title: Synovial fluid mononuclear cells of ERA patient 6

description: miRNA expression profile in synovial fluid mononuclear cells of patient 6 with enthesitis related arthritis

source_name: Synovial fluid mononuclear cells of patient 6 with enthesitis related arthritis

value: 6 Yrs


title: Wnt+ rectal tumor 12 [GE]

status: Public on Oct 30 2017

type: RNA

city: HYDERABAD

first: Murali

middle: Dharan

last: Bashyam

state: (Click to Select US State)

address: MJ MARKET

country: India

institute: CDFD

description:
2145
Microsatellite stable Wnt+ rectal adenocarcinoma

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505B scanner Images were quantified using Agilent Feature Extraction Software (version v10.7)

data_processing: Agilent Feature Extraction Software (v10.7) was used for background subtraction and LOWESS normalization

molecule: total RNA

organism: Homo sapiens

source_name: Surgically removed rectum

label_protocol: 2μg each of total RNA from tumors along with equal quantity of universal reference RNA (pooled up RNA from 11 cell lines (Bashyam et al., 2005)) were differentially labeled with Cy5 and Cy3 dyes using Quickamp labeling kit (Agilent Technologies, CA, USA) following manufacturer's instructions

growth_protocol: Not applicable

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

tag: Sex

value: Male

tag: age

tag: tissue

value: Rectal adenocarcinoma

tag: Stage

tag: grade

source_name: pooled 11 cell line

tag: reference

value: Universal reference RNA


title: Wnt+ rectal tumor 14 [GE]

description:
2215
Microsatellite stable Wnt+ rectal adenocarcinoma

value: Female


title: Wnt- rectal tumor 9 [GE]

description:
2141
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt+ rectal tumor 11 [GE]

description:
2107
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Wnt- rectal tumor 11 [GE]

description:
2189
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt- rectal tumor 8 [GE]

description:
2071
Microsatellite stable Wnt- rectal adenocarcinoma


title: Peripheral blood mononuclear cells of HC 1

city: Lucknow

first: Sushma

last: Singh

state: Uttar Pradesh

address: Raebareli Road

department: Clinical Immunology

institute: Sanjay Gandhi Post Graduate Institute of Medical Sciences

description: miRNA expression profile in peripheral blood mononuclear cells of healthy control 1

hyb_protocol: The dried sample was resuspended in nuclease free water and mixed with Hybridization Mix containing blocking and Hi-RPM Hybridization Buffer  and incubated at 100oC for 5 minutes followed by snap chill on ice for 5 minutes.  The samples were hybridized on the Human miRNA 8x15k Arrays. The hybridization was carried out at 55°C for 20 hours. After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 5 minutes and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37oC for 5 minutes. The slides were then washed with Acetonitrile for 30 seconds. The microarray slide was scanned on a G2505C scanner (Agilent Technologies)

data_processing: The normalization was done using GeneSpring GX  Software. 90th Percentile Shift Normalization

source_name: Peripheral blood mononuclear cells of healthy control 1

label_protocol: The miRNA labeling was performed using miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Part Number: 5190-0456). The total RNA sample was diluted to 50ng/ul in nuclease free water. 100ng of total RNA was dephosphorylated using Calf Intestinal Alkaline Phosphatase (CIP) master by incubating at 37oC for 30 minutes. The dephosphorylated miRNA sample was denatured by adding Dimethyl Sulfoxide and heating at 100 oC for 10 minutes and transferred to ice-water bath. The Ligation master mix containing Cyanine 3-pCp was added to the denatured miRNA sample and incubated at 16oC for 2 hours. The Cyanine 3-pCp labeled miRNA sample was dried completely in the vacuum concentrator (Eppendorf, Concentrator Plus) at 45oC for 2 hour.

extract_protocol: Peripheral blood and synovial fluid mononuclear cells (PBMC and SFMCs) were isolated by density gradient centrifugation using Histopaque 1077 (Sigma-Aldrich,  St. Louis, MO, USA). PBMCs and SFMCs were stored at -80ºC in Trizol (Life Technologies Inc., USA) at a concentration of 5-6 x 106/ ml and RNA was isolated using Trizol (Life  Technologies Inc., USA) according to the manufacturer’s protocol. Quantification and purity of RNA was checked by measuring absorbance at 260, 230  and 280 nm using Nanodrop spectrophotometer (Nanodrop Inc., Wilmington, DE, USA) and calculating 260/230 and 260/280 ratio. The quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: diagnosis

value: healthy

value: Peripheral blood

tag: gender

tag: age on collection of sample

value: 23 Yrs

tag: duration of disease

value: 0 Yr


title: Wnt+ rectal tumor 10 [GE]

description:
2105
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Peripheral blood mononuclear cells of HC 5

description: miRNA expression profile in peripheral blood mononuclear cells of healthy control 5

scan_protocol: The microarray slide was scanned on a G2505C scanner (Agilent Technologies)

source_name: Peripheral blood mononuclear cells of healthy control 5

value: 22 Yrs


title: Synovial fluid mononuclear cells of ERA patient 3

description: miRNA expression profile in synovial fluid mononuclear cells of patient 3 with enthesitis related arthritis

source_name: Synovial fluid mononuclear cells of patient 3 with enthesitis related arthritis

value: enthesitis related arthritis

value: Synovial fluid

value: 16 Yrs

value: 7 Yrs


title: Synovial fluid mononuclear cells of ERA patient 2

description: miRNA expression profile in synovial fluid mononuclear cells of patient 2 with enthesitis related arthritis

source_name: Synovial fluid mononuclear cells of patient 2 with enthesitis related arthritis

value: 14 Yrs


title: Synovial fluid mononuclear cells of ERA patient 1

description: miRNA expression profile in synovial fluid mononuclear cells of patient 1 with enthesitis related arthritis

source_name: Synovial fluid mononuclear cells of patient 1 with enthesitis related arthritis

value: 15 Yrs


title: Peripheral blood mononuclear cells of ERA patient 3

description: miRNA expression profile in peripheral blood mononuclear cells of patient 3 with enthesitis related arthritis

source_name: Peripheral blood mononuclear cells of patient 3 with enthesitis related arthritis


title: Peripheral blood mononuclear cells of ERA patient 2

description: miRNA expression profile in peripheral blood mononuclear cells of patient 2 with enthesitis related arthritis

source_name: Peripheral blood mononuclear cells of patient 2 with enthesitis related arthritis


title: Wnt+ rectal tumor 7 [GE]

description:
2011
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Peripheral blood mononuclear cells of ERA patient 1

description: miRNA expression profile in peripheral blood mononuclear cells of patient 1 with enthesitis related arthritis

source_name: Peripheral blood mononuclear cells of patient 1 with enthesitis related arthritis


title: Wnt- rectal tumor 6 [GE]

description:
1402
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt+ rectal tumor 9 [GE]

description:
2063
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Wnt+ rectal tumor 8 [GE]

description:
2033
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Wnt+ rectal tumor 5 [GE]

description:
1095
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Wnt+ rectal tumor 6 [GE]

description:
1097
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Wnt+ rectal tumor 3 [GE]

description:
1043
Microsatellite stable Wnt+ rectal adenocarcinoma


title: Wnt- rectal tumor 5 [GE]

description:
1055
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt+ rectal tumor 4 [GE]

description:
1085
Microsatellite stable Wnt+ rectal adenocarcinoma


title: VDw0 vs VDw4P_4

city: Pathum Thani

first: umaporn

last: uawisetwathana

address: 113 Thailand Science Park

department: Biosensing Technology Research Unit

country: Thailand

institute: National Center for Genetic Engineering and Biotechnology

hyb_protocol: The probe was resuspended in hybridization solution (50% Formamide; 5x SSC; 0.1% SDS; 0.2 mg/ml Salmon sperm DNA; 0.2 mg/ml yeast tRNA; 10mM Tris, pH 7.5) and placed onto the post-processed slides.  The slides were hybridized at 42°C for 16 hrs before they were washed with home-made buffer.

scan_protocol: The slides were scanned with GenePix 4000B (Molecular Devices, Sunnyvale, CA).  Microarray spots on scanned images are located using GenePix Pro version 6.1.

data_processing: All “empty” and “bad” spots were removed from the analysis.  “Empty” spots were failed PCR products whereas “bad” spots were flagged by visual inspection of the spot images.  From the remaining spots, only the spots with intensities more than one standard deviation above the background intensity were further analyzed.  The processed data were normalized within each array by the median-nomalization method, and across arrays, using the Aroma package (Bengtsson, available from: http://www.maths.lth.se/help/R/aroma/) run in R project environment (http://cran.r-project.org).  The normalized data were further analyzed by multivariate statistical analysis, gene ontology (GO) analysis, hierarchical clustering analysis and significance analysis of microarray (SAM) analysis in order to identify differentially expressed genes. Logarithmic base 2 values of intensities from both Cy3- and Cy5- samples (M values) were used as inputs for clustering.  Cluster program was used to perform hierarchical clustering and Treeview program was used to visualized the clustered results (Eisen et al., 1998)

organism: Penaeus monodon

source_name: pooled vas deferens from 10 domesticated 17-month-old shrimp at week 0 before feeding

label_protocol: RNA samples were extracted from testes and vas deferens of domesticated 17-month-old before feeding (week 0, pooled from n=10 each organ) and after feeding between commercial pellet and polychaetes at week 4 (individual, 4 replicates each organ) from Shrimp Genetic Improvement Center, Thailand. The RNA from testes and vas deferens at week 0 were labeled with Cy3 dye as a reference and those of testes and vas deferens at week 4 were labeled with Cy5 dye.  The Cy3- and Cy5-samples were mixed together and hybridized onto the arrays overnight. The hybridized slides were washed with home-made washing buffer I, II and III .

growth_protocol: Domesticated male brooders (17-month-old, Broodstock Multiplication Center, Burapha University, Chanthaburi, Thailand) and the domesticated female brooders (17-month-old, Shrimp Genetic Improvement Center (SGIC), Suratthani, Thailand) were transferred to a commercial hatchery farm (Bunjonk farm, Chachoengsao, Thailand) and acclimatized to the experiment condition for one month prior to the experiment.

extract_protocol: RNA samples were extracted from testes and vas deferens of domesticated 17-month-old before comparing 2 different feeds at week 0(w0) and after feeding with commercial pellet (C) and polychaetes (P) at week 4 (w4). Contaminated genomic DNA was removed by treatment with DNase I at 0.15 U/μg total RNA at 37°C for 30 min.

treatment_protocol: Briefly, the domesticated male black tiger shrimp (17-month-old) were randomly divided into two groups: one fed with commercial pellet and the other fed with polychaetes. Both groups were fed for one month.

value: 17 months

value: pooled vas deferens

source_name: individual vas deferens from 1 domesticated 17-month-old shrimp after polychaetes feeding at week 4

value: individual vas deferens


title: Wnt- rectal tumor 4 [GE]

description:
1025
Microsatellite stable Wnt- rectal adenocarcinoma

value: Rectal adenocarcinoma


title: VDw0 vs VDw4P_3


title: Wnt- rectal tumor 3 [GE]

description:
1012
Microsatellite stable Wnt- rectal adenocarcinoma

value: Universal reference RNA


title: VDw0 vs VDw4P_1


title: VDw0 vs VDw4P_2


title: Wnt- rectal tumor 29 [CGH]

type: genomic

description:
2521
Gender matched control

hyb_protocol: Samples were hybridized to HEEBO arrays and were incubated at 65 °C for 40 hours in rotating microarray hybridization oven. After hybridization, slides were washed sequential.

scan_protocol: Scanned on Genepix 4000B scanner. Images were quantified using Spot Reader (Niles scientific, USA) software.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. snapCGH package in R was used.

molecule: genomic DNA

label_protocol: Using Cy-5 and Cy-3 fluorescent dyes (GE Healthcare Lifesciences, NJ, USA) and BioPrime DNA labeling system (Invitrogen Inc., Carlsbad, CA, USA) as per manufacturer’s protocol.

extract_protocol: DNA was isolated using DNeasy blood & tissue kit (Qiagen Gmbh, Hilden, Germany) as per manufacturer’s protocol.

treatment_protocol: DNA was isolated using DNeasy tissue kit (Qiagen Gmbh, Hilden, Germany) as per manufacturer’s protocol and labeled using BioPrime DNA labeling system (Invitrogen Inc., Carlsbad, CA, USA)

value: Male

source_name: Total DNA from matched gender normal

value: Blood


title: Wnt- rectal tumor 1 [GE]

description:
T150
Microsatellite stable Wnt- rectal adenocarcinoma

value: Female


title: Wnt+ rectal tumor 23 [CGH]

description:
2495
Gender matched control


title: Wnt- rectal tumor 2 [GE]

description:
T156
Microsatellite stable Wnt- rectal adenocarcinoma


title: Wnt+ rectal tumor 25 [CGH]

description:
2517
Gender matched control


title: Wnt- rectal tumor 26 [CGH]

description:
2491
Gender matched control


title: VDw0 vs VDw4C_4

source_name: individual vas deferens from 1 domesticated 17-month-old shrimp after commercial pellet feeding at week 4


title: Wnt+ rectal tumor 22 [CGH]

description:
2445
Gender matched control


title: Wnt- rectal tumor 25 [CGH]

description:
2473
Gender matched control


title: Wnt- rectal tumor 17 [CGH]

description:
2308
Gender matched control


title: Wnt- rectal tumor 28 [CGH]

description:
2513
Gender matched control


title: VDw0 vs VDw4C_3


title: VDw0 vs VDw4C_2


title: Wnt- rectal tumor 24 [CGH]

description:
2455
Gender matched control


title: Wnt- rectal tumor 16 [CGH]

description:
2303
Gender matched control


title: Wnt- rectal tumor 22 [CGH]

description:
2409
Gender matched control


title: Wnt+ rectal tumor 19 [CGH]

description:
2397
Gender matched control


title: Wnt+ rectal tumor 16 [CGH]

description:
2265
Gender matched control


title: Wnt- rectal tumor 14 [CGH]

description:
2255
Gender matched control


title: Wnt+ rectal tumor 17 [CGH]

description:
2299
Gender matched control


title: Wnt- rectal tumor 23 [CGH]

description:
2433
Gender matched control


title: Wnt+ rectal tumor 20 [CGH]

description:
2403
Gender matched control


title: Wnt+ rectal tumor 14 [CGH]

description:
2215
Gender matched control


title: Wnt- rectal tumor 21 [CGH]

description:
2401
Gender matched control


title: Wnt+ rectal tumor 18 [CGH]

description:
2389
Gender matched control


title: VDw0 vs VDw4C_1


title: Wnt- rectal tumor 10 [CGH]

description:
2177
Gender matched control


title: Wnt- rectal tumor 19 [CGH]

description:
2379
Gender matched control


title: TTw0 vs TTw4P_1

source_name: pooled testes from 10 domesticated 17-month-old shrimp at week 0 before feeding

value: pooled testes

source_name: individual testis from 1 domesticated 17-month-old shrimp after polychaetes feeding at week 4

value: individual testis


title: Wnt- rectal tumor 9 [CGH]

description:
2141
Gender matched control


title: TTw0 vs TTw4P_4


title: TTw0 vs TTw4P_2


title: TTw0 vs TTw4P_3


title: TTw0 vs TTw4C_4

source_name: individual testis from 1 domesticated 17-month-old shrimp after commercial pellet feeding at week 4


title: Wnt- rectal tumor 18 [CGH]

description:
2353
Gender matched control

source_name: Surgically removed rectum


title: TTw0 vs TTw4C_1


title: TTw0 vs TTw4C_3


title: TTw0 vs TTw4C_2


title: Wnt- rectal tumor 13 [CGH]

description:
2251
Gender matched control


title: Wnt- rectal tumor 8 [CGH]

description:
2071
Gender matched control


title: Wnt+ rectal tumor 11 [CGH]

description:
2107
Gender matched control


title: Wnt- rectal tumor 15 [CGH]

description:
2295
Gender matched control


title: Wnt- rectal tumor 20 [CGH]

description:
2387
Gender matched control


title: Wnt+ rectal tumor 10 [CGH]

description:
2105
Gender matched control


title: Wnt- rectal tumor 7 [CGH]

description:
1612
Gender matched control


title: Wnt- rectal tumor 1 [CGH]

description:
T150
Gender matched control


title: Wnt+ rectal tumor 1 [CGH]

description:
T177
Gender matched control


title: Wnt- rectal tumor 2 [CGH]

description:
T156
Gender matched control


title: Wnt- rectal tumor 12 [CGH]

description:
2243
Gender matched control


title: Wnt- rectal tumor 11 [CGH]

description:
2189
Gender matched control


title: Wnt- rectal tumor 5 [CGH]

description:
1055
Gender matched control


title: Wnt- rectal tumor 6 [CGH]

description:
1402
Gender matched control


title: Wnt+ rectal tumor 7 [CGH]

description:
2011
Gender matched control


title: Patient ID #6: Tumor

status: Public on Oct 28 2017

city: Columbus

first: Steve

last: Oghumu

address: 1841 Neil Ave

country: USA

institute: Ohio State University

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Affymetrix Eukaryotic Hybridization Controls (Affymetrix) and Oligo B2, 3nM (Affymetrix) •Heat 65oC for 5 minutes, 99oC for 5 minutes, 45oC for 5 minutes centrifuge top speed for 5 minutes  •Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0002

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G using AGCC

data_processing: Background correction and quantile normalization was performed to adjust technical bias, and expression levels were summarized over probeset using RMA method. A filtering method based on percentage of arrays above noise cutoff was applied to filter out low expression genes. Affymetrix software Expression Console and statistical package R was used for the analysis.

label: biotin

source_name: oral tumor

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

growth_protocol: Samples were obtained from oral squamous cell carcinoma patients (N = 6) enrolled in a Phase 0 clinical trial study (ClinicalTrials.gov ID NCT01465776) approved by the Internal Review Board at the Ohio State University Wexner Medical Center

extract_protocol: Total RNA was isolated from tumor and adjacent non-tumor tissue from OSCC patients using an RNeasy Fibrous Tissue Kit (Qiagen, Valencia, CA, USA). RNA quantity, quality and integrity were confirmed by Nanodrop and Agilent Bioanalyzer before inclusion in the array

treatment_protocol: Oral tumors and adjacent non-tumor oral tissue were obtained from each patient enrolled in the study

tag: patient id

value: Patient ID #6

value: squamous cell carcinoma


title: Wnt+ rectal tumor 6 [CGH]

description:
1097
Gender matched control


title: Patient ID #6: Adjacent Normal

source_name: adjacent non-tumor oral tissue


title: Patient ID #5: Adjacent Normal

value: Patient ID #5


title: SS43.P3

status: Public on Oct 26 2017

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

description: bone marrow CLP plate 4 cell 94

data_processing: Ct values calculated and exported using Fluidigm Biomark software. Data normalized by subtraction of the median Ct per cell followed by z-score scaling.

label: FAM

organism: Mus musculus

source_name: bone marrow CLP

label_protocol: Upon thawing, Taq/SSIII enzyme reaction mix (CellsDirect One-Step RT-qPCR kit, Invitrogen) and 96 TaqMan assays at a final dilution of 0.025x were added to each well, excluding 4 wells where no-reverse-transcription control of Taq enzyme (Invitrogen) reaction mix was added. Pre-amplification cycling was preformed according to previously described protocols (Pina et al. 2012) with minor alterations, the first cycle, 50°C at 15min, was extended to 60min.The pre-amplified single-cells were loaded on to a 96.96 Dynamic Array Chip for Gene Expression (Fluidigm) with 96 TaqMan assays and analyzed on BioMark HD (Fluidigm).

extract_protocol: Cells were sorted into 96 well plates with 4µl lysis buffer (10%NP40, 10mM dNTP, 0.1M DTT, RNAsout (Invitrogen) and nuclease free water) and immediately frozen at -80°C.

treatment_protocol: Single cell suspension of BM cells were FACS sorted to obtain CLP cells

tag: strain

tag: genotype/variation

value: wt

tag: cell type

value: CLP

tag: cell subtype

value: Lin- B220- Flt3+ Il7r+ Kitlow Sca1low

tag: sample type

value: single cell


title: SS45.P3

description: bone marrow CLP plate 4 cell 90


title: SS51.P3

description: bone marrow CLP plate 4 cell 89


title: SS50.P3

description: bone marrow CLP plate 4 cell 91


title: Patient ID #5: Tumor


title: SS44.P3

description: bone marrow CLP plate 4 cell 92


title: Patient ID #2: Tumor

value: Patient ID #2


title: SS49.P3

description: bone marrow CLP plate 4 cell 93


title: Patient ID #1: Adjacent Normal

value: Patient ID #1


title: Erlo 3h, biological replicate 2

city: Vienna

first: Florian

middle: Leopold

last: Klinglmueller

address: Spitalgasse 23

department: Medizinische Statistik und Informatik

country: Austria

institute: Medizinische Universitaet Wien

description: erlotinib treated cells

hyb_protocol: Affymetrix GeneChip® Human Gene 1.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.

data_processing: Data were preprocessed using quantile normalization to account for latent batch effects and RMA to summarize probesets. Analysis was performed using R and Biconductor.

source_name: Erlotinib-treated

label_protocol: 100ng of total RNA were amplified and labeled using the Ambion Whole Transcript Expression Kit (Catalog Number 4411973, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900670, Affymetrix, Santa Clara, CA)

growth_protocol: HCC-1.2 cells were grown in DMEM at 37°C until 80% confluency

extract_protocol: RNA was extracted by Trizol according to manufacturer protocol and cleaned by DNAse set (Quiagen, Venlo, The Netherlands)

treatment_protocol: 3 hours 10µM erlotinib or solvent control

tag: cell line

value: hepatocarcinoma


title: SS46.P3

description: bone marrow CLP plate 4 cell 88


title: Ko 3h, biological replicate 3

description: solvent treated control cells


title: Patient ID #3: Tumor

value: Patient ID #3


title: Patient ID #3: Adjacent Normal


title: Patient ID #1: Tumor


title: SS52.P3

description: bone marrow CLP plate 4 cell 87


title: Erlo 3h, biological replicate 1

description: erlotinib treated cells


title: Ko 3h, biological replicate 2

description: solvent treated control cells


title: Patient ID #2: Adjacent Normal


title: Patient ID #4: Tumor

value: Patient ID #4


title: Patient ID #4: Adjacent Normal


title: Erlo 3h, biological replicate 3

description: erlotinib treated cells


title: SS47.P3

description: bone marrow CLP plate 4 cell 86


title: Ko 3h, biological replicate 1

description: solvent treated control cells


title: SS48.P3

description: bone marrow CLP plate 4 cell 84


title: SS53.P3

description: bone marrow CLP plate 4 cell 85


title: SS37.P3

description: bone marrow CLP plate 4 cell 82


title: SS55.P3

description: bone marrow CLP plate 4 cell 81


title: SS38.P3

description: bone marrow CLP plate 4 cell 80


title: SS56.P3

description: bone marrow CLP plate 4 cell 79


title: SS41.P3

description: bone marrow CLP plate 4 cell 74


title: SS39.P3

description: bone marrow CLP plate 4 cell 78


title: SS59.P3

description: bone marrow CLP plate 4 cell 73


title: SS31.P3

description: bone marrow CLP plate 4 cell 70


title: SS57.P3

description: bone marrow CLP plate 4 cell 77


title: SS58.P3

description: bone marrow CLP plate 4 cell 75


title: noRT1.P3

description: bone marrow CLP plate 4 cell 71

value: No RT control


title: SS62.P3

description: bone marrow CLP plate 4 cell 65


title: SS61.P3

description: bone marrow CLP plate 4 cell 67


title: SS32.P3

description: bone marrow CLP plate 4 cell 68


title: SS33.P3

description: bone marrow CLP plate 4 cell 66


title: SS60.P3

description: bone marrow CLP plate 4 cell 69


title: SS63.P3

description: bone marrow CLP plate 4 cell 63


title: SS64.P3

description: bone marrow CLP plate 4 cell 61


title: SS35.P3

description: bone marrow CLP plate 4 cell 62


title: SS25.P3

description: bone marrow CLP plate 4 cell 58


title: SS26.P3

description: bone marrow CLP plate 4 cell 56


title: SS66.P3

description: bone marrow CLP plate 4 cell 57


title: SS67.P3

description: bone marrow CLP plate 4 cell 55


title: SS28.P3

description: bone marrow CLP plate 4 cell 52


title: SS68.P3

description: bone marrow CLP plate 4 cell 53


title: SS27.P3

description: bone marrow CLP plate 4 cell 54


title: SS42.P3

description: bone marrow CLP plate 4 cell 72


title: SS40.P3

description: bone marrow CLP plate 4 cell 76


title: SS34.P3

description: bone marrow CLP plate 4 cell 64


title: SS29.P3

description: bone marrow CLP plate 4 cell 50


title: SS65.P3

description: bone marrow CLP plate 4 cell 59


title: SS69.P3

description: bone marrow CLP plate 4 cell 51


title: SS20.P3

description: bone marrow CLP plate 4 cell 44


title: SS72.P3

description: bone marrow CLP plate 4 cell 43


title: noRT2.P3

description: bone marrow CLP plate 4 cell 47


title: SS71.P3

description: bone marrow CLP plate 4 cell 45


title: SS36.P3

description: bone marrow CLP plate 4 cell 60


title: SS30.P3

description: bone marrow CLP plate 4 cell 48


title: SS19.P3

description: bone marrow CLP plate 4 cell 46


title: SS22.P3

description: bone marrow CLP plate 4 cell 40


title: SS13.P3

description: bone marrow CLP plate 4 cell 34


title: SS77.P3

description: bone marrow CLP plate 4 cell 33


title: SS73.P3

description: bone marrow CLP plate 4 cell 41


title: SS74.P3

description: bone marrow CLP plate 4 cell 39


title: SS76.P3

description: bone marrow CLP plate 4 cell 35


title: SS24.P3

description: bone marrow CLP plate 4 cell 36


title: SS14.P3

description: bone marrow CLP plate 4 cell 32


title: SS23.P3

description: bone marrow CLP plate 4 cell 38


title: SS75.P3

description: bone marrow CLP plate 4 cell 37


title: SS78.P3

description: bone marrow CLP plate 4 cell 31


title: SS54.P3

description: bone marrow CLP plate 4 cell 83


title: SS70.P3

description: bone marrow CLP plate 4 cell 49


title: SS79.P3

description: bone marrow CLP plate 4 cell 29


title: SS80.P3

description: bone marrow CLP plate 4 cell 27


title: SS16.P3

description: bone marrow CLP plate 4 cell 28


title: SS21.P3

description: bone marrow CLP plate 4 cell 42


title: SS81.P3

description: bone marrow CLP plate 4 cell 25


title: SS18.P3

description: bone marrow CLP plate 4 cell 24


title: SS17.P3

description: bone marrow CLP plate 4 cell 26


title: noRT3.P3

description: bone marrow CLP plate 4 cell 23


title: SS8.P3

description: bone marrow CLP plate 4 cell 21


title: SS9.P3

description: bone marrow CLP plate 4 cell 20


title: SS82.P3

description: bone marrow CLP plate 4 cell 19


title: SS7.P3

description: bone marrow CLP plate 4 cell 22


title: SS10.P3

description: bone marrow CLP plate 4 cell 18


title: 10CELLS.P3

description: 10 bone marrow CLP

value: 10 cell control


title: SS83.P3

description: bone marrow CLP plate 4 cell 17


title: SS15.P3

description: bone marrow CLP plate 4 cell 30


title: SS84.P3

description: bone marrow CLP plate 4 cell 15


title: SS1.P3

description: bone marrow CLP plate 4 cell 12


title: SS3.P3

description: bone marrow CLP plate 4 cell 8


title: SS89.P3

description: bone marrow CLP plate 4 cell 5


title: SS4.P3

description: bone marrow CLP plate 4 cell 6


title: SS88.P3

description: bone marrow CLP plate 4 cell 7


title: SS2.P3

description: bone marrow CLP plate 4 cell 10


title: SS5.P3

description: bone marrow CLP plate 4 cell 4


title: 20CELLS.P3

description: 20 bone marrow CLP

value: 20 cell control


title: SS90.P3

description: bone marrow CLP plate 4 cell 3


title: SS49.P2

description: bone marrow CLP plate 3 cell 93


title: SS6.P3

description: bone marrow CLP plate 4 cell 2


title: SS43.P2

description: bone marrow CLP plate 3 cell 94


title: SS12.P3

description: bone marrow CLP plate 4 cell 14


title: SS11.P3

description: bone marrow CLP plate 4 cell 16


title: SS86.P3

description: bone marrow CLP plate 4 cell 11


title: SS44.P2

description: bone marrow CLP plate 3 cell 92


title: SS87.P3

description: bone marrow CLP plate 4 cell 9


title: SS85.P3

description: bone marrow CLP plate 4 cell 13


title: SS45.P2

description: bone marrow CLP plate 3 cell 90


title: SS48.P2

description: bone marrow CLP plate 3 cell 84


title: SS50.P2

description: bone marrow CLP plate 3 cell 91


title: SS51.P2

description: bone marrow CLP plate 3 cell 89


title: SS46.P2

description: bone marrow CLP plate 3 cell 88


title: SS52.P2

description: bone marrow CLP plate 3 cell 87


title: SS53.P2

description: bone marrow CLP plate 3 cell 85


title: SS55.P2

description: bone marrow CLP plate 3 cell 81


title: SS37.P2

description: bone marrow CLP plate 3 cell 82


title: noRT4.P3

description: bone marrow CLP plate 4 cell 1


title: SS38.P2

description: bone marrow CLP plate 3 cell 80


title: SS54.P2

description: bone marrow CLP plate 3 cell 83


title: SS57.P2

description: bone marrow CLP plate 3 cell 77


title: SS58.P2

description: bone marrow CLP plate 3 cell 75


title: SS41.P2

description: bone marrow CLP plate 3 cell 74


title: SS47.P2

description: bone marrow CLP plate 3 cell 86


title: SS59.P2

description: bone marrow CLP plate 3 cell 73


title: SS42.P2

description: bone marrow CLP plate 3 cell 72


title: SS60.P2

description: bone marrow CLP plate 3 cell 69


title: SS32.P2

description: bone marrow CLP plate 3 cell 68


title: SS61.P2

description: bone marrow CLP plate 3 cell 67


title: noRT1.P2

description: bone marrow CLP plate 3 cell 71


title: SS31.P2

description: bone marrow CLP plate 3 cell 70


title: SS62.P2

description: bone marrow CLP plate 3 cell 65


title: SS33.P2

description: bone marrow CLP plate 3 cell 66


title: SS56.P2

description: bone marrow CLP plate 3 cell 79


title: SS39.P2

description: bone marrow CLP plate 3 cell 78


title: SS34.P2

description: bone marrow CLP plate 3 cell 64


title: SS40.P2

description: bone marrow CLP plate 3 cell 76


title: SS65.P2

description: bone marrow CLP plate 3 cell 59


title: SS64.P2

description: bone marrow CLP plate 3 cell 61


title: SS35.P2

description: bone marrow CLP plate 3 cell 62


title: SS66.P2

description: bone marrow CLP plate 3 cell 57


title: SS63.P2

description: bone marrow CLP plate 3 cell 63


title: SS67.P2

description: bone marrow CLP plate 3 cell 55


title: SS36.P2

description: bone marrow CLP plate 3 cell 60


title: SS26.P2

description: bone marrow CLP plate 3 cell 56


title: SS68.P2

description: bone marrow CLP plate 3 cell 53


title: SS27.P2

description: bone marrow CLP plate 3 cell 54


title: SS69.P2

description: bone marrow CLP plate 3 cell 51


title: SS29.P2

description: bone marrow CLP plate 3 cell 50


title: SS70.P2

description: bone marrow CLP plate 3 cell 49


title: noRT2.P2

description: bone marrow CLP plate 3 cell 47


title: SS19.P2

description: bone marrow CLP plate 3 cell 46


title: SS30.P2

description: bone marrow CLP plate 3 cell 48


title: SS71.P2

description: bone marrow CLP plate 3 cell 45


title: SS20.P2

description: bone marrow CLP plate 3 cell 44


title: SS25.P2

description: bone marrow CLP plate 3 cell 58


title: SS21.P2

description: bone marrow CLP plate 3 cell 42


title: SS73.P2

description: bone marrow CLP plate 3 cell 41


title: SS22.P2

description: bone marrow CLP plate 3 cell 40


title: SS72.P2

description: bone marrow CLP plate 3 cell 43


title: SS23.P2

description: bone marrow CLP plate 3 cell 38


title: SS74.P2

description: bone marrow CLP plate 3 cell 39


title: SS24.P2

description: bone marrow CLP plate 3 cell 36


title: SS75.P2

description: bone marrow CLP plate 3 cell 37


title: SS28.P2

description: bone marrow CLP plate 3 cell 52


title: SS76.P2

description: bone marrow CLP plate 3 cell 35


title: SS15.P2

description: bone marrow CLP plate 3 cell 30


title: SS13.P2

description: bone marrow CLP plate 3 cell 34


title: SS78.P2

description: bone marrow CLP plate 3 cell 31


title: SS14.P2

description: bone marrow CLP plate 3 cell 32


title: SS16.P2

description: bone marrow CLP plate 3 cell 28


title: SS79.P2

description: bone marrow CLP plate 3 cell 29


title: SS81.P2

description: bone marrow CLP plate 3 cell 25


title: SS80.P2

description: bone marrow CLP plate 3 cell 27


title: SS18.P2

description: bone marrow CLP plate 3 cell 24


title: SS7.P2

description: bone marrow CLP plate 3 cell 22


title: SS8.P2

description: bone marrow CLP plate 3 cell 21


title: SS9.P2

description: bone marrow CLP plate 3 cell 20


title: 20CELLS.P2

description: 20 bone marrow CLP


title: SS82.P2

description: bone marrow CLP plate 3 cell 19


title: 10CELLS.P2

description: 10 bone marrow CLP


title: SS77.P2

description: bone marrow CLP plate 3 cell 33


title: SS10.P2

description: bone marrow CLP plate 3 cell 18


title: SS11.P2

description: bone marrow CLP plate 3 cell 16


title: SS12.P2

description: bone marrow CLP plate 3 cell 14


title: SS83.P2

description: bone marrow CLP plate 3 cell 17


title: SS86.P2

description: bone marrow CLP plate 3 cell 11


title: SS17.P2

description: bone marrow CLP plate 3 cell 26


title: noRT3.P2

description: bone marrow CLP plate 3 cell 23


title: SS1.P2

description: bone marrow CLP plate 3 cell 12


title: SS85.P2

description: bone marrow CLP plate 3 cell 13


title: SS84.P2

description: bone marrow CLP plate 3 cell 15


title: SS3.P2

description: bone marrow CLP plate 3 cell 8


title: SS87.P2

description: bone marrow CLP plate 3 cell 9


title: SS89.P2

description: bone marrow CLP plate 3 cell 5


title: SS4.P2

description: bone marrow CLP plate 3 cell 6


title: SS88.P2

description: bone marrow CLP plate 3 cell 7


title: SS5.P2

description: bone marrow CLP plate 3 cell 4


title: SS2.P2

description: bone marrow CLP plate 3 cell 10


title: SS49.P1

description: bone marrow CLP plate 2 cell 93


title: noRT4.P2

description: bone marrow CLP plate 3 cell 1


title: SS6.P2

description: bone marrow CLP plate 3 cell 2


title: SS90.P2

description: bone marrow CLP plate 3 cell 3


title: SS44.P1

description: bone marrow CLP plate 2 cell 92


title: SS50.P1

description: bone marrow CLP plate 2 cell 91


title: SS43.P1

description: bone marrow CLP plate 2 cell 94


title: SS51.P1

description: bone marrow CLP plate 2 cell 89


title: SS45.P1

description: bone marrow CLP plate 2 cell 90


title: SS46.P1

description: bone marrow CLP plate 2 cell 88


title: SS37.P1

description: bone marrow CLP plate 2 cell 82


title: SS47.P1

description: bone marrow CLP plate 2 cell 86


title: SS52.P1

description: bone marrow CLP plate 2 cell 87


title: SS53.P1

description: bone marrow CLP plate 2 cell 85


title: SS55.P1

description: bone marrow CLP plate 2 cell 81


title: SS54.P1

description: bone marrow CLP plate 2 cell 83


title: SS48.P1

description: bone marrow CLP plate 2 cell 84


title: SS56.P1

description: bone marrow CLP plate 2 cell 79


title: SS38.P1

description: bone marrow CLP plate 2 cell 80


title: SS39.P1

description: bone marrow CLP plate 2 cell 78


title: SS57.P1

description: bone marrow CLP plate 2 cell 77


title: SS40.P1

description: bone marrow CLP plate 2 cell 76


title: SS41.P1

description: bone marrow CLP plate 2 cell 74


title: SS58.P1

description: bone marrow CLP plate 2 cell 75


title: noRT1.P1

description: bone marrow CLP plate 2 cell 71


title: SS59.P1

description: bone marrow CLP plate 2 cell 73


title: SS42.P1

description: bone marrow CLP plate 2 cell 72


title: SS61.P1

description: bone marrow CLP plate 2 cell 67


title: SS31.P1

description: bone marrow CLP plate 2 cell 70


title: SS60.P1

description: bone marrow CLP plate 2 cell 69


title: SS32.P1

description: bone marrow CLP plate 2 cell 68


title: SS62.P1

description: bone marrow CLP plate 2 cell 65


title: SS34.P1

description: bone marrow CLP plate 2 cell 64


title: SS35.P1

description: bone marrow CLP plate 2 cell 62


title: SS63.P1

description: bone marrow CLP plate 2 cell 63


title: SS33.P1

description: bone marrow CLP plate 2 cell 66


title: SS64.P1

description: bone marrow CLP plate 2 cell 61


title: SS36.P1

description: bone marrow CLP plate 2 cell 60


title: SS65.P1

description: bone marrow CLP plate 2 cell 59


title: SS25.P1

description: bone marrow CLP plate 2 cell 58


title: SS26.P1

description: bone marrow CLP plate 2 cell 56


title: SS67.P1

description: bone marrow CLP plate 2 cell 55


title: SS66.P1

description: bone marrow CLP plate 2 cell 57


title: SS28.P1

description: bone marrow CLP plate 2 cell 52


title: SS68.P1

description: bone marrow CLP plate 2 cell 53


title: SS69.P1

description: bone marrow CLP plate 2 cell 51


title: SS29.P1

description: bone marrow CLP plate 2 cell 50


title: SS70.P1

description: bone marrow CLP plate 2 cell 49


title: SS30.P1

description: bone marrow CLP plate 2 cell 48


title: noRT2.P1

description: bone marrow CLP plate 2 cell 47


title: SS20.P1

description: bone marrow CLP plate 2 cell 44


title: SS71.P1

description: bone marrow CLP plate 2 cell 45


title: SS19.P1

description: bone marrow CLP plate 2 cell 46


title: SS72.P1

description: bone marrow CLP plate 2 cell 43


title: SS21.P1

description: bone marrow CLP plate 2 cell 42


title: SS73.P1

description: bone marrow CLP plate 2 cell 41


title: SS22.P1

description: bone marrow CLP plate 2 cell 40


title: SS23.P1

description: bone marrow CLP plate 2 cell 38


title: SS13.P1

description: bone marrow CLP plate 2 cell 34


title: SS74.P1

description: bone marrow CLP plate 2 cell 39


title: SS15.P1

description: bone marrow CLP plate 2 cell 30


title: SS76.P1

description: bone marrow CLP plate 2 cell 35


title: SS24.P1

description: bone marrow CLP plate 2 cell 36


title: SS27.P1

description: bone marrow CLP plate 2 cell 54


title: SS75.P1

description: bone marrow CLP plate 2 cell 37


title: SS14.P1

description: bone marrow CLP plate 2 cell 32


title: SS78.P1

description: bone marrow CLP plate 2 cell 31


title: SS79.P1

description: bone marrow CLP plate 2 cell 29


title: SS16.P1

description: bone marrow CLP plate 2 cell 28


title: SS77.P1

description: bone marrow CLP plate 2 cell 33


title: SS80.P1

description: bone marrow CLP plate 2 cell 27


title: SS17.P1

description: bone marrow CLP plate 2 cell 26


title: SS18.P1

description: bone marrow CLP plate 2 cell 24


title: noRT3.P1

description: bone marrow CLP plate 2 cell 23


title: SS81.P1

description: bone marrow CLP plate 2 cell 25


title: SS7.P1

description: bone marrow CLP plate 2 cell 22


title: 20CELLS.P1

description: 20 bone marrow CLP


title: SS9.P1

description: bone marrow CLP plate 2 cell 20


title: 10CELLS.P1

description: 10 bone marrow CLP


title: SS82.P1

description: bone marrow CLP plate 2 cell 19


title: SS10.P1

description: bone marrow CLP plate 2 cell 18


title: SS83.P1

description: bone marrow CLP plate 2 cell 17


title: SS84.P1

description: bone marrow CLP plate 2 cell 15


title: SS1.P1

description: bone marrow CLP plate 2 cell 12


title: SS88.P1

description: bone marrow CLP plate 2 cell 7


title: SS3.P1

description: bone marrow CLP plate 2 cell 8


title: SS11.P1

description: bone marrow CLP plate 2 cell 16


title: SS85.P1

description: bone marrow CLP plate 2 cell 13


title: SS2.P1

description: bone marrow CLP plate 2 cell 10


title: SS5.P1

description: bone marrow CLP plate 2 cell 4


title: SS87.P1

description: bone marrow CLP plate 2 cell 9


title: noRT4.P1

description: bone marrow CLP plate 2 cell 1


title: SS6.P1

description: bone marrow CLP plate 2 cell 2


title: SS12.P1

description: bone marrow CLP plate 2 cell 14


title: SS90.P1

description: bone marrow CLP plate 2 cell 3


title: SS43.P0

description: bone marrow CLP plate 1 cell 94


title: SS4.P1

description: bone marrow CLP plate 2 cell 6


title: SS89.P1

description: bone marrow CLP plate 2 cell 5


title: SS45.P0

description: bone marrow CLP plate 1 cell 90


title: SS8.P1

description: bone marrow CLP plate 2 cell 21


title: SS46.P0

description: bone marrow CLP plate 1 cell 88


title: SS51.P0

description: bone marrow CLP plate 1 cell 89


title: SS49.P0

description: bone marrow CLP plate 1 cell 93


title: SS52.P0

description: bone marrow CLP plate 1 cell 87


title: SS86.P1

description: bone marrow CLP plate 2 cell 11


title: SS50.P0

description: bone marrow CLP plate 1 cell 91


title: SS53.P0

description: bone marrow CLP plate 1 cell 85


title: SS47.P0

description: bone marrow CLP plate 1 cell 86


title: SS48.P0

description: bone marrow CLP plate 1 cell 84


title: SS44.P0

description: bone marrow CLP plate 1 cell 92


title: SS54.P0

description: bone marrow CLP plate 1 cell 83


title: SS55.P0

description: bone marrow CLP plate 1 cell 81


title: SS38.P0

description: bone marrow CLP plate 1 cell 80


title: SS57.P0

description: bone marrow CLP plate 1 cell 77


title: SS40.P0

description: bone marrow CLP plate 1 cell 76


title: SS58.P0

description: bone marrow CLP plate 1 cell 75


title: SS42.P0

description: bone marrow CLP plate 1 cell 72


title: SS37.P0

description: bone marrow CLP plate 1 cell 82


title: SS60.P0

description: bone marrow CLP plate 1 cell 69


title: SS31.P0

description: bone marrow CLP plate 1 cell 70


title: SS63.P0

description: bone marrow CLP plate 1 cell 63


title: SS33.P0

description: bone marrow CLP plate 1 cell 66


title: noRT1.P0

description: bone marrow CLP plate 1 cell 71


title: SS32.P0

description: bone marrow CLP plate 1 cell 68


title: SS41.P0

description: bone marrow CLP plate 1 cell 74


title: SS36.P0

description: bone marrow CLP plate 1 cell 60


title: SS59.P0

description: bone marrow CLP plate 1 cell 73


title: SS34.P0

description: bone marrow CLP plate 1 cell 64


title: SS61.P0

description: bone marrow CLP plate 1 cell 67


title: SS62.P0

description: bone marrow CLP plate 1 cell 65


title: SS25.P0

description: bone marrow CLP plate 1 cell 58


title: SS35.P0

description: bone marrow CLP plate 1 cell 62


title: SS65.P0

description: bone marrow CLP plate 1 cell 59


title: SS66.P0

description: bone marrow CLP plate 1 cell 57


title: SS67.P0

description: bone marrow CLP plate 1 cell 55


title: SS26.P0

description: bone marrow CLP plate 1 cell 56


title: SS56.P0

description: bone marrow CLP plate 1 cell 79


title: SS27.P0

description: bone marrow CLP plate 1 cell 54


title: SS39.P0

description: bone marrow CLP plate 1 cell 78


title: SS28.P0

description: bone marrow CLP plate 1 cell 52


title: SS29.P0

description: bone marrow CLP plate 1 cell 50


title: SS70.P0

description: bone marrow CLP plate 1 cell 49


title: SS68.P0

description: bone marrow CLP plate 1 cell 53


title: SS71.P0

description: bone marrow CLP plate 1 cell 45


title: SS64.P0

description: bone marrow CLP plate 1 cell 61


title: SS19.P0

description: bone marrow CLP plate 1 cell 46


title: SS30.P0

description: bone marrow CLP plate 1 cell 48


title: SS69.P0

description: bone marrow CLP plate 1 cell 51


title: SS73.P0

description: bone marrow CLP plate 1 cell 41


title: SS21.P0

description: bone marrow CLP plate 1 cell 42


title: noRT2.P0

description: bone marrow CLP plate 1 cell 47


title: SS72.P0

description: bone marrow CLP plate 1 cell 43


title: SS24.P0

description: bone marrow CLP plate 1 cell 36


title: SS23.P0

description: bone marrow CLP plate 1 cell 38


title: SS20.P0

description: bone marrow CLP plate 1 cell 44


title: SS22.P0

description: bone marrow CLP plate 1 cell 40


title: SS76.P0

description: bone marrow CLP plate 1 cell 35


title: SS74.P0

description: bone marrow CLP plate 1 cell 39


title: SS75.P0

description: bone marrow CLP plate 1 cell 37


title: SS77.P0

description: bone marrow CLP plate 1 cell 33


title: SS14.P0

description: bone marrow CLP plate 1 cell 32


title: SS78.P0

description: bone marrow CLP plate 1 cell 31


title: SS15.P0

description: bone marrow CLP plate 1 cell 30


title: SS80.P0

description: bone marrow CLP plate 1 cell 27


title: SS16.P0

description: bone marrow CLP plate 1 cell 28


title: SS13.P0

description: bone marrow CLP plate 1 cell 34


title: PBMC_HLNRA_Grp IV, biological rep 5

city: Mumbai

first: Birajalaxmi

last: Das

state: Maharashtra

address: Trombay

department: LLRRS, RB&HSD

institute: Bhabha Atomic Research Centre

description:
Human_HL_Grp IV_5
Gene expression data from PBMC of HLNRA individuals receiving annual background dose of >15.0 mGy/year.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree Celsius on Human Genome U133 Plus 2.0 Gene Chip expression arrays as per Affymetrix protocol.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were normalized with Robust multichip analysis (RMA) algorithm.

source_name: PBMC, HLNRA, Grp IV

label_protocol: Biotin labelled cRNA/aRNA was prepared using Gene Chip®3' IVT Express Labeling Kit (Affymetrix, Santa Clara, CA, USA) as per manufacturer's protocol.

extract_protocol: Isolation of total RNA using RNeasy Mini Kit (Qiagen) as per manufacturer's instructions.

treatment_protocol: PBMCs were isolated from whole blood of each individual using HistopaqueTM separation medium (Sigma) as per manufacturer's instruction. Cells were washed with phosphate-buffered saline (PBS) and stored in RNAlater solution.

value: Blood

value: Peripheral blood mononuclear cells (PBMC)

tag: Sex

value: Male

tag: annual background radiation dose


title: PBMC_HLNRA_Grp IV, biological rep 6

description:
Human_HL_Grp IV_6
Gene expression data from PBMC of HLNRA individuals receiving annual background dose of >15.0 mGy/year.

tag: tissue


title: PBMC_HLNRA_Grp IV, biological rep 3

description:
Human_HL_Grp IV_3
Gene expression data from PBMC of HLNRA individuals receiving annual background dose of >15.0 mGy/year.


title: noRT3.P0

description: bone marrow CLP plate 1 cell 23


title: 10CELLS.P0

description: 10 bone marrow CLP cells


title: SS81.P0

description: bone marrow CLP plate 1 cell 25


title: PBMC_HLNRA_Grp IV, biological rep 7

description:
Human_HL_Grp IV_7
Gene expression data from PBMC of HLNRA individuals receiving annual background dose of >15.0 mGy/year.


title: SS7.P0

description: bone marrow CLP plate 1 cell 22


title: PBMC_HLNRA_Grp IV, biological rep 2

description:
Human_HL_Grp IV_2
Gene expression data from PBMC of HLNRA individuals receiving annual background dose of >15.0 mGy/year.


title: PBMC_HLNRA_Grp IV, biological rep 4

description:
Human_HL_Grp IV_4
Gene expression data from PBMC of HLNRA individuals receiving annual background dose of >15.0 mGy/year.


title: PBMC_HLNRA_Grp III, biological rep 11

description:
Human_HL_Grp III_11
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 5.01-15.0 mGy/year.

source_name: PBMC, HLNRA, Grp III


title: PBMC_HLNRA_Grp III, biological rep 9

description:
Human_HL_Grp III_9
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 5.01-15.0 mGy/year.


title: PBMC_HLNRA_Grp III, biological rep 4

description:
Human_HL_Grp III_4
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 5.01-15.0 mGy/year.


title: PBMC_HLNRA_Grp III, biological rep 8

description:
Human_HL_Grp III_8
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 5.01-15.0 mGy/year.


title: SS8.P0

description: bone marrow CLP plate 1 cell 21


title: PBMC_HLNRA_Grp III, biological rep 10

description:
Human_HL_Grp III_10
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 5.01-15.0 mGy/year.


title: PBMC_HLNRA_Grp III, biological rep 7

description:
Human_HL_Grp III_7
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 5.01-15.0 mGy/year.


title: PBMC_HLNRA_Grp III, biological rep 5

description:
Human_HL_Grp III_5
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 5.01-15.0 mGy/year.


title: SS79.P0

description: bone marrow CLP plate 1 cell 29


title: PBMC_HLNRA_Grp III, biological rep 6

description:
Human_HL_Grp III_6
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 5.01-15.0 mGy/year.


title: SS17.P0

description: bone marrow CLP plate 1 cell 26


title: SS82.P0

description: bone marrow CLP plate 1 cell 19


title: 20CELLS.P0

description: 20 bone marrow CLP cells


title: SS9.P0

description: bone marrow CLP plate 1 cell 20


title: SS18.P0

description: bone marrow CLP plate 1 cell 24


title: SS10.P0

description: bone marrow CLP plate 1 cell 18


title: SS83.P0

description: bone marrow CLP plate 1 cell 17


title: PBMC_HLNRA_Grp IV, biological rep 1

description:
Human_HL_Grp IV_1
Gene expression data from PBMC of HLNRA individuals receiving annual background dose of >15.0 mGy/year.


title: PBMC_HLNRA_Grp III, biological rep 2

description:
Human_HL_Grp III_2
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 5.01-15.0 mGy/year.


title: SS85.P0

description: bone marrow CLP plate 1 cell 13


title: PBMC_HLNRA_Grp III, biological rep 3

description:
Human_HL_Grp III_3
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 5.01-15.0 mGy/year.


title: SS12.P0

description: bone marrow CLP plate 1 cell 14


title: SS1.P0

description: bone marrow CLP plate 1 cell 12


title: SS86.P0

description: bone marrow CLP plate 1 cell 11


title: PBMC_HLNRA_Grp III, biological rep 1

description:
Human_HL_Grp III_1
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 5.01-15.0 mGy/year.


title: PBMC_HLNRA_Grp II, biological rep 7

description:
Human_HL_Grp II_7
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 1.51-5.0 mGy/year.

source_name: PBMC, HLNRA, Grp II


title: SS2.P0

description: bone marrow CLP plate 1 cell 10


title: PBMC_HLNRA_Grp II, biological rep 4

description:
Human_HL_Grp II_4
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 1.51-5.0 mGy/year.


title: SS3.P0

description: bone marrow CLP plate 1 cell 8


title: SS87.P0

description: bone marrow CLP plate 1 cell 9


title: PBMC_HLNRA_Grp II, biological rep 9

description:
Human_HL_Grp II_9
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 1.51-5.0 mGy/year.


title: PBMC_HLNRA_Grp II, biological rep 8

description:
Human_HL_Grp II_8
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 1.51-5.0 mGy/year.


title: SS11.P0

description: bone marrow CLP plate 1 cell 16


title: SS84.P0

description: bone marrow CLP plate 1 cell 15


title: PBMC_HLNRA_Grp II, biological rep 5

description:
Human_HL_Grp II_5
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 1.51-5.0 mGy/year.


title: PBMC_HLNRA_Grp II, biological rep 1

description:
Human_HL_Grp II_1
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 1.51-5.0 mGy/year.


title: PBMC_HLNRA_Grp II, biological rep 2

description:
Human_HL_Grp II_2
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 1.51-5.0 mGy/year.


title: PBMC_HLNRA_Grp II, biological rep 3

description:
Human_HL_Grp II_3
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 1.51-5.0 mGy/year.


title: PBMC_HLNRA_Grp II, biological rep 6

description:
Human_HL_Grp II_6
Gene expression data from PBMC of HLNRA individuals receiving annual background dose between 1.51-5.0 mGy/year.


title: PBMC_NLNRA_Grp I, biological rep 7

description:
Human_NL_Grp I_7
Gene expression data from PBMC of NLNRA individuals receiving annual background dose of ≤ 1.5 mGy/year.

source_name: PBMC, NLNRA, Grp I


title: PBMC_NLNRA_Grp I, biological rep 8

description:
Human_NL_Grp I_8
Gene expression data from PBMC of NLNRA individuals receiving annual background dose of ≤ 1.5 mGy/year.


title: PBMC_NLNRA_Grp I, biological rep 6

description:
Human_NL_Grp I_6
Gene expression data from PBMC of NLNRA individuals receiving annual background dose of ≤ 1.5 mGy/year.


title: SS89.P0

description: bone marrow CLP plate 1 cell 5


title: PBMC_NLNRA_Grp I, biological rep 4

description:
Human_NL_Grp I_4
Gene expression data from PBMC of NLNRA individuals receiving annual background dose of ≤ 1.5 mGy/year.


title: PBMC_NLNRA_Grp I, biological rep 9

description:
Human_NL_Grp I_9
Gene expression data from PBMC of NLNRA individuals receiving annual background dose of ≤ 1.5 mGy/year.


title: SS90.P0

description: bone marrow CLP plate 1 cell 3


title: SS6.P0

description: bone marrow CLP plate 1 cell 2


title: SS88.P0

description: bone marrow CLP plate 1 cell 7


title: SS4.P0

description: bone marrow CLP plate 1 cell 6


title: noRT4.P0

description: bone marrow CLP plate 1 cell 1


title: PBMC_NLNRA_Grp I, biological rep 5

description:
Human_NL_Grp I_5
Gene expression data from PBMC of NLNRA individuals receiving annual background dose of ≤ 1.5 mGy/year.


title: SS5.P0

description: bone marrow CLP plate 1 cell 4


title: PBMC_NLNRA_Grp I, biological rep 2

description:
Human_NL_Grp I_2
Gene expression data from PBMC of NLNRA individuals receiving annual background dose of ≤ 1.5 mGy/year.


title: d3lacZ1

status: Public on Oct 25 2017

type: SRA

city: WAUWATOSA

first: ZIQING

last: LIU

state: WI

address: 8701 W Watertown Plank Rd, BSB 5320

department: Biology

institute: Medical College of Wisconsin

library_source: transcriptomic

data_processing:
QC: Qualities of de-barcoded raw sequence reads were checked by fastqc.
Mapping: Mapping to the merged genome of mm10 was performed with Tophat2 (2.1.0) using default settings.
Counting: Gene expression was counted with Htseq-count (0.6.1p1) using the union mode and counts per million were calculated for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing CPM for each gene in each sample.

molecule: polyA RNA

source_name: d3CF transduced with empty vector

growth_protocol: P1.5 neonatal hearts were isolated from CD1 mice and cardiac fibroblasts were isolated with the enzyme digestion method followed by MACS purification of Thy1+ cells. P1.5 cardiomyocytes were isolated using the neonatal cardiomyocytes isolation system (Worthington Biochemical Corporation). For reprogramming, CF cells were seeded onto 0.1% gelatin-coated plates at 2 x 104/cm2 in fibroblast media (IMDM + 20% FBS). After overnight culturing, media was replaced before retroviral transduction to remove unattached cells.

extract_protocol:
After three days, cells were collected and lysed in TRIzol.
Illumina libraries were prepared for sequencing using the TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Retroviruses encoding MGT were packaged by transfecting platE cells (Cell Biolabs) with lipofectamine 2000 (Life Technology) and lentiviruses encoding non-targeting shRNA control (shRNA) or shPtbp1 were packaged by transfecting 293T cells. Viruses collected from one 10 cm2 dish were resuspended in 100 µl iCM media. For RNA-seq of Ptbp1-silencing experiments, 2.5 x 105 CF were seeded into one well in a 6-well plate. On the following day, 50 µl of pMXs-puro/ pMXs-puro-MGT or 50 µl each of pMXs-puro-MGT and shNT/ shPtbp1-271 were added to the cells.

tag: age

tag: transduction

value: empty vector


title: d3MGT2

source_name: d3CF transduced with MGT

value: MGT


title: CF2

source_name: neonatal cardiac fibroblasts


title: CM1

source_name: neonatal cardiomyocytes


title: d3MGT-shPtbp1-1

source_name: d3CF transduced with MGT and shPtbp1

value: MGT and shPtbp1


title: d3MGT1


title: d3MGT-shNT2

source_name: d3CF transduced with MGT and shNT

value: MGT and shNT


title: CM2


title: d3MGT-shNT1


title: d3lacZ2


title: PBMC_NLNRA_Grp I, biological rep 3

description:
Human_NL_Grp I_3
Gene expression data from PBMC of NLNRA individuals receiving annual background dose of ≤ 1.5 mGy/year.


title: MEH098

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: Gene expression data from tumors derived from aP2-expressing cells

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Affymetrix Titan scanner

data_processing: The data were rma normalized  by Partek Genomics Suite 6.6

source_name: mouse tumor model

label_protocol: Biotinylated cRNA were prepared using  standard Affymetrix protocols

extract_protocol: RNA was extracted with miRNeasy mini kit (Qiagen), in accordance with themanufacturer's protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: mixed C57Bl/6 and 129X1/SvJ

tag: tissue type

value: tumor

tag: genotype


title: MEH099


title: MEH088

description: Gene expression data from normal skeletal muscle

source_name: normal skeletal muscle

value: sternocleidomastoid

value: wild type


title: MEH085

value: quadriceps femoris


title: MEH086


title: MEH097


title: MEH082


title: MEH087


title: MEH074

description: Gene expression data from normal aorta

source_name: normal aorta

value: aorta


title: MEH076

description: Gene expression data from normal aorta


title: PBMC_NLNRA_Grp I, biological rep 1

description:
Human_NL_Grp I_1
Gene expression data from PBMC of NLNRA individuals receiving annual background dose of ≤ 1.5 mGy/year.


title: MEH084


title: MEH083


title: MEH072


title: MEH075

description: Gene expression data from normal aorta


title: MEH073

description: Gene expression data from normal aorta


title: MEH089


title: S. clavuligerus pSCL4-_70.5h_rep1

type: mixed

city: León

first: Paloma

middle: Liras

last: Padín

state: Spain

address: Vegazana Campus

department: Molecular Biology

country: Spain

institute: University of León

description: Biological replicate 1 of 2. pSCL4-_70.5h-rep1

hyb_protocol: Cy3-cDNA (300 ng) and Cy5-labeled gDNA (2,5 pmol) were mixed, resuspended in 32 μl of hybridization solution (Agilent) and applied on the microarray surface. Hybridizations were carried out at 55°C and extended to 60 h to improve the quality of the results.

scan_protocol: Scanned on an Agilent DNA Microarray Scanner G2565BA. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Microarrays data were processed with the Bioconductor package limma (Smyth and Speed 2003; Smyth 2004). Background corrected signals (the median background signal was substracted from the mean foreground signal) were log2-transformed and normalized with the global median procedure (within arrays), and with the cyclic loess procedure (between arrays). The Mg value is the normalized log2 of Cy3/Cy5 intensities, which is proportional to the abundance of the transcript for a particular gene.

organism: Streptomyces clavuligerus

source_name: pSCL4-_70.5h _totalRNA

label_protocol: Labelling reactions were performed according to the recommendations described by BioPrime® Array CGH Genomic Labeling Systems (Life Technologies). Total RNA was labelled with Cy3-dCTP (Amersham) using random primers and SuperScript™ II reverse transcriptase (Invitrogen). gDNA was labelled with Cy5-dCTP (Amersham) from random primers extended with the Klenow fragment of DNA polymerase (Roche). The final products were purified with MinElute columns (Qiagen) and labelling efficiencies were quantified spectrophotometrically.

growth_protocol: Culture conditions were optimized using SA medium (Starch-Asparagine, Aido et al., 1994) and the samples to extract RNA were collected at 12h, 22.5h, 36h, 46.5h, 60 h and 70.5h of the cultures.

extract_protocol:
lisozime 30 mg/ml in TE was added to stabilized culture samples. After 10 min, 600 µl RLT-β-mercaptoethanol was added to samples, mixed with vortex and, samples within microtubes containing silica beads were processed in FastPrep equipment with the following program: 30 s 6.5 m/s, 1 min at 0 °C, 30 s 6.5 m/s, 1 min at 0 °C. The preparation was extracted with one volume of phenol/chloroform-isoamilic alcohol and the aqueous-phase was applied to RNeasy Mini Kit Columns (Qiagen) according to the manufacturer’s instructions. RNA preparations were incubated with DNaseI (Qiagen) to eliminate DNA contamination. Sample quantification was done with a NanoDrop ND-1000 UV-Vis Spectrophotometer and the integrity of the RNA was determined in a Bioanalyzer 2100 (Agilent Technologies). Only RNAs with an RNA integrity value above 7.0 were used.
Genomic DNA from a stationary phase culture was purified by the salting out procedure (Pospiech, and Neumann, 1995).

treatment_protocol: Samples from the Streptomyces cultures were stabilized with two volumes of RNA Protect Bacteria Reagent (Qiagen) for 5 min

tag: time

source_name: ATCC 27064_ Stationary growth phase _genomicDNA [reference]

value: Stationary growth phase


title: S. clavuligerus pSCL4-_22.5h_rep2

description: Biological replicate 2 of 2. pSCL4-_22.5h-rep2

source_name: pSCL4-_22.5h _totalRNA


title: S. clavuligerus pSCL4-_36.0h_rep2

description: Biological replicate 2 of 2. pSCL4-_36.0h-rep2

source_name: pSCL4-_36.0h _totalRNA


title: S. clavuligerus pSCL4-_36.0h_rep1

description: Biological replicate 1 of 2. pSCL4-_36.0h-rep1


title: S. clavuligerus pSCL4-_12.0h_rep2

description: Biological replicate 2 of 2. pSCL4-_12.0h-rep2

source_name: pSCL4-_12.0h _totalRNA


title: S. clavuligerus pSCL4-_70.5h_rep2

description: Biological replicate 2 of 2. pSCL4-_70.5h-rep2


title: S. clavuligerus pSCL4-_46.5h_rep1

description: Biological replicate 1 of 2. pSCL4-_46.5h-rep1

source_name: pSCL4-_46.5h _totalRNA


title: S. clavuligerus pSCL4-_60.0h_rep1

description: Biological replicate 1 of 2. pSCL4-_60.0h-rep1

source_name: pSCL4-_60.0h _totalRNA


title: S. clavuligerus pSCL4-_46.5h_rep2

description: Biological replicate 2 of 2. pSCL4-_46.5h-rep2


title: S. clavuligerus pSCL4-_60.0h_rep2

description: Biological replicate 2 of 2. pSCL4-_60.0h-rep2


title: S. clavuligerus pSCL4-_12.0h_rep1

description: Biological replicate 1 of 2. pSCL4-_12.0h-rep1


title: MEH067


title: MEH069


title: MEH070


title: S. clavuligerus ATCC 27064_36.0h_rep2

description: Biological replicate 2 of 2. Wild type strain. WT_36.0h-rep2


title: S. clavuligerus pSCL4-_22.5h_rep1

description: Biological replicate 1 of 2. pSCL4-_22.5h-rep1


title: S. clavuligerus ATCC 27064_70.5h_rep2

description: Biological replicate 2 of 2. Wild type strain. WT_70.5h-rep2


title: S. clavuligerus ATCC 27064_12.0h_rep1

description: Biological replicate 1 of 2. Wild type strain. WT_12.0h-rep1

extract_protocol:
RNA: lisozime 30 mg/ml in TE was added to stabilized culture samples. After 10 min, 600 µl RLT-β-mercaptoethanol was added to samples, mixed with vortex and, samples within microtubes containing silica beads were processed in FastPrep equipment with the following program: 30 s 6.5 m/s, 1 min at 0 °C, 30 s 6.5 m/s, 1 min at 0 °C. The preparation was extracted with one volume of phenol/chloroform-isoamilic alcohol and the aqueous-phase was applied to RNeasy Mini Kit Columns (Qiagen) according to the manufacturer’s instructions. RNA preparations were incubated with DNaseI (Qiagen) to eliminate DNA contamination. Sample quantification was done with a NanoDrop ND-1000 UV-Vis Spectrophotometer and the integrity of the RNA was determined in a Bioanalyzer 2100 (Agilent Technologies). Only RNAs with an RNA integrity value above 7.0 were used.
Genomic DNA from a stationary phase culture was purified by the salting out procedure (Pospiech, and Neumann, 1995).


title: S. clavuligerus ATCC 27064_12.0h_rep2

description: Biological replicate 2 of 2. Wild type strain. WT_12.0h-rep2


title: S. clavuligerus ATCC 27064_36.0h_rep1

description: Biological replicate 1 of 2. Wild type strain. WT_36.0h-rep1


title: S. clavuligerus ATCC 27064_70.5h_rep1

description: Biological replicate 1 of 2. Wild type strain. WT_70.5h-rep1


title: Subject 24205, IUS

city: Boston

first: Alvin

middle: T.

last: Kho

state: MA

address: 320 Longwood Avenue

department: Informatics Program

institute: Boston Children's Hospital

description:
Subject 24205, IUS
ST-01010176

hyb_protocol: Not applicable.

scan_protocol: Not applicable.

data_processing:
Raw output values in triplets for each sample: Ct on base 2 exponent, Cq confidence Cq_Conf, amplification score Amp_Score. Triplets with any “Undetermined” value, or Cq-Conf<0.8, or Amp_Score<1.24 are disregarded in subsequent analyses.
In the Normalized data matrix, we have CT_QNORM which CT values from the Non-Normalized data matrix that have CQ_CONF>0.8 and AMP_SCORE>1.24 (otherwise they are null-valued) and then quantile normalized.

source_name: whole lung human fetus

label_protocol: Not applicable.

extract_protocol: Total RNA was isolated from lung tissue RNeasy Mini Kit (Qiagen, Valencia, CA) and quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. We averaged around 4 ng/ul of total RNA in 20 ul measured by RiboGreen. Isolated RNA was reverse-transcribed and the product was pre-amplified using Megaplex PreAmp Primers and TaqMan PreAmp Master Mix (Applied Biosystems).

value: lung

tag: developmental stage

value: fetus

tag: subject id

tag: sex from y chromosome gene expression

value: Female

value: 85 dpc

tag: cotinine (ng/g placenta)

tag: cotinine (ng/ml lung)

tag: processing date

tag: batch id


title: Subject 24191, IUS

description:
Subject 24191, IUS
ST-01010172

value: 91 dpc


title: Subject 24227, IUS

description:
Subject 24227, IUS
ST-01010179

value: 108 dpc


title: Subject 21334, no IUS

description:
Subject 21334, no IUS
ST-01010047

value: Male

value: 76 dpc


title: Subject 21883, IUS

description:
Subject 21883, IUS
ST-01010108

value: 115 dpc


title: Subject 24071, IUS

description:
Subject 24071, IUS
ST-01010135

value: 67 dpc


title: Subject 24159, IUS

description:
Subject 24159, IUS
ST-01010162

value: 96 dpc


title: Subject 21628, no IUS

description:
Subject 21628, no IUS
ST-01010072

value: 74 dpc


title: Subject 24190, IUS

description:
Subject 24190, IUS
ST-01010171

value: 105 dpc


title: Subject 18354, IUS_Rep1

description:
Subject 18354, IUS
ST-01010028_Rep1


title: Subject 21092, no IUS

description:
Subject 21092, no IUS
ST-01010045


title: Subject 20676, no IUS

description:
Subject 20676, no IUS
ST-01010036


title: Subject 18354, IUS_Rep2

description:
Subject 18354, IUS
ST-01010028_Rep2


title: Subject 21602, no IUS

description:
Subject 21602, no IUS
ST-01010068


title: Subject 21531, no IUS

description:
Subject 21531, no IUS
ST-01010056


title: Subject 21341, no IUS

description:
Subject 21341, no IUS
ST-01010004

value: 72 dpc


title: Subject 21004, no IUS_Rep2

description:
Subject 21004, no IUS
ST-01009975_Rep2


title: Subject 21055, IUS

description:
Subject 21055, IUS
ST-01010044

value: 80 dpc


title: Subject 21004, no IUS_Rep1

description:
Subject 21004, no IUS
ST-01009975_Rep1


title: Subject 20731, no IUS

description:
Subject 20731, no IUS
ST-01009942

value: 87 dpc


title: Subject 20734, no IUS

description:
Subject 20734, no IUS
ST-01009945


title: Subject 20764, no IUS

description:
Subject 20764, no IUS
ST-01009947


title: Subject 20152, IUS

description:
Subject 20152, IUS
ST-01009889


title: Subject 21364, no IUS

description:
Subject 21364, no IUS
ST-00008773


title: Subject 20908, no IUS

description:
Subject 20908, no IUS
ST-00008762


title: Subject 21349, no IUS

description:
Subject 21349, no IUS
ST-00008772

value: 101 dpc


title: Subject 20717, no IUS

description:
Subject 20717, no IUS
ST-00008749

value: lung

value: 89 dpc


title: Subject 20773, IUS

description:
Subject 20773, IUS
ST-01009948

value: fetus

value: Female


title: Subject 20197, IUS

description:
Subject 20197, IUS
ST-00008727

value: 110 dpc


title: Subject 20445, IUS

description:
Subject 20445, IUS
ST-00008742


title: Subject 20108, IUS

description:
Subject 20108, IUS
ST-00008721


title: Subject 20225, IUS

description:
Subject 20225, IUS
ST-00008728

value: 82 dpc


title: AML 26 DAY 1

city: Bergen

first: Hakon

last: Reikvam

address: Jonas Lies vei 65

department: Department of Clinical Science

country: Norway

institute: University of Bergen

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were quantile-normalised (http://www.molmine.com/magma/loading/illumina.html) using J-Express version 2012 (http://jexpress.bioinfo.no/site/)

source_name: Leukemic blasts

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit from Thermo Fisher Scientific

extract_protocol: RNA isolation was performed according to QIAgen's instructions in the RNeasy with DNase treatment protocol for the QIAcube.

tag: cell type

value: Leukemic blasts

tag: disease state

value: Acute myeloid leukemia

tag: gender

value: M

tag: aml status

value: Relapse

tag: fab

value: Pos

tag: cytogenetics

value: Normal


title: AML 17 DAY 8

value: F

tag: age

value: de novo

value: Neg


title: control group 3

city: Detroit

middle: H

last: Gorski

state: MI

address: 840.2 HWCRC

department: Surgery

institute: Wayne State University School of Medicine

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: non-silenced vector_MDA-MB-231

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA Amplification Kit

growth_protocol: Cells were cultured in RPMI media supplemented with 5% FBS, 50 U/ml penicillin, 50 mg/ml streptomycin and 250 ng/ml amphotericin B

extract_protocol: RNA was extracted  with the QIAGEN Rneasy Plus kit according to manufacturer's instructions and quality assessed using the Agilent 2100 Bioanalyzer

treatment_protocol: Cells were transduced with GIPZ Lentiviral vectors expressing either GRM1 shRNA or a non-silencing vector and a stable cell culture established using puromycin (10 ug/ml) for two weeks prior to RNA extraction

tag: cell line

value: triple-negative breast cancer cell line

tag: tranduced with

value: GIPZ Lentiviral vectors expressing control non-silencing vector


title: AML 26 DAY 8


title: AML 8 DAY 3


title: AML 14 DAY 3

value: Secondary (MDS)

value: Nt


title: GRM1 silenced group 3

source_name: GRM1 silenced_MDA-MB-231

value: GIPZ Lentiviral vectors expressing GRM1 shRNA


title: AML 38 DAY 8

value: Li Fraumeni, chemotherapy

value: Multiple


title: AML 8 DAY 8


title: AML 42 DAY 3


title: AML 26 DAY 3


title: AML 31 DAY 3

value: Secondary (CMF)


title: AML 14 DAY 8

value: Leukemic blasts


title: AML 43

value: Acute myeloid leukemia


title: AML 42

value: M


title: AML 23 DAY 3

value: Secondary (chemo)


title: AML 23 DAY 8


title: AML 17 DAY 3

value: Pos


title: control group 1


title: AML 33

value: Normal


title: GRM1 silenced group 1


title: GRM1 silenced group 2


title: AML 34

value: Seconday (MDS)


title: AML 42 DAY 1

value: de novo


title: control group 2


title: AML 38 DAY 3

value: F


title: AML 31 DAY 8


title: AML 42 DAY 8


title: AML 38


title: AML 38 DAY 1


title: AML 28

value: Relapse


title: AML 32

value: Secondary (PV)

value: Trisomy 13


title: AML 24

value: Nt


title: AML 31 DAY 1


title: AML 26


title: AML 19


title: AML 23 DAY 1

value: Neg


title: H2A.Z

status: Public on Oct 24 2017

city: Kisarazu

first: Kazuto

last: Kugou

state: Chiba

address: 2-6-7 KazusaKamatatri

department: Department of Frontier Research

country: Japan

institute: Kazusa DNA Research Institute

description: H2A.Z / WCE, meiosis 4h

hyb_protocol: 16 h at 45C using a hybridization oven 640 (affymetrix) as described in the Affymetrix Chromatin Immunoprecipitation Assay Protocol (P/N 702238)

scan_protocol: Fluidics station 400 protocol EukGE-WS2v5 (affymetrix) was performed to wash and stain arrays. The arrays were scanned on GeneChip Scanner 3000 7G (affymetrix).

data_processing: Data were quantile normalized and smoothed with Affymetrix Tiling Analysis Software

organism: Schizosaccharomyces pombe

source_name: H2A.Z ChIP DNA from cells harvested 4h after meiosis induction

label_protocol: Amplified DNA were labeled with biotin as described (Katou et al., Nature 424:1078-83)

growth_protocol: Cells in a pat1-114 background were induced to enter meiosis by the haploid meiosis system, and harvested four hours after the induction.

extract_protocol: Cells were crosslinked with formaldehyde and ChIPs were performed as previously described (Yamada et al., EMBO J 23: 1792-803) except for using anti-H2A.Z antibodies (Abcam).

tag: antibody

source_name: Input DNA from cells harvested 4h after meiosis induction

value: input


title: pht1d-meiosis3h

description: Gene expression data of meiotic cells

hyb_protocol: After fragmentation, 5 ug of biotin labeled cRNA were hybridized for 16 hours at 45C on GeneChip® Yeast Genome 2.0 Array (Affymetrix). GeneChips were washed and stained using Mini_euk2v3 protocol in the Affymetrix Fluidics Station 400 (Affymetrix).

scan_protocol: GeneChips were scanned with the GeneChip® Scanner 3000 G7 (Affymetrix). Image processing was performed with GeneChip® Operating Software (GCOS 1.4) using default settings

data_processing: Expression values were obtained from CEL file by performing background correction, normalization, and summarization with rma method  in the platform R and bioconductor.

source_name: pht1delta diploid, meiosis 3 hr

label_protocol: Biotin-labeled cRNA was synthesized from 1 ug of mRNA by using Affymetrix One-Cycle cDNA synthesis kit.

growth_protocol: Meiosis was induced in h+/h- diploid cells by nitrogen withdrawal and wild-type and pht1Δ diploid cells were harvested 1.5 and 3 hours after the induction.

extract_protocol: Total RNA was extracted with phenol:chloroform:isoamyl alcohol (25:24:1, v/v) and treated with RQ1 DNase I (Promega). mRNA was purified with OligotexTM-dT30 Super mRNA Purification Kit (TaKaRa).

tag: genotype

tag: cell cycle

value: 3 hr after meiosis induction


title: AML 25


title: AML 18


title: AML 22


title: AML 15


title: pht1d-meiosis1.5h

description: Gene expression data of meiotic cells

source_name: pht1delta diploid, meiosis 1.5 hr

value: 1.5 hr after meiosis induction


title: AML 7

value: Leukemic blasts

value: Multiple


title: wt-meiosis3h

description: Gene expression data of meiotic cells

source_name: wild type diploid, meiosis 3 hr


title: wt-meiosis1.5h

description: Gene expression data of meiotic cells

source_name: wild type diploid, meiosis 1.5 hr


title: AML 1

value: Acute myeloid leukemia

value: M


title: AML 13

value: Pos


title: AML 8 DAY 1

value: Normal


title: AML 16


title: AML 17 DAY 1


title: AML 4

value: Seconday (MDS)


title: AML 14 DAY 1

value: Secondary (MDS)


title: AML 20

value: F

value: de novo


title: AML 3


title: AML 5


title: AML 11

value: Secondary (PV)

value: Monosomi 7/-7


title: Non-Dormant_water_T_6h_rep2

status: Public on Oct 23 2017

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

hyb_protocol: GeneChip® 3' IVT Express kit (cat. # 901229) was used for hybridisation, washing and staining of the cartridges.

scan_protocol: Scanning of the arrays was performed using the Affimetrix 3000G scanner.

data_processing: The GeneChip data were analyzed using the R statistical programming environment and Bioconductor packages. The data were normalized using the RMA algorithm. The P values were adjusted for multiple testing with the Benjamini and Hochberg method to control for false positives.

organism: Arabidopsis thaliana

source_name: DELAY Of GERMINATION 1 NIL

label_protocol: RNA was processed and cRNA synthesized according to the 3’ GeneChips OneCycle kit.

growth_protocol: For the transcriptome and  transcriptome analyses NILDOG1 were grown in a randomized complete block design with three replicates. Each replicate consisted of a bulk of eight plants.

extract_protocol: The total RNA and polysomal RNA were purified with TriPure Isolation Reagent (Roche, Basel, Switzerland), further purified using RNeasy Mini spin columns (Qiagen, Hilden, Germany) and dissolved in RNase-free H2O for further analyses.

treatment_protocol: RNA was extracted from freshly harvested, dry seeds of three biological replicates of each genotype.

tag: genetic background

value: Landsberg erecta

tag: tissue

value: seed

tag: dormancy level

value: Non-dormant seeds

tag: treatment

value: water

tag: time course (hours)

tag: rna type

value: Total RNA


title: Non-Dormant_water_T_6h_rep3


title: Non-Dormant_water_T_6h_rep1


title: Non-Dormant_water_T_24h_rep1


title: Dormant_water_T_6h_rep1

value: dormant seeds


title: Non-Dormant_cordycepin_T_6h_rep3

value: Cordycepin


title: Non-Dormant_cordycepin_T_6h_rep1


title: Non-Dormant_water_T_24h_rep2


title: Dormant_water_T_24h_rep2


title: Dormant_water_T_6h_rep3


title: Dormant_water_T_24h_rep3


title: Non-Dormant_cordycepin_T_6h_rep2


title: Non-Dormant_water_T_24h_rep3


title: Dormant_water_T_24h_rep1


title: Dormant_cordycepin_T_24h_rep3


title: Dormant_water_T_6h_rep2


title: Non-Dormant_cordycepin_T_24h_rep2


title: Non-Dormant_cordycepin_T_24h_rep1


title: Non-Dormant_water_P_24h_rep3

value: Polysomal RNA


title: Non-Dormant_water_P_6h_rep1


title: Dormant_cordycepin_T_6h_rep3


title: Dormant_cordycepin_T_6h_rep2


title: Dormant_cordycepin_T_24h_rep2


title: Non-Dormant_water_P_24h_rep1


title: Dormant_cordycepin_T_24h_rep1


title: Dormant_cordycepin_T_6h_rep1


title: Non-Dormant_cordycepin_T_24h_rep3


title: Non-Dormant_water_P_24h_rep2


title: Non-Dormant_water_P_6h_rep3


title: Dormant_water_P_6h_rep3


title: Dormant_water_P_6h_rep2


title: Dormant_water_P_6h_rep1


title: Dormant_water_P_24h_rep1


title: Dormant_water_P_24h_rep2


title: Non-Dormant_cordycepin_P_6h_rep1


title: Non-Dormant_cordycepin_P_6h_rep3


title: Non-Dormant_cordycepin_P_24h_rep2


title: Dormant_cordycepin_P_6h_rep3


title: Dormant_cordycepin_P_24h_rep1


title: Dormant_cordycepin_P_6h_rep1


title: Dormant_cordycepin_P_24h_rep2


title: Non-Dormant_cordycepin_P_24h_rep1


title: Dormant_cordycepin_P_6h_rep2


title: Non-Dormant_cordycepin_P_6h_rep2


title: 90-8TL_combo_2

first: Clare

last: Malone

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School -  Brigham Women's Hospital

description: Gene Expression Data from combo treated cells

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: BRB array tools

label_protocol: standard Affymetrix protocol

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and l-glutamine

extract_protocol: Total RNA was extracted using a trizol extraction followed by Qiagen RNeasy purification

treatment_protocol: Cells were treated with DMSO (vehicle), 100nM INK-128, 2μM Vorinostat, or the combination of INK-128 and Vorinostat for 24 hours prior to harvest.

value: human MPNST cells (90-8TL)

value: 3X INK-128 + Vorinostat


title: NCC_CH2 biological rep1

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

institute: Keio University School of Medicine

hyb_protocol: biotin- labeled, and hybridized to a Human Genome U133 Plus 2.0 Array (Affymetrix Inc., Santa Clara, CA, USA), which was subsequently washed and stained in a Fluidics Station 450 according to the manufacturer’s instructions

scan_protocol: using a GeneChip Scanner 3000 7G

data_processing: RMA algorithm implemented background correction, normalization across arrays, and log2 transformation to the raw image files.

source_name: iPSC derived neural crest cells

growth_protocol: iPSCs were differentiated into neural crest cells as previously described. [8] Briefly, iPSCs were incubated with 2 mg/ml collagenase IV. Once iPSCs were detached, clusters were broken into pieces consisting of 100–200 cells and plated onto a 100mm petridish (B&D) in hNCC differentiation medium consisting o f 1:1 Neurobasal medium and DMEM/F-12 medium (Invitrogen) containing 1x Glutamax(Invitrogen), 5mg/ml insulin(Sigma), 0.5% P/S, and 0.5x GEM 21, 0.5x N2 supplement containing 20ug/ml hrEGF and 20ug/ml hrFGF2. Medium was changed every other day. After seven days of differentiation, migratory neural crest cells appeared from attached spheres. 3–4 days after their appearance, the cells were used for subsequent analysis.

extract_protocol: Purified with the RNeasy mini kit (Qiagen Inc., Hilgen, Germany).

treatment_protocol: Total RNA was isolated from day10 NCs using Trizol® according to the manufacturer’s protocol

tag: genotype/variation

value: patient


title: NCC_201B7 biological rep2

label_protocol: biotin- labeled, and hybridized to a Human Genome U133 Plus 2.0 Array (Affymetrix Inc., Santa Clara, CA, USA), which was subsequently washed and stained in a Fluidics Station 450 according to the manufacturer’s instructions

value: wild type


title: NCC_CH1 biological rep1


title: NCC_CH2 biological rep2


title: NCC_WD39 biological rep1


title: 90-8TL_Vor_3

description: Gene Expression Data from vorinostat treated cells

value: 3X Vorinostat


title: NCC_CH1 biological rep2


title: 90-8TL_combo_3


title: 90-8TL_combo_1


title: NCC_201B7 biological rep1


title: 90-8TL_Vor_1


title: 90-8TL_Vor_2


title: NCC_WD39 biological rep2


title: Non-Dormant_water_P_6h_rep2


title: 90-8TL_INK_1

description: Gene Expression Data from INK-128 treated cells


title: 90-8TL_Vehicle_3

description: Gene Expression Data from vehicle treated cells

value: DMSO


title: Oesophageal Adenocarcinoma 11

status: Public on Oct 22 2017

city: Bedford Park

first: Damian

middle: James

last: Hussey

address: Flinders Drive

country: Australia

institute: Flinders University

description: serum from patient with Oesophageal Adenocarcinoma

data_processing:
Expression data were processed using OpenArray® Real-Time qPCR Analysis Software (BioTrove™, version 1.0.4). CSV files were generated by the software with the cycle threshold (Ct) values for each microRNA with a setting of Ct confidence value threshold of 150.
The CSV files were imported into Realtime Statminer® software (Integromics, Philadelphia, Pa., USA) for  quality checking. Data in the CSV files was then analysed using R version 3.0.2 and SPSS v19 (IBM Inc) for Mac.  Only microRNAs which amplified in every sample were analysed for further analysis.
Data were analysed in R version 3.0.2 and SPSS v19 (IBM Inc.). The relative expression of each miRNA was calculated as 2(40-Ct). All possible permutations of miRNA ratios were generated from the relative expression values using R version 3.0.2.  Mann-Whitney U tests (p<0.05), linear regression (regression coefficient p<0.05), and area under the curve (AUC>0.7) of Receiver Operating Characteristic curves (ROC)  were used to generate a list of differentially expressed microRNAs for control and Barrett's oesoghagus vs. oesophageal adenocarcinoma.
Stepwise forward regression (SPSS v19; IBM Inc) was used to select a panel of microRNA ratios that differentiated controls and Barrett's oesophagus from oesophageal adenocarcinoma.
Matrix normalized worksheet reports the miRNA ratio expression values generated by R version 3.0.2
Fold Change worksheet reports the fold difference of expression of the microRNA ratios between the indicated study groups

label: FAMTM

source_name: peripheral blood serum exosomes

label_protocol: PCR assays were performed by following the protocol for TaqMan@OpenArray Human MicroRNA Panel (4461104, Life technologies). For each sample, 3μl of RNA was reverse transcribed using pre-defined RT-primers (MegaplexTM Primer Human Pool A and Pool B) and the TaqMan® microRNA Reverse Transcription Kit (Life technologies, #4366596). Pre-amplifications were carried out with MegaplexTM PreAmp Pools and TaqMan PreAmp Master Mix on 7.5μl cDNA/ sample for each pool. The pre-amplified products (4μl per sample) were diluted at the recommended 1:40 dilution with 156μl of RNase-free ultra pure water before loading onto the 384-well TaqMan OpenArray loading plate. PCR runs were performed on XXX.

extract_protocol: Exosomes were isolated from the serum samples using ExoquickTm (System Biosciences, EXOQ20A-1). Extraction of miRNA from exosomes was performed using a  miRNeasy Serum/Plasma kit (Qiagen, #217184) with a final elution volume of 24 microlitres ultra pure water

treatment_protocol: Peripheral blood was collected into serum clot activator tubes

tag: disease state

value: Oesophageal Adenocarcinoma

tag: tumour stage

value: locally advanced oesophageal adenocarcinoma


title: Oesophageal Adenocarcinoma 13


title: Oesophageal Adenocarcinoma 12


title: Oesophageal Adenocarcinoma 18


title: Oesophageal Adenocarcinoma 15


title: SKMEL5_siMITF_2

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Samples were prepared for hybridization using 10 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human PrimeView, Affymetrix 901837) were hybridized in a GeneChip Hybridization Oven at 45C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console. A Primeview CDF that included probe information for the ERCC controls (GPL16043), provided by Affymetrix, was used to generate .CEL files.

data_processing: A CDF provided by Affymetrix, which contained the ERCC probes (PrimeView_withERCC_binary.cdf) was used instead of the standard PrimeView cdf. The data were analyzed with Bioconductor using the MAS5 normalization method. Then, these data were renormalized to the external spike-ins. See Loven, Orlando et al., Cell, 2012 for additional details.

source_name: melanoma

label_protocol: For microarray analysis, 100 ng of total RNA containing ERCC RNA Spike-In Mix (see above) was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (30 IVT Express Kit, Affymetrix 901228). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: Cells were grown in DMEM supplemented with 10%FCS to appr. 80% confluency

extract_protocol: Total RNA from DMSO or drug –treated cells was extracted using a RNeasy Mini kit with QIAshredder spin column for homogenization and an on-column DNase digestion (79254, Qiagen) following the manufacturer’s instructions and re-suspended in 30 μL nuclease-free water (Ambion, AM9938). Total RNA was spiked-in with ERCC RNA Spike-In Mix (Ambion, 4456740) proportional to cell number (Loven et al., 2012), treated with DNA-freeTM DNase I (Ambion, AM1906), and analyzed on Agilent 2100 Bioanalyzer for integrity.

treatment_protocol: Transfected with siRNA against MITF

value: siMITF


title: Oesophageal Adenocarcinoma 10


title: Oesophageal Adenocarcinoma 9


title: Oesophageal Adenocarcinoma 8


title: SKMEL5_siCtrl_1

treatment_protocol: Transfected with non-targeting control siRNA (Dharmacon/GE)

value: siCtrl


title: Oesophageal Adenocarcinoma 16


title: Oesophageal Adenocarcinoma 17


title: SKMEL5_THZ1_250nM_2

treatment_protocol: THZ1 250nM + 25uM DMSO for 6 hours


title: SKMEL5_siMITF_1


title: 90-8TL_Vehicle_1


title: 90-8TL_Vehicle_2


title: 90-8TL_INK_3


title: SKMEL5_DMSO_2

treatment_protocol: 25uM DMSO


title: Oesophageal Adenocarcinoma 14


title: Barrett's oesophagus 10

description: serum from patient with non-dysplastic Barrett's Oesophagus

value: non-dysplastic Barrett's Oesophagus


title: Oesophageal Adenocarcinoma 2


title: Oesophageal Adenocarcinoma 1


title: Oesophageal Adenocarcinoma 5


title: Oesophageal Adenocarcinoma 6


title: Oesophageal Adenocarcinoma 7


title: Oesophageal Adenocarcinoma 4


title: Oesophageal Adenocarcinoma 3


title: Barrett's oesophagus 7


title: Barrett's oesophagus 6


title: Barrett's oesophagus 9


title: Barrett's oesophagus 8


title: Barrett's oesophagus 2


title: Barrett's oesophagus 1


title: SKMEL5_THZ1_250nM_1


title: SKMEL5_siCtrl_2


title: SKMEL5_DMSO_1


title: Barrett's oesophagus 4


title: Control 19

description: serum from patient without Barrett's Oesophagus or Cancer


title: Control 18


title: Control 17


title: Control 14


title: Control 13


title: Control 16


title: Control 8


title: Control 10


title: Control 9


title: Barrett's oesophagus 5


title: Control 11


title: Barrett's oesophagus 3


title: Control 15


title: Control 1


title: Control 2


title: Control 4


title: Control 12


title: Control 5


title: Control 6


title: 90-8TL_INK_2


title: Control 3


title: Oa_CTR_T40_5

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

institute: AstraZeneca

description: Blood samples were aseptically collected in Paxgene blood collection tubes, allowed to rest for 2 hours at room temperature, then stored at –20 °C till the extraction process.

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5 and normalized using R2.15.0 statistical software.

organism: Ovis aries

source_name: Sheep, Ovis aries, female, 3-4 y old,  control

label_protocol: Amplification and labelling was done according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol.

extract_protocol: RNA from blood samples was isolated using Paxgene RNA extraction kit, according to manufacturer's instruction. Isolated RNA was purified using Qiagen RNeasy Mini Kit protocol.

tag: gender

value: female

value: 3-4 y old

value: Blood sample


title: Oa_CTR_T40_4


title: Oa_CTR_T40_2


title: Oa_CTR_T40_1


title: MCF10A_RhoC_dox_7d_2

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

data_processing: All arrays were normalized together using the quantile normalization algorithm without background subtraction using the R Bioconductor beadarray package

label: Biotin

source_name: MCF10A with RhoC shRNA with dox after 7 days, rep2

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

growth_protocol: MCF10A cells were purchased from ATCC. MCF10Atet cells, constitutively expressing a Tet-regulated transcriptional transactivator, were provided by  T. Brummer (IMMZ, Freiburg, Germany). Both wild-type and stably transfected cell lines were maintained in growth medium consisting of DMEM/F12 supplemented with 5% horse serum, 10 µg/ml insulin, 0.5 µg/ml hydrocortisone, 20 ng/ml EGF and 0.1 µg/ml cholera toxin. Stable cell lines inducible for Rho overexpression were generated via nucleofection (AMAXA®) with the AhdI-linearized pWHE636 vector containing wild-type cDNA of RhoA or RhoC along with GFP and promoter binding sites for the Tet-regulated transcriptional transactivator (cf. Herr et al., Cell Comm Signaling, 2011 and Danke et al., J Gene Med, 2010).

extract_protocol: Total RNA was isolated from isolated tumor cells using the RNeasy Plus Mini Kit (Qiagen, 74136)

treatment_protocol: Doxycycline for the induction of transgenic overexpression was purchased from Sigma and added at 2 ug/ml before harvesting the cells at 1 and 7 days. CNF toxins were purified as described previously and used at 2 nM for the indicated time periods of 1 and 7 days (Reipschläger et al., JBC 2012). Inhibitors, toxins and inducers were renewed every 2-3 days with every medium exchange.

tag: replicate

value: Replicate 2

tag: stimulus duration

value: 7 Days

tag: transfection

value: RhoC shRNA

tag: stimulus

value: Doxycyclin

tag: array id


title: Oa_CTR_T0_3

tag: age


title: Oa_CTR_T0_2


title: Oa_ZINC_T40_8

source_name: Sheep, Ovis aries, female, 3-4 y old, supplemented (ZINC 212 mg/animal/day)


title: Oa_CTR_T0_5


title: Oa_ZINC_T40_9


title: Oa_CTR_T0_4


title: Oa_ZINC_T40_10


title: MCF10A_RhoC_7d_2

source_name: MCF10A with RhoC shRNA w/o dox after 7 days, rep2

tag: cell line


title: MCF10A_RhoA_dox_7d_2

source_name: MCF10A with RhoA shRNA with dox after 7 days, rep2

value: Replicate 3

value: RhoA shRNA


title: MCF10A_RhoC_dox_7d_1

source_name: MCF10A with RhoC shRNA with dox after 7 days, rep1

value: Replicate 1


title: Oa_CTR_T40_3


title: Oa_ZINC_T40_6


title: MCF10A_RhoA_7d_2

source_name: MCF10A with RhoA shRNA w/o dox after 7 days, rep2


title: Oa_ZINC_T40_7


title: Oa_CTR_T0_1


title: MCF10A_RhoA_dox_1d_2

source_name: MCF10A with RhoA shRNA with dox after 1 day, rep2

value: 1 Day


title: MCF10A_RhoC_1d_2

source_name: MCF10A with RhoC shRNA w/o dox after 1 day, rep2


title: MCF10A_RhoA_7d_1

source_name: MCF10A with RhoA shRNA w/o dox after 7 days, rep1


title: MCF10A_RhoC_dox_1d_1

source_name: MCF10A with RhoC shRNA with dox after 1 day, rep1


title: MCF10A_RhoC_dox_1d_2

source_name: MCF10A with RhoC shRNA with dox after 1 day, rep2


title: MCF10A_RhoC_1d_1

source_name: MCF10A with RhoC shRNA w/o dox after 1 day, rep1


title: MCF10A_RhoA_dox_7d_1

source_name: MCF10A with RhoA shRNA with dox after 7 days, rep1


title: MCF10A_RhoA_dox_1d_1

source_name: MCF10A with RhoA shRNA with dox after 1 day, rep1


title: MCF10A_RhoC_7d_1

source_name: MCF10A with RhoC shRNA w/o dox after 7 days, rep1


title: Oa_ZINC_T40_3


title: Oa_ZINC_T0_9

source_name: Sheep, Ovis aries, female, 3-4 y old, unsupplemented control


title: Oa_ZINC_T40_4


title: Oa_ZINC_T40_1


title: Oa_ZINC_T40_5


title: Oa_ZINC_T0_1


title: Oa_ZINC_T40_2


title: Oa_ZINC_T0_6


title: Oa_ZINC_T0_8


title: Oa_ZINC_T0_7


title: Oa_ZINC_T0_3


title: MCF10A_LV_7d_1

source_name: MCF10A with empty vector w/o dox after 7 days, rep1

value: empty vector


title: MCF10A_LV_dox_7d_1

source_name: MCF10A with empty vector with dox after 7 days, rep1


title: Oa_ZINC_T0_4


title: Oa_ZINC_T0_10


title: Oa_ZINC_T0_5


title: Oa_ZINC_T0_2


title: MCF10A_RhoA_1d_1

source_name: MCF10A with RhoA shRNA w/o dox after 1 day, rep1


title: MCF10A_LV_1d_2

source_name: MCF10A with empty vector w/o dox after 1 day, rep2


title: MCF10A_LV_dox_7d_2

source_name: MCF10A with empty vector with dox after 7 days, rep2


title: MCF10A_CNFY_7d_1

source_name: MCF10A CNFY treated after 7 days, rep1

value: untransfected

value: CNFY


title: MCF10A_LV_1d_1

source_name: MCF10A with empty vector w/o dox after 1 day, rep1


title: MCF10A_LV_dox_1d_2

source_name: MCF10A with empty vector with dox after 1 day, rep2


title: MCF10A_LV_7d_2

source_name: MCF10A with empty vector w/o dox after 7 days, rep2


title: MCF10A_RhoA_1d_2

source_name: MCF10A with RhoA shRNA w/o dox after 1 day, rep2


title: MCF10A_LV_dox_1d_1

source_name: MCF10A with empty vector with dox after 1 day, rep1


title: MCF10A_CNFY_7d_2

source_name: MCF10A CNFY treated after 7 days, rep2


title: MCF10A_CNFY_1d_2

source_name: MCF10A CNFY treated after 1 day, rep2


title: MCF10A_CNFY_1d_1

source_name: MCF10A CNFY treated after 1 day, rep1


title: Control 7

source_name: peripheral blood serum exosomes