title: PF_male gametocyte D12_Rep2

description:
raw data file: SG12454250_254853210016_S001_GE2_1105_Oct12_1_4.txt (Cy3 channel)
This sample is of Plasmodium falciparum male gametocyte at stage V. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: Plasmodium falciparum, male gametocyte, D12, Rep2

tag: age


title: 69

status: Public on Jan 28 2016

type: genomic

city: salamanca

first: Juan

middle: Luis

last: Garcia

address: Campus Miguel de Unamuno

country: Spain

institute: Center Cancer Research

description: Muestra 72

hyb_protocol: Hybridization was performed according to the instructions in the NimbleGen Array User Guide

scan_protocol: Scanning was performed according to the instructions in the NimbleGen Array User Guide

data_processing: Arrays were processed using Nimblegen's standard protocol and segmented using the WAVICGH tool.

molecule: genomic DNA

organism: Homo sapiens

source_name: DNA from Colorectal cancer tissue

label_protocol: Samples were denatured and labeled in parallel with Cy3 for the test group and Cy5 for the control group, each through a random priming method, using Klenow fragments (NimbleGen Dual-Color DNA Labeling Kit, Roche NimbleGen, Inc., Madison, WI, USA)

extract_protocol: The genomic DNA was extracted from colo rectal cancer tissues  with QIAmp DNA Mini Kit (Qiagen,  16 Valencia, CA, USA) following the manufacturer’s instructions

tag: gender

value: Male

tag: disease

value: Late-Onset Colorectal cancer

tag: age group

tag: genetic subtype

value: Not applicable

source_name: commercially available genomic DNA

tag: reference dna source

value: Human Genomic DNA, Male, Promega, Madison, WI, USA


title: 58

description: Muestra 61

value: Female


title: 72

description: Muestra 75

value: Human Genomic DNA, Female, Promega, Madison, WI, USA


title: 68

description: Muestra 71


title: 65

description: Muestra 68


title: 60

description: Muestra 63


title: 57

description: Muestra 60


title: 70

description: Muestra 73


title: 56

description: Muestra 59-


title: Control 3 Control 003

type: RNA

city: Chongqing

first: Zhenhua

last: Guo

address: No.136, 2nd Zhongshan Road, Yuzhong District

country: China

institute: Children's Hospitoal of Chongqing Medical University

description: Replicated miRNAs were averaged and miRNAs that intensities>=41 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

hyb_protocol: Mixing 12.5ul labeled sample, 90ul 2×Hybridization buffer, 77.5ul Nuclease-free Buffer in a PCR tube. Incubate at 95°C for 2 min. During the incubation the target preparation should be protected from light. Leave on ice for at least 2 min. and up to 15min. Briefly spin the reaction after ice incubation. Take cover slide out of the package. Carefully laid the miRCURYTM Array on top of the assembly of cover slide and spacer, where the printed side of array should be facing toward the cover slide, to form a hybridization assembly. The printed side of array is on the side of the label. Insert the hybridization assembly into a (3.1 x 9cm) heat-shrank hybridization (hyb.) bag. Sample loading side of the hybridization assembly should face the opening side of film bag. Lower the assembly to the end of the bag (Assembly viewed from the other side). Clip the bag with a clipper “securely” from the opening end. Immerse the assembly to the rim of the slide in 95℃ hot water swiftly (approximately 2~5 sec). Do not dip the assembly too far into the water to avoid water leaking into the assembly. The hyb. bag will shrink and tightly wrap around the assembly. Remove the assembly from water and wipe off the water from the assembly. Trim off the excess film from the top of the assembly. Keep the assembly in a 50℃ oven for at least 10 minutes. Load the180ul target hybridization mix into the assembly through the sample loading opening. Fill up the hybridization space with 1X Hybridization buffer till the liquid level reaches to approximately 5 mm (0.5cm) away from the top rim.Cut the second Hyb. Bag to approximately one-half of its original length.Keep the assembly vertical and slip on the shortened hyb. bag from step 11 all the way until the assembly reaches the end of the hyb. bag.Use a pair of forceps to hold onto the top of the assembly. Immerse the entire assembly into 95℃ hot water with the assembly in upright position.Place the hybridization assembly into a 56℃ oven and set it on a rotator. Remember to rotate the assembly at 2 rotations per minute (RPM) for overnight.After hybridization, disassembled the hybridization assembly, and wash the slides at 56℃ for 2min. using Wash buffer A.Wash briefly at room temperature in Wash buffer B.Wash for 2min. at room temperature in Wash buffer B.Wash for 2min. at room temperature in Wash buffer C.Wash briefly in water.Dry the slides by centrifugation for 5 min. at 200* g(1000rpm).

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

data_processing: The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged.b) We use Median Normalization Method to obtain “Normalized Data”, Normalized Data= (Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 30 in all samples after background correction. After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test. Unsupervised hierarchical clustering and Correlation analysis was performed on miRNA data.

molecule: total RNA

source_name: Control without Hirschsprung's Disease

label_protocol: One ug total RNA was diluted in 3ul H2O and then combined with 0.5ul Calf Intestine Phosphartase (CIP) buffer and 0.5ul CIP enzyme in an RNase-free microcentrifuge tube and should be mixed by pipetting up and down to ensure that all reagents are mixed thoroughly. Incubate 30 min.at 37℃, using a PCR cycler with heated lid. Stop the enzyme reaction and denaturate the RNA by incubation at 95℃ followed by snap cooling on ice. Leave on ice for at least 2 min. Briefly spin the reaction after incubation on ice. Four ul CIP reaction from the above reaction mixed with 3ul Labeling buffer, 1.5ul Fluorescent label(Hy3), 2ul DMSO and 2ul Labeling enzyme. Mix the reagents by gentle vortexing or by pipetting up and down to ensure that all reagents are mixed thoroughly. Incubate at 16°C for 1hour, using a PCR cycler with heated lid. Protect the reaction from light. Incubate for 15 min. at 65°C. After stopping the labeling procedure, briefly spin the reaction and leave it at 4°C. The labeled sample is now ready for hybridization on the array. Hybridization on the array. Hybridization should preferably occur within 1-2h.

extract_protocol: Six stenotic colon segment samples, three control samples (anastomotic normal colon segments) from HSCR patients, and three normal colon tissues from subjects without HSCR  prepared for the extraction of total RNA. Cryopulverizated of tissue using the Biopulverizer and homogenization using the Mini-Bead-Beater-16,  the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization. Transfer the upper, aqueous phase to a new collection tube. Add 1.5 volume of 100% ethanol, and mix thoroughly by pipitting up and down several times. Do not centrifuge. 4. Pipet up to 700 μl of the sample, including any precipitate that may have formed, into an RNeasy Mini spin column in a 2 ml collection tube. Close the lid gently, and centrifuge for 15 s at ≥8000 x g at room temperature. Discard the flow-through. 5. Add 700ul Buffer RWT to the RNeasy Mini spin column. Close the lid gently and centrifuge for 15s at ≥8000 x g at room temperature to wash the column. Discard the flow-through.  Add 500 μl Buffer RPE to the spin column. Close the lid gently, and centrifuge for 15 s at ≥8000 x g to wash the spin column membrane. Discard the flow-through.Add another 500ul Buffer RPE onto the spin column. Close the lid gently and centrifuge for 2min at ≥8000 x g to dry the RNeasy Mini spin column membrane.Place the RNeasy Mini spin column into a new 2ml collection tube, and discard the old collection tube with the flow-through. Centrifuge in a microcentrifuge at full speed for 1min.Transfer the RNeasy Mini spin column to a new 1.5ml collection tube. Pipet 20ul RNase-free water directly onto the RNeasy Mini spin column membrane. Close the lid gently and centrifuge for 1min at ≥8000 x g to elute the RNA.

tag: tissue

value: colon

tag: segment

value: normal colon segments from patient without Hirschsprung's Disease

value: 9 months


title: Control 2 Control 002

description: Replicated miRNAs were averaged and miRNAs that intensities>=40 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

value: 1 year


title: Control 1 Control 001

description: Replicated miRNAs were averaged and miRNAs that intensities>=39 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

value: 3 years


title: Patient 3 HSCR 003 (anastomotic normal colon)

description: Replicated miRNAs were averaged and miRNAs that intensities>=38 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

source_name: Hirschsprung's Disease

value: anastomotic normal colon segments from Hirschsprung's Disease patient

value: 1 year 3 months


title: PF_Female gametocyte D12_Rep1

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

country: USA

institute: University of South Florida

description:
raw data file: SG12454250_254853210016_S001_GE2_1105_Oct12_1_3.txt (Cy5 channel)
This sample is of Plasmodium falciparum female gametocyte at stage V. It is the first of two biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by Genomics Core Facility of Pennsylvania State University according to the manufacturer’s instructions (Agilent).

scan_protocol: Scanning was performed by Genomics Core Facility of Pennsylvania State University by using Axon GenePix 4000B.

data_processing: The raw data was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in DNASTAR software-ArrayStar 11 (dnastar.com).

organism: Plasmodium falciparum

source_name: Plasmodium falciparum, female gametocyte, D12, Rep1

label_protocol: Labeling was done by Genomics Core Facility of Pennsylvania State Univerity. Amplify 1ug of each sample using the Ambion (Life Technologies) Amino Allyl MessageAmp II aRNA Amplification Kit. Dye couple 15 ug of aRNA with Cy3 or Cy5 (GE Health Care #RPN5661), as appropriate, and subsequently purify according to the Ambion Kit instructions.(AM1753).

growth_protocol:
P. falciparum parasites were maintained as described previously (Trager and Jensen, 1976)
Induction of gametocytogenesis was performed as described (Fivelman et al., 2007).  Gametocytes were harvested at  Day 12 (stage V).

extract_protocol: The male and female gametocytes were separated by cell-sorter based on GFP intensity. Total RNA was extracted using the Trizol reagent (invirtogen.com)

tag: strain

value: Day 12

tag: cell type

value: gametocyte


title: PF_male gametocyte D12_Rep1

description:
raw data file: SG12454250_254853210016_S001_GE2_1105_Oct12_1_3.txt (Cy3 channel)
This sample is of Plasmodium falciparum male gametocyte at stage V. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: Plasmodium falciparum, male gametocyte, D12, Rep1


title: Patient 1 HSCR 001 (anastomotic normal colon)

description: Replicated miRNAs were averaged and miRNAs that intensities>=36 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

value: 3 years 4 months


title: Patient 6 HSCR 006

description: Replicated miRNAs were averaged and miRNAs that intensities>=35 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

value: stenotic colon segment from Hirschsprung's Disease patient

value: 3 years 1 months


title: Patient 2 HSCR 002 (anastomotic normal colon)

description: Replicated miRNAs were averaged and miRNAs that intensities>=37 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

value: 6 months

value: Male


title: 53

description: Muestra 56

value: Late-Onset Colorectal cancer

value: Not applicable


title: 54

description: Muestra 57

value: Female

value: Human Genomic DNA, Male, Promega, Madison, WI, USA


title: Patient 2 HSCR 002

description: Replicated miRNAs were averaged and miRNAs that intensities>=31 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

value: colon

value: 6 month


title: Patient 3 HSCR 003

description: Replicated miRNAs were averaged and miRNAs that intensities>=32 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.


title: Patient 4 HSCR 004

description: Replicated miRNAs were averaged and miRNAs that intensities>=33 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

value: 1 year 6 months


title: 50

description: Muestra 53


title: Patient 5 HSCR 005

description: Replicated miRNAs were averaged and miRNAs that intensities>=34 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.

value: 8 months


title: 49

description: Muestra 52

value: Human Genomic DNA, Female, Promega, Madison, WI, USA


title: 52

description: Muestra 55


title: Patient 1 HSCR 001

description: Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization.


title: 51

description: Muestra 54


title: 45

description: Muestra 48


title: 48

description: Muestra 51


title: 44

description: Muestra 47


title: 47

description: Muestra 50-


title: 43

description: Muestra 46


title: 46

description: Muestra 49


title: 59

description: Muestra 62


title: 40

description: Muestra 43-


title: 55

description: Muestra 58


title: P1_MRD

city: Pamplona

first: Bruno

last: Paiva

address: Av. Pio XII, 55

institute: Clinica Universidad de Navarra

description: Multiple Myeloma Plasma Cells. Sample 15. Minimal Residual Disease.

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: primary data description: Weighted Log2 Ratios from ChAS console

label: biotin

source_name: Bone marrow

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix

extract_protocol: Genomic DNA was digested with Nsp I and Sty I restriction enzymes, ligated to adapters with T4 DNA ligase and amplified. PCR products were concentrated and fragmented (DNAsal), and then end-labeled with deoxynucleotidil transferase

treatment_protocol: A total of 40 elderly, transplant-ineligible patients with newly-diagnosed symptomatic MM staged according to the International Myeloma Working Group criteria 24 were prospectively studied after inclusion in the GEM2010MAS65 trial. In all patients, bone marrow (BM) aspirates were collected at diagnosis and after 9 cycles of induction therapy. In brief, patients treatment consisted of bortezomib, melphalan, prednisone (VMP) and lenalidomide plus low-dose dexamethasone (Rd), given in a sequential (n=21) or alternating (n=19) manner.

tag: tumor

value: Multiple myeloma

tag: sample type

value: Minimal Residual Disease

value: Clonal Plasma Cells


title: 42

description: Muestra 45


title: 39

description: Muestra 42


title: 41

description: Muestra 44


title: 36

description: Muestra 38-


title: 38

description: Muestra 41


title: P7_MRD

description: Multiple Myeloma Plasma Cells. Sample 14. Minimal Residual Disease.


title: P1_D

description: Multiple Myeloma Plasma Cells. Sample 15. Diagnosis.

value: Diagnosis


title: P7_D

description: Multiple Myeloma Plasma Cells. Sample 14. Diagnosis.


title: 35

description: Muestra 37


title: 34

description: Muestra 36-


title: 32

description: Muestra 34


title: 31

description: Muestra 33


title: 37

description: Muestra 40


title: P6_MRD

description: Multiple Myeloma Plasma Cells. Sample 11. Minimal Residual Disease.


title: P6_D

description: Multiple Myeloma Plasma Cells. Sample 11. Diagnosis.


title: 30

description: Muestra 32-


title: 29

description: Muestra 31


title: P3_MRD

description: Multiple Myeloma Plasma Cells. Sample 10. Minimal Residual Disease.


title: P3_D

description: Multiple Myeloma Plasma Cells. Sample 10. Diagnosis.


title: P4_MRD

description: Multiple Myeloma Plasma Cells. Sample 8. Minimal Residual Disease.


title: 33

description: Muestra 35


title: 27

description: Muestra 29


title: 26

description: Muestra 28


title: 25

description: Muestra 27-


title: P2_MRD

description: Multiple Myeloma Plasma Cells. Sample 6. Minimal Residual Disease.


title: 28

description: Muestra 30


title: 24

description: Muestra 26


title: P5_MRD

description: Multiple Myeloma Plasma Cells. Sample 5. Minimal Residual Disease.


title: P5_D

description: Multiple Myeloma Plasma Cells. Sample 5. Diagnosis.


title: 21

description: Muestra 23


title: 20

description: Muestra 22


title: P8_MRD

description: Multiple Myeloma Plasma Cells. Sample 1. Minimal Residual Disease.


title: P2_D

description: Multiple Myeloma Plasma Cells. Sample 6. Diagnosis.


title: P8_D

description: Multiple Myeloma Plasma Cells. Sample 1. Diagnosis.


title: 18

description: Muestra 20


title: 22

description: Muestra 24


title: 23

description: Muestra 25


title: 19

description: Muestra 21


title: 13

description: Muestra 15


title: P15_MRD

hyb_protocol: Labeled RNA was hybridized to Human Gene 1.0 ST Array

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing:
Expression value for each probe set was calculated using Affymetrix Expression Console that uses RMA (Robust Multi-Array Average) algorithm.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: Tumors were extracted and cells were collected. Total RNA from disgregated cells was extracted using Buffer RLT plus (Qiagen, CA, USA) and purified with All prep DNA/RNA mini Kit (Qiagen, CA, USA).


title: 15

description: Muestra 17


title: 14

description: Muestra 16


title: 12

description: Muestra 14


title: P15_DCO


title: 16

description: Muestra 18


title: 11

description: Muestra 13-


title: 17

description: Muestra 19


title: P14_MRD


title: P14_DCO


title: P11_DCO


title: P10_MRD


title: P11_MRD


title: 10

description: Muestra 12


title: P10_DCO


title: 7

description: Muestra 9


title: 9

description: Muestra 11


title: P8_MRD


title: 5

description: Muestra 6


title: 8

description: Muestra 10


title: 6

description: Muestra 8


title: P8_DCO

description: Multiple Myeloma Plasma Cells. Sample 8. Diagnosis.


title: P7_DCO

description: Multiple Myeloma Plasma Cells. Sample 7. Diagnosis.


title: P7_MRD

description: Multiple Myeloma Plasma Cells. Sample 7. Minimal Residual Disease.


title: 2

description: Muestra 3


title: samples collected from U87 ROCK1 KD after 24h (rep 1)

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

country: United Kingdom

institute: University of Birmingham

hyb_protocol: RNA was hybridized using the Agilent hybridization protocol

scan_protocol: Agilent Technologies Scanner G2505C US92200305

data_processing: data was read and quantile normalized

source_name: U87 cells

label_protocol: RNA was labelled using the Agilent LIQA-Quickamp Protocol

growth_protocol: U87 cells were grown in a dish until 70% confluency

extract_protocol: RNA was extracted using Qiagen (Valencia, CA) RNeasy columns

treatment_protocol: siRNA reverse transfection using lipofectamine RNAimax in U87 cells

tag: cell line

tag: treatment

value: ROCK KD

tag: time


title: samples collected from U87 ROCK1 KD after 24h (rep 2)


title: samples collected from U87 RhoE KD after 24h (rep 3)

value: RhoE KD


title: 4

description: Muestra 5


title: samples collected from U87 ROCK1 KD after 24h (rep 3)


title: samples collected from U87 NSC after 24h (ROCK control rep 2)

value: control


title: samples collected from U87 NSC after 24h (ROCK control rep 3)


title: P4_D


title: samples collected from U87 NSC after 48h (rep 1)


title: samples collected from U87 NSC after 24h (ROCK control rep 1)


title: P12_D

data_processing:
ChAS console from Affymetrix was used to assess genome wide copy number frequencies
Weighted Log2 Ratios from ChAS console


title: P4_MRD

description: Multiple Myeloma Plasma Cells. Sample 4. Minimal Residual Disease.


title: samples collected from U87 NSC after 24h (rep 3)


title: samples collected from U87 RhoE KD after 24h (rep 2)


title: samples collected from U87 NSC after 24h (rep 2)


title: P10_MRD


title: samples collected from U87 RhoE KD after 48h (rep 1)


title: 3

description: Muestra 4

value: Male


title: samples collected from U87 RhoE KD after 24h (rep 1)


title: 1

description: Muestra 2

value: Late-Onset Colorectal cancer


title: P12_MRD


title: H_RT-PCR 43

city: London

first: Silvana

last: Debernardi

address: Charterhouse Square

department: Molecular Oncology

institute: Barts Cancer Institute

description: circulating smallRNA

hyb_protocol: Hybridization to the GeneChip microRNA array, staining, washing and scanning was performed according to standard protocols on Affymetrix workstation.

scan_protocol: GeneChip® Scanner 3000 7G

data_processing: Raw data files were first analyzed with the Expression Console Software v 1.2 (Affymetrix);

source_name: Urine

label_protocol: 100ng of LMW RNAs were labeled using FlashTag Biotin HSR RNA Labeling Kit according to the manufacturer’s protocol (www.affymetrix.com).

extract_protocol: LMW RNAs (<200bp) were extracted from 3-5 ml of cryopreserved urine, using the Urine microRNA Purification Kit from NORGEN, followed by concentration with RNAstable (Biomatrica).

tag: disease state

value: Healthy

value: F


title: P11_MRD


title: P9_MRD


title: P10_D


title: H_RT-PCR 39

description: circulating smallRNA


title: H_RT-PCR 38

description: circulating smallRNA

value: M


title: H_RT-PCR 37

description: circulating smallRNA


title: H_RT-PCR 32B, RNA extraction 2, rep2

description: circulating smallRNA


title: H_RT-PCR 32C, RNA extraction 3

description: circulating smallRNA


title: samples collected from U87 NSC after 24h (rep 1)


title: H_RT-PCR 32B, RNA extraction 2, rep1

description: circulating smallRNA


title: CP_RT-PCR 28

description:
circulating smallRNA
ETOH Chronic Pancreatitis

value: CP


title: CP_RT-PCR 21

description:
circulating smallRNA
Autoimmune pancreatitis


title: CP_RT-PCR 20

description:
circulating smallRNA
Chronic pancreatitis


title: CP_RT-PCR 31

description:
circulating smallRNA
Recurrent acute pancreatitis


title: CP_RT-PCR 27

description:
circulating smallRNA
Chronic calcific pancreatitis


title: PDAC_RT-PCR 101

description: circulating smallRNA

value: PDAC

tag: tumor stage

value: Stage IA

tag: tnm


title: H_RT-PCR 32A, RNA extraction 1, rep2

description: circulating smallRNA

tag: gender

tag: age


title: H_RT-PCR 42

description: circulating smallRNA


title: H_RT-PCR 32A, RNA extraction 1, rep1

description: circulating smallRNA


title: CP_RT-PCR 30

description:
circulating smallRNA
Cystic lesion in pancreas


title: PDAC_RT-PCR 14

description: circulating smallRNA

value: Stage IV


title: PDAC_RT-PCR 15

description: circulating smallRNA


title: PDAC_RT-PCR 17

description:
circulating smallRNA
metastatic


title: PDAC_RT-PCR 12

description: circulating smallRNA


title: P9_D


title: P11_D


title: Shoot, Mut, Zn++, Rep3

city: Vairao

first: Antonio

last: Muñoz

state: Porto

address: Rua Padre Armando Quintas, 7 (Campus Agrario)

country: Portugal

institute: CIBIO-InBIO (University of Porto)

hyb_protocol: Samples were hybridized to the ATH1 gene chip for 16 h, as recommended by the supplier (Gene expression analysis manual; Affymetrix).

scan_protocol: GenChips were scanned using the GeneChip Scanner 3000 7G

data_processing: Raw data files were processed in Bioconductor/R using packages Affy and Limma. Background correction and quantile normalization were performed using the Robust Multichip Average (RMA) function.

organism: Arabidopsis thaliana

source_name: Shoots_Zn mutant_high levels of Zinc

label_protocol: Targets were prepared with the one-cycle cDNA synthesis kit followed by biotin-labeling with the IVT labeling kit (GeneChip One-cycle target labeling and control reagents; Affymetrix).

growth_protocol: Arabidopsis thaliana ecotype Columbia (Col-0), and an Arabidopsis T-DNA insertion double mutant (bzip19 bzip23, were grown in a climate chamber with a long day photoperiod (16 h light at 22°C, 8 h dark at 20°C), at 120 μmol photon m−2 s−1, and 50% relative humidity. Before germination, seeds were subjected to a 3-day stratification treatment in a cold room at 4°C, in the dark, to promote uniform germination. Seeds were sown onto 0.55% (w/v) agar-filled microtubes, and grown in hydropony on a modified half-strength Hoagland’s nutrient solution containing 2 μM ZnSO4 (Zn+). The hydroponic system consisted of 8-L-capacity containers (46×31×8 cm), with a non-translucent 3-mm-thick plastic lid containing holes for placement of agar-filled tubes. Three plants were grown in each container. The nutrient solution was replaced once in the first week, and twice a week in weeks thereafter.

extract_protocol: RNA was extracted with the RNeasy Plant Mini kit (Qiagen). For cDNA synthesis, 1 μg of total RNA was used as starting material.

treatment_protocol: The two genotypes, i.e. wild-type (Col-0) and double mutant (bzip19 bzip23), were grown for three weeks with normal zinc supply (Zn+, 2 μM ZnSO4) and then one week with low (Zn-, 0.05 μM ZnSO4), normal (Zn+) or excess zinc supply (Zn++, 25 μM ZnSO4). For each genotype and treatment (Zn-/Zn+/Zn++), roots or shoots of six plants (two containers) were pooled.

tag: ecotype

value: Columbia (Col-0)

tag: genotype/variation

value: double mutant bzip19 bzip23

value: 4 weeks old

tag: zinc level

value: excess zinc supply (Zn++, 25 μM ZnSO4)

value: Shoots


title: PDAC_RT-PCR 11

description: circulating smallRNA

value: Stage IB


title: PDAC_RT-PCR 8

description: circulating smallRNA

value: Stage II


title: PDAC_RT-PCR 10

description: circulating smallRNA


title: Shoot, Mut, Zn++, Rep2

tag: tissue


title: PDAC_RT-PCR 1

description: circulating smallRNA


title: PDAC_RT-PCR 7

description: circulating smallRNA


title: PDAC_RT-PCR 6

description: circulating smallRNA


title: PDAC_RT-PCR 5

description: circulating smallRNA


title: P4_DCO

description: Multiple Myeloma Plasma Cells. Sample 4. Diagnosis.

value: Multiple myeloma

value: Diagnosis

value: Clonal Plasma Cells


title: Shoot, WT, Zn++, Rep3

source_name: Shoots_wild type_high levels of Zinc

value: wild type


title: Shoot, WT, Zn++, Rep2


title: normal-3

city: Seoul

first: Bongkun

last: Choi

address: Olympic-ro 43-gil

department: Department of Biomedical Sciences

country: South Korea

institute: Asan Medical Center, University of Ulsan College of Medicine

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Gene 2.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: aortic valve

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

extract_protocol: Protocol not provided

tag: diagnosis

value: normal

tag: tissue type

value: aortic valve


title: Shoot, WT, Zn++, Rep1


title: Shoot, Mut, Zn-, Rep1

source_name: Shoots_Zn mutant_low levels of Zinc

value: low zinc supply (Zn-, 0.05 μM ZnSO4)


title: calcified-3

value: calcific aortic valve disease (CAVD)


title: Shoot, WT, Zn+, Rep3

source_name: Shoots_wild type_normal levels of Zinc

value: normal zinc supply (Zn+, 2 μM ZnSO4)


title: normal-6


title: calcified-8


title: calcified-2


title: Shoot, Mut, Zn-, Rep2


title: Shoot, Mut, Zn+, Rep2

source_name: Shoots_Zn mutant_normal levels of Zinc


title: Shoot, Mut, Zn++, Rep1


title: Shoot, WT, Zn+, Rep1


title: Shoot, WT, Zn-, Rep3

source_name: Shoots_wild type_low levels of Zinc


title: Shoot, Mut, Zn+, Rep1


title: Shoot, Mut, Zn-, Rep3


title: Shoot, Mut, Zn+, Rep3


title: Shoot, WT, Zn-, Rep2


title: normal-2


title: Shoot, WT, Zn+, Rep2


title: H_RT-PCR 41

description: circulating smallRNA

value: Healthy

value: F


title: Root, Mut, Zn++, Rep4

source_name: Roots_Zn mutant_high levels of Zinc

value: Columbia (Col-0)

value: double mutant bzip19 bzip23

value: Roots


title: Root, Mut, Zn++, Rep3

value: 4 weeks old

value: excess zinc supply (Zn++, 25 μM ZnSO4)


title: Root, WT, Zn++, Rep3

source_name: Roots_wild type_high levels of Zinc


title: Shoot, WT, Zn-, Rep1

value: Shoots


title: Root, WT, Zn++, Rep2


title: Root, WT, Zn++, Rep1


title: Root, Mut, Zn++, Rep1


title: Root, WT, Zn++, Rep4


title: Root, Mut, Zn+, Rep4

source_name: Roots_Zn mutant_normal levels of Zinc


title: Root, Mut, Zn+, Rep3


title: Root, Wt, Zn+, Rep4

source_name: Roots_wild type_normal levels of Zinc


title: Root, Wt, Zn+, Rep2


title: Root, Mut, Zn+, Rep2


title: Root, Wt, Zn+, Rep3


title: Root, Wt, Zn+, Rep1


title: Root, Mut, Zn+, Rep1


title: Root, Mut, Zn-, Rep4

source_name: Roots_Zn mutant_low levels of Zinc


title: Root, Mut, Zn-, Rep3


title: Root, Mut, Zn-, Rep2


title: Root, WT, Zn- ,Rep3

source_name: Roots_wild type_low levels of Zinc


title: Root, Mut, Zn-, Rep1


title: Root, WT, Zn-, Rep4


title: Dhp1-1_rep2

city: Canberra

first: Tamas

last: Fischer

state: ACT

address: Building 131, Garran Rd

department: The John Curtin School of Medical Research

country: Australia

institute: The Australian National University

hyb_protocol: Hybridization, blocking, and washing was performed following the Agilent instructions

scan_protocol: Scanning of arrays was performed using Agilent DNA Microarray Scanner and Agilent Scan control software (v A.8.4.1.)

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) Protocol: GE2_107_Sep09 with modifications; Background Substraction Method - Local Background; Detrend on Replicates Only - False; Robust Neg Ctrl Stats? - True; Choose universal error, or the most conservative - Use Universal Error Model; Dye Normalization Probe Selection Method/Variable Rank Tolerance - True; Max Number Ranked Probes - -1; Normalization Correction Method - Lowess Only; Spikein Target Used - False p-value filtering (p<=0.05) and background filtering (BG=median of negative control probes for green channel and red channel, probes with gProcessedSignal < 2x gBG AND rProcessedSignal < 2x rBG are filtered out) Filtered probes value set to 1

organism: Schizosaccharomyces pombe

source_name: rRNA depleted RNA of Dhp1-1

label_protocol: The cDNAs from WT and mutant strains were labeled with Cy3(WT) and Cy5(mutant) (GE Healthcare)

growth_protocol: 30ºC liquid cultures grown to log phase in full media (YEA)

extract_protocol: Ribosomal RNA was depleted from total RNA extracts of all strains using a mixture of 5' biotinylated rRNA probes. The rRNA-depleted samples were reverse transcribed to cDNA using the SuperScriptTM Indirect cDNA labeling system (Life Technologies) with anchored oligo(dT)20 and random hexamers.

treatment_protocol: RNA was isolated from either wildtype strains or deletion mutants using TRI Reagent (Sigma Aldrich) following the manufacturers instructions

tag: strain

source_name: rRNA depleted RNA of wildtype

value: wildtype


title: din1∆

source_name: rRNA depleted RNA of din1∆


title: Root, WT, Zn-, Rep2


title: Dhp1-1_rep1


title: Root, WT, Zn-, Rep1


title: Mm_CNS_MB-SHH (MM12_ARN0014)

status: Public on Jan 27 2016

city: Paris

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

country: France

institute: Institut Curie

hyb_protocol: Hybridization performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

scan_protocol: Scanning were performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

data_processing: Arrays were normalized by the GCRMA procedure using Brainarray annotations (V.16.0.0, ENTREZG)

organism: Mus musculus

source_name: Medulloblastoma Shh mouse tumor

label_protocol: According to the standard Affymetrix protocol

extract_protocol: Total RNAs were collected from samples using the miRNeasy kit (Qiagen) according to the manufacturer's instructions


title: Mm_CNS_MB-SHH (MM18_ARN0008)


title: Mm_CNS_Smarcb1def-Tumor (MM31_ARN0012)

source_name: Smarcb1-deficient Brain tumor mouse tumor


title: Mm_CNS_Smarcb1def-Tumor (MM31_ARN0017)


title: Mm_CNS_Smarcb1def-Tumor (MM31_ARN0005)


title: Mm_CNS_Smarcb1def-Tumor (MM31_ARN0013)


title: Mm_CNS_Smarcb1def-Tumor (MM31_ARN0006)


title: Mm_CNS_MB-SHH (MM12_ARN0013)


title: Mm_CNS_Smarcb1def-Tumor (MM31_ARN0010)


title: Mm_CNS_Smarcb1def-Tumor (MM31_ARN0001)


title: Mm_soft-tissue_Smarcb1def-T-Cell_Lymphoma (MM18_ARN0011)

source_name: Smarcb1-deficient T-Cell lymphoma mouse tumor


title: Mm_CNS_Smarcb1def-Tumor (MM31_ARN0004)


title: Mm_soft-tissue_Smarcb1def-T-Cell_Lymphoma (MM18_ARN0010)


title: Root, Mut, Zn++, Rep2


title: T3

city: Changwon

first: Gi Cheol

last: Park

address: Samsung Changwon Hospital, 158, Paryong-ro, MasanHoewon-Gu

department: Otolaryngology-Head and Neck Surgery

institute: Samsung Changwon Hospital, Sungkyunkwan University School of Medicine

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0). Analysis also performed with R 2.15.1 (www.r-project.org). Detection p-value > 0.05 was considered above background while <= 0.05 was considered below background. Probes with <= 0.05 detection p-value in more than 50% of the samples were considered low quality. Raw data were log2 transformed and quantile normalized.

source_name: palatine tonsil

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use.

value: palatine tonsil

value: Male


title: Mm_soft-tissue_Smarcb1def-T-Cell_Lymphoma (MM18_ARN0006)


title: A1

source_name: abdominal fat

value: abdominal fat

value: Female


title: Mm_soft-tissue_Smarcb1def-T-Cell_Lymphoma (MM18_ARN0002)


title: B3

source_name: BM

value: bone marrow


title: T2


title: Mm_soft-tissue_Smarcb1def-T-Cell_Lymphoma (MM18_ARN0003)


title: Mm_soft-tissue_Smarcb1def-T-Cell_Lymphoma (MM18_ARN0004)


title: T1


title: B4


title: B1

source_name: bone marrow (iliac crest)

value: bone marrow (iliac crest)


title: B2


title: A4


title: A3


title: T4


title: A2


title: Mm_soft-tissue_Smarcb1def-T-Cell_Lymphoma (MM12_ARN0005)


title: Mm_soft-tissue_Smarcb1def-T-Cell_Lymphoma (MM12_ARN0006)


title: Mm_soft-tissue_Smarcb1def-T-Cell_Lymphoma (MM12_ARN0002)


title: Mm_soft-tissue_Smarcb1def-T-Cell_Lymphoma (MM18_ARN0001)


title: Mm_soft-tissue_Smarcb1def-T-Cell_Lymphoma (MM12_ARN0004)


title: Mm_soft-tissue_Smarcb1def-T-Cell_Lymphoma (MM12_ARN0003)


title: Mm_soft-tissue_Smarcb1def-T-Cell_Lymphoma (MM12_ARN0008)


title: Mm_soft-tissue_Smarcb1def-T-Cell_Lymphoma (MM12_ARN0001)


title: Mm_soft-tissue_Smarcb1def-T-Cell_Lymphoma (MM12_ARN0007)


title: genomic DNA from DF.iPSC.283.79.E

first: Lee

last: Butcher

address: 72 Huntley Street

institute: University College London

description: batch = 3, Sentrix_ID = 9704031125, Sentrix_Position = R04C02

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner settings

data_processing: ChAMP analysis pipeline [T. J. Morris et al., Bioinformatics (2013)]

label: Cy5 and Cy3

source_name: iPSC

label_protocol: Standard Illumina Protocol

growth_protocol: see L. Vallier et al., Stem Cells (2009) for details

extract_protocol: batch = 1 | 2: Sigma GenElute Mammalian DNA Miniprep Kit; batch = 3; Qiagen AllPrep DNA/RNA Mini Kit

tag: donor id

tag: cell line #

tag: donor cell type

value: dermal fibroblast

tag: reprogramming method

value: episomal

tag: Sex

value: male

tag: replicate #

tag: differentiation capacity

value: HDC


title: genomic DNA from EB.iPSC.447.64.S

description: batch = 3, Sentrix_ID = 9704031163, Sentrix_Position = R02C01

treatment_protocol: see L. Vallier et al., Stem Cells (2009) for details

value: erythroblast

value: Sendai virus


title: genomic DNA from DF-700_5

description: batch = 1, Sentrix_ID = 6042316019, Sentrix_Position = R03C02

source_name: dermal fibroblast


title: genomic DNA from DF.iPSC.447.39.E

description: batch = 3, Sentrix_ID = 9704031163, Sentrix_Position = R05C01

value: LDC


title: genomic DNA from EB.iPSC.283.78.S

description: batch = 3, Sentrix_ID = 9704031163, Sentrix_Position = R04C01


title: genomic DNA from DF.iPSC.983.15.E

description: batch = 3, Sentrix_ID = 9704031163, Sentrix_Position = R05C02

value: female


title: genomic DNA from DF-700_3

description: batch = 1, Sentrix_ID = 6042308004, Sentrix_Position = R04C02


title: genomic DNA from DF-852_5

description: batch = 2, Sentrix_ID = 7766130080, Sentrix_Position = R05C01


title: genomic DNA from EB.iPSC.685.68.S

description: batch = 3, Sentrix_ID = 9704031125, Sentrix_Position = R05C02


title: genomic DNA from DF-263_1

description: batch = 2, Sentrix_ID = 7766130107, Sentrix_Position = R05C02


title: genomic DNA from DF-700_2

description: batch = 1, Sentrix_ID = 5911874002, Sentrix_Position = R02C02


title: genomic DNA from DF-627_3

description: batch = 1, Sentrix_ID = 6042308004, Sentrix_Position = R02C01


title: genomic DNA from FF-832_5

description: batch = 1, Sentrix_ID = 6042316019, Sentrix_Position = R01C02

source_name: foreskin fibroblast

value: foreskin fibroblast


title: genomic DNA from DF-852_4

description: batch = 2, Sentrix_ID = 7766130097, Sentrix_Position = R05C02


title: genomic DNA from FF-832_2

description: batch = 1, Sentrix_ID = 5911874001, Sentrix_Position = R03C02


title: genomic DNA from DF-627_2

description: batch = 1, Sentrix_ID = 6042316068, Sentrix_Position = R06C01


title: genomic DNA from DF-852_3

description: batch = 2, Sentrix_ID = 7766130079, Sentrix_Position = R06C01


title: genomic DNA from FF-832_4

description: batch = 1, Sentrix_ID = 5911874019, Sentrix_Position = R04C01


title: genomic DNA from DF-263_4

description: batch = 2, Sentrix_ID = 7766130145, Sentrix_Position = R05C01


title: genomic DNA from FF-832_3

description: batch = 1, Sentrix_ID = 6042308024, Sentrix_Position = R05C01


title: genomic DNA from DF-700_1

description: batch = 1, Sentrix_ID = 6042316020, Sentrix_Position = R04C01


title: genomic DNA from EB.iPSC.844.53.S

description: batch = 3, Sentrix_ID = 9704031163, Sentrix_Position = R01C01


title: genomic DNA from DF-263_2

description: batch = 2, Sentrix_ID = 7766130108, Sentrix_Position = R05C02


title: genomic DNA from DF-852_1

description: batch = 2, Sentrix_ID = 7766130106, Sentrix_Position = R05C01


title: genomic DNA from DF-852_2

description: batch = 2, Sentrix_ID = 7766130106, Sentrix_Position = R02C01


title: genomic DNA from DF-263_3

description: batch = 2, Sentrix_ID = 7766130079, Sentrix_Position = R01C02


title: bmMSC2

city: Leiden

first: Danielle

last: Leuning

address: Albinusdreef 2

department: Nephrology

country: Netherlands

institute: LUMC

hyb_protocol: cDNA and cRNA synthesis, labeling and subsequent hybridization on the Human HT12 V4 Gene Expression Beadchips (Illumina Inc., San Diego, USA) were performed according to manufacturer’s protocols.

scan_protocol: Standard Illumina scanning protocol;The beadchips, targeting more than 47000 gene transcripts, were scanned using iSCAN system (Illumina Inc., San Diego, USA) and fluorescence intensities were uploaded into GenomeStudio Software (Illumina Inc, San Diego, USA)

data_processing: Genes with a detection p-value of >0.05 for all samples were excluded. Subsequent data was quantile normalized in Genome Studio. Differential expression was analyzed using the gene expression module of Genome Studio (Illumina).

growth_protocol: Human bmMSCs and kPSCs were grown in 5% platelet lysates

extract_protocol: RNA was isolated from biological triplicates using Trizol reagent (Life Technologies, Bleiswijk, the Netherlands) and the RNeasy kit (Qiagen, Heidelberg, Germany) according to the manufacturer’s protocol. The quality and quantity of RNA was assessed using a Nanodrop

treatment_protocol: Cells were grown untill passage 5-7. No specific treatments were applied.

tag: cell type

value: bone marrow mesenchymal stem cells


title: bmMSC3

label_protocol: cDNA and cRNA synthesis, labeling and subsequent hybridization on the Human HT12 V4 Gene Expression Beadchips (Illumina Inc., San Diego, USA) were performed according to manufacturer’s protocols.


title: genomic DNA from DF-700_4

description: batch = 1, Sentrix_ID = 6042316019, Sentrix_Position = R04C01


title: genomic DNA from FF-832_1

description: batch = 1, Sentrix_ID = 6042316068, Sentrix_Position = R05C01


title: kPSC3

value: human kidney derived perivascular stromal cells


title: genomic DNA from FF-832_6

description: batch = 1, Sentrix_ID = 5911874002, Sentrix_Position = R04C01


title: bmMSC1


title: kPSC2


title: genomic DNA from EP-230_5

description: batch = 1, Sentrix_ID = 5911874019, Sentrix_Position = R06C01

source_name: endothelial precursor

value: endothelial precursor


title: genomic DNA from DF-263_5

description: batch = 2, Sentrix_ID = 7766130095, Sentrix_Position = R04C02


title: Liver_mouse_WT_vehicle_rep6

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description:
A410_H5_LIVER_8_WT_VEHICLE.CEL
Liver tissue from wild-type mouse treated with vehicle (1% methyl cellulose) by oral gavage for 7 days.

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.34.0).

source_name: liver, wild-type, vehicle for 7 days

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Male C57BL/6 wild-type (WT) and FXR-/- mice [PMID: 11030617] were housed in a room with controlled temperature (20-24°C), relative humidity (55%±15%) and a 12h light dark cycle. Mice were fed chow and demineralized water ad libitum.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: At the age of 9-12 weeks, mice received a daily oral gavage with the semi-synthetic FXR agonist obeticholic acid (OCA, INT-747, 6α-ethyl-chenodeoxycholic acid; 10 mg/kg/day), or vehicle (1% methyl cellulose) for 7 days. Livers were then isolated, snap frozen in liquid nitrogen, and stored at -80°C.

tag: strain/background

value: wild type

tag: gender

value: liver

tag: treatment

value: vehicle (1% methyl cellulose)

tag: time point

value: 7 days


title: Liver_mouse_FXRKO_vehicle_rep6

description:
A410_H7_LIVER_34_FXRKO_VEHICLE.CEL
Liver tissue from FXR knockout mouse treated with vehicle (1% methyl cellulose) by oral gavage for 7 days.

source_name: liver, FXR knockout, vehicle for 7 days

tag: genotype/variation

value: FXR KO


title: genomic DNA from EP-230_4

description: batch = 1, Sentrix_ID = 5911874002, Sentrix_Position = R06C02


title: Liver_mouse_WT_vehicle_rep5

description:
A410_G5_LIVER_7_WT_VEHICLE.CEL
Liver tissue from wild-type mouse treated with vehicle (1% methyl cellulose) by oral gavage for 7 days.

tag: tissue


title: Liver_mouse_FXRKO_vehicle_rep5

description:
A410_G7_LIVER_29_FXRKO_VEHICLE.CEL
Liver tissue from FXR knockout mouse treated with vehicle (1% methyl cellulose) by oral gavage for 7 days.


title: Liver_mouse_FXRKO_INT747_rep6

description:
A410_H9_LIVER_44_FXRKO_INT747_2.CEL
Liver tissue from FXR knockout mouse treated with the FXR agonist OCA (INT-747) (10 mg/kg/day, dissolved in 1% methyl cellulose) by oral gavage for 7 days.

source_name: liver, FXR knockout, FXR agonist OCA (INT-747) for 7 days


title: Liver_mouse_FXRKO_vehicle_rep4

description:
A410_F7_LIVER_28_FXRKO_VEHICLE.CEL
Liver tissue from FXR knockout mouse treated with vehicle (1% methyl cellulose) by oral gavage for 7 days.


title: Liver_mouse_FXRKO_INT747_rep4

description:
A410_F9_LIVER_42_FXRKO_INT747.CEL
Liver tissue from FXR knockout mouse treated with the FXR agonist OCA (INT-747) (10 mg/kg/day, dissolved in 1% methyl cellulose) by oral gavage for 7 days.


title: Liver_mouse_FXRKO_INT747_rep3

description:
A410_E9_LIVER_41_FXRKO_INT747_2.CEL
Liver tissue from FXR knockout mouse treated with the FXR agonist OCA (INT-747) (10 mg/kg/day, dissolved in 1% methyl cellulose) by oral gavage for 7 days.


title: Liver_mouse_FXRKO_INT747_rep5

description:
A410_G9_LIVER_43_FXRKO_INT747_2.CEL
Liver tissue from FXR knockout mouse treated with the FXR agonist OCA (INT-747) (10 mg/kg/day, dissolved in 1% methyl cellulose) by oral gavage for 7 days.


title: Liver_mouse_FXRKO_vehicle_rep3

description:
A410_E7_LIVER_26_FXRKO_VEHICLE.CEL
Liver tissue from FXR knockout mouse treated with vehicle (1% methyl cellulose) by oral gavage for 7 days.


title: kPSC1


title: genomic DNA from EP-230_3

description: batch = 1, Sentrix_ID = 5911874001, Sentrix_Position = R05C01


title: genomic DNA from DF-230_5

description: batch = 1, Sentrix_ID = 6042308024, Sentrix_Position = R04C02

value: dermal fibroblast


title: Liver_mouse_WT_INT747_rep5

description:
A410_E5_LIVER_5_WT_INT747.CEL
Liver tissue from wild-type mouse treated with the FXR agonist OCA (INT-747) (10 mg/kg/day, dissolved in 1% methyl cellulose) by oral gavage for 7 days.

source_name: liver, wild-type, FXR agonist OCA (INT-747) for 7 days


title: Liver_mouse_FXRKO_INT747_rep2

description:
A410_D9_LIVER_40_FXRKO_INT747.CEL
Liver tissue from FXR knockout mouse treated with the FXR agonist OCA (INT-747) (10 mg/kg/day, dissolved in 1% methyl cellulose) by oral gavage for 7 days.


title: Liver_mouse_WT_INT747_rep6

description:
A410_F5_LIVER_6_WT_INT747.CEL
Liver tissue from wild-type mouse treated with the FXR agonist OCA (INT-747) (10 mg/kg/day, dissolved in 1% methyl cellulose) by oral gavage for 7 days.


title: genomic DNA from DF-230_3

description: batch = 1, Sentrix_ID = 6042308009, Sentrix_Position = R01C02


title: genomic DNA from EP-230_1

description: batch = 1, Sentrix_ID = 5911874001, Sentrix_Position = R05C02


title: Liver_mouse_WT_vehicle_rep3

description:
A410_C7_LIVER_11_WT_VEHICLE.CEL
Liver tissue from wild-type mouse treated with vehicle (1% methyl cellulose) by oral gavage for 7 days.


title: genomic DNA from DF-230_6

description: batch = 1, Sentrix_ID = 6042316020, Sentrix_Position = R05C01


title: genomic DNA from DF-230_2

description: batch = 1, Sentrix_ID = 6042308004, Sentrix_Position = R03C01


title: Liver_mouse_WT_INT747_rep4

description:
A410_D5_LIVER_4_WT_INT747_2.CEL
Liver tissue from wild-type mouse treated with the FXR agonist OCA (INT-747) (10 mg/kg/day, dissolved in 1% methyl cellulose) by oral gavage for 7 days.


title: genomic DNA from DF-230_4

description: batch = 1, Sentrix_ID = 6042308003, Sentrix_Position = R02C02


title: Liver_mouse_FXRKO_vehicle_rep2

description:
A410_B9_LIVER_36_FXRKO_VEHICLE.CEL
Liver tissue from FXR knockout mouse treated with vehicle (1% methyl cellulose) by oral gavage for 7 days.


title: genomic DNA from DF-230_1

description: batch = 1, Sentrix_ID = 6042308004, Sentrix_Position = R01C02


title: genomic DNA from EP-230_2

description: batch = 1, Sentrix_ID = 6042308003, Sentrix_Position = R05C01


title: Liver_mouse_WT_vehicle_rep2

description:
A410_B7_LIVER_10_WT_VEHICLE.CEL
Liver tissue from wild-type mouse treated with vehicle (1% methyl cellulose) by oral gavage for 7 days.


title: Liver_mouse_FXRKO_INT747_rep1

description:
A410_C9_LIVER_39_FXRKO_INT747.CEL
Liver tissue from FXR knockout mouse treated with the FXR agonist OCA (INT-747) (10 mg/kg/day, dissolved in 1% methyl cellulose) by oral gavage for 7 days.


title: genomic DNA from DF-iPSC-367-32-R_1

description: batch = 2, Sentrix_ID = 7766130133, Sentrix_Position = R03C01

value: retorviral

value: high


title: genomic DNA from DF-iPSC-367-32-R_5

description: batch = 2, Sentrix_ID = 7766130106, Sentrix_Position = R02C02

value: male


title: Liver_mouse_WT_INT747_rep2

description:
A410_B5_LIVER_2_WT_INT747.CEL
Liver tissue from wild-type mouse treated with the FXR agonist OCA (INT-747) (10 mg/kg/day, dissolved in 1% methyl cellulose) by oral gavage for 7 days.


title: genomic DNA from FF-iPSC-832-44-R_6

description: batch = 1, Sentrix_ID = 5911874019, Sentrix_Position = R05C02


title: Liver_mouse_WT_vehicle_rep4

description:
A410_D7_LIVER_12_WT_VEHICLE.CEL
Liver tissue from wild-type mouse treated with vehicle (1% methyl cellulose) by oral gavage for 7 days.


title: Liver_mouse_FXRKO_vehicle_rep1

description:
A410_A9_LIVER_35_FXRKO_VEHICLE.CEL
Liver tissue from FXR knockout mouse treated with vehicle (1% methyl cellulose) by oral gavage for 7 days.


title: Liver_mouse_WT_vehicle_rep1

description:
A410_A7_LIVER_9_WT_VEHICLE.CEL
Liver tissue from wild-type mouse treated with vehicle (1% methyl cellulose) by oral gavage for 7 days.


title: Liver_mouse_WT_INT747_rep1

description:
A410_A5_LIVER_1_WT_INT747.CEL
Liver tissue from wild-type mouse treated with the FXR agonist OCA (INT-747) (10 mg/kg/day, dissolved in 1% methyl cellulose) by oral gavage for 7 days.


title: genomic DNA from FF-iPSC-832-44-R_5

description: batch = 1, Sentrix_ID = 6042308004, Sentrix_Position = R06C01


title: genomic DNA from DF-iPSC-367-32-R_6

description: batch = 2, Sentrix_ID = 7766130102, Sentrix_Position = R02C01


title: genomic DNA from FF-iPSC-832-44-R_4

description: batch = 1, Sentrix_ID = 6042308009, Sentrix_Position = R01C01


title: genomic DNA from DF-iPSC-367-32-R_4

description: batch = 2, Sentrix_ID = 7766130003, Sentrix_Position = R05C02


title: genomic DNA from ESC-H9_6

description: batch = 1, Sentrix_ID = 6042316019, Sentrix_Position = R04C02

source_name: ESC

value: embryonic stem cell


title: genomic DNA from FF-iPSC-832-44-R_3

description: batch = 1, Sentrix_ID = 5911874002, Sentrix_Position = R05C02


title: Liver_mouse_WT_INT747_rep3

description:
A410_C5_LIVER_3_WT_INT747.CEL
Liver tissue from wild-type mouse treated with the FXR agonist OCA (INT-747) (10 mg/kg/day, dissolved in 1% methyl cellulose) by oral gavage for 7 days.


title: genomic DNA from ESC-H9_5

description: batch = 1, Sentrix_ID = 6042308024, Sentrix_Position = R06C01


title: genomic DNA from FF-iPSC-832-44-R_1

description: batch = 1, Sentrix_ID = 6042308004, Sentrix_Position = R01C01


title: genomic DNA from ESC-H9_4

description: batch = 1, Sentrix_ID = 5911874002, Sentrix_Position = R05C01


title: genomic DNA from DF-iPSC-367-32-R_3

description: batch = 2, Sentrix_ID = 7766130106, Sentrix_Position = R06C01


title: genomic DNA from DF-iPSC-700-62-S_5

description: batch = 2, Sentrix_ID = 7766130147, Sentrix_Position = R01C01

value: Sendai virus


title: genomic DNA from DF-iPSC-367-32-R_2

description: batch = 2, Sentrix_ID = 7766130128, Sentrix_Position = R03C01


title: genomic DNA from ESC-H9_2

description: batch = 1, Sentrix_ID = 6042316019, Sentrix_Position = R02C02


title: genomic DNA from DF-iPSC-700-62-S_3

description: batch = 2, Sentrix_ID = 7766130108, Sentrix_Position = R04C02


title: genomic DNA from DF-iPSC-700-62-S_4

description: batch = 2, Sentrix_ID = 7766130079, Sentrix_Position = R01C01


title: genomic DNA from DF-iPSC-700-62-S_2

description: batch = 2, Sentrix_ID = 7766130056, Sentrix_Position = R03C01


title: genomic DNA from ESC-H9_1

description: batch = 1, Sentrix_ID = 5911874002, Sentrix_Position = R01C02


title: genomic DNA from EPC-iPSC-700-54-S_5

description: batch = 2, Sentrix_ID = 7766130133, Sentrix_Position = R04C02

value: endothelial progenitor


title: genomic DNA from EPC-iPSC-700-54-S_2

description: batch = 2, Sentrix_ID = 7766130056, Sentrix_Position = R01C01


title: genomic DNA from EP-iPSC-700-54-S_6

description: batch = 2, Sentrix_ID = 7766130128, Sentrix_Position = R05C02


title: genomic DNA from FF-iPSC-832-44-R_2

description: batch = 1, Sentrix_ID = 6042316020, Sentrix_Position = R02C02


title: genomic DNA from EPC-iPSC-700-54-S_4

description: batch = 2, Sentrix_ID = 7766130079, Sentrix_Position = R03C01


title: genomic DNA from EPC-iPSC-700-59-R_5

description: batch = 2, Sentrix_ID = 7766130147, Sentrix_Position = R01C02


title: genomic DNA from DF-iPSC-700-62-S_1

description: batch = 2, Sentrix_ID = 7766130147, Sentrix_Position = R04C02


title: genomic DNA from DF-iPSC-700-47-R_1

description: batch = 1, Sentrix_ID = 5911874019, Sentrix_Position = R05C01


title: genomic DNA from DF-iPSC-700-47-R_3

description: batch = 1, Sentrix_ID = 6042308009, Sentrix_Position = R04C02


title: genomic DNA from EPC-iPSC-700-59-R_3

description: batch = 2, Sentrix_ID = 7766130097, Sentrix_Position = R06C01


title: genomic DNA from EPC-iPSC-700-54-S_3

description: batch = 2, Sentrix_ID = 7766130102, Sentrix_Position = R01C02


title: genomic DNA from EPC-iPSC-700-59-R_4

description: batch = 2, Sentrix_ID = 7766130077, Sentrix_Position = R04C01


title: genomic DNA from EPC-iPSC-700-59-R_6

description: batch = 2, Sentrix_ID = 7766130105, Sentrix_Position = R06C01


title: genomic DNA from DF-iPSC-700-47-R_5

description: batch = 1, Sentrix_ID = 6042308003, Sentrix_Position = R04C01


title: genomic DNA from EPC-iPSC-700-54-S_1

description: batch = 2, Sentrix_ID = 7766130080, Sentrix_Position = R02C01


title: genomic DNA from DF-iPSC-700-47-R_6

description: batch = 1, Sentrix_ID = 5911874001, Sentrix_Position = R01C01


title: genomic DNA from EP-iPSC-700-89-R_3

description: batch = 1, Sentrix_ID = 6042316019, Sentrix_Position = R06C01


title: genomic DNA from EPC-iPSC-700-59-R_2

description: batch = 2, Sentrix_ID = 7766130056, Sentrix_Position = R06C02


title: genomic DNA from EPC-iPSC-700-59-R_1

description: batch = 2, Sentrix_ID = 7766130108, Sentrix_Position = R01C01


title: genomic DNA from DF-iPSC-700-47-R_4

description: batch = 1, Sentrix_ID = 6042308003, Sentrix_Position = R03C01


title: NC_MCF7_JHU_PPT_5nM_8h_NC200539_R1

city: Santa Clara

first: Rick

middle: A

last: Fasani

state: CA

address: 5301 Stevens Creek Blvd

institute: Agilent Technologies

description: Gene expression in MCF-7, exposed to PPT, 5nM, 8h

hyb_protocol: Probes were hybridized to Agilent SurePrint G3 human whole genome 8x60K microarray (Agilent) following manufacture’s protocol.

scan_protocol: Microarrays were scanned with an Agilent microarray scanner.

data_processing: Images were processed using Feature Extraction software, version 11.5.1.1 (Agilent).

label_protocol: cRNA probes were synthesized and Cy3 labeled using Agilent LowInput QuickAmp Labeling Kit (Agilent) from 100 ng of total RNA. After purification, RNA probe concentration and dye incorporation were measured using NanoDrop ND-1000 spectrophotometer.

growth_protocol: MCF-7 cells were seeded at a density of 300,000 cells/well in 6-well plates and allowed to grow for 72 hours in complete growth medium composed of DMEM/F12 media supplemented with 10% fetal bovine serum (FBS, Atlanta Biologicals, Flowery Branch, GA), non-essential amino acids, 10µg/mL bovine insulin and gentamicin.

extract_protocol: Total RNA from MCF-7 cells was extracted using TRIzol Reagent (Sigma Aldrich, no. T9424) according to manufacturer’s instruction, and purified using RNeasy Mini Kit (Qiagen). Purified RNA was quantified by using NanoDrop ND-1000 spectrophotometer and the quality of RNA was analyzed by using Agilent Bioanalyzer (Agilent).

treatment_protocol: After 72 hours, cells were rinsed with PBS and placed in treatment medium composed of DMEM/F12 supplemented with 5% dextran charcoal stripped fetal bovine serum (DCC, Gemini Bio-products, Sacramento, CA, US, no. 100-119), nonessential amino acids, 6ng/mL bovine insulin and gentamicin for 48 hours. Cells were then exposed to 0.01 nM, 0.1 nM or 1nM 17β estradiol (E2, SigmaAldrich, St. Louis, MO, USA, no. E8875), 5 nM propyl pyrazole triol (PPT, Tocris, Minneapolis, MN, USA, no 1426) or vehicle control (dimethylsulfoxide , DMSO, Sigma Aldrich, no. D8418) in fresh treatment medium for 4 or 8 hours.

tag: cell line

tag: lab

value: JHU

value: PPT


title: NC_MCF7_JHU_PPT_5nM_8h_NC200540_R1


title: NC_MCF7_JHU_PPT_5nM_8h_NC200538_R1


title: genomic DNA from DF-iPSC-700-13-R_4

description: batch = 1, Sentrix_ID = 6042308024, Sentrix_Position = R02C01


title: genomic DNA from DF-iPSC-700-13-R_2

description: batch = 1, Sentrix_ID = 6042308003, Sentrix_Position = R06C02


title: genomic DNA from EP-iPSC-700-89-R_5

description: batch = 1, Sentrix_ID = 6042316019, Sentrix_Position = R01C01


title: genomic DNA from DF-iPSC-700-13-R_3

description: batch = 1, Sentrix_ID = 6042308004, Sentrix_Position = R03C02


title: NC_MCF7_JHU_PPT_5nM_4h_NC200529_R1

description: Gene expression in MCF-7, exposed to PPT, 5nM, 4h


title: NC_MCF7_JHU_PPT_5nM_4h_NC200530_R1


title: genomic DNA from DF-iPSC-700-47-R_2

description: batch = 1, Sentrix_ID = 5911874002, Sentrix_Position = R04C02


title: genomic DNA from DF-iPSC-700-13-R_1

description: batch = 1, Sentrix_ID = 6042308003, Sentrix_Position = R05C02


title: NC_MCF7_JHU_PPT_5nM_4h_NC200531_R1


title: genomic DNA from EP-iPSC-700-89-R_1

description: batch = 1, Sentrix_ID = 5911874002, Sentrix_Position = R03C01


title: genomic DNA from DF-iPSC-700-25-R_6

description: batch = 1, Sentrix_ID = 6042316020, Sentrix_Position = R03C02


title: genomic DNA from DF-iPSC-700-13-R_6

description: batch = 1, Sentrix_ID = 6042316020, Sentrix_Position = R04C02


title: genomic DNA from DF-iPSC-700-13-R_5

description: batch = 1, Sentrix_ID = 5911874019, Sentrix_Position = R02C01


title: genomic DNA from DF-iPSC-700-25-R_3

description: batch = 1, Sentrix_ID = 6042308009, Sentrix_Position = R02C01


title: genomic DNA from EP-iPSC-700-89-R_2

description: batch = 1, Sentrix_ID = 6042308009, Sentrix_Position = R05C02


title: genomic DNA from DF-iPSC-700-25-R_5

description: batch = 1, Sentrix_ID = 5911874019, Sentrix_Position = R06C02


title: genomic DNA from DF-iPSC-700-25-R_4

description: batch = 1, Sentrix_ID = 6042316020, Sentrix_Position = R03C01


title: NC_MCF7_JHU_PPT_0nM_8h_NC200534_R1

description: Gene expression in MCF-7, exposed to PPT, 0nM, 8h


title: NC_MCF7_JHU_PPT_0nM_8h_NC200533_R1


title: genomic DNA from DF-iPSC-700-25-R_1

description: batch = 1, Sentrix_ID = 6042316019, Sentrix_Position = R05C02


title: genomic DNA from DF-iPSC-627-36-R_6

description: batch = 1, Sentrix_ID = 6042308009, Sentrix_Position = R04C01

value: female


title: genomic DNA from DF-iPSC-700-25-R_2

description: batch = 1, Sentrix_ID = 6042308009, Sentrix_Position = R02C02


title: genomic DNA from DF-iPSC-627-46-R_5

description: batch = 1, Sentrix_ID = 5911874001, Sentrix_Position = R01C02


title: NC_MCF7_JHU_PPT_0nM_8h_NC200532_R1


title: genomic DNA from DF-iPSC-627-36-R_4

description: batch = 1, Sentrix_ID = 6042308004, Sentrix_Position = R06C02


title: genomic DNA from DF-iPSC-627-36-R_3

description: batch = 1, Sentrix_ID = 6042316019, Sentrix_Position = R03C01


title: NC_MCF7_JHU_PPT_0nM_4h_NC200524_R1

description: Gene expression in MCF-7, exposed to PPT, 0nM, 4h


title: genomic DNA from DF-iPSC-627-36-R_1

description: batch = 1, Sentrix_ID = 5911874002, Sentrix_Position = R01C01


title: NC_MCF7_BU_PPT_5nM_8h_NC100425_R1

description: Gene expression in MCF-7, exposed to PPT, 5nM, 8h

value: BU


title: NC_MCF7_JHU_PPT_0nM_4h_NC200525_R1


title: genomic DNA from DF-iPSC-627-36-R_2

description: batch = 1, Sentrix_ID = 6042316020, Sentrix_Position = R01C01


title: NC_MCF7_JHU_PPT_0nM_4h_NC200523_R1


title: genomic DNA from DF-iPSC-627-46-R_4

description: batch = 1, Sentrix_ID = 6042316068, Sentrix_Position = R01C01


title: NC_MCF7_BU_PPT_5nM_4h_NC100419_R1

description: Gene expression in MCF-7, exposed to PPT, 5nM, 4h


title: NC_MCF7_BU_PPT_5nM_8h_NC100423_R1


title: genomic DNA from DF-iPSC-627-36-R_5

description: batch = 1, Sentrix_ID = 5911874002, Sentrix_Position = R06C01


title: NC_MCF7_BU_PPT_5nM_4h_NC100417_R1


title: NC_MCF7_BU_PPT_0nM_8h_NC100421_R1


title: genomic DNA from DF-iPSC-627-46-R_6

description: batch = 1, Sentrix_ID = 6042308024, Sentrix_Position = R02C02


title: NC_MCF7_BU_PPT_5nM_4h_NC100418_R1


title: NC_MCF7_BU_PPT_0nM_8h_NC100422_R1


title: NC_MCF7_BU_PPT_5nM_8h_NC100424_R1


title: NC_MCF7_BU_PPT_0nM_4h_NC100416_R1


title: NC_MCF7_BU_PPT_0nM_4h_NC100415_R1


title: genomic DNA from DF-iPSC-627-46-R_2

description: batch = 1, Sentrix_ID = 6042308024, Sentrix_Position = R04C01


title: NC_MCF7_BU_PPT_0nM_4h_NC100414_R1


title: NC_MCF7_JHU_E2_1nM_8h_NC200536_R1

description: Gene expression in MCF-7, exposed to E2, 1nM, 8h


title: NC_MCF7_JHU_E2_1nM_8h_NC200535_R1


title: NC_MCF7_BU_PPT_0nM_8h_NC100420_R1

description: Gene expression in MCF-7, exposed to PPT, 0nM, 8h


title: NC_MCF7_JHU_E2_1nM_8h_NC200537_R1


title: genomic DNA from DF-iPSC-627-10-R_4

description: batch = 1, Sentrix_ID = 6042316019, Sentrix_Position = R06C02


title: genomic DNA from DF-iPSC-627-10-R_3

description: batch = 1, Sentrix_ID = 6042308003, Sentrix_Position = R01C02


title: NC_MCF7_BU_E2_1nM_8h_NCBU-36_R2


title: genomic DNA from DF-iPSC-852-94-R_4

description: batch = 2, Sentrix_ID = 7766130056, Sentrix_Position = R05C02

value: low


title: genomic DNA from DF-iPSC-627-46-R_3

description: batch = 1, Sentrix_ID = 6042316020, Sentrix_Position = R06C02


title: genomic DNA from DF-iPSC-627-10-R_1

description: batch = 1, Sentrix_ID = 6042308004, Sentrix_Position = R05C01


title: NC_MCF7_BU_E2_1nM_8h_NCBU-35_R1


title: genomic DNA from DF-iPSC-852-94-R_6

description: batch = 2, Sentrix_ID = 7766130079, Sentrix_Position = R04C01


title: genomic DNA from DF-iPSC-852-94-R_2

description: batch = 2, Sentrix_ID = 7766130147, Sentrix_Position = R03C02


title: genomic DNA from DF-iPSC-852-94-R_5

description: batch = 2, Sentrix_ID = 7766130095, Sentrix_Position = R01C02


title: NC_MCF7_BU_E2_1nM_8h_NCBU-36_R1


title: genomic DNA from DF-iPSC-627-10-R_5

description: batch = 1, Sentrix_ID = 6042316020, Sentrix_Position = R06C01


title: NC_MCF7_BU_E2_1nM_8h_NCBU-34_R1


title: genomic DNA from DF-iPSC-852-87-R_4

description: batch = 2, Sentrix_ID = 7766130107, Sentrix_Position = R05C01


title: NC_MCF7_BU_E2_1nM_8h_NCBU-36_R3


title: genomic DNA from DF-iPSC-627-10-R_6

description: batch = 1, Sentrix_ID = 5911874002, Sentrix_Position = R03C02


title: genomic DNA from DF-iPSC-852-87-R_6

description: batch = 2, Sentrix_ID = 7766130080, Sentrix_Position = R06C01


title: genomic DNA from DF-iPSC-627-46-R_1

description: batch = 1, Sentrix_ID = 5911874019, Sentrix_Position = R01C02


title: genomic DNA from DF-iPSC-852-87-R_3

description: batch = 2, Sentrix_ID = 7766130147, Sentrix_Position = R02C02


title: genomic DNA from DF-iPSC-852-94-R_3

description: batch = 2, Sentrix_ID = 7766130133, Sentrix_Position = R02C01


title: NC_MCF7_BU_E2_0nM_8h_NC100185_R1

description: Gene expression in MCF-7, exposed to E2, 0nM, 8h


title: NC_MCF7_BU_E2_0nM_8h_NC100183_R1


title: genomic DNA from DF-iPSC-852-87-R_5

description: batch = 2, Sentrix_ID = 7766130108, Sentrix_Position = R05C01


title: NC_MCF7_BU_E2_0nM_8h_NC100186_R1


title: NC_MCF7_BU_E2_0nM_8h_NC100182_R3


title: genomic DNA from DF-iPSC-852-94-R_1

description: batch = 2, Sentrix_ID = 7766130105, Sentrix_Position = R03C02


title: HCC line infected with pLKO-shKLF6; Infection 3

city: Worcester

first: Brian

middle: C

last: Lewis

state: Massachusetts

address: 364 Plantation Street; LRB 521

department: PGFE

institute: University of Massachusetts Medical School

hyb_protocol: GeneChip Hybridization Oven 320

scan_protocol: GeneChip Scanner 3000

data_processing: RMA method in Affy package from Bioconductor was used in R to summarize the probe level data and normalize

source_name: HCC cell line

label_protocol: Affymetrix 3' IVT Express Kit

growth_protocol: HCC cells are grown in DMEM medium with 10%FBS

extract_protocol: RNA was isolated from selected cell lines using Trizol

treatment_protocol: HCC cells were infected with virus containing pLKO-shGFP or pLKO-shKLF6; This infection was repeated 3 times

value: hepatocellular carcinoma


title: genomic DNA from DF-iPSC-852-64-R_4

description: batch = 2, Sentrix_ID = 7766130003, Sentrix_Position = R06C02


title: NC_MCF7_BU_E2_0nM_8h_NC100184_R1


title: genomic DNA from DF-iPSC-852-87-R_2

description: batch = 2, Sentrix_ID = 7766130107, Sentrix_Position = R03C02


title: genomic DNA from DF-iPSC-852-64-R_6

description: batch = 2, Sentrix_ID = 7766130102, Sentrix_Position = R01C01


title: genomic DNA from DF-iPSC-852-64-R_5

description: batch = 2, Sentrix_ID = 7766130095, Sentrix_Position = R06C01


title: genomic DNA from DF-iPSC-852-64-R_3

description: batch = 2, Sentrix_ID = 7766130145, Sentrix_Position = R04C01


title: HCC line infected with pLKO-shKLF6; Infection 1


title: genomic DNA from DF-iPSC-627-10-R_7

description: batch = 1, Sentrix_ID = 6042308009, Sentrix_Position = R03C02


title: genomic DNA from DF-iPSC-263-55-R_4

description: batch = 2, Sentrix_ID = 7766130105, Sentrix_Position = R01C02


title: genomic DNA from DF-iPSC-263-55-R_2

description: batch = 2, Sentrix_ID = 7766130106, Sentrix_Position = R05C02


title: NC_MCF7_BU_E2_0nM_8h_NC100182_R2


title: HCC line infected with pLKO-shGFP; Infection 3


title: genomic DNA from DF-iPSC-852-64-R_2

description: batch = 2, Sentrix_ID = 7766130097, Sentrix_Position = R03C02


title: HCC line infected with pLKO-shGFP; Infection 1


title: genomic DNA from DF-iPSC-852-64-R_1

description: batch = 2, Sentrix_ID = 7766130105, Sentrix_Position = R05C02


title: NC_MCF7_BU_E2_0.1nM_8h_NC100214_R1

description: Gene expression in MCF-7, exposed to E2, 0.1nM, 8h


title: HCC line infected with pLKO-shKLF6; Infection 2


title: genomic DNA from DF-iPSC-263-55-R_3

description: batch = 2, Sentrix_ID = 7766130077, Sentrix_Position = R02C02


title: genomic DNA from DF-iPSC-852-87-R_1

description: batch = 2, Sentrix_ID = 7766130108, Sentrix_Position = R04C01


title: Subclone line, I1_2

source_name: HCC cell line_Subclone_line_I1

treatment_protocol: M1 and I1 cells are selected migratory subpopulations of the parent BL185 cell line

value: Hepatocellular carcinoma


title: HCC line infected with pLKO-shGFP; Infection 2


title: NC_MCF7_BU_E2_0.1nM_8h_NC100213_R1


title: Subclone line, I1_1


title: Subclone line, M1_2

source_name: HCC cell line_Subclone_line_M1


title: Parent line, BL185_1

source_name: HCC cell line_Parent_line_BL185


title: Ammonium vs nitrogen starvation

city: Córdoba

first: Victor M.

last: Luque

address: Edificio Severo Ochoa 1ª planta, Campus de Rabanales

department: Departamento de Bioquímica y Biología Molecular

institute: Universidad de Córdoba

description: Sample H

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5).

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

organism: Ectopseudomonas oleovorans CECT 5344

source_name: Ammonium chloride

label_protocol: Two-color microarray-based LowInput QuickAmp Labeling (Agilent)

growth_protocol: P. pseudoalcaligenes CECT5344 cells were cultured in minimal medium M9 with 50 mM acetate as carbon source and 2 mM ammonium chloride as nitrogen source. After 24 h, ammonium was depleted and different nitrogen sources (2 mM concentration) were added to independent cultures, including sodiun cyanide, a cyanurated jewelry wastewater and ammonium chloride. An experiment without added nitrogen source was also carried out. P. pseudoalcaligenes cells were grown at 30°C on a rotatory shaker at 220 rpm.

extract_protocol: Total RNA was extracted using the RNAeasy Midi Kit (Qiagen) and following manufacturer's instructions. DNase incubation was carried out in the column with RNase-free DNase set (Qiagen) and an additional post-column treatment was required with DNase I (Ambion). The concentration and purity of the RNA samples were measured by using a ND1000 spectrophotometer (Nanodrop Technologies).

treatment_protocol: P. pseudoalcaligenes cells were harvested and washed in TEG buffer containing 25 mM Tris-HCl (pH 8.0) with 1% glucose and 10 mM EDTA. Pellets were kept at -80 °C until use.

tag: nitrogen source

value: Ammonium chloride

tag: replicate

value: Biological replicate 4 of 4

source_name: Nitrogen starvation

value: none (Nitrogen starvation)


title: genomic DNA from DF-iPSC-263-55-R_1

description: batch = 2, Sentrix_ID = 7766130080, Sentrix_Position = R05C02

tag: donor id

tag: cell line #

value: dermal fibroblast


title: Nitrogen starvation vs wastewater

description: Sample F

value: Biological replicate 1 of 4

source_name: cyanide-containing wastewater

value: Jewelry wastewater (cyanide-containing wastewater)


title: NC_MCF7_BU_E2_0nM_8h_NC100182_R1

description: Gene expression in MCF-7, exposed to E2, 0nM, 8h


title: NC_MCF7_BU_E2_0.1nM_8h_NC100212_R1


title: Wastewater vs cyanide

description: Sample D

source_name: Sodium cyanide

value: Sodium cyanide


title: NC_MCF7_BU_E2_0.01nM_8h_NC100202_R1

description: Gene expression in MCF-7, exposed to E2, 0.01nM, 8h


title: Parent line, BL185_2


title: genomic DNA from DF-iPSC-263-92-R_5

description: batch = 2, Sentrix_ID = 7766130128, Sentrix_Position = R06C01

source_name: iPSC

tag: donor cell type

tag: reprogramming method

value: retorviral


title: Cyanide vs wastewater

description: Sample C

value: Biological replicate 3 of 4

value: Biological replicate 2 of 4


title: Nitrogen starvation vs ammonium

description: Sample G


title: NC_MCF7_BU_E2_0.1nM_8h_NC100211_R1


title: PCLS_subject 5_INT747_rep3

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.30.0).

source_name: precision-cut liver slices, after 24h incubation with obeticholic acid (OCA; INT-747)

growth_protocol: Liver biopsies were collected from obese patients undergoing bariatric surgery. After collection, biopsies were immediately placed in ice-cold oxygenated Belzer UW Cold Storage Solution and quickly transferred to the laboratory for further processing. 5 mm cylindrical liver cores were prepared with a surgical biopsy punch and sectioned to 200 μm slices using a Krumdieck tissue slicer.

extract_protocol: Total RNA was prepared from the liver slices using TRIzol reagent and purified using Qiagen RNeasy columns. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Liver slices were incubated in William's E Medium in 6-well plates at 37°C/5% CO2/80% O2 under continuous shaking (70 rpm). Duplicate wells were used per donor with 3 liver slices per well. After 1 hour, the media was replaced with fresh William's E Medium in the presence or absence of obeticholic acid (OCA, INT-747, 6α-ethyl-chenodeoxycholic acid) (1 μM) dissolved in dimethyl sulfoxide (DMSO, final concentration 0.1%). After 24 h incubation, liver slices were snap-frozen in liquid nitrogen and stored in -80°C for RNA isolation.

value: liver

value: 1 uM OCA (INT-747)

tag: age (yr)

tag: bmi


title: NC_MCF7_BU_E2_0.1nM_8h_NC100210_R1


title: Wastewater vs nitrogen starvation

description: Sample E


title: Ammonium vs cyanide

description: Sample B


title: Subclone line, M1_1

tag: cell type


title: Cyanide vs ammonium

description: Sample A


title: genomic DNA from DF-iPSC-263-92-R_4

description: batch = 2, Sentrix_ID = 7766130095, Sentrix_Position = R04C01

tag: Sex

value: female

tag: replicate #

tag: differentiation capacity


title: NC_MCF7_BU_E2_0.01nM_8h_NC100200_R1

value: BU

tag: treatment


title: PCLS_subject 5_DMSO_rep3

source_name: precision-cut liver slices, after 24h incubation with vehicle

value: vehicle (0.1% DMSO)

tag: time point

tag: gender


title: NC_MCF7_BU_E2_0.01nM_8h_NC100201_R1

tag: cell line


title: PCLS_subject 3_INT747_rep1

tag: tissue


title: PCLS_subject 4_INT747_rep2


title: genomic DNA from DF-iPSC-263-92-R_3

description: batch = 2, Sentrix_ID = 7766130116, Sentrix_Position = R03C01

value: low


title: IL-2_3, rep3

city: Bloomington

first: Rafael

middle: F

last: Guerrero

state: IN - Indiana

address: 1001 E 3rd St

department: Biology

institute: Indiana University

hyb_protocol: Standard

scan_protocol: Affy GCOS

data_processing: CEL files were processed using the rma() function from the Affy package in R, with default settings.

organism: Solanum lycopersicum x Solanum pennellii

source_name: Carpels seven days after pollination

label_protocol: Single cycle

growth_protocol: Standard greenhouse cultivation. Three-week seedlings were transferred to individual 3.75L pots, grown in climate-controlled facility. Watered daily, feritlized weekly

extract_protocol: Trizol, RNAeasy purification (Qiagen) following manufacturer's instructions

treatment_protocol: All plants were treated equally. Collected tissue was frozen in liquid nitrogen.

value: Carpel

tag: line


title: IL-2_3, rep4


title: PCLS_subject 3_DMSO_rep1


title: Hs_CNS_MB-SHH (hMB._.MB147)

source_name: Medulloblastoma SHH


title: genomic DNA from DF-iPSC-263-92-R_1

description: batch = 2, Sentrix_ID = 7766130079, Sentrix_Position = R02C01


title: PCLS_subject 4_DMSO_rep2


title: genomic DNA from DF-iPSC-973-92-R_6

description: batch = 2, Sentrix_ID = 7766130095, Sentrix_Position = R01C01


title: genomic DNA from DF-iPSC-263-92-R_6

description: batch = 2, Sentrix_ID = 7766130106, Sentrix_Position = R03C01


title: Hs_CNS_MB-SHH (hMB._.MB146)


title: IL-2_3, rep2


title: IL-2_3, rep1


title: IL-1_4, rep3


title: Hs_CNS_MB-SHH (hMB._.MB141)


title: IL-1_4, rep2


title: genomic DNA from DF-iPSC-263-92-R_2

description: batch = 2, Sentrix_ID = 7766130116, Sentrix_Position = R04C01


title: Hs_CNS_MB-SHH (hMB._.MB107)


title: IL-1_1, rep4


title: genomic DNA from DF-iPSC-973-92-R_5

description: batch = 2, Sentrix_ID = 7766130105, Sentrix_Position = R02C02


title: genomic DNA from DF-iPSC-973-92-R_4

description: batch = 2, Sentrix_ID = 7766130080, Sentrix_Position = R01C02


title: IL-1_4, rep1


title: genomic DNA from DF-iPSC-973-92-R_3

description: batch = 2, Sentrix_ID = 7766130147, Sentrix_Position = R05C01


title: IL-1_1, rep3


title: IL-1_1, rep2


title: genomic DNA from DF-iPSC-973-92-R_2

description: batch = 2, Sentrix_ID = 7766130097, Sentrix_Position = R05C01


title: NC_MCF7_BU_E2_0.1nM_8h_NC100209_R1

description: Gene expression in MCF-7, exposed to E2, 0.1nM, 8h

tag: lab


title: IL-1_1, rep1


title: Seed Control M82, rep6

organism: Solanum lycopersicum

value: parental


title: Seed Control M82, rep5


title: genomic DNA from DF-iPSC-657-48-R_2

description: batch = 2, Sentrix_ID = 7766130108, Sentrix_Position = R06C01

tag: donor id

value: male


title: genomic DNA from DF-iPSC-657-48-R_3

description: batch = 2, Sentrix_ID = 7766130003, Sentrix_Position = R02C02

tag: cell line #


title: Seed Control M82, rep4


title: Seed Control M82, rep1


title: Seed Control M82, rep3


title: IL-8_1_1,rep4

description: Gene expression data from anthers from introgression line IL-8_1

source_name: Anthers one day preanthesis

value: Anthers (pollen)


title: genomic DNA from DF-iPSC-973-92-R_1

description: batch = 2, Sentrix_ID = 7766130102, Sentrix_Position = R06C01

tag: donor cell type

value: dermal fibroblast


title: IL-8_1_1,rep3


title: IL-8_1_1,rep2


title: genomic DNA from DF-iPSC-657-19-R_5

description: batch = 2, Sentrix_ID = 7766130105, Sentrix_Position = R06C02

tag: reprogramming method


title: genomic DNA from DF-iPSC-657-48-R_4

description: batch = 2, Sentrix_ID = 7766130107, Sentrix_Position = R02C01


title: genomic DNA from DF-iPSC-657-48-R_6

description: batch = 2, Sentrix_ID = 7766130107, Sentrix_Position = R04C02


title: genomic DNA from DF-iPSC-657-19-R_6

description: batch = 2, Sentrix_ID = 7766130080, Sentrix_Position = R03C02


title: IL-8_1_1,rep1


title: genomic DNA from DF-iPSC-657-19-R_3

description: batch = 2, Sentrix_ID = 7766130145, Sentrix_Position = R03C02


title: genomic DNA from DF-iPSC-657-19-R_2

description: batch = 2, Sentrix_ID = 7766130105, Sentrix_Position = R03C01


title: IL-7_2, rep3

description: Gene expression data from anthers from introgression line IL-7_2


title: IL-7_2, rep4


title: genomic DNA from DF-iPSC-657-48-R_5

description: batch = 2, Sentrix_ID = 7766130080, Sentrix_Position = R03C01


title: genomic DNA from DF-iPSC-657-48-R_1

description: batch = 2, Sentrix_ID = 7766130147, Sentrix_Position = R03C01


title: genomic DNA from DF-iPSC-657-19-R_4

description: batch = 2, Sentrix_ID = 7766130128, Sentrix_Position = R03C02


title: genomic DNA from DF-iPSC-657-75-R_3

description: batch = 2, Sentrix_ID = 7766130133, Sentrix_Position = R05C01


title: IL-7_2, rep2


title: IL-7_2, rep1


title: genomic DNA from DF-iPSC-657-19-R_1

description: batch = 2, Sentrix_ID = 7766130102, Sentrix_Position = R05C02


title: Seed Control M82, rep2


title: IL-4_2, rep4

description: Gene expression data from anthers from introgression line IL-4_2


title: IL-4_2, rep2


title: genomic DNA from DF-iPSC-657-75-R_4

description: batch = 2, Sentrix_ID = 7766130056, Sentrix_Position = R04C01


title: IL-4_2, rep3


title: IL-4_2, rep1


title: genomic DNA from ESC-hSF6_4

description: batch = 2, Sentrix_ID = 7766130079, Sentrix_Position = R05C02

value: embryonic stem cell


title: genomic DNA from DF-iPSC-657-75-R_1

description: batch = 2, Sentrix_ID = 7766130108, Sentrix_Position = R02C01


title: genomic DNA from ESC-hSF6_5

description: batch = 2, Sentrix_ID = 7766130056, Sentrix_Position = R06C01


title: genomic DNA from EP-iPSC-230-57-R_5

description: batch = 1, Sentrix_ID = 6042316019, Sentrix_Position = R02C01

value: endothelial precursor


title: IL-1_1_3, rep2

description: Gene expression data from anthers from introgression line IL-1_1


title: IL-1_1_3, rep3


title: genomic DNA from ESC-FES22_1

description: batch = 1, Sentrix_ID = 6042316068, Sentrix_Position = R02C01


title: genomic DNA from ESC-FES22_3

description: batch = 1, Sentrix_ID = 6042316068, Sentrix_Position = R03C01


title: IL-1_1_3, rep1


title: genomic DNA from DF-iPSC-657-75-R_2

description: batch = 2, Sentrix_ID = 7766130108, Sentrix_Position = R03C01


title: Pollen Control M82, rep6

description: Gene expression data from anthers from domesticated tomato (control)


title: genomic DNA from ESC-hSF6_2

description: batch = 2, Sentrix_ID = 7766130080, Sentrix_Position = R01C01


title: genomic DNA from ESC-hSF6_3

description: batch = 2, Sentrix_ID = 7766130080, Sentrix_Position = R06C02


title: Pollen Control M82, rep5


title: Pollen Control M82, rep3


title: genomic DNA from ESC-hSF6_1

description: batch = 2, Sentrix_ID = 7766130102, Sentrix_Position = R05C01


title: Pollen Control M82, rep1


title: genomic DNA from ESC-FES22_2

description: batch = 1, Sentrix_ID = 5911874001, Sentrix_Position = R02C02


title: RA-16

city: Nijmegen

first: Mathijs

last: Broeren

address: Geert Grootplein 28

department: Department of Rheumatology

institute: Radboud university medical Center

hyb_protocol: Hybridization to U133Plus 2.0 was performed according to the Affymetrix Expression Analysis Technical Manual for two-cycle amplification.

scan_protocol: The arrays were scanned using a GeneChip Scanner (Affymetrix)

data_processing: The arrays were analyzed using Affymetrix GeneChip Operating Software version 1.4. Array normalization and expression value calculation were performed using DNA-Chip Analyzer version 1.3. The Invariant Set Normalization method and the model-based method were used for computing expression values.

source_name: RA, synovium

label_protocol: Biotinylated cRNA was generated according to the Affymetrix Expression Analysis Technical Manual for two-cycle amplification.

extract_protocol: Total RNA was isolated from the synovial samples using the Rneasy kit for fibrous tissue according the manufacturer's protocol (Qiagen, Venlo, Netherlands).

tag: disease state

value: Rheumatoid arthritis

value: synovium


title: Pollen Control M82, rep4


title: genomic DNA from EP-iPSC-230-57-R_6

description: batch = 1, Sentrix_ID = 6042308004, Sentrix_Position = R04C01

value: retorviral


title: Pollen Control M82, rep2


title: genomic DNA from DF-iPSC-230-25-R_5

description: batch = 1, Sentrix_ID = 6042308009, Sentrix_Position = R06C02


title: RA-15


title: genomic DNA from EP-iPSC-230-57-R_4

description: batch = 1, Sentrix_ID = 6042308003, Sentrix_Position = R04C02


title: RA-14


title: RA-13


title: H2-3° HARS category, 2nd day after irr., baboon 5

city: Munich

first: Michael

last: Abend

state: Bavaria

address: Neuherbergstr. 11

country: Germany

institute: Bundeswehr Institute of Radiobiology

hyb_protocol: Following cRNA clean-up and quantification 600 ng of each Cyanine-3-labeled cRNA sample was fragmented and prepared for one-color-based hybridization (Gene Expression Hybridization Kit, Agilent Technologies).  Labeled cRNA samples were hybridized at 65°C for 17 hrs on separate Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays (AMADID 039494).  Afterwards, microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).

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

data_processing:
The software tools Feature Extraction 10.7.3.1, GeneSpring GX 12.6 (both Agilent Technologies), Excel 2010 (Microsoft) and the IMGM internal tool marfin v1.8 were used for RS-280 21-Oct-2013 Page 11 of 75  quality control, statistical data analysis, filtering of differentially expressed transcript, RNA annotation and visualization.  Furthermore, the online tool VENNY (http://bioinfo.genotoul.fr/index.php?id=116) was applied for Venn analysis in order to elucidate overlaps of the effects of the two different shRNAs on gene expression.  PANTHER website, release 8.1 was used for functional analysis of differentially expressed genes. Quantile normalization was applied to the data set. After normalization, the microarray probes were filtered according to the flag information provided by Feature Extraction 10.7.3.1 software.
The non-parametric Mann Whitney (MW) test was used to compare gene expression across H1-2 and H2-3 groups employing H0-group as the reference (control). We did not adjust the p-values for multiple comparisons. Only those gene transcripts that had a call “present” in at least 50% of RNA specimens were included in the analysis of gene expression and only genes with MW p-values < 0.05 and a > 2-fold gene expression difference among compared groups were considered to represent a candidate gene for validation in phase II.

organism: Papio papio

source_name: peripheral whole blood

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

growth_protocol: Adult male baboons (average age: 8.1 years, +/- 3.3 years) weighing 23.7 + 5.2 kg were bred by the Centre National de la Recherche Scientifique (Rousset sur Arc, France). In the nonhuman primate facility of the French Army Biomedical Research Institute, baboons were placed in individual cages at 21°C, with a relative humidity of 55% and a 12h/12h light-dark schedule. The animals received fresh fruit and solid food twice a day, and had access to water ad libitum.

extract_protocol: Whole blood samples (2.5 ml) were processed following the PAXgene Blood RNA system (BD Diagnostics, PreAnalytiX GmbH, Hombrechtikon, Switzerland). In brief, blood was drawn into a PAXgene Blood RNA tube at the French Army Biomedical Research Institute. The tube was gently inverted (10 times), settled at room temperature overnight and stored at -20°. After collecting all samples needed the PaxGene tubes were sent to Germany for further processing. After thawing, washing and centrifugation, cells in the supernatant became lysed (Proteinase K) followed by adding Lysis/Binding Solution taken from the mirVana Kit (Life Technologies, Darmstadt, Germany). With the mirVana kit total RNA including small RNA species was isolated by combining a Phenol-Chloroform RNA precipitation with further processing using a silica membrane. After several washing procedures DNA residuals became digested on the membrane (RNAse free DNAse Set, Qiagen, Hilden, Germany), washed, RNA was eluted in a collection tube and frozen at -80°C. Quality and quantity of isolated total RNA were measured spectrophotometrically (NanoDrop, PeqLab Biotechnology, Erlangen, Germany). RNA integrity was assessed by the 2100 Agilent Bioanalyser (Life Science Group, Penzberg, Germany) and DNA contamination was controlled by conventional PCR using actin primer.

treatment_protocol: The animals were anesthetized before irradiation. Then, the baboons were placed in restraint chairs, sitting orthogonally, front to a horizontal and homogeneous field of gamma rays delivered by a 60Co source (IRDI 4000; Alsthom, Levallois, France) to perform either total body irradiation (TBI) or partial body irradiation (PBI). Equivalent whole body dose was either 2.5 Gy or 5 Gy.

value: peripheral whole blood

tag: hars category

value: H2-3 (medium-severe degree HARS)

tag: days after exposure

value: 2 days after exposure


title: RA-12


title: genomic DNA from EP-iPSC-230-57-R_2

description: batch = 1, Sentrix_ID = 5911874001, Sentrix_Position = R03C01

tag: Sex

value: female


title: H2-3° HARS category, 2nd day after irr., baboon 4


title: genomic DNA from DF-iPSC-230-25-R_6

description: batch = 1, Sentrix_ID = 6042308004, Sentrix_Position = R02C02

tag: replicate #


title: genomic DNA from EP-iPSC-230-57-R_3

description: batch = 1, Sentrix_ID = 5911874019, Sentrix_Position = R04C02

tag: differentiation capacity


title: RA-11


title: genomic DNA from DF-iPSC-230-25-R_3

description: batch = 1, Sentrix_ID = 6042316020, Sentrix_Position = R02C01


title: H2-3° HARS category, 2nd day after irr., baboon 3


title: genomic DNA from DF-iPSC-230-96-R_5

description: batch = 1, Sentrix_ID = 6042308003, Sentrix_Position = R03C02


title: genomic DNA from EP-iPSC-230-57-R_1

description: batch = 1, Sentrix_ID = 6042308009, Sentrix_Position = R06C01


title: RA-8


title: H2-3° HARS category, 2nd day after irr., baboon 1


title: genomic DNA from DF-iPSC-230-25-R_1

description: batch = 1, Sentrix_ID = 6042316020, Sentrix_Position = R01C02


title: H2-3° HARS category, 2nd day after irr., baboon 2


title: genomic DNA from DF-iPSC-230-25-R_2

description: batch = 1, Sentrix_ID = 5911874001, Sentrix_Position = R02C01


title: RA-7


title: Hs_CNS_MRT (hNA._.INI39)

source_name: Malignant Rhabdoid Tumor

value: MRT


title: H2-3° HARS category, 1st day after irr., baboon 3

value: 1 day after exposure


title: H2-3° HARS category, 1st day after irr., baboon 4


title: genomic DNA from DF-iPSC-230-96-R_1

description: batch = 1, Sentrix_ID = 6042308024, Sentrix_Position = R03C01

value: low


title: RA-5


title: RA-6


title: RA-9


title: genomic DNA from DF-iPSC-230-79-R_3

description: batch = 1, Sentrix_ID = 5911874002, Sentrix_Position = R02C01


title: H2-3° HARS category, 1st day after irr., baboon 5


title: genomic DNA from DF-iPSC-230-79-R_6

description: batch = 1, Sentrix_ID = 6042308009, Sentrix_Position = R05C01


title: genomic DNA from DF-iPSC-230-96-R_2

description: batch = 1, Sentrix_ID = 6042308009, Sentrix_Position = R03C01


title: RA-4


title: genomic DNA from DF-iPSC-230-79-R_5

description: batch = 1, Sentrix_ID = 6042308003, Sentrix_Position = R02C01


title: genomic DNA from DF-iPSC-230-79-R_2

description: batch = 1, Sentrix_ID = 6042308004, Sentrix_Position = R05C02


title: genomic DNA from DF-iPSC-230-25-R_4

description: batch = 1, Sentrix_ID = 6042308024, Sentrix_Position = R03C02


title: H2-3° HARS category, 1st day after irr., baboon 2


title: H2-3° HARS category, 1st day after irr., baboon 1


title: H1-2° HARS category, 2nd day after irr., baboon 3

value: H1-2 (low-medium degree HARS)


title: RA-3


title: HC-7

source_name: HC, synovium

value: Healthy control


title: RA-2


title: HC-6


title: H1-2° HARS category, 2nd day after irr., baboon 4

value: male


title: H1-2° HARS category, 2nd day after irr., baboon 1


title: H1-2° HARS category, 2nd day after irr., baboon 2


title: genomic DNA from DF-iPSC-230-79-R_1

description: batch = 1, Sentrix_ID = 5911874019, Sentrix_Position = R01C01


title: RA-1


title: H1-2° HARS category, 1st day after irr., baboon 4


title: H1-2° HARS category, 1st day after irr., baboon 3


title: genomic DNA from DF-iPSC-230-79-R_4

description: batch = 1, Sentrix_ID = 6042308024, Sentrix_Position = R01C01


title: genomic DNA from DF-iPSC-230-96-R_3

description: batch = 1, Sentrix_ID = 6042316020, Sentrix_Position = R05C02


title: HC-4


title: HC-3


title: HC-1


title: HC-2


title: H1-2° HARS category, 1st day after irr., baboon 1


title: H0 HARS category, before irr., baboon 5

value: H0 (healthy, no exposure)

value: before irradiation


title: H1-2° HARS category, 1st day after irr., baboon 2


title: H0 HARS category, before irr., baboon 2


title: H0 HARS category, before irr., baboon 3


title: H0 HARS category, before irr., baboon 4


title: HC-5


title: CON-F-1

status: Public on Jan 26 2016

city: Lucknow

first: Neetu

last: Singh

address: Chowk

department: Center for Advance Research

country: India

institute: King George's Medical University

hyb_protocol: Following fragmentation, 5.5 ug of single stranded cDNA were hybridized for 16 hr at 45C on Human Transcripptome Array 2.0. GeneChips were washed and stained in the Gene Chip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Chip Scanner, Affymetrix

data_processing: The data were analyzed with Transcriptome Analysis Console 3.0 using settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Control F-1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (GeneChip WT expression Array Manual,  Affymetrix).

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

treatment_protocol: All patients were commenced to Imatinib treatment alone or in combination with Hydrea/Hydroxyurea. Importantly, in some cases when patients failed to achieve time dependent molecular targets we switched to nilotinib or high dose Imatinib. Clinical outcomes included molecular response on the basis of BCR-ABL1

value: Control

value: Blood

tag: phase

value: CONTROL

tag: treatment

tag: age


title: CP-UT-63

value: CML

value: Chronic Phase

value: Under Treatment-Imatinib for 7 months

value: 37 years

tag: gender


title: CON-M-2

source_name: Control M-2

tag: tissue


title: CP-UT-65

value: Under Treatment-Imatinib for 7.9 years

value: 43 years


title: CP-UT-93

value: Under Treatment-Imatinib for 11 months

value: 60 years


title: CP


title: CP-UT-6

value: Under Treatment-Imatinib treated 7 months

value: 24 years


title: CP-UT-68

value: Under Treatment-Imatinib for 4 months

value: 28 years


title: AP-UT-62

value: Accelerated Phase

value: Under Treatment-Uridrea, Imatinib and since February 2014 Nilotinib treated for 4.4 years

value: 42 years

value: male


title: CP-UT-4

value: Blood

value: Under Treatment-Imatinib 10 months

value: 14 years


title: CON-M-1

source_name: Control M-1

value: Control

value: CONTROL


title: CON-F-2

source_name: Control F-2

value: female


title: CP-UT-91

value: CML

value: Chronic Phase

value: Under Treatment-Imatinib 6 months

value: 66 years


title: CP-UT-7

value: Under Treatment-Imatinib for 7.2 years

value: 41 years


title: CP-UT-57

value: Under Treatment-Hydroxyurea, Zyloric and Imatinib treated


title: CP-UT-87

value: Under Treatment- Imatinib treated 2.9 years

value: 45 years


title: H0 HARS category, before irr., baboon 1

value: peripheral whole blood

value: H0 (healthy, no exposure)

value: before irradiation


title: CP-UT-36

value: Blood

value: Under Treatment-Hydab and Imatinib treated for 6.10 years

value: 23 years

value: male


title: CP-UT-56

value: Under Treatment-Hydroxyurea , Zyloric and  Imatinib treated one year

value: 43 years

value: female


title: CP-UT-2

value: CML

value: Chronic Phase

value: Under Treatment-Droxygel (Antacid), Unidrea and Imatinib treated

value: 50 years


title: B-NEW-19

value: Blast

value: NEW

value: 28 years


title: AP-UT-59

value: Under Treatment-Hydroxyurea , Zyloric and Imatinib treated 3months

value: 15 years


title: CP-UT-20

value: Under Treatment Imatinib one month

value: 33 years


title: CP-UT-55

value: Blood

value: Under Treatment-Imatinib treated for 3 months

value: 60 years


title: B-NEW-11

value: 20 years

value: male


title: CP-UT-13

value: Under Treatment-Droxygel (Antacid), Unidrea and Imatinib treated for 7.1 years


title: CP-NEW-14

value: CML

value: 35 years

value: female


title: B-NEW-34

value: 24 years


title: AP-UT-1

value: Accelerated Phase

value: Under Treatment- Imatinib for 1.8 years


title: CP-NEW-10

value: Chronic Phase

value: NEW

value: 46 years


title: AP-UT-32

value: Under Treatment-Initially treated with Myeleron, Hydab irocos, Zyloric since may 2005 on Imatinib treated for 15 years

value: 27 years