studies by conditioned place preference test with under-threshold cocaine dosage (5 mg/kg) , extinction and withdrawal.

extract_protocol: Mouse blood was collected via sub-mandibular puncture in EDTA tubes. PBMC were extracted from blood samples using Red Blood Cell lysis buffer and RNA was subsequently isolated using Total RNA purification Plus Kit (Norgen Biotek, Thorold, Canada)

tag: tissue

value: blood

tag: cell type

value: PBMC

tag: gender

value: female

tag: type of stress

value: SI

tag: mouse id #


title: HRSRNAPilot-10

tag: age (yrs)

tag: female

tag: black

tag: bmi


title: HRSRNAPilot-4

tag: diabcvdcastr

tag: smoke

tag: alcohol

tag: loneliness


title: HRSRNAPilot-9

tag: optimism

tag: pessimism

tag: anxiety

tag: cesd


title: HRSRNAPilot-5

tag: hispanic

tag: lifesatisfaction

tag: pa


title: PBMC of SI male mouse #7

description: Gene expression of PBMC from male SI mouse #7

source_name: male SI 7

tag: tissue

tag: cell type

tag: gender

value: male

tag: type of stress


title: HRSRNAPilot-6

tag: age (yrs)

tag: female

tag: black


title: HRSRNAPilot-1

tag: bmi

tag: diabcvdcastr

tag: smoke


title: HRSRNAPilot-12

tag: alcohol

tag: loneliness

tag: optimism


title: HRSRNAPilot-2

tag: pessimism

tag: anxiety

tag: cesd


title: PBMC of SS female mouse #22

description: Gene expression of PBMC from female SS mouse #22

source_name: female SS 22

value: SS

tag: mouse id #


title: PBMC of SS male mouse #2

description: Gene expression of PBMC from male SS mouse #2

source_name: male SS 2

tag: tissue


title: PBMC of SS female mouse #23

description: Gene expression of PBMC from female SS mouse #23

source_name: female SS 23

tag: cell type


title: PBMC of SI male mouse #5

description: Gene expression of PBMC from male SI mouse #5

source_name: male SI 5

tag: gender


title: PBMC of SI female mouse #28

description: Gene expression of PBMC from female SI mouse #28

source_name: female SI 28

tag: type of stress


title: PBMC of SS female mouse #20

description: Gene expression of PBMC from female SS mouse #20

source_name: female SS 20


title: PBMC of SS male mouse #01b

description: Gene expression of PBMC from male SS mouse #01b

source_name: male SS 01b


title: HRSRNAPilot-13

tag: age (yrs)

tag: hispanic

tag: lifesatisfaction

tag: pa


title: PBMC of SS male mouse #3

description: Gene expression of PBMC from male SS mouse #3

source_name: male SS 3


title: HRSRNAPilot-7

tag: female

tag: black

tag: bmi

tag: diabcvdcastr


title: PBMC of SS female mouse #21

description: Gene expression of PBMC from female SS mouse #21

source_name: female SS 21


title: HRSRNAPilot-8

tag: smoke

tag: alcohol

tag: loneliness

tag: optimism


title: Knockdown Control#2 rep3

city: Beijing

first: Guifeng

last: Wei

state: Beijing

address: 15 Datun Road

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

description:
control#2_rep3
raw data file: US10313827_255290910047_S01_GE2_107_Sep09_1_2.txt

hyb_protocol: (1) Reverse transcribed into first strand cDNA with the T7-oligo(dT) primer and T7-random primer. (2) systhesis of the second cDNA (3) in vitro transcribed into cRNA with T7 Enzyme mix (4) cRNA purification (5) reverse transcription using the cRNA as template with random primers (6) labelling the cDNA with Klenow Fragment Enzyme, as well as the Cy3 or Cy5-labelled dNTPs.

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner and processed with the Agilent Feature Extraction v10.7

data_processing: The microarray data were quantile normalized using the R limma package. The fold change and two-tailed Student’s t test were applied for statistical analysis of differentially expressed genes. Heatmap and Scatterplot were drawn with the functions in R. GSEA (v2.0.13) analysis were conducted with two classes (OverExpression vs Control) against the c2 and hallmark v5.0 of MSigDB.

source_name: siRNA control#2

label_protocol: 500 ng RNAs were used to generate fluorescence-labelled cDNA for hybridization according to the Agilent standard workflow

growth_protocol: RKO cells were cultured in MEM medium supplemented with 10% FBS.

extract_protocol: Total RNA was isolated using the Trizol following the manufacturer’s instructions and RNA integrity assessed on a Nanodrop 2000

treatment_protocol: siRNAs targeting the Lnc_ASNR sequence or control were transfected into RKO using Lipofectamine 2000.

tag: cell line

value: RKO

value: human colorectal carcinoma

tag: transfected with

value: control siRNA#2


title: Knockdown Lnc_ASNR#b rep3

description:
siRNA_LncASNR#b_rep3
raw data file: US10313827_255290910047_S01_GE2_107_Sep09_1_2.txt

tag: cell type


title: HRSRNAPilot-3

tag: pessimism

tag: anxiety

tag: cesd


title: HRSRNAPilot-18

tag: age (yrs)

tag: hispanic


title: Knockdown Lnc_ASNR#a rep3

description:
siRNA_LncASNR#a_rep3
raw data file: US10313827_255290910047_S01_GE2_107_Sep09_1_1.txt


title: Knockdown Lnc_ASNR#b rep2

description:
siRNA_LncASNR#b_rep2
raw data file: US10313827_255290910046_S01_GE2_107_Sep09_1_4.txt


title: HRSRNAPilot-22

tag: lifesatisfaction

tag: pa


title: PBMC of SS male mouse #1

description: Gene expression of PBMC from male SS mouse #1

source_name: male SS 1

tag: tissue

tag: gender

tag: type of stress

tag: mouse id #


title: Knockdown Lnc_ASNR#a rep2

description:
siRNA_LncASNR#a_rep2
raw data file: US10313827_255290910046_S01_GE2_107_Sep09_1_3.txt


title: Knockdown Control#1 rep3

description:
control#1_rep3
raw data file: US10313827_255290910047_S01_GE2_107_Sep09_1_1.txt

value: control siRNA#1


title: Knockdown Lnc_ASNR#b rep1

description:
siRNA_LncASNR#b_rep1
raw data file: US10313827_255290910046_S01_GE2_107_Sep09_1_2.txt


title: Knockdown Lnc_ASNR#a rep1

description:
siRNA_LncASNR#a_rep1
raw data file: US10313827_255290910046_S01_GE2_107_Sep09_1_1.txt


title: PBMC of SI male mouse #6

description: Gene expression of PBMC from male SI mouse #6

source_name: male SI 6


title: Knockdown Control#1 rep2

description:
control#1_rep2
raw data file: US10313827_255290910046_S01_GE2_107_Sep09_1_3.txt

source_name: siRNA control#1


title: Knockdown Control#2 rep2

description:
control#2_rep2
raw data file: US10313827_255290910046_S01_GE2_107_Sep09_1_4.txt


title: PBMC of SI male mouse #4

description: Gene expression of PBMC from male SI mouse #4

source_name: male SI 4


title: Control liver progenitor sample 2

city: Philadelphia

first: Pichai

last: Raman

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description: Control liver progenitors were isolated by Flow cytometry with a combination of surface markers

hyb_protocol: Amplifified cRNA was streptavidin-labeled, fragmented and hybridized to Affymetrix 430-2.0 arrays as recommended by the manufacturer

scan_protocol: Gene CHIP Scanner 3000

data_processing: The raw data for microarray results were normalized using RMA from the R/Bioconductor package ‘affy’.

source_name: Mouse control liver progenitor 2

label_protocol: As recommended by the Manufacturer (Affymetrix)

growth_protocol: in vivo

extract_protocol: Liver progenitor cells were sorted into Trizol LS and classical trizol extraction was performed to obtain total RNA

treatment_protocol: Tamoxifen treated mice for 5 days (1mgr/day), 2 weeks before harvesting the liver

value: liver


title: Control liver progenitor sample 1

source_name: Mouse control liver progenitor 1


title: Knockdown Control#2 rep1

description:
control#2_rep1
raw data file: US10313827_255290910046_S01_GE2_107_Sep09_1_2.txt


title: Rb family triple Knock Out liver progenitor sample 1

description: Mutant liver progenitors were isolated by Flow cytometry with a combination of surface markers

source_name: Mouse mutant liver progenitor 1


title: Rb family triple Knock Out liver progenitor sample 2

source_name: Mouse mutant liver progenitor 2


title: Control liver progenitor sample 3

source_name: Mouse control liver progenitor 3


title: DF_EC10.3

status: Public on Nov 14 2015

city: Antwerp

first: Melissa

last: Penninck

address: Groenenborgerlaan 171

country: Belgium

institute: University of Antwerp

description: Biological replicate 3 of 3. Exposed sample.

hyb_protocol: Gene Expression Hybridization Kit (Agilent)

scan_protocol: Genepix Personal 4100 (Axon Instruments)

data_processing: Data was processed as normalized log2 based fold change Cy5/Cy3

organism: Daphnia magna

source_name: EC10 exposure 3,4-DICHLOROPHENOL, whole body extracts, 96h

label_protocol: Low Input Quick Amp Labeling Kit (Two Color, Agilent); Starting material = 100 ng

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions followed by a DNAse treatment using 1U RNAse-free DNAse and 1U RNAse inhibitor (Fermentas, Germany) per 30µl sample and subsequent phenol/chloroform extractions.

treatment_protocol: Daphnia magna neonates (between 0 and 24h old) were exposed for 96h in glass recipients to each chemicals’ respective EC10-96h (determined based on 96h immobilization experiments) to allow multi-level effect assessment. The experiments were performed in triplicate at a density of 1 daphnid/5ml of reconstituted fresh water CaCl2.2H2O, 2mM; MgSO4.7H2O, 500μM; NaHCO3, 771μM; KCl, 77.1μM; water hardness, 250 mg CaCO3; pH 7.8; OECD guideline 203, annex 2). Test media were renewed every 48h for the anilines. Organisms were fed every other day with a mixture of P. subcapitata and C. reinhardtii in a 3:1 ratio. 30 pooled daphnids per replica were used for gene transcription analyses.

value: whole body extracts (30 organisms)

tag: age

value: day 4

source_name: Reference, whole body extracts, 96h


title: Cd_CONT.1

description: Biological replicate 1 of 3. Control sample.

source_name: Controle, whole body extracts, 96h


title: Cd_EC10.1

description: Biological replicate 1 of 3. Exposed sample.

source_name: EC10 exposure CADMIUM, whole body extracts, 96h


title: Cd_EC10.3


title: genomic DNA from aGBM primary culture 11

type: genomic

city: Toronto

first: Peter

middle: B

last: Dirks

state: Ontario

address: 555 University Avenue

department: Developmental and Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina 450k Human Methylation Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Raw data (idat files) generated by Illumina GenomeStudio Software were imported into R program and Bioconductor package minfi was used to obtain methylated and unmethylated signals (non-normalized_data.txt)  as well as beta and detection p-values (sample data table). We removed probes on the sex chromosomes and those with more than 90% sequence similarity to multiple genomic locations were excluded. The final dataset comprised of 392,879 autosomal probes.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: aGBM primary culture 11

label_protocol: Standard Illumina Protocol

growth_protocol: Cells were grown as monolayers in NS-A basal media (Stem Cell Technologies) supplemented with N2, B27, 75 μg/mL BSA (Sigma), 10 ng/mL rhEGF (Sigma), 10 ng/mL bFGF (Sigma) and 2 μg/mL heparin (Sigma).

extract_protocol: genomic DNA was extracted from cells using Qiagen DNeasy Kit according to standard instructions

value: adult aGBM primary culture


title: DF_EC10.1


title: Cd_CONT.3

description: Biological replicate 3 of 3. Control sample.


title: Cd_EC10.2

description: Biological replicate 2 of 3. Exposed sample.


title: DF_CONT.3


title: DF_EC10.2


title: genomic DNA from aGBM primary culture 3

description: SAMPLE 3; aGBM3

data_processing: Raw data (idat files) generated by Illumina GenomeStudio Software were imported into R program and Bioconductor package minfi was used to obtain methylated and unmethylated signals (non-normalized_data.txt) as well as beta and detection p-values (sample data table). We removed probes on the sex chromosomes and those with more than 90% sequence similarity to multiple genomic locations were excluded. The final dataset comprised of 392,879 autosomal probes.

source_name: aGBM primary culture 3

value: adult GBM primary culture


title: Knockdown Control#1 rep1

description:
control#1_rep1
raw data file: US10313827_255290910046_S01_GE2_107_Sep09_1_1.txt


title: TCA_EC10.2

source_name: EC10 exposure 2,3,4_TRICHLOROANILINE, whole body extracts, 96h


title: TCA_EC10.1

source_name: EC10 exposure 2,3,4-TRICHLOROANILINE, whole body extracts, 96h


title: genomic DNA from aGBM primary culture 14

source_name: aGBM primary culture 14


title: genomic DNA from aGBM primary culture 4

description: SAMPLE 4; aGBM4

source_name: aGBM primary culture 4


title: DF_CONT.2

description: Biological replicate 2 of 3. Control sample.


title: genomic DNA from aGBM primary culture 7

source_name: aGBM primary culture 7


title: genomic DNA from aGBM primary culture 6

source_name: aGBM primary culture 6


title: genomic DNA from aGBM primary culture 8

source_name: aGBM primary culture 8


title: genomic DNA from aGBM primary culture 2

description: SAMPLE 2; aGBM2

source_name: aGBM primary culture 2


title: genomic DNA from aGBM primary culture 13

source_name: aGBM primary culture 13


title: genomic DNA from aGBM primary culture 5

source_name: aGBM primary culture 5


title: genomic DNA from aGBM primary culture 10

source_name: aGBM primary culture 10


title: genomic DNA from aGBM primary culture 9

source_name: aGBM primary culture 9


title: genomic DNA from aGBM primary culture 12

source_name: aGBM primary culture 12


title: DA_EC10.2

source_name: EC10 exposure 3,5-DICHLOROANILINE, whole body extracts, 96h

source_name: Reference, whole body extracts, 96h


title: TCA_EC10.3


title: TCA_CONT.3

source_name: Controle, whole body extracts, 96h


title: CA_EC10.2

source_name: EC10 exposure 4-CHLOROANILINE, whole body extracts, 96h


title: CA_CONT.2


title: DA_EC10.3


title: TCA_CONT.1


title: DA_CONT.1


title: TCA_CONT.2


title: DF_CONT.1


title: CA_CONT.3


title: CA_EC10.1


title: DA_CONT.3


title: CA_CONT.1


title: CA_EC10.3


title: A_EC10.3

source_name: EC10 exposure ANILINE, whole body extracts, 96h


title: CP_EC10.2

source_name: EC10 exposure 3-CHLOROPROPANOL, whole body extracts, 96h


title: CP_EC10.3


title: A_EC10.2


title: CP_CONT.3


title: CP_EC10.1


title: CP_CONT.1


title: A_CONT.2


title: DA_CONT.2


title: genomic DNA from aGBM primary culture 1

description: SAMPLE 1; aGBM1

source_name: aGBM primary culture 1


title: DA_EC10.1


title: CP_CONT.2


title: A_CONT.3


title: A_EC10.1


title: IB_EC10.2

source_name: EC10 exposure ISOBUTANOL, whole body extracts, 96h


title: IB_CONT.3


title: IB_CONT.2


title: IB_CONT.1


title: IB_EC10.1


title: A_CONT.1


title: IB_EC10.3


title: Cd_CONT.2


title: Smoking TiOblast2 DAY7

city: Chapel Hill

first: Lyndon

last: Cooper

state: NC

address: 330 Brauer Hall, CB#7450

department: Prosthodontics

institute: UNC School of Dentistry

hyb_protocol: The Encore Biotin Module V2-NuGen/Affymetrix Human gene 1.1 ST Array

scan_protocol: Affymetrix GeneChip Scanner 3000 7G Plus with Autoloader

data_processing: The data was analyzed using GeneSpring software v.12.0

source_name: implant adherent cells-alveolar bone-microroughosurface implant-day7-Smoking

label_protocol: Samples were processed and hybridized to the Affymetrix Human gene 1.1 ST Array at the UNC core facility following the manufacturer’s recommended protocols and reagents (Affymetrix, San Clara,CA). Labeling used Nugen Encore Biotin Module

growth_protocol: 11 Healthy non-smoking  and 10 smoking human subjects missing 2 or more teeth were included.Following anesthesia(Lidocaine 2% with epinephrine (1:100,000)), two separate crestal incisions approximately 6mm in length were made and full thickness mucoperiosteal flaps were raised. Each subject received two TIO and two OS implants. Two osteotomies were prepared per site to allow placement of one implant of each surface (1 TiO and 1 Os). This paired surgical design permitted the retrieval of the first 2 implants (1 of each surface) at the earlier time point without disturbing the healing of the other 2 implants. Drilling was completed using a 2.0 mm twist osteotomy drill under profuse irrigation with sterile saline. Single use osteotomy drills were used on each subject. All implants were placed by a self-tapping procedure and primary stability at the time of implant placement was insured. A submerged implant installation technique was used and the mucosal tissues were closed primarily with 4-0 chromic gut sutures.

extract_protocol: At 3 and 7 days following surgery, one surgical site was chosen at random, re-entered and the paired (One TIO and one OS) implants were removed by reverse threading. The implants were then immediately rinsed in cold PBS and then placed into 1000 ul of Tri-reagent (Invitrogen, Carlsbad, CA). Cell lysates were snap frozen, and stored at -80°C until further use.   Total RNA was isolated from the lysates using the standard Tri-reagent protocol and collected by ethanol precipitation. This was followed by purification using RNeasy MinElute Clean up kit (Qiagen, Valencia, CA, USA).  RNA was assessed for quality and quantity using a bioanalyzer (Agilent, Santa Clara, CA, USA) and nanodrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE) respectively.

treatment_protocol: Eighty-four implants (cp titanium) were placed in the alveolar bone of 11 systemically non-smoking and 10 smoking human subjects missing 2 or more teeth.Following anesthesia(Lidocaine 2% with epinephrine (1:100,000)), two separate crestal incisions approximately 6mm in length were made and full thickness mucoperiosteal flaps were raised. Each subject received two TIO and two OS implants. Two osteotomies were prepared per site to allow placement of one implant of each surface (1 TiO and 1 Os). This paired surgical design permitted the retrieval of the first 2 implants (1 of each surface) at the earlier time point without disturbing the healing of the other 2 implants. Drilling was completed using a 2.0 mm twist osteotomy drill under profuse irrigation with sterile saline. Single use osteotomy drills were used on each subject. All implants were placed by a self-tapping procedure and primary stability at the time of implant placement was insured. A submerged implant installation technique was used and the mucosal tissues were closed primarily with 4-0 chromic gut sutures

value: alveolar bone

value: implant adherent cells

tag: subject

value: Smoking subject


title: Smoking Osseospeed6 DAY7

source_name: implant adherent cells-alveolar bone-nanosurface implant-day7-Smoking


title: Smoking TiOblast6 DAY7


title: Smoking TiOblast4 DAY7


title: Smoking TiOblast10 DAY7


title: Smoking Osseospeed9 DAY7


title: Smoking Osseospeed8 DAY7


title: Smoking Osseospeed2 DAY7


title: Smoking TiOblast8 DAY7


title: Smoking TiOblast7 DAY7


title: Smoking TiOblast5 DAY7


title: Smoking Osseospeed4 DAY7


title: Smoking Osseospeed7 DAY7


title: Smoking TiOblast1 DAY7


title: Smoking Osseospeed3 DAY7


title: Smoking TiOblast3 DAY7


title: Smoking Osseospeed1 DAY7


title: Smoking TiOblast7 DAY3

source_name: implant adherent cells-alveolar bone-microroughosurface implant-day3-Smoking


title: Smoking Osseospeed5 DAY7


title: Smoking Osseospeed10 DAY7


title: Smoking TiOblast9 DAY3


title: Smoking TiOblast6 DAY3


title: Smoking TiOblast10 DAY3


title: Smoking TiOblast2 DAY3


title: Smoking TiOblast5 DAY3


title: Smoking TiOblast4 DAY3


title: Smoking TiOblast8 DAY3


title: Smoking TiOblast3 DAY3


title: Smoking Osseospeed9 DAY3

source_name: implant adherent cells-alveolar bone-nanosurface implant-day3-Smoking


title: Smoking Osseospeed8 DAY3


title: Smoking Osseospeed2 DAY3


title: Smoking Osseospeed10 DAY3


title: Smoking Osseospeed4 DAY3


title: Smoking Osseospeed5 DAY3


title: Smoking Osseospeed7 DAY3


title: Healthy TiOblast5 DAY7

source_name: implant adherent cells-alveolar bone-microroughosurface implant-day7-Non-smoking

value: Non-smoking subject


title: Smoking Osseospeed3 DAY3


title: Healthy TiOblast6 DAY7


title: Healthy TiOblast11 DAY7


title: Healthy TiOblast10 DAY7


title: Smoking TiOblast1 DAY3


title: Healthy TiOblast8 DAY7


title: Smoking Osseospeed6 DAY3


title: Healthy TiOblast9 DAY7


title: Smoking Osseospeed1 DAY3


title: Healthy TiOblast7 DAY7


title: Healthy TiOblast4 DAY7


title: Healthy TiOblast2 DAY7


title: Healthy Osseospeed11 DAY7

source_name: implant adherent cells-alveolar bone-nanosurface implant-day7-Non-smoking


title: Healthy TiOblast3 DAY7


title: Healthy TiOblast1 DAY7


title: Healthy Osseospeed6 DAY7


title: Healthy Osseospeed9 DAY7


title: Healthy Osseospeed7 DAY7


title: Smoking TiOblast9 DAY7


title: Healthy Osseospeed5 DAY7


title: Healthy Osseospeed4 DAY7


title: Healthy Osseospeed1 DAY7


title: Healthy Osseospeed10 DAY7


title: Healthy Osseospeed3 DAY7


title: Healthy TiOblast10 DAY3

source_name: implant adherent cells-alveolar bone-microroughosurface implant-day3-Non-smoking


title: Healthy TiOblast5 DAY3


title: Healthy TiOblast2 DAY3


title: Cy3-E19, Cy5-E16

first: Zhong

last: Zheng

address: 675 Charles E Young Dr, South

institute: UCLA

hyb_protocol: Corresponding Cy3 and Cy5 labeled cRNAs were combined in hybridization buffer and samples were and hybridized overnight (17 hours, 65°C) to an Agilent Rat Genome Oligo Microarrays (4x44K, Design ID 014879) using Agilent’s recommended hybridization chamber and oven.Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Scanner G2505B US22502695 (Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 9.5.1.1) was used to read out and process the microarray image files. For data normalization and determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware). The applied normalization that was based on the Rosetta error model (Weng et al., 2006, Bioinformatics, Vol. 22 no. 9 2006, pages 1111–1121).

organism: Rattus norvegicus

source_name: E19 fetal skin

label_protocol: Agilent Low RNA Input Linear Amp Kit

growth_protocol: E16 (day 16.5) or E19 (day 18.5) fetal SD rat skin

extract_protocol: NucleoSpin® RNA II

treatment_protocol: Not applicable

tag: strain

value: Sprague Dawley

value: E19 fetal skin

source_name: E16 fetal skin

value: E16 fetal skin


title: Cy3-E16, Cy5-E19


title: Healthy Osseospeed8 DAY7


title: Healthy TiOblast3 DAY3


title: Healthy Osseospeed2 DAY7


title: Healthy TiOblast4 DAY3


title: Healthy Osseospeed11 DAY3

source_name: implant adherent cells-alveolar bone-nanosurface implant-day3-Non-smoking


title: Healthy TiOblast11 DAY3


title: Healthy TiOblast9 DAY3


title: Healthy TiOblast6 DAY3


title: Healthy TiOblast1 DAY3


title: Healthy Osseospeed10 DAY3


title: Healthy TiOblast7 DAY3


title: Fed brain rep4

city: Setagaya-ku

first: Kosuke

last: Tanegashima

state: Tokyo

address: 2-1-6 Kamikitazawa

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

hyb_protocol: 0.60 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression Microarray 8x60K Ver.2.0 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44K array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Fed brain

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Brain were dissoluved in TRIZOL, and total RNA were extracted with standerd protcol. RNA was further purified with Rnasy kit.

value: brain


title: Healthy Osseospeed8 DAY3


title: Fed brain rep2


title: Healthy TiOblast8 DAY3


title: Fed brain rep3


title: Healthy Osseospeed6 DAY3


title: Healthy Osseospeed7 DAY3


title: Healthy Osseospeed5 DAY3


title: Control-1

status: Public on Nov 13 2015

city: Charlestown

first: Yan

last: Feng

state: MA

address: 149 13th Street, Rm4423

department: Anesthesia, Critical Care and Pain Medicine

institute: MGH

description:
Sham-1
microRNAs
First background subtraction was performed using the data from four negative control wells containing water. The samples were then normalized using the signals of mir-20a-5p, mir-24-3p, mir-93-5p

hyb_protocol: Firefly Smart Particles (35 μL) are added to fresh wells of a 96-well filter plate and filtered. Next, 100 μL of Hybridization Buffer is added to each well followed by 40 μL of the PCR product. The plate is incubated at 37°C for 30 minutes with 750 rpm shaking. After rinsing twice with 200 μL of 1X Rinse Buffer, 175 μL of Run Buffer is added to each well.

scan_protocol: The assay was scanned using an EMD Millipore Guava 8HT flow cytometer

data_processing: The data was analyzed using the Firefly Analysis Workbench. Normalization is applied by first using the geometric average of the three selected normalization targets (mir-20a-5p, mir-24-3p, mir-93-5p) to form a synthetic normalizer, which is deflated to an average value of 1.0 across all wells to be normalized. All targets are then divided by the deflated normalizer in that well.

source_name: EDTA-treated Plasma_sham

label_protocol: Sample (40 μL) is mixed with 36 μL Digest Buffer and 4 μL 10% Protease Mix and incubated at 60°C for 30 minutes with 750 rpm shaking.  For each sample, Firefly Particles (35 μL) are added to a well of a 96-well filter plate and filtered. Next, 25 μL of Hybridization Buffer is added to each well followed by 25 μL of sample. The plate is incubated at 37°C for 60 minutes with 750 rpm shaking. After rinsing twice with 200 μL of 1X Buffer A, 75 μL of 1X Labeling Buffer is added to each well. The plate is incubated at room temperature for 60 minutes with 750 rpm shaking. After two rinses with Buffer B followed by one rinse with 1X Buffer A, a catch plate is added to the vacuum manifold and the filter plate is put under constant vacuum. 75 μL of 95°C RNAse-free water is added twice to each well. 30 μL of this eluant is added to a clean PCR plate and mixed with 20 μL PCR master mix containing a Cy5-labeled primer. The mixture undergoes 27 cycles of PCR amplification followed by 6 cycles of asymmetric amplification.

extract_protocol: No RNA extraction was required

treatment_protocol: Sham mice only underwent laparotomy, whereas CLP mice had cecal ligation and puncture procedure. EDTA-treated plasma were harvested at 24 h after the procedure.

value: Plasma

tag: Sex

value: male

value: 10 weeks


title: Control-2

description:
Sham-2
microRNAs
First background subtraction was performed using the data from four negative control wells containing water. The samples were then normalized using the signals of mir-20a-5p, mir-24-3p, mir-93-5p


title: CLP mice-4

description:
CLP-4
microRNAs
First background subtraction was performed using the data from four negative control wells containing water. The samples were then normalized using the signals of mir-20a-5p, mir-24-3p, mir-93-5p

source_name: EDTA-treated Plasma_CLP


title: CLP mice-5

description:
CLP-5
microRNAs
First background subtraction was performed using the data from four negative control wells containing water. The samples were then normalized using the signals of mir-20a-5p, mir-24-3p, mir-93-5p


title: Fasting brain rep4

source_name: Fasting brain


title: IR mice-8

description:
microRNAs
First background subtraction was performed using the data from four negative control wells containing water. The samples were then normalized using the signals of let-7d-5p, let-7g-5p, let-7i-5p

data_processing: The data was analyzed using the Firefly Analysis Workbench. Normalization is applied by first using the geometric average of the three selected normalization targets (let-7d-5p, let-7g-5p, let-7i-5p) to form a synthetic normalizer, which is deflated to an average value of 1.0 across all wells to be normalized. All targets are then divided by the deflated normalizer in that well.

source_name: EDTA-treated Plasma_I/R_injury

treatment_protocol: Sham mice only underwent the left thoracotomy without coronary artery ligation, whereas I/R mice had 45 min ischemia (left anterior descending coronary artery ligation) followed by 4 h reperfusioin

value: plasma


title: CLP mice-3

description:
CLP-3
microRNAs
First background subtraction was performed using the data from four negative control wells containing water. The samples were then normalized using the signals of mir-20a-5p, mir-24-3p, mir-93-5p


title: CLP mice-2

description:
CLP-2
microRNAs
First background subtraction was performed using the data from four negative control wells containing water. The samples were then normalized using the signals of mir-20a-5p, mir-24-3p, mir-93-5p


title: Control-3

description:
Sham-3
microRNAs
First background subtraction was performed using the data from four negative control wells containing water. The samples were then normalized using the signals of mir-20a-5p, mir-24-3p, mir-93-5p


title: Control-4

description:
Sham-4
microRNAs
First background subtraction was performed using the data from four negative control wells containing water. The samples were then normalized using the signals of mir-20a-5p, mir-24-3p, mir-93-5p


title: CLP mice-1

description:
CLP-1
microRNAs
First background subtraction was performed using the data from four negative control wells containing water. The samples were then normalized using the signals of mir-20a-5p, mir-24-3p, mir-93-5p


title: Fasting brain rep3


title: Fed brain rep1


title: IR mice-5


title: Fasting brain rep2


title: Healthy Osseospeed2 DAY3


title: Healthy Osseospeed3 DAY3


title: IR mice-7


title: Healthy Osseospeed1 DAY3


title: IR mice-6


title: IR mice-4


title: IR mice-3


title: Healthy Osseospeed9 DAY3


title: Healthy Osseospeed4 DAY3


title: Sham mice-1


title: IR mice-1


title: Sham mice-4


title: Sham mice-2


title: IR mice-2


title: Sham mice-5


title: Sham mice-3


title: Sham mice-6


title: Fasting brain rep1


title: 2192-T

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

hyb_protocol: Hybridization of genomic DNA onto the Agilent 244K CGH (Agilent Technologies) was performed according to Agilent's Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: normalized and background corrected intensities were used to calculate log2 ratios for each probe. The normalized log2 ratio (Cy5/Cy3) representing test/reference corresponds to the 11th column in the Agilent Feature Extraction output files provided by Agilent.

source_name: Early stage lung cancer

label_protocol: DNA concentration was assessed using the Quant-iT PicoGreen dsDNA Assay kit (Life Technologies). 2.5 ug of tumor DNA (A260/A280ratio of 1.8-2.0) was labelled with Cy5 (red). The normal reference (Human Genomic DNA, Female, Promega, Inc., Cat #G1521). was labeled with Cy3 (green). Labelled DNA was hybridized on Agilent Human Genome CGH Microarray 244A (high-definition 244K array).

extract_protocol: Snap-Frozen tumor tissue were processed on cryostat to generate multiple 5-micron thick shavings. After trimming excess OCT the shavings are homogenized and further processed using the Qiagen QIAamp DNA Mini kit (Qiagen Inc.) according to the manufacturer's instructions.

value: Lung

value: Adenocarcinoma

tag: race

value: Caucasian

value: M

tag: tumor stage

value: IB

value: Female


title: 850-T

tag: cell type

value: F

value: IIIB

source_name: Human Genomic DNA, Female, Promega, Inc., Cat #G1521


title: 1330-T

value: Squamous

value: IIIA


title: 386-T

value: IA


title: 2244-T

value: African American

value: IIB


title: 1311-T


title: 2239-T


title: Tumor_183

city: Oslo

first: Maria

middle: Moksnes

last: Bjaanæs

address: Ullernchausseen 70

department: Department of genetics

country: Norway

institute: Oslo Universitetssykehus

hyb_protocol: The labeled cRNA were hybridized to slides that were incubated for 17 hours at 65°C.

scan_protocol: Arrays were scanned by using Agilent Microarray Scanner (Agilent technologies) and the raw data were preprocessed with the Agilent's Feature Extraction Software with default parameters (Agilent feature extraction version 10.7.3.1).

data_processing: The gene expression values were log 2 transformed and normalized between arrays by using the 75th percentile method in Genespring GX analysis Software v.12.1 (Agilent technology).

label_protocol: Total RNA from each tumor sample (50ng) was converted to cDNA through reverse transcription with the use of a T7-oligo (dT) primer. By using quick-AMP labeling kit (Agilent technologies), amplified and Cy3-labeled cRNA were produced.

extract_protocol: Standard TRIZOL methods (Invitrogen, Carlsbad, CA, USA) were used to extract total RNA and the procedure was done according to manufacturer's instruction.

treatment_protocol: Tissue obtained at the surgery were snap frozen in liquid nitrogen and stored at –80°C until DNA and RNA isolation.

tag: smoking

value: Smoker

value: Lung adenocarcinoma tissue

tag: Stage

value: IIIa

tag: tp53 mutation

value: mutated

tag: egfr mutation

value: wild type

tag: kras mutation


title: 1095-T

value: Lung


title: 2024-T

value: Adenocarcinoma

value: Caucasian


title: 819-T


title: 1736-T

value: IB


title: 2269-T

value: M

value: Female


title: 2167-T

value: F


title: 717-T


title: 495-T


title: IR mice-9

value: plasma

value: male

value: 10 weeks


title: 1454-T

value: IIIA


title: 602-T

value: Squamous

value: IA


title: Tumor_182

tag: age (yrs)

value: Smoker

value: Lung adenocarcinoma tissue

value: IIa


title: 555-T

tag: tissue

value: IIB


title: 440-T

value: Lung

tag: gender


title: 940-T

value: Adenocarcinoma


title: 2212-T

value: Asian


title: Tumor_181

value: wild type


title: 1510-Tx

value: Caucasian

value: M

value: IB


title: 2247-T

value: IIIB

value: Female


title: 1282-T

value: F


title: 363-T


title: 1325-T


title: Tumor_179

value: Ia

value: mutated


title: 1761-T

value: IIIA


title: Tumor_177

value: Never

value: Male

value: Ib


title: Tumor_174

value: Smoker

value: Lung adenocarcinoma tissue


title: 1714-T

value: Lung

value: Adenocarcinoma

value: IIB


title: 2309-T

value: Caucasian


title: Tumor_175

value: IIIa

value: wild type


title: 259-T

value: African American

value: IB


title: 1238-T

value: Asian or Pacific Islander

value: F

value: Female


title: 1265-T

value: M

value: IA


title: Tumor_173

value: Ia

value: mutated


title: Tumor_169

value: Smoker

value: Ib


title: 1551-T

value: Lung


title: 1844-T

value: Squamous

value: IIIA


title: 2204-T

value: Adenocarcinoma

value: Caucasian


title: Tumor_172

value: Male

value: Lung adenocarcinoma tissue

value: wild type


title: Tumor_167


title: 1671-T

value: IIIB


title: Tumor_168


title: Tumor_165


title: 1498-T

value: F

value: IB


title: 2211-T

value: M

value: IIB

value: Female


title: 670-T

value: Hispanic

value: IA


title: 1332-T

value: African American


title: 2299-T

value: Lung


title: Tumor_164

value: Smoker

value: IIa

value: mutated


title: Tumor_170

value: IIIa


title: Tumor_162


title: 1405-T

value: Adenocarcinoma

value: Caucasian

value: IIIA


title: Tumor_180

value: Lung adenocarcinoma tissue

value: Ib

value: wild type


title: Tumor_163

value: Male

value: Ia


title: Tumor_161

value: Female


title: Tumor_160


title: Tumor_159


title: Tumor_176


title: 917-T

value: Squamous

value: F

value: IB


title: 1908-T

value: Lung


title: 2278-T

value: M

value: IV


title: 1601-T


title: Tumor_155

value: Smoker

value: mutated


title: Tumor_156

value: IIIa


title: Tumor_157


title: 1161-T

value: Adenocarcinoma

value: Caucasian

value: IIIB


title: Tumor_153

value: Lung adenocarcinoma tissue

value: Ib


title: 1502-T2

value: IIA


title: Tumor_149

value: Never

value: wild type


title: 2280-T

value: Squamous

value: Female


title: 2076-T


title: 1978-T

value: F

value: IIIA


title: Tumor_147

value: Male

value: Ia


title: Tumor_151

value: Smoker


title: 2006-T

value: Lung

value: M


title: 2281-T

value: Adenocarcinoma

value: IIB


title: Tumor_142

value: IIa


title: 999-T

value: Caucasian

value: IB


title: 1038-T2


title: 2279-T

value: IA


title: Tumor_148

value: Lung adenocarcinoma tissue


title: 1930-T

value: African American


title: Tumor_152

value: IIb

value: mutated

value: wild type


title: Tumor_143

value: Female


title: 1168-T

value: IIA


title: Tumor_137

value: Never

value: Male


title: Tumor_146

value: Smoker

value: IIIa


title: Tumor_140

value: Ib


title: Tumor_145


title: Tumor_138

value: Ia


title: 697-T

value: Lung

value: Adenocarcinoma

value: F

value: IIB


title: 1183-T

value: Caucasian

value: M

value: IA


title: Tumor_139

value: Lung adenocarcinoma tissue

value: IIb

value: mutated


title: 722-T

value: Squamous

value: IIIB

value: Female


title: Tumor_135

value: Smoker

value: Male

value: wild type


title: Tumor_133

value: Ib


title: 309-T

value: Lung


title: 1966-T

value: Adenocarcinoma

value: African American

value: IA & IA


title: Tumor_132

value: Never

value: IIIa


title: 1052-T

value: Caucasian

value: M

value: IB


title: 1353-T

value: F


title: 1477-T

value: Squamous


title: 2307-T

value: IIB


title: Tumor_128

value: Female

value: Lung adenocarcinoma tissue

value: Ia

value: mutated


title: Tumor_123

value: Ib

value: wild type


title: Tumor_118

value: Smoker

value: IIb


title: Tumor_127

value: Male


title: Tumor_129


title: Tumor_121


title: Tumor_130


title: 2029-T

value: Lung

value: IIIA


title: 1793-T

value: Adenocarcinoma

value: Caucasian


title: Tumor_126

value: Never

value: IIIa


title: Tumor_120


title: Tumor_93


title: 2303-T

value: Squamous

value: F

value: IA


title: Tumor_92

value: Female

value: Lung adenocarcinoma tissue


title: Tumor_91

value: Ia

value: mutated


title: 1284-T

value: M

value: IIIB


title: 497-T

value: IIB


title: 539-T


title: Tumor_90

value: Smoker

value: Male

value: Ib

value: wild type


title: 1303-T

value: Lung

value: Adenocarcinoma

value: Caucasian

value: IB


title: Tumor_88

value: Never


title: 1213-T

value: Squamous

value: IIIA


title: 993-T

value: Female


title: 1041-T

value: African American

value: F


title: 1598-T2

value: IIIB vs IV


title: 590-T

value: IIA


title: 1992-T

value: M

value: IA


title: 952-T


title: Tumor_89

value: Smoker

value: Male

value: Lung adenocarcinoma tissue

value: Ia


title: Tumor_87

value: IIIa

value: mutated

value: wild type


title: Tumor_86

value: Ib


title: Tumor_85

value: Never

value: IIa


title: 2135-T

value: Lung

value: Adenocarcinoma

value: Asian

value: IIIB

value: Female


title: 1443-T

value: Caucasian

value: F

value: IB


title: Tumor_82

value: Male


title: Tumor_83

value: Smoker

value: Lung adenocarcinoma tissue


title: Tumor_80

value: Ia


title: 399-T

value: M


title: 686-T

value: Squamous


title: 1129-T

value: IIA


title: 485-T

value: Hispanic

value: IIB


title: 412-T

value: Lung

value: IIIA


title: 1476-T

value: Adenocarcinoma


title: Tumor_75

value: Ib

value: mutated

value: wild type


title: 2313-T

value: Caucasian

value: F

value: IA

value: Female


title: Tumor_78

value: Smoker

value: Lung adenocarcinoma tissue


title: Tumor_79

value: IV


title: Tumor_74

value: Ia


title: 1378-T


title: Tumor_73

value: Never

value: Male


title: 1496-T

value: IB


title: 1921-T

value: Lung

value: M

value: IIA


title: Tumor_71

value: Ib


title: 756-T1

value: Squamous

value: IIIA


title: Tumor_68

value: wild type

value: mutated


title: 250-T

value: Adenocarcinoma

value: Caucasian


title: Tumor_69

value: Smoker

value: Female


title: Tumor_70

value: Lung adenocarcinoma tissue


title: Tumor_72

value: Ia


title: Tumor_66

value: IIa


title: 1956-T

value: F


title: Tumor_67

value: Male


title: 814-T

value: Lung


title: 1355-T

value: IB


title: Tumor_64


title: Tumor_84

value: IIIa


title: Tumor_60

value: Ib


title: Tumor_63


title: 1824-T

value: Squamous

value: M


title: Tumor_61

value: wild type


title: 1237-T


title: 1346-T

value: IV


title: 416-T

value: Adenocarcinoma

value: IIIA


title: Tumor_59

value: Smoker

value: mutated


title: Tumor_58

value: Female

value: Lung adenocarcinoma tissue


title: 568-T

value: Caucasian


title: 1623-T

value: IIIB


title: 2257-T

value: IIA


title: 1809-T

value: Lung


title: Tumor_56

value: Ia


title: 720-T

value: F


title: Tumor_57


title: 393-T

value: IB


title: 2308-T

value: IIB


title: 1888-T

value: M


title: Tumor_53

value: Never

value: Ib

value: wild type


title: 475-T

value: Adenocarcinoma


title: Tumor_49

value: Smoker


title: Tumor_54

value: Male

value: IIb

value: mutated


title: Tumor_51

value: Lung adenocarcinoma tissue


title: Tumor_50


title: 2230-T

value: Caucasian

value: Female


title: Tumor_55


title: 1662-T

value: Lung

value: Hispanic


title: Tumor_45

value: IIIa


title: Tumor_48

value: IIa


title: 1576-T

value: F

value: IIB


title: Tumor_52


title: Tumor_43

value: IV


title: Tumor_42

value: Ia


title: 15-T

value: M

value: IIIA


title: 1853-T

value: Adenocarcinoma

value: IIIB


title: 1240-T

value: IA & IA


title: Tumor_40

value: Smoker

value: Male

value: wild type


title: 1549-T

value: Caucasian

value: IB

value: Female


title: Tumor_35

value: Lung adenocarcinoma tissue

value: IIIa


title: Tumor_36

value: IIa

value: mutated


title: Tumor_39


title: 1964-T

value: Lung


title: Tumor_31

value: Ib


title: 1273-T

value: Squamous

value: M


title: Tumor_32

value: Ia


title: 18-T

value: IIIA


title: 582-T


title: 1350-T


title: Tumor_27


title: 501-T


title: Tumor_30


title: 1289-T

value: Adenocarcinoma

value: F


title: 556-T


title: 1402-T

value: IA


title: HCC026N

first: Yuanfeng

last: Li

address: No.38 shengmingyuan Road

institute: Beijing Institute of Radiation Medicine

description: non-tumor liver tissue

hyb_protocol: Hybridization was performed for 16 hrs using the MES_EukGE-WS2v5_450-DEV fluidics wash and stain script.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip scanner 3000 7G

data_processing:
RMA (Robust Multiple chip Average) integrated in Expression Console was used to extract the signal from core probes representing 22,012 transcript clusters nd perform the preprocessing. Only transcript clusters with the signal above 50 in at least 50% of the samples were kept for further analysis. Gene symbol identifiers of Human Genome 18 were used to match the transcript clusters to their representative genes, while inconsistent genes were filtered during the process. Then GRSN (Global Rank-invariant Set Normalization) was employed to eliminate the intensity-dependent bias of the transcript clusters data set.
HuEx-1_0-st-v2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: non-tumor liver tissue

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

growth_protocol: non-tumor liver tissues from 31 HBV-related HCC patients

extract_protocol: not applicable

treatment_protocol: not applicable

value: Male


title: Tumor_37

value: Smoker

value: wild type


title: HCC029N

description: non-tumor liver tissue


title: HCC028N

description: non-tumor liver tissue


title: HCC027N

description: non-tumor liver tissue


title: 1833-T

value: Caucasian

value: IB

value: Female


title: Tumor_25

value: Lung adenocarcinoma tissue


title: Tumor_23

value: IIa

value: mutated


title: 654-T2

value: Lung


title: Tumor_28


title: 1729-T


title: HCC030N

description: non-tumor liver tissue


title: 1434-T


title: Tumor_22

value: Ib


title: HCC024N

description: non-tumor liver tissue


title: 2078-T

value: M


title: HCC023N

description: non-tumor liver tissue


title: HCC019N

description: non-tumor liver tissue


title: HCC021N

description: non-tumor liver tissue


title: HCC020N

description: non-tumor liver tissue


title: Tumor_20


title: HCC018N

description: non-tumor liver tissue


title: 1380-T


title: HCC022N

description: non-tumor liver tissue


title: Tumor_21

value: IIb


title: HCC017N

description: non-tumor liver tissue


title: HCC016N

description: non-tumor liver tissue


title: Tumor_19


title: HCC015N

description: non-tumor liver tissue


title: 1839-T


title: Tumor_18

value: Ia


title: 1872-T

value: Adenocarcinoma

value: IV


title: 96-T

value: IIIB


title: 1858-T2

value: African American

value: F

value: IA


title: HCC014N

description: non-tumor liver tissue


title: 1804-T

value: Hispanic


title: HCC013N

description: non-tumor liver tissue

value: Male


title: Tumor_17

value: Smoker

value: wild type


title: 1375-T

value: Squamous

value: Caucasian

value: Female


title: HCC012N

description: non-tumor liver tissue


title: HCC011N

description: non-tumor liver tissue


title: HCC008N

description: non-tumor liver tissue


title: Tumor_13

value: Lung adenocarcinoma tissue

value: IIIa

value: mutated


title: Tumor_29

value: IIb


title: Tumor_12

value: Ib


title: HCC009N

description: non-tumor liver tissue


title: HCC010N

description: non-tumor liver tissue


title: Tumor_7


title: 1974-T

value: Lung

value: M

value: IIIA


title: HCC007N

description: non-tumor liver tissue


title: Tumor_11


title: Tumor_6

value: Never

value: Ia


title: Tumor_14

value: IIa


title: Tumor_9


title: 1718-T

value: Adenocarcinoma

value: IB


title: 566-T


title: HCC006N

description: non-tumor liver tissue


title: HCC005N

description: non-tumor liver tissue

value: Male


title: 1727-T

value: African American

value: IA


title: HCC004N

description: non-tumor liver tissue

value: Female


title: 1884-T

value: Squamous

value: Caucasian

value: F

value: IIIB


title: 1591-T

value: IIA


title: HCC003N

description: non-tumor liver tissue


title: 1266-T

value: Lung


title: HCC002N

description: non-tumor liver tissue


title: HCC031N

description: non-tumor liver tissue


title: HCC025N

description: non-tumor liver tissue


title: N_0_5microg_mlAgNO3

city: Berlin

first: Linda

last: Böhmert

address: Max-Dohrn-Straße 8-10

country: Germany

institute: Federal Institute for risk assessment

description: differentiated (21 days post-confluence) Caco-2 cells (p22) in 75 cm² cell culture flask, 24 h incubated in 20 mL DMEM with 1 % ITS (Insulin, Transferin, Selen) and 1 % Penecillin/Streptomycin and 0.5 µg/mL silver ions (AgNO3)

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Human array (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000

data_processing: Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).

source_name: differentiated (21 days post-confluence) Caco-2 cells, 0.5 µg/mL silver ions (AgNO3)

label_protocol: Biotinylated cRNA was prepared from 250 ng total RNA according to the 3`IVT express kit Affymetrix protocol.

growth_protocol: differentiated (21 days post-confluence) Caco-2 cells (p22) in 75 cm² cell culture flask, medium change every 2 days, DMEM with 10 % heat inactivated fetal calf serum and 1 % Penecillin/Streptomycin

extract_protocol: mRNA was extracted and purified using a commercial system from Quiagen

tag: cell line

value: colon carcinoma cell line Caco-2

tag: agent

value: silver ions (AgNO3)

tag: dose

value: 0.5 µg/mL


title: O_0_5microg_mlAgNO3

treatment_protocol: 24 h incubated in 20 mL DMEM with 1 % ITS (Insulin, Transferin, Selen) and 1 % Penecillin/Streptomycin


title: 426-T

value: M


title: L_25_microg_mlAgPure

description: differentiated (21 days post-confluence) Caco-2 cells (p22) in 75 cm² cell culture flask, 24 h incubated in 20 mL DMEM with 1 % ITS (Insulin, Transferin, Selen) and 1 % Penecillin/Streptomycin and 25 µg/mL surfactant coated silver nanoparticles (AgPURE)

source_name: differentiated (21 days post-confluence) Caco-2 cells, 25 µg/mL surfactant coated silver nanoparticles (AgPURE)

value: 25 µg/mL


title: 296-T

value: Adenocarcinoma


title: K_25_microg_mlAgPure

value: surfactant coated silver nanoparticles (AgPURE)


title: 1987-T


title: 1692-T

value: IB


title: I_25_microg_mlAgPure


title: 1462-T

value: IIB


title: 758-T1

value: IIIA


title: G_2_5 microg_mlAgPure

description: differentiated (21 days post-confluence) Caco-2 cells (p22) in 75 cm² cell culture flask, 24 h incubated in 20 mL DMEM with 1 % ITS (Insulin, Transferin, Selen) and 1 % Penecillin/Streptomycin and 2.5 µg/mL surfactant coated silver nanoparticles (AgPURE)

source_name: differentiated (21 days post-confluence) Caco-2 cells, 2.5 µg/mL surfactant coated silver nanoparticles (AgPURE)

value: 2.5 µg/mL


title: 1933-T

value: African American

value: Female


title: E_2_5 microg_mlAgPure


title: 1309-T

value: Caucasian

value: F


title: P_0_5microg_mlAgNO3


title: D_Medium

description: differentiated (21 days post-confluence) Caco-2 cells (p22) in 75 cm² cell culture flask, 24 h incubated in 20 mL DMEM with 1 % ITS (Insulin, Transferin, Selen) and 1 % Penecillin/Streptomycin als medium control

source_name: differentiated (21 days post-confluence) Caco-2 cells, medium control

value: control


title: F_2_5 microg_mlAgPure


title: 482-T

value: Lung


title: 1805-T


title: 2190-T

value: Hispanic

value: IA


title: 771-T

value: Squamous


title: C_Medium

value: colon carcinoma cell line Caco-2


title: 1465-T


title: VGH-Med

city: New Taipei

first: Chih-Cheng

last: Chien

address: No 2, Ln 59, Jian-Cheng Rd, Sijhih Dist

country: Taiwan

institute: Sijhih Cathay General Hospital

hyb_protocol: 1.65 μg of Cy3-labeled cRNA was fragmented to an average size of approximately 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes, and then differently fragmented cRNA was independently hybridized with Agilent Human Whole Genome Oligo 4X44K Microarray system (Agilent Technologies) at 65°C for 17 hours.

scan_protocol: After washing and drying by nitrogen gun blowing, the microarrays were scanned with an Agilent Technologies Scanner G2505C US85003611 (Agilent Technologies) at 535 nm, according to Agilent's standard protocols.

data_processing: The scanned images were analyzed with Agilent Feature Extraction software (Agilent Technologies), version 10.5.1.1. Image analysis and normalization software were used to quantify the signal and background intensity for each feature. Each expression data was applied to 75 percentile normalization and log2 transformation. After global normalization, probes with intensity <70 were filtered out.

source_name: VGH-Med medullobastoma cell line

label_protocol: 1 μg of total RNA was amplified into cRNA using a Low Input Quick-Amp Labeling kit (Agilent Technologies) and was labeled with Cy3-deoxycytidine triphosphate during the in vitro transcription process.

extract_protocol: Total RNA from each culture was independently extracted using the RNeasy Mini Kit, according to the manufacturer's instructions (Qiagen, Valencia, CA, USA). Before microarray hybridization, each extract of total RNA was quantified using a NanoDrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE, USA) and a Bioanalyzer RNA Nano 6000 chip (Agilent Technologies, Palo Alto, CA, USA).

value: brain cell line


title: 764-T

value: Adenocarcinoma


title: B_Medium


title: Daoy

source_name: Daoy medulloblasoma cell line

value: brain/cerebellum cell line

value: ATCC; HTB-186


title: A967_07_4-1_Wt4

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: wt CD4+CD62L+ T cells, replicate 4

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: R/Bioconductor, rma normalization, default parameters

source_name: wt CD4+CD62L+ T cells

label_protocol: Standard Affymetrix protocol.

growth_protocol: Mice were bred under SPF conditions

extract_protocol: T cells were sorted from MLNs as CD45.1+ CD45.2- and CD45.1- CD45.2+ CD3+ CD4+ T cells 14 days after cotransfer into Rag1-/- mice using the Aria III (BD Bioscience). Purity was above 99.5 %. RNA was isolated using TRIzol ® according to the manufactures protocol (Invitrogen, Karlsruhe, Germany)

treatment_protocol: Colitis was induced by transfer of 3*105 CD4+ CD62L+ T cells into Rag1-/- mice as previously described (PMID:22057112). Bodyweight and consistency of stool was monitored throughout the experiments to detect colitis induction. In cotransfer experiments, equal numbers (3*105) of wt (CD45.1) and Irak1-/- (CD45.2) CD4+CD62L+ T cells were injected (i.p.) into Rag1-/- mice. For microarray analysis, T cells were FACS sorted using a BDFACSAria (BD BiosciencesHeidelberg, Germany). 2 recipient mice were pooled in each microarray experiment

tag: genotype

value: wt

tag: batch


title: 2319-T

value: IB


title: A967_08_4-2_Ko4

description: Irak1-/-  CD4+CD62L+ T cells, replicate 4

source_name: Irak1-/-  CD4+CD62L+ T cells

tag: strain


title: normal_brain_2

description: 13 males and 10 females aged 23-86 years, Cat. No. AM7000, Ambion

value: brain


title: 1064-T

tag: race


title: normal_brain_1

description: two males aged 47 and 55 years, Cat. No. 636530; Clontech


title: A967_05_3-1_Wt3

description: wt CD4+CD62L+ T cells, replicate 3


title: A967_06_3-2_Ko3

description: Irak1-/-  CD4+CD62L+ T cells, replicate 3


title: WT C064 + 3

city: New York

first: Gaurav

last: Pandey

state: New York

address: 1 Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: Specific pathogen free lung CD64+ macrophages- rep 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Mouse derived primary cells

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

extract_protocol: RNA was extracted with Trizol using manufacturers' instructions, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit Quality control was performed with Agilent Bioanalyser.

tag: sample type

value: Primary cells


title: GF CD24T 2

description: Germ free lung CD24+ dendritic cells- rep 2

tag: cell type

value: Germ free lung CD24+ dendritic cells


title: A967_01_1-1_Wt1

description: wt CD4+CD62L+ T cells, replicate 1


title: WT C024 + 3

description: Specific pathogen free lung CD24+ dendritic cells- rep 3


title: A967_03_2-1_Wt2

description: wt CD4+CD62L+ T cells, replicate 2


title: A967_02_1-2_Ko1

description: Irak1-/-  CD4+CD62L+ T cells, replicate 1


title: GF CD103T 2

description: Germ free lung CD103+ dendritic cells- rep 2

value: Germ free lung CD103+ dendritic cells


title: WT C0103 + 3

description: Specific pathogen free lung CD103+ dendritic cells- rep 3


title: HCC001N

description: non-tumor liver tissue

value: Female

tag: age


title: WT CD103T 2

description: Specific pathogen free lung CD103+ dendritic cells- rep 2


title: GF C024 T 1

description: Germ free lung CD24+ dendritic cells- rep 1


title: GF CD64T 2

description: Germ free lung CD64+ macrophages- rep 2

value: Germ free lung CD64+ macrophages


title: WT C024 T 1

description: Specific pathogen free lung CD24+ dendritic cells- rep 1


title: WT C064 T 1

description: Specific pathogen free lung CD64+ macrophages- rep 1


title: A967_04_2-2_Ko2

description: Irak1-/-  CD4+CD62L+ T cells, replicate 2


title: WT CD64T 2

description: Specific pathogen free lung CD64+ macrophages- rep 2


title: GF C0103 T 1

description: Germ free lung CD103+ dendritic cells- rep 1


title: RNA-IP of wild-type flies, replicate 2

city: Regensburg

first: Julia

middle: C

last: Engelmann

address: Josef-Engert-Str. 9

department: Statistical Bioinformatics

institute: University of Regensburg

description:
immunoprecipitated RNA
transcripts from negative control IP

hyb_protocol: 1.9 to 2.8 µg fragmented and labeled sense-strand cDNA were hybridized to Affymetrix GeneChip Drosophila Gene 1.0 arrays for 16 h at 45 °C in a GeneChip hybridization oven 640.

scan_protocol: GeneChips were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled the by the Affymetrix GeneChip Command Console software v3.2 (AGCC)

data_processing: The intensities of the CEL files were normalized with the VSN algorithm (Huber, 2002) and summarized to expression levels based on entrez transcript identifiers using the chip description file from BrainArray (Dai, 2005) (see publication for details).

organism: Drosophila melanogaster

source_name: embryos

label_protocol: The Affymetrix GeneChip WT PLUS Reagent Kit protocol was used to generate fragmented and biotinylated sense-strand cDNA from immunoprecipitated RNA.

growth_protocol: Virgins of da::GAL4 and UAS::Flag-myc-Brat males were mated at 25C. Wt or Flag-myc-expressing embryos were harvested after 24 hours.

extract_protocol: RNA was extracted by proteinase K digestion followed by phenol chloroform extraction.

treatment_protocol: Embryos (0-24hrs) were dechorinated using bleach, quick frozen in liquid nitrogen and stored at -80C until further use. Embryos were lysed and subjected to immunoprecipitation using a combination of Flag and myc antibodies pre-bound to protein G dynabeads for 90 min at 4C. After extensive washing RNA was extracted by Proteinase K digestion.

value: dechorinated embryos

value: embryos 0-24 hrs post egg laying


title: WT CD24T 2

description: Specific pathogen free lung CD24+ dendritic cells- rep 2


title: Ago2 Hem KO LSK cells (SAMPLE 2)

first: Chozha Vendan

last: Rathinam

state: NY

address: 701 W 168th street

department: Genetics & Development

institute: Columbia University Medical Center

data_processing: The images are analyzed using Illumina Beadstudio software. Quality control and data analysis are carried out according to the instructions provided by Illumina.

source_name: LSK cells

label_protocol: RNA was amplified and labeled with Illumina total prep RNA amplification kit.

extract_protocol: RNA was extracted with Qiagen RNeasy micro kit.  RNA Quality control was performed with Agilent Bioanalyser.

value: Bone Marrow

value: lineage- Sca1+ c-Kit+ (LSK) cells

value: Ago2 Hem KO


title: Control LSK cells (SAMPLE 1)

value: Control


title: RNA-IP of Flag-myc-BRAT expressing flies, replicate 2

description:
immunoprecipitated RNA
enriched transcripts from Brat-IP


title: RNA-IP of wild-type flies, replicate 1


title: RNA-IP of Flag-myc-BRAT expressing flies, replicate 1


title: WT C0103 T 1

description: Specific pathogen free lung CD103+ dendritic cells- rep 1


title: PCC6803_#642_isoprene_producer_rep1

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocol GE1_107_Sep09  for one-color arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensity was normexp background corrected and quantile normalized

organism: Synechocystis sp. PCC 6803

label_protocol: The RNA was labeled directly, without cDNA synthesis with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Axenic cultures of the cyanobacterium Synechocystis sp. PCC 6803 were grown photoautotrophically under continuous illumination of 175 µmol photons/m2 s (warm white fluorescent tubes, Osram L 32) at 29° C. For isoprene production, cultures were pre-cultivated at high CO2 (5%) in BG11 medium. After 24 h, the pre-cultures were used to inoculate the main cultures in closed 0,1 L Schott flasks at OD750 of about 1 in 50 ml of BG11 supplemented with 50 mM NaHCO3. The cultures were incubated at 30° C, with an illumination of about 150 µmol photons/m2 s under continuous stirring with 150 rpm. After 24 h, samples were taken for RNA isolation

extract_protocol: Synechocystis 6803 cells were collected by centrifugation (4000 rpm, 4°C, 4 min) and the cells were dissolved in 500 µl PGTX solution (Pinto et al., 2009) with the following composition: 39.6% (w/v) phenol, 7% (v/v) glycerol, 7 mM 8-hydroxyquinoline, 20 mM EDTA, 97.5 mM sodium acetate, 0.8 M guanidine thiocyanate, 0.48 M guanidine hydrochloride. The samples were incubated for 15 min at 65°C and put on ice for 5 minutes. After addition of 500 µl chloroform/isoamylalcohol (24:1), samples were incubated at room temperature for 10 minutes. Samples were centrifuged at 6,000 rpm, 20°C for 10 min. The upper aqueous phase was transferred into a new tube and the same volume of chloroform/isoamylalcohol (24:1) was added and mixed. Samples were centrifuged as described above and the aqueous phase removed again and combined with an equal volume of isopropanol. After gently inverting the tube, RNA was precipitated over night at -20°C. RNA was pelleted through centrifugation (13,000 rpm, 4°C, 30 min). The pellet was washed with 1 ml of 70% ethanol (13,000 rpm, 20°C, 5 min), allowed to air dry for approximately 10 min and resuspended in 30 µl H2O.

treatment_protocol: no special treatment was applied

value: ispS+


title: PCC6803_WT_rep1

value: WT


title: PCC6803_WT_rep2


title: PCC6803_#642_isoprene_producer_rep2


title: GF C064 T 1

description: Germ free lung CD64+ macrophages- rep 1


title: T48 RPH_Rat2_replicate2

status: Public on Nov 12 2015

city: Indianapolis

first: Jeffrey

last: Sutherland

state: IN

address: Lilly Corporate Center

institute: Lilly Research Laboratories

hyb_protocol: Affymetrix hyb protocol: EukGE-WS2v5_450

scan_protocol: .CEL files generated using GCOS software

data_processing: MAS5 signal intensities were generated using Bioconductor's Affy package. Data was scaled to a target of 500.

source_name: untreated RPHs_48hrs post-seeding

label_protocol: RNA was then labeled and hybridized to RG230-2 microarrays (Affymetrix) according to the manufacturer’s instructions

extract_protocol: Samples were homogenized in Trizol, and RNA isolated per manufacturer's protocol. Impurities were removed from the resulting RNA using Qiagen RNeasy columns.

value: Sprague Dawley

tag: rat id

value: male

tag: tissue/cell type

value: rat primary hepatocytes (RPH)

tag: time in culture

value: 48hrs post-seeding


title: T48 RPH_Rat3_replicate2


title: T48 RPH_Rat3_replicate1


title: T48 RPH_Rat1_replicate3


title: T48 RPH_Rat1_replicate1


title: T24 RPH_Rat3_replicate1

source_name: untreated RPHs_24hrs post-seeding

value: 24hrs post-seeding


title: T48 RPH_Rat3_replicate3


title: T24 RPH_Rat3_replicate3


title: T24 RPH_Rat2_replicate1


title: T24 RPH_Rat1_replicate3


title: T24 RPH_Rat2_replicate2


title: T48 RPH_Rat1_replicate2


title: T4 RPH_Rat3_replicate3

source_name: untreated RPHs_4hrs post-seeding

value: 4hrs post-seeding


title: T48 RPH_Rat2_replicate1


title: T24 RPH_Rat3_replicate2


title: T4 RPH_Rat3_replicate1


title: T24 RPH_Rat1_replicate2


title: T4 RPH_Rat2_replicate1


title: T4 RPH_Rat2_replicate2


title: T4 RPH_Rat2_replicate3


title: T0 RPH_Rat3_replicate3

source_name: untreated RPHs_uncultured cell pellet

value: 0hrs (untreated)


title: T4 RPH_Rat1_replicate2


title: T4 RPH_Rat1_replicate1


title: T0 RPH_Rat3_replicate1


title: T4 RPH_Rat1_replicate3


title: T24 RPH_Rat2_replicate3


title: T0 RPH_Rat2_replicate3


title: Liver_Rat3_replicate2

source_name: untreated liver

value: Liver


title: T0 RPH_Rat1_replicate3


title: T0 RPH_Rat1_replicate2


title: Liver_Rat3_replicate1


title: T0 RPH_Rat2_replicate1


title: T0 RPH_Rat2_replicate2


title: Liver_Rat3_replicate3


title: T0 RPH_Rat1_replicate1


title: T0 RPH_Rat3_replicate2


title: Liver_Rat2_replicate3


title: Liver_Rat1_replicate3


title: Liver_Rat1_replicate2


title: Left ventricle sham FA rep3

first: Georgios

last: Kararigas

address: Hessische Str. 3-4

institute: Charite University Hospital

description:
Sample name: 07M
Left ventricle sham FA rep3

hyb_protocol: Biotinylated cRNA was prepared and hybridized according to the standard Affymetrix processing protocol.

scan_protocol: The array was scanned in a GeneChip Scanner 3000.

data_processing: The data were normalized and transformed using R version 2.14.2, the Bioconductor package 'vsn' and the vsnrma algorithm with all defualt values, i.e. library('vsn') vsnrmadata = vsnrma(object = data).

source_name: Left ventricle sham FA rep3

growth_protocol: The mice were kept on a 12-hour light, 12-hour dark cycle in temperature-controlled rooms with water ad libitum.

extract_protocol: Total RNA was isolated using the RNeasy Fibrous Tissue Mini kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: Left ventricles were snap frozen in liquid nitrogen and stored at -80°C until further analysis.

value: Male

value: 2-mo old

tag: intervention

value: Sham

tag: treatment

value: FA

value: Left ventricle


title: Liver_Rat2_replicate2


title: Left ventricle DOXO FA rep4

description:
Sample name: 18M
Left ventricle DOXO FA rep4

source_name: Left ventricle DOXO FA rep4

label_protocol: Biotinylated cRNA was prepared and hybridized according to the standard Affymetrix processing protocol.

value: DOX

tag: tissue


title: Left ventricle DOXO FA rep5

description:
Sample name: 19M
Left ventricle DOXO FA rep5

source_name: Left ventricle DOXO FA rep5

tag: gender


title: Left ventricle sham FA rep4

description:
Sample name: 08M
Left ventricle sham FA rep4

source_name: Left ventricle sham FA rep4


title: Left ventricle DOXO FA rep1

description:
Sample name: 15M
Left ventricle DOXO FA rep1

source_name: Left ventricle DOXO FA rep1


title: Liver_Rat2_replicate1


title: Left ventricle sham FA rep2

description:
Sample name: 06M
Left ventricle sham FA rep2

source_name: Left ventricle sham FA rep2


title: Left ventricle DOXO plac rep3

description:
Sample name: 11M
Left ventricle DOXO plac rep3

source_name: Left ventricle DOXO plac rep3

value: Plac


title: Left ventricle DOXO FA rep2

description:
Sample name: 16M
Left ventricle DOXO FA rep2

source_name: Left ventricle DOXO FA rep2


title: Left ventricle DOXO FA rep6

description:
Sample name: 20M
Left ventricle DOXO FA rep6

source_name: Left ventricle DOXO FA rep6


title: Left ventricle DOXO plac rep4

description:
Sample name: 12M
Left ventricle DOXO plac rep4

source_name: Left ventricle DOXO plac rep4


title: Left ventricle DOXO plac rep5

description:
Sample name: 13M
Left ventricle DOXO plac rep5

source_name: Left ventricle DOXO plac rep5


title: Left ventricle DOXO plac rep2

description:
Sample name: 10M
Left ventricle DOXO plac rep2

source_name: Left ventricle DOXO plac rep2


title: Left ventricle sham plac rep2

description:
Sample name: 02M
Left ventricle sham plac rep2

source_name: Left ventricle sham plac rep2


title: Left ventricle sham plac rep4

description:
Sample name: 04M
Left ventricle sham plac rep4

source_name: Left ventricle sham plac rep4


title: Left ventricle sham plac rep3

description:
Sample name: 03M
Left ventricle sham plac rep3

source_name: Left ventricle sham plac rep3


title: Left ventricle DOXO plac rep1

description:
Sample name: 09M
Left ventricle DOXO plac rep1

source_name: Left ventricle DOXO plac rep1


title: Left ventricle sham FA rep1

description:
Sample name: 05M
Left ventricle sham FA rep1

source_name: Left ventricle sham FA rep1


title: Left ventricle DOXO FA rep3

description:
Sample name: 17M
Left ventricle DOXO FA rep3

source_name: Left ventricle DOXO FA rep3


title: Left ventricle DOXO plac rep6

description:
Sample name: 14M
Left ventricle DOXO plac rep6

source_name: Left ventricle DOXO plac rep6


title: T24 RPH_Rat1_replicate1

source_name: untreated RPHs_24hrs post-seeding


title: KA0717_SOX2_CD_0.2ug/ml DOX_d10

city: Münster

first: Boris

last: Greber

address: Von-Esmarch-Str. 54

institute: Max Planck Institute for Molecular Biomedicine

description:
human ES cells subjected to standard cardiac differentiation in presence of 0.2µg/ml doxycycline, replicate 1
SAMPLE 12

hyb_protocol: 18 hours according to manufacturer's instructions (Illumina)

scan_protocol: Default settings on a HiScan SQ (Illumina)

data_processing: Cubic spline normalization with background subtration in GenomeStudio (Illumina)

source_name: differentiated cell line

label_protocol: Illumina TotalPrep RNA Amplification Kit (Life Technologies); 14h of in-vitro transcription

growth_protocol: Undifferentiated hPSCs were in chemically defined FTDA medium. Differentiation was induced upon replating cells on Matrigel-coated 24-well plates in a defined serum and serum albumin-free medium based on Knockout-DMEM

extract_protocol: Qiagen RNeasy columns with on-column DNA-digestion

treatment_protocol: Insulin was added to the cells on day 0 and withdrawn from day 1 onwards. Specific differentiation-inducing factors were: 10 ng/ml FGF2, 1 ng/ml BMP4, and 1µM CHIR00921 - added to all samples during the first 24 hours. Samples were  treated with a WNT inhibitor (IWP-2, 2µM) on days 1 and 2 . SOX2,  in the indicated samples was overexpressed by doxycycline-mediated transgene induction throughout the differentiation.

tag: cell line

tag: time point


title: KA0717_SOX2_CD_0.2ug/ml DOX_d6

description:
human ES cells subjected to standard cardiac differentiation in presence of 0.2µg/ml doxycycline, replicate 1
SAMPLE 10


title: KA0717_SOX2_CD_d10

description:
human ES cells subjected to standard cardiac differentiation, replicate 1
SAMPLE 11


title: Left ventricle sham plac rep1

description:
Sample name: 01M
Left ventricle sham plac rep1

source_name: Left ventricle sham plac rep1


title: KA0717_SOX2_CD_d6

description:
human ES cells subjected to standard cardiac differentiation, replicate 1
SAMPLE 9


title: KA0717_SOX2_CD_0.2ug/ml DOX_d3

description:
human ES cells subjected to standard cardiac differentiation in presence of 0.2µg/ml doxycycline, replicate 1
SAMPLE 8


title: Liver_Rat1_replicate1

source_name: untreated liver


title: 0.5 ng/ml BMP4 / 0.25 µM CHIR00921 [14d]

description:
0.5 ng/ml BMP4 / 0.25 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 17

growth_protocol: Undifferentiated human ES cells (line HuES6) were in chemically defined FTDA medium. Differentiation was induced upon replating cells on Matrigel-coated 24-well plates in a defined serum and serum albumin-free medium based on Knockout-DMEM. Samples were harvested after two weeks of differentiation

treatment_protocol: Insulin was added to the cells on day 0 and withdrawn from day 1 onwards. Specific differentiation-inducing factors were: diverse concentrations of BMP4 during the first 24 hours (see sample descriptions), diverse concentrations of CHIR00921 during the first 24 hours (see sample descriptions), 10 ng/ml FGF2 during the first 24 hours (to all samples), and addition of 2µM WNT inhibitor IWP-2 on days 2 and 3 (to all samples)

tag: time-point

value: day 2

value: ES


title: KA0717_SOX2_FTDA_0.2ug/ml DOX_24hr

description:
human ES cells grown in FTDA in presence of 0.2µg/ml doxycycline for 24 hours, replicate 2
SAMPLE 2

source_name: undifferentiated cell line


title: KA0717_SOX2_CD_d3

description:
human ES cells subjected to standard cardiac differentiation, replicate 1
SAMPLE 7


title: KA0717_SOX2_CD_0.2ug/ml DOX_d2

description:
human ES cells subjected to standard cardiac differentiation in presence of 0.2µg/ml doxycycline, replicate 1
SAMPLE 6


title: KA0717_SOX2_CD_d2

description:
human ES cells subjected to standard cardiac differentiation, replicate 1
SAMPLE 5


title: 1 ng/ml BMP4 / 0.5 µM CHIR00921 [14d]

description:
1 ng/ml BMP4 / 0.5 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 13

value: day 5


title: KA0717_SOX2_CD_d1

description:
human ES cells subjected to standard cardiac differentiation, replicate 1
SAMPLE 3


title: 0.25 ng/ml BMP4 / 0.25 µM CHIR00921 [14d]

description:
0.25 ng/ml BMP4 / 0.25 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 16

value: day 1


title: SOX2 KD_48hr

description:
human ES cells grown in FTDA and harvested 48 hours after SOX2 siRNA transfection, replicate 1
SAMPLE 2

source_name: undifferentiated hESCs

growth_protocol: Undifferentiated hPSCs were in chemically defined FTDA medium.

treatment_protocol: SOX2 knockdown was performed using pooled siRNAs. Culture medium was replaced 24 hours after transfection and cells were harvested on the following day.

tag: sirna

value: SOX2 siRNA


title: KA0717_SOX2_FTDA

description:
human ES cells grown in FTDA, replicate 1
SAMPLE 1


title: WT

description:
human ES cells grown in FTDA and harvested 48 hours after scrambled siRNA transfection, replicate 1
SAMPLE 1

value: scrambled siRNA


title: 1 ng/ml BMP4 / 0.25 µM CHIR00921 [14d]

description:
1 ng/ml BMP4 / 0.25 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 18

value: day 3


title: 4 ng/ml BMP4 / 1 µM CHIR00921 [14d]

description:
4 ng/ml BMP4 / 1 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 10


title: 4 ng/ml BMP4 / 0.5 µM CHIR00921 [14d]

description:
4 ng/ml BMP4 / 0.5 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 15

value: day 8


title: 2 ng/ml BMP4 / 1 µM CHIR00921 [14d]

description:
2 ng/ml BMP4 / 1 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 9


title: 0.5 ng/ml BMP4 / 0.5 µM CHIR00921 [14d]

description:
0.5 ng/ml BMP4 / 0.5 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 12

value: day 4


title: 2 ng/ml BMP4 / 0.25 µM CHIR00921 [14d]

description:
2 ng/ml BMP4 / 0.25 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 19


title: KA0717_SOX2_CD_0.2ug/ml DOX_d1

description:
human ES cells subjected to standard cardiac differentiation in presence of 0.2µg/ml doxycycline, replicate 1
SAMPLE 4


title: 4 ng/ml BMP4 / 0.25 µM CHIR00921 [14d]

description:
4 ng/ml BMP4 / 0.25 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 20


title: 0.25 ng/ml BMP4 / 0.5 µM CHIR00921 [14d]

description:
0.25 ng/ml BMP4 / 0.5 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 11


title: 1 ng/ml BMP4 / 1 µM CHIR00921 [14d]

description:
1 ng/ml BMP4 / 1 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 8


title: 0.5 ng/ml BMP4 / 1 µM CHIR00921 [14d]

description:
0.5 ng/ml BMP4 / 1 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 7

value: day 6


title: 0.25 ng/ml BMP4 / 1 µM CHIR00921 [14d]

description:
0.25 ng/ml BMP4 / 1 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 6


title: 4 ng/ml BMP4 / 2 µM CHIR00921 [14d]

description:
4 ng/ml BMP4 / 2 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 5


title: 1 ng/ml BMP4 / 2 µM CHIR00921 [14d]

description:
1 ng/ml BMP4 / 2 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 3


title: 0.25 ng/ml BMP4 / 2 µM CHIR00921 [14d]

description:
0.25 ng/ml BMP4 / 2 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 1

value: day 0


title: 4 ng/ml BMP4 / 0.25 µM CHIR00921 [36 hours]

growth_protocol: Undifferentiated human ES cells (line HuES6) were in chemically defined FTDA medium. Differentiation was induced upon replating cells on Matrigel-coated 24-well plates in a defined serum and serum albumin-free medium based on Knockout-DMEM. Samples were harvested after 36 hours of differentiation

treatment_protocol: Insulin was added to the cells on day 0 and withdrawn on day 1 Specific differentiation-inducing factors were: variable concentrations of BMP4 during the first 24 hours (see sample descriptions), variable concentrations of CHIR00921 during the first 24 hours (see sample descriptions), as well as 10 ng/ml FGF2 during the first 24 hours (in all samples)


title: 0.5 ng/ml BMP4 / 2 µM CHIR00921 [14d]

description:
0.5 ng/ml BMP4 / 2 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 2


title: 0.25 ng/ml BMP4 / 0.25 µM CHIR00921 [36 hours]

description:
0.25 ng/ml BMP4 / 0.25 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 16


title: 1 ng/ml BMP4 / 0.25 µM CHIR00921 [36 hours]

description:
1 ng/ml BMP4 / 0.25 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 18


title: 2 ng/ml BMP4 / 0.5 µM CHIR00921 [36 hours]

description:
2 ng/ml BMP4 / 0.5 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 14


title: 0.25 ng/ml BMP4 / 1 µM CHIR00921 [36 hours]


title: 2 ng/ml BMP4 / 0.25 µM CHIR00921 [36 hours]


title: 0.25 ng/ml BMP4 / 0.5 µM CHIR00921 [36 hours]


title: 4 ng/ml BMP4 / 1 µM CHIR00921 [36 hours]

description:
4 ng/ml BMP4 / 1 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 10


title: 4 ng/ml BMP4 / 2 µM CHIR00921 [36 hours]


title: 1 ng/ml BMP4 / 0.5 µM CHIR00921 [36 hours]

description:
1 ng/ml BMP4 / 0.5 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 13


title: 1 ng/ml BMP4 / 2 µM CHIR00921 [36 hours]


title: 0.5 ng/ml BMP4 / 0.25 µM CHIR00921 [36 hours]

description:
0.5 ng/ml BMP4 / 0.25 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 17


title: 4 ng/ml BMP4 / 0.5 µM CHIR00921 [36 hours]

description:
4 ng/ml BMP4 / 0.5 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 15


title: 0.5 ng/ml BMP4 / 2 µM CHIR00921 [36 hours]


title: 1 ng/ml BMP4 / 1 µM CHIR00921 [36 hours]


title: 2 ng/ml BMP4 / 1 µM CHIR00921 [36 hours]

description:
2 ng/ml BMP4 / 1 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 9


title: FW-induced day 6

description:
differentiating human ES cells induced with FGF + WNT, day 6
SAMPLE 28

treatment_protocol: Insulin was added to the cells on day 0 and withdrawn from day 1 onwards. Specific differentiation-inducing factors were: 10 ng/ml FGF2 on day 0, 1 ng/ml BMP4 on day 0, 1µM CHIR00921 on day 0, and 2µM WNT inhibitor IWP-2 on days 2 and 3


title: 0.5 ng/ml BMP4 / 0.5 µM CHIR00921 [36 hours]

description:
0.5 ng/ml BMP4 / 0.5 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 12


title: 0.25 ng/ml BMP4 / 2 µM CHIR00921 [36 hours]


title: FW-induced day 8

description:
differentiating human ES cells induced with FGF + WNT, day 8
SAMPLE 29


title: 0.5 ng/ml BMP4 / 1 µM CHIR00921 [36 hours]

description:
0.5 ng/ml BMP4 / 1 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 7


title: 2 ng/ml BMP4 / 2 µM CHIR00921 [36 hours]

description:
2 ng/ml BMP4 / 2 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 4


title: FW-induced day 4

description:
differentiating human ES cells induced with FGF + WNT, day 4
SAMPLE 26


title: FW-induced day 5

description:
differentiating human ES cells induced with FGF + WNT, day 5
SAMPLE 27


title: BW-induced day 4

description:
differentiating human ES cells induced with BMP + WNT, day 4
SAMPLE 19


title: BW-induced day 3

description:
differentiating human ES cells induced with BMP + WNT, day 3
SAMPLE 18


title: BW-induced day 5

description:
differentiating human ES cells induced with BMP + WNT, day 5
SAMPLE 20


title: BW-induced day 1

description:
differentiating human ES cells induced with BMP + WNT, day 1
SAMPLE 16


title: FB-induced day 8

description:
differentiating human ES cells induced with FGF + BMP, day 8
SAMPLE 15


title: BW-induced day 8

description:
differentiating human ES cells induced with BMP + WNT, day 8
SAMPLE 22


title: BW-induced day 2

description:
differentiating human ES cells induced with BMP + WNT, day 2
SAMPLE 17


title: FB-induced day 3

description:
differentiating human ES cells induced with FGF + BMP, day 3
SAMPLE 11


title: FW-induced day 3

description:
differentiating human ES cells induced with FGF + WNT, day 3
SAMPLE 25


title: BW-induced day 6

description:
differentiating human ES cells induced with BMP + WNT, day 6
SAMPLE 21


title: FB-induced day 6

description:
differentiating human ES cells induced with FGF + BMP, day 6
SAMPLE 14


title: FW-induced day 2

description:
differentiating human ES cells induced with FGF + WNT, day 2
SAMPLE 24


title: FW-induced day 1

description:
differentiating human ES cells induced with FGF + WNT, day 1
SAMPLE 23


title: FB-induced day 4

description:
differentiating human ES cells induced with FGF + BMP, day 4
SAMPLE 12


title: FB-induced day 5

description:
differentiating human ES cells induced with FGF + BMP, day 5
SAMPLE 13


title: FB-induced day 2

description:
differentiating human ES cells induced with FGF + BMP, day 2
SAMPLE 10


title: FBW-induced day 4

description:
differentiating human ES cells induced with FGF + BMP + WNT, day 4
SAMPLE 5


title: 2 ng/ml BMP4 / 0.5 µM CHIR00921 [14d]

description:
2 ng/ml BMP4 / 0.5 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 14


title: 2 ng/ml BMP4 / 2 µM CHIR00921 [14d]

description:
2 ng/ml BMP4 / 2 µM CHIR00921 used for the initial induction of differentiation in human ES cells
SAMPLE 4


title: FBW-induced day 5

description:
differentiating human ES cells induced with FGF + BMP + WNT, day 5
SAMPLE 6


title: FB-induced day 1

description:
differentiating human ES cells induced with FGF + BMP, day 1
SAMPLE 9


title: - WNT inh. R2

description:
human ES cells subjected to cardiac differentiation without intermediate WNT inhibitor treatment, replicate 2
SAMPLE 6

treatment_protocol: Insulin was added to the cells on day 0 and withdrawn from day 1 onwards. Specific differentiation-inducing factors were: 10 ng/ml FGF2, 1 ng/ml BMP4, and 1µM CHIR00921 - added to all samples during the first 24 hours. Samples were either treated with a WNT inhibitor (IWP-2, 2µM) on days 1 and 2 (or, alternatively, on days 2 and 3) or not treated with the WNT inhibitor, as indicated in sample description. In some samples, MSX1 or CDX2 were selectively overexpressed by doxycycline-mediated transgene induction during the time-window of WNT inhibition


title: FBW-induced day 6

description:
differentiating human ES cells induced with FGF + BMP + WNT, day 6
SAMPLE 7
duplicate of GSM1640346 [the two series share the same control sample time-course, i.e. the two series are to be analyzed in different contexts.]


title: FBW-induced day 3

description:
differentiating human ES cells induced with FGF + BMP + WNT, day 3
SAMPLE 4
duplicate of GSM1640343 [the two series share the same control sample time-course, i.e. the two series are to be analyzed in different contexts.]


title: FBW-induced day 2

description:
differentiating human ES cells induced with FGF + BMP + WNT, day 2
SAMPLE 3


title: FBW-induced day 1

description:
differentiating human ES cells induced with FGF + BMP + WNT, day 1
SAMPLE 2


title: - WNT inh. R1

description:
human ES cells subjected to cardiac differentiation without intermediate WNT inhibitor treatment, replicate 1
SAMPLE 5


title: + WNT inh. R4

description:
human ES cells subjected to cardiac differentiation with WNT inhibitor treatment on days 2 and 3, replicate 4
SAMPLE 4


title: + WNT inh. + CDX2 (DOX)

description:
human ES cells subjected to cardiac differentiation with WNT inhibitor treatment on days 2 and 3. CDX2 expression was concomitantly induced by doxycycline treatment during the same time window
SAMPLE 8


title: + WNT inh. R3

description:
human ES cells subjected to cardiac differentiation with WNT inhibitor treatment on days 2 and 3, replicate 3
SAMPLE 3


title: day 0

description:
undifferentiated human ES cells (line HuES6)
SAMPLE 1

source_name: cultured cell line


title: FBW-induced day 8

description:
differentiating human ES cells induced with FGF + BMP + WNT, day 8
SAMPLE 8


title: time-course 2, - IWP-2 on days 1 and 2, day 5

description:
time-course 2, differentiating human ES cells induced with FGF + BMP + WNT, no IWP-2 added on days 1 and 2, day 5
SAMPLE 25

treatment_protocol: Insulin was added to the cells on day 0 and withdrawn from day 1 onwards. Specific differentiation-inducing factors were: 10 ng/ml FGF2, 1 ng/ml BMP4, and 1µM CHIR00921 - all added during the first 24 hours of differentiation. WNT inhibitor IWP-2 (µM) was either added or not added on days 2 and 3 (time-course 1) or on days 1 and 2 (time-course 2)


title: time-course 2, - IWP-2 on days 1 and 2, day 4

description:
time-course 2, differentiating human ES cells induced with FGF + BMP + WNT, no IWP-2 added on days 1 and 2, day 4
SAMPLE 24


title: time-course 2, - IWP-2 on days 1 and 2, day 8

description:
time-course 2, differentiating human ES cells induced with FGF + BMP + WNT, no IWP-2 added on days 1 and 2, day 8
SAMPLE 27


title: time-course 2, + IWP-2 on days 1 and 2, day 8

description:
time-course 2, differentiating human ES cells induced with FGF + BMP + WNT, IWP-2 added on days 1 and 2, day 8
SAMPLE 21


title: time-course 2, - IWP-2 on days 1 and 2, day 2

description:
time-course 2, differentiating human ES cells induced with FGF + BMP + WNT, no IWP-2 added on days 1 and 2, day 2
SAMPLE 22


title: + WNT inh. + MSX1 (DOX)

description:
human ES cells subjected to cardiac differentiation with WNT inhibitor treatment on days 2 and 3. MSX1 expression was concomitantly induced by doxycycline treatment during the same time window
SAMPLE 7


title: + WNT inh. R1

description:
human ES cells subjected to cardiac differentiation with WNT inhibitor treatment on days 2 and 3, replicate 1
SAMPLE 1


title: time-course 2, + IWP-2 on days 1 and 2, day 6

description:
time-course 2, differentiating human ES cells induced with FGF + BMP + WNT, IWP-2 added on days 1 and 2, day 6
SAMPLE 20


title: time-course 2, - IWP-2 on days 1 and 2, day 3

description:
time-course 2, differentiating human ES cells induced with FGF + BMP + WNT, no IWP-2 added on days 1 and 2, day 3
SAMPLE 23


title: + WNT inh. R2

description:
human ES cells subjected to cardiac differentiation with WNT inhibitor treatment on days 1 and 2, replicate 2
SAMPLE 2


title: time-course 2, + IWP-2 on days 1 and 2, day 4

description:
time-course 2, differentiating human ES cells induced with FGF + BMP + WNT, IWP-2 added on days 1 and 2, day 4
SAMPLE 18


title: time-course 2, + IWP-2 on days 1 and 2, day 5

description:
time-course 2, differentiating human ES cells induced with FGF + BMP + WNT, IWP-2 added on days 1 and 2, day 5
SAMPLE 19


title: time-course 1, + IWP-2 on days 2 and 3, day 8

description:
time-course 1, differentiating human ES cells induced with FGF + BMP + WNT, IWP-2 added on days 2 and 3, day 8
SAMPLE 8


title: time-course 1, - IWP-2 on days 2 and 3, day 8

description:
time-course 1, differentiating human ES cells induced with FGF + BMP + WNT, no IWP-2 added on days 2 and 3, day 8
SAMPLE 13


title: time-course 1, + IWP-2 on days 2 and 3, day 5

description:
time-course 1, differentiating human ES cells induced with FGF + BMP + WNT, IWP-2 added on days 2 and 3, day 5
SAMPLE 6


title: HB2_62_exp11

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

description: Human cells with treated with control and GNG12-AS1 siRNA against exon1, exon7 or exon9 to find differentially expressed genes after knock-down of lncRNA GNG12-AS1.

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.

source_name: Human mammary epithelial cells (HB2)

growth_protocol: Human mammary epithelial cells (HB2 cell line) were cultured in Dulbecco’s modified Eagle’s medium (DMEM, GIBCO) supplemented with 10% Fetal bovine serum (FBS), 10 ml/l penicillin-streptomycin solution (P/S), 5 mg/ml insulin (Sigma), and 1 mg/ml hydrocortisone (HC, Sigma). The cells were from American Type Culture Collection (ATCC) and were cultured at 37 °C with 5% CO2.

extract_protocol: RNA was extracted and reverse transcribed with the RNeasy Kit and the QuantiTect Reverse Transcription Kit (QIAGEN). Quantitative real-time PCR was performed on a 7900HT Fast Real-Time PCR System (Applied Biosystems) with Fast SYBR Green Master Mix (Invitrogen).

treatment_protocol: The cells were transfected with control siRNA (Life Technologies, 4390084) and GNG12-AS1 siRNAs targeting different exons (exon 1, exon 7 and exon 9, Life Technologies, Silencer select) using DharmaFECT 3 (Thermo-Scientific) transfection reagent following the manufacturer's instructions. RNA was collected 48 hr after transfection. The siRNAs were used at a final concentration of 50 nM.

tag: samplegroup

value: mammary epithelial


title: time-course 1, - IWP-2 on days 2 and 3, day 4

description:
time-course 1, differentiating human ES cells induced with FGF + BMP + WNT, no IWP-2 added on days 2 and 3, day 4
SAMPLE 10


title: HB2_122_exp5


title: HB2_62_exp5


title: time-course 1, + IWP-2 on days 2 and 3, day 6

description:
time-course 1, differentiating human ES cells induced with FGF + BMP + WNT, IWP-2 added on days 2 and 3, day 6
SAMPLE 7
duplicate of GSM1640381 [the two series share the same control sample time-course, i.e. the two series are to be analyzed in different contexts.]


title: time-course 2, day 1

description:
time-course 2, differentiating human ES cells induced with FGF + BMP + WNT, day 1
SAMPLE 15


title: time-course 1, - IWP-2 on days 2 and 3, day 6

description:
time-course 1, differentiating human ES cells induced with FGF + BMP + WNT, no IWP-2 added on days 2 and 3, day 6
SAMPLE 12


title: time-course 1, + IWP-2 on days 2 and 3, day 3

description:
time-course 1, differentiating human ES cells induced with FGF + BMP + WNT, IWP-2 added on days 2 and 3, day 3
SAMPLE 4
duplicate of GSM1640378 [the two series share the same control sample time-course, i.e. the two series are to be analyzed in different contexts.]


title: time-course 1, - IWP-2 on days 2 and 3, day 5

description:
time-course 1, differentiating human ES cells induced with FGF + BMP + WNT, no IWP-2 added on days 2 and 3, day 5
SAMPLE 11


title: time-course 2, + IWP-2 on days 1 and 2, day 3

description:
time-course 2, differentiating human ES cells induced with FGF + BMP + WNT, IWP-2 added on days 1 and 2, day 3
SAMPLE 17


title: HB2_123_exp5


title: time-course 1, day 2

description:
time-course 1, differentiating human ES cells induced with FGF + BMP + WNT, day 2
SAMPLE 3