title: genomic DNA from cord blood 101

description: normal cord blood sample

source_name: cord blood 101


title: genomic DNA from cord blood 106

status: Public on May 31 2017

type: genomic

city: Berkeley

first: Nina

last: Holland

state: CA

address: 733 University Hall

country: USA

institute: University of California, Berkeley

description: normal cord blood sample

hyb_protocol: DNA was whole genome amplified, enzymatically fragmented, purified, and hybridised to the Illumina Infinium HumanMethylation450 BeadChips according to the Illumina methylation protocol

scan_protocol: 450K BeadChips were handled by robotics and analyzed using the Illumina Hi-Scan system

data_processing:
Probe signal intensities were extracted by Illumina GenomeStudio software (version XXV2011.1, Methylation Module 1.9) methylation module and background subtracted. The All Sample Mean Normalization (ASMN) algorithm was used to adjust for color channel bias, batch effects, and difference in Infinium chemistry [Yousefi et al. 2013]. This was followed by Beta Mixture Quantile (BMIQ) normalization for differences between type I and type II probes [Teschendorff et al. 2013]. Samples were retained only if 95% of sites assayed had detection P-values > 0.01. Sites with annotated probe SNPs (n=65) and with common SNPs (minor allele frequency >5%) within 50bp of the target identified in the MXL (Mexican ancestry in Los Angeles, California) HapMap population (n=49,748), and cross-reactive probes identified by Chen et al. [Chen et al. 2013] (n=25,248). Probes where 95% of samples had detection P-values >0.01 were also dropped (n= 460).
Normalized (ASMN and BMIQ) Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: cord blood 106

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from the banked non-heparinized umbilical cord blood clot samples using QIAamp DNA Blood Maxi Kits according to the manufacturer’s protocol

tag: cohort

value: Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS)

tag: tissue

value: cord blood


title: Slide 58_Anaerobic culture_CORM-401_biol rep 1_Cy3 20 Cy5 0

type: RNA

city: Sheffield

first: Robert

last: Poole

state: South Yorkshire

address: Firth Court, Western Bank

department: Molecular Biology & Biotechnology

country: United Kingdom

institute: University of Sheffield

hyb_protocol: For hybridization to the microarray slides, 400 ng cDNA was added to 25 μl 2 x Hi-RMP Hybridization Buffer and 5 μl 10 x Gene Expression Blocking Agent (Agilent Technologies) to give 50 μl total volume. Custom Gene Expression Microarray slides each containing 8 x 15K arrays were purchased from Agilent Technologies. For hybridization one 8 x Gasket Slide was placed inside a Microarray Hybridization Chamber and samples loaded for 8 different conditions, followed by placement of the microarray slide over the gasket. After sealing the chamber the arrays were incubated at 65 °C, rotating at 10 rpm for ~17 h. Following incubation, the slides were washed in Gene Expression Wash Buffer 1 for 1 min, followed by washing in Gene Expression Wash Buffer 2 for 1 min. Slides were dried and scanned in a microarray scanner (Agilent).

scan_protocol: Scanned on an Agilent DNA microarray scanner with SureScan high-resolution technology

data_processing: Agilent Feature Extraction Software (v 10.10.1.1) was used for background subtraction and LOWESS normalization.

molecule: total RNA

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Continuous anaerobically grown cultures in Evans medium, CORM-401 samples or samples prior to addition of CORM-401

label_protocol: cDNA synthesis was carried out using 16 μg of RNA, primed with 5 μg Random Primers (Invitrogen). Reaction mixes (30 μl) containing 0.5 mM dATP, dTTP, and dGTP, 0.2 mM dCTP, and 67 μM Cy-3 or Cy-5-dCTP were incubated at 25 °C for 5 min, then at 50 °C overnight with 300 U of Superscript III Reverse Transcriptase (Invitrogen). Following synthesis, cDNA was purified using a PCR purification kit (Qiagen).

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

tag: strain

value: Wild type strain MG1655

tag: agent

tag: time

value: 20 min

tag: culture conditions

value: anaerobic

value: control

value: 0 min


title: T-34

city: seoul

first: minhee

last: park

address: shinchondong

country: South Korea

institute: student

description: sample name: 08-15457T

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: biotin

source_name: colorectal carcinoma-34

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

extract_protocol: RNA was extracted with Trizol reagent, followed by  Dnase digestion and clean-up procedures. Quality control was performed with Agilent Bioanalyser.

value: colorectal carcinoma

tag: patient diagnosis

tag: disease stage

value: stageIII

tag: gender

value: male


title: Slide 58_Anaerobic culture_CORM-401_biol rep 1_Cy3 10 Cy5 0

value: 10 min


title: T-35

description: sample name: 08-17736T

source_name: colorectal carcinoma-35


title: genomic DNA from cord blood 100

description: normal cord blood sample

source_name: cord blood 100


title: Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 5 Cy5 0

value: 5 min


title: genomic DNA from cord blood 99

description: normal cord blood sample

source_name: cord blood 99


title: genomic DNA from cord blood 98

description: normal cord blood sample

source_name: cord blood 98


title: Chicken miR Embryo Breast sample L10_61

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

country: Germany

institute: FBN Dummerstorf

description: microRNA expression of broiler M. longissimus dorsi treat by varience incubation temperature

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42°C on  GeneChip® miRNA-3_0-st-v3 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

organism: Gallus gallus

source_name: Musculus  pectoralis

label_protocol: Biotinylated cRNA were prepared from miRNA according to FlashTag Biotin RNA Labeling Kit for Affymetrix GeneChip miRNA arrays (Genisphere, Hatfield, PA, USA) according to the manufacturer’s recommendations Affymetrix GeneChip miRNA Array protocols (Affymetrix, Santa Clara, CA, USA)

extract_protocol: Total RNA was isolated using Qiagen miReasy Mini kit TRI Reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol for small-RNA. Then small RNA was cleaned up using the Rneasy MinElute Clean up kit  (Qiagen, Hilden, Germany).

tag: stage/age of sampling

value: Embryo

tag: incubation temperature in treatment interval

value: Low 36.8 C

tag: time interval of varied incubation temperature


title: genomic DNA from cord blood 97

description: normal cord blood sample

source_name: cord blood 97


title: Chicken miR Embryo Breast sample L10_60


title: Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 40

value: 40 min


title: T-33

description: sample name: 08-12530T

source_name: colorectal carcinoma-33


title: Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 20


title: T-28

description: sample name: 08-04971T

source_name: colorectal carcinoma-28


title: Chicken miR Embryo Breast sample L13_73


title: Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 10


title: Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 80

value: 80 min


title: Chicken miR Embryo Breast sample L13_74


title: Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 5


title: T-31

description: sample name: 08-08956T

source_name: colorectal carcinoma-31

value: female


title: Chicken miR Embryo Breast sample L13_72


title: genomic DNA from cord blood 96

description: normal cord blood sample

source_name: cord blood 96

value: Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS)


title: T-29

description: sample name: 08-06979T

source_name: colorectal carcinoma-29


title: Chicken miR Embryo Breast sample L13_75


title: T-26

description: sample name: 08-03607T

source_name: colorectal carcinoma-26


title: Chicken miR Embryo Breast sample L13_77


title: T-24

description: sample name: 07-42862T

source_name: colorectal carcinoma-24


title: Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 2.5 Cy5 0

value: 2.5 min


title: T-25

description: sample name: 08-01837T

source_name: colorectal carcinoma-25


title: Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 80

source_name: Continuous aerobically grown cultures in Evans medium, CORM-401 samples or samples prior to addition of CORM-401

value: Wild type strain MG1655

value: aerobic


title: genomic DNA from cord blood 95

description: normal cord blood sample

source_name: cord blood 95

value: cord blood


title: genomic DNA from cord blood 94

description: normal cord blood sample

source_name: cord blood 94


title: T-30

description: sample name: 08-07305T

source_name: colorectal carcinoma-30


title: Chicken miR Embryo Breast sample L13_76


title: genomic DNA from cord blood 93

description: normal cord blood sample

source_name: cord blood 93


title: Slide 70_Anaerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 2.5

source_name: Continuous anaerobically grown cultures in Evans medium, CORM-401 samples or samples prior to addition of CORM-401

value: control

value: anaerobic


title: Chicken miR Mature Breast sample C10_30

value: Mature

value: Control 37.8 C


title: genomic DNA from cord blood 92

description: normal cord blood sample

source_name: cord blood 92


title: Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 5

value: 0 min


title: T-32

description: sample name: 08-09193T

source_name: colorectal carcinoma-32

value: colorectal carcinoma

value: stageIII

value: male


title: Chicken miR Mature Breast sample C10_90

source_name: Musculus  pectoralis


title: T-27

description: sample name: 08-04760T

source_name: colorectal carcinoma-27


title: genomic DNA from cord blood 91

description: normal cord blood sample

source_name: cord blood 91


title: Chicken miR Mature Breast sample C13_29


title: genomic DNA from cord blood 90

description: normal cord blood sample

source_name: cord blood 90


title: genomic DNA from cord blood 89

description: normal cord blood sample

source_name: cord blood 89


title: Chicken miR Mature Breast sample C13_70


title: T-20

description: sample name: 07-15174T

source_name: colorectal carcinoma-20


title: Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 80 Cy5 0


title: Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 2.5


title: Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 40


title: T-22

description: sample name: 07-31446T

source_name: colorectal carcinoma-22


title: Chicken miR Mature Breast sample C13_68


title: T-21

description: sample name: 07-16184T

source_name: colorectal carcinoma-21


title: Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 20 Cy5 0

value: 20 min


title: genomic DNA from cord blood 88

description: normal cord blood sample

source_name: cord blood 88


title: Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 40 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, CORM-401 samples or samples prior to addition of CORM-401

value: 40 min


title: Chicken miR Mature Breast sample C13_77


title: T-23

description: sample name: 07-41576T

source_name: colorectal carcinoma-23


title: T-19

description: sample name: 07-13626T

source_name: colorectal carcinoma-19


title: Chicken miR Mature Breast sample C13_81


title: T-18

description: sample name: 07-07559T

source_name: colorectal carcinoma-18


title: Slide 46_Aerobic culture_CORM-401_biol rep 2_Cy3 2.5 Cy5 0


title: Slide 46_Aerobic culture_CORM-401_biol rep 2_Cy3 5 Cy5 0

value: 5 min


title: Slide 48_Aerobic culture_CORM-401_biol rep 2_Cy3 10 Cy5 0

value: 10 min


title: genomic DNA from cord blood 87

description: normal cord blood sample

source_name: cord blood 87

value: Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS)


title: T-17

description: sample name: 07-05689T

source_name: colorectal carcinoma-17

value: female


title: Chicken miR Mature Breast sample H10_11

value: High 38.8 C


title: Chicken miR Mature Breast sample H10_13


title: Chicken miR Mature Breast sample C13_83


title: Slide 46_Aerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 20

value: Wild type strain MG1655

value: aerobic


title: T-16

description: sample name: 07-03802T

source_name: colorectal carcinoma-16


title: Slide 46_Aerobic culture_CORM-401_biol rep 2_Cy3 0 Cy5 10

value: control


title: T-15

description: sample name: 07-02140T

source_name: colorectal carcinoma-15


title: Chicken miR Mature Breast sample H10_15

source_name: Musculus  pectoralis


title: genomic DNA from cord blood 84

description: normal cord blood sample

source_name: cord blood 84

value: cord blood


title: genomic DNA from cord blood 85

description: normal cord blood sample

source_name: cord blood 85


title: genomic DNA from cord blood 82

description: normal cord blood sample

source_name: cord blood 82


title: genomic DNA from cord blood 83

description: normal cord blood sample

source_name: cord blood 83


title: T-14

description: sample name: 06-44202T

source_name: colorectal carcinoma-14


title: Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 80 Cy5 0

value: 80 min


title: Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 40 Cy5 0


title: Chicken miR Mature Breast sample H10_66

value: Mature


title: Chicken miR Mature Breast sample H10_67


title: Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 10 Cy5 0

value: 0 min


title: T-13

description: sample name: 06-43826T

source_name: colorectal carcinoma-13

value: colorectal carcinoma


title: T-11

description: sample name: 06-40108T

source_name: colorectal carcinoma-11

value: stageIII


title: Chicken miR Mature Breast sample H10_3


title: Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 20 Cy5 0


title: Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 5 Cy5 0


title: T-12

description: sample name: 06-40868T

source_name: colorectal carcinoma-12


title: genomic DNA from cord blood 80

description: normal cord blood sample

source_name: cord blood 80


title: T-10

description: sample name: 06-39891T

source_name: colorectal carcinoma-10


title: Chicken miR Mature Breast sample H10_72


title: genomic DNA from cord blood 79

description: normal cord blood sample

source_name: cord blood 79


title: Chicken miR Mature Breast sample H10_74


title: genomic DNA from cord blood 81

description: normal cord blood sample

source_name: cord blood 81


title: genomic DNA from cord blood 78

description: normal cord blood sample

source_name: cord blood 78


title: Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 2.5 Cy5 0

source_name: Continuous aerobically grown cultures in Evans medium, CORM-401 samples or samples prior to addition of CORM-401

value: 2.5 min


title: Chicken miR Mature Breast sample H13_31


title: genomic DNA from cord blood 77

description: normal cord blood sample

source_name: cord blood 77


title: Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 80


title: T-9

description: sample name: 06-38659T

source_name: colorectal carcinoma-9

value: male


title: genomic DNA from cord blood 76

description: normal cord blood sample

source_name: cord blood 76


title: genomic DNA from cord blood 86

description: normal cord blood sample

source_name: cord blood 86


title: Slide 54_Aerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 40

value: 40 min


title: T-8

description: sample name: 06-38301T

source_name: colorectal carcinoma-8


title: Chicken miR Mature Breast sample H13_39

source_name: Musculus  pectoralis


title: Chicken miR Mature Breast sample H13_34


title: T-7

description: sample name: 06-37384T

source_name: colorectal carcinoma-7


title: Slide 53_Aerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 2.5


title: genomic DNA from cord blood 75

description: normal cord blood sample

source_name: cord blood 75


title: genomic DNA from cord blood 74

description: normal cord blood sample

source_name: cord blood 74


title: Chicken miR Mature Breast sample H13_43


title: Chicken miR Mature Breast sample H13_58


title: Chicken miR Mature Breast sample H13_50


title: Slide 53_Aerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 5

value: 5 min


title: genomic DNA from cord blood 71

description: normal cord blood sample

source_name: cord blood 71


title: T-4

description: sample name: 06-23384T

source_name: colorectal carcinoma-4


title: Slide 53_Aerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 10

value: 10 min


title: T-5

description: sample name: 06-30651T

source_name: colorectal carcinoma-5


title: Chicken miR Mature Breast sample H13_53


title: T-6

description: sample name: 06-34696T

source_name: colorectal carcinoma-6


title: T-2

description: sample name: 06-04381T

source_name: colorectal carcinoma-2


title: T-1

description: sample name: 06-00692T

source_name: colorectal carcinoma-1


title: T-3

description: sample name: 06-14028T

source_name: colorectal carcinoma-3


title: Chicken miR Mature Breast sample H13_60


title: Slide 53_Aerobic culture_CORM-401_biol rep 1_Cy3 0 Cy5 20

source_name: Continuous aerobically grown cultures in Evans medium, CORM-401 samples or samples prior to addition of CORM-401

value: 20 min


title: genomic DNA from cord blood 70

description: normal cord blood sample

source_name: cord blood 70

value: Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS)


title: genomic DNA from cord blood 73

description: normal cord blood sample

source_name: cord blood 73


title: genomic DNA from cord blood 66

description: normal cord blood sample

source_name: cord blood 66


title: Chicken miR Mature Breast sample L10_145

value: Low 36.8 C


title: Chicken miR Mature Breast sample L10_116


title: Chicken miR Mature Breast sample L10_51


title: genomic DNA from cord blood 69

description: normal cord blood sample

source_name: cord blood 69


title: N-31

description: sample name: 11-42848N

source_name: normal mucosa-31

value: normal colon mucosa

value: female


title: genomic DNA from cord blood 68

description: normal cord blood sample

source_name: cord blood 68


title: genomic DNA from cord blood 67

description: normal cord blood sample

source_name: cord blood 67


title: N-34

description: sample name: 11-67012N

source_name: normal mucosa-34


title: Chicken miR Mature Breast sample L13_161

source_name: Musculus  pectoralis


title: N-35

description: sample name: 11-67303N

source_name: normal mucosa-35


title: Chicken miR Mature Breast sample L10_170


title: genomic DNA from cord blood 65

description: normal cord blood sample

source_name: cord blood 65


title: genomic DNA from cord blood 62

description: normal cord blood sample

source_name: cord blood 62


title: Chicken miR Mature Breast sample L10_153


title: Chicken miR Mature Breast sample L10_155


title: genomic DNA from cord blood 61

description: normal cord blood sample

source_name: cord blood 61


title: genomic DNA from cord blood 64

description: normal cord blood sample

source_name: cord blood 64


title: Chicken miR Mature Breast sample L10_64


title: genomic DNA from cord blood 63

description: normal cord blood sample

source_name: cord blood 63


title: N-33

description: sample name: 11-54129N

source_name: normal mucosa-33


title: N-28

description: sample name: 11-27404N

source_name: normal mucosa-28


title: Chicken miR Mature Breast sample L13_122


title: N-32

description: sample name: 11-52318N

source_name: normal mucosa-32


title: N-30

description: sample name: 11-40633N

source_name: normal mucosa-30


title: Chicken miR Mature Breast sample L10_76


title: N-26

description: sample name: 11-20764N

source_name: normal mucosa-26


title: Chicken miR Mature Breast sample L13_163


title: Chicken miR Mature Breast sample L13_127


title: Chicken miR Mature Breast sample L13_178


title: N-27

description: sample name: 11-24177N

source_name: normal mucosa-27


title: N-29

description: sample name: 11-34678N

source_name: normal mucosa-29


title: genomic DNA from cord blood 59

description: normal cord blood sample

source_name: cord blood 59


title: genomic DNA from cord blood 60

description: normal cord blood sample

source_name: cord blood 60


title: genomic DNA from cord blood 58

description: normal cord blood sample

source_name: cord blood 58


title: genomic DNA from cord blood 57

description: normal cord blood sample

source_name: cord blood 57


title: N-24

description: sample name: 11-17727N

source_name: normal mucosa-24


title: N-25

description: sample name: 11-17775N

source_name: normal mucosa-25


title: Thalassiosira_T=8h_rep2

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

hyb_protocol: 1650 ng cRNA from each sample was fragmented and hybridized on a custom made 8x15K Thalassiosira pseudonana whole-genome 60-mer oligonucleotide microarrays (Agilent Technologies, design ID: Agilent-048448) in an Agilent G2545A Hybridization rotary oven (10 rpm, 65°C, 17.5 h). Hybridization was performed with the Gene Expression Hybridization Kit (Agilent p/n 5188-5242). The slides were washed with buffer 1 & 2 from Gene Expression Wash Buffer kit (Agilent p/n 5188-5327) according to the manufacturer's description.

scan_protocol: The microarray sides were scanned twice at 5 µm resolution on a laser scanner (G2505 B from Agilent Technologies), using the dynamic range expander option in the scanner software. The resulting images were processed using Agilent Feature Extraction software v9.5.

data_processing: The median signal intensities (gMedianSignal) were normalized using the quantile method, and no background subtraction was performed. Spots identified as feature outliers were excluded from analysis, and weak or non-detected spots were given reduced weight (0.5). Genes with statistically significant differential expression were identified using the Limma package (version 3.4) and R (version 3.0.3).

organism: Thalassiosira pseudonana

source_name: Thalassiosira, Si-plus, 8h

label_protocol: Total RNA (83-200 ng) was reverse transcribed, amplified and labelled with Cy3-CTP using the Low Input Quick Amp Labelling Kit, One-Color (Agilent p/n 5190-2305).

growth_protocol: Thalassiosira pseudonana (CCAP 1085/2) was grown in axenic cultures at 20°C, illuminated with 130 µmol photons m-2 s-1 provided by fluorescent tubes (Philips Master TL-D 36W/840) in light:dark cycles of 16:8 hours. Both experiments were initiated at least 4 hours after beginning of the light phase, and all consecutive samplings were performed within the same light period. Cultivation medium was made from natural seawater filtered through 0.2-µm Tuffryn membrane capsules (Pall Gelman) before nutrient amendment and autoclaving. Nutrient amendment was according to the f/2 recipe of Guillard (1975), except that the PO43- concentration was increased to 1.25 of the original recipe to prevent limitation at any time during the experiment. Cultures were grown in 2000 mL Nalgene optically clear flasks and aerated to prevent settling of cells and carbon limitation. During the experiments pH was stable in the range 7.5 to 8.0. Si-free medium was made as follows: A 10 L batch of seawater medium (f/2 without Si addition) was used to grow a culture of T. pseudonana until the Si was depleted. The cells were harvested by filtration through a 1 µm filter, and the remaining Si-depleted medium was further filtered through a 0.22 µm filter before it was autoclaved and stored at 4°C in the dark. The Si-depleted medium contained 0.7 µM Si, and was used to prepare the experimental medium for the shift-down experiment following the modified f/2 recipe, but with no Si added.

extract_protocol: For the RNA isolation, 50 ml samples of the biological replicates were quickly harvested through vacuum filtration on Durapore membrane filters (DVPP, 0.65 µm, Merck Millipore). The cells were resuspended in 1 mL of f/2 medium and transferred to 2 mL tubes and centrifuged at 18,000 g for 1 min, and the supernatant was removed. The remaining cell pellet was flash frozen in liquid nitrogen and stored at -80°C. Total RNA was isolated from the samples using the RNeasy Plant Mini kit (QIAgen).

treatment_protocol: For the shift-up experiment, 1000 mL pre-cultures were cultivated as batch cultures in medium with f/4-levels of Si (approximately 55-60 µM Si, including a seawater background of 4 µM) for three weeks prior to the experiment; the cultures were diluted with fresh medium when the Si was depleted. The Si shift-up experiment was initiated by adding a pulse of Si to each culture (t=0). The new [Si] was approximately 300 µM. For the shift-down experiment, 1000 mL pre-cultures were grown under semi-continuous batch conditions for three weeks prior to the experiment with daily dilutions of approx. 70% of the volume and with surplus of Si. The cells were spun down by gentle centrifugation (7500 g, 3x10 min) and the resulting cell slurry was transferred to Si-free medium (t=0). At each sampling time, two aliquots of approx. 50 mL were removed. Silicon shift-up experimental cultures were sampled right before Si addition, and then every hour or every half hour as the biomass began to increase. Based on the time course of the culture, the time points -0.25 (-15 min, control), 0.25, 0.5, 1, 2, 4, 6, and 8 hours relative to the silicate shift-up were selected for further analyses. The silicon shift-down experiment was sampled before centrifugation (-2 h) and thereafter samples were taken every hour or half hour for 7.5 hours after resuspension in silicate-free medium. Samples from time point 72 h were also included. The time points -2, 0.33, 1, 2, 4, 7.5, and 72 hours were selected for further analyses.

tag: clone

tag: treatment

value: Siicon shift-up

tag: time point


title: Thalassiosira_T=8h_rep1


title: genomic DNA from cord blood 56

description: normal cord blood sample

source_name: cord blood 56

value: cord blood


title: Thalassiosira_T=4h_rep2

source_name: Thalassiosira, Si-plus, 4h


title: N-23

description: sample name: 11-13680N

source_name: normal mucosa-23


title: Thalassiosira_T=6h_rep1

source_name: Thalassiosira, Si-plus, 6h


title: Chicken miR Mature Breast sample L13_6

source_name: Musculus  pectoralis


title: Thalassiosira_T=6h_rep2


title: N-22

description: sample name: 11-10575N

source_name: normal mucosa-22


title: Chicken miR Mature Breast sample L13_91


title: Thalassiosira_T=2h_rep2

source_name: Thalassiosira, Si-plus, 2h


title: N-20

description: sample name: 08-45631N

source_name: normal mucosa-20


title: genomic DNA from cord blood 54

description: normal cord blood sample

source_name: cord blood 54


title: genomic DNA from cord blood 55

description: normal cord blood sample

source_name: cord blood 55


title: N-21

description: sample name: 08-50942N

source_name: normal mucosa-21


title: Thalassiosira_T=4h_rep1


title: N-19

description: sample name: 08-45024N

source_name: normal mucosa-19


title: Thalassiosira_T=1h_rep2

source_name: Thalassiosira, Si-plus, 1h


title: N-18

description: sample name: 08-43732N

source_name: normal mucosa-18


title: genomic DNA from cord blood 51

description: normal cord blood sample

source_name: cord blood 51


title: Chicken miR Mature Breast sample L13_179


title: genomic DNA from cord blood 52

description: normal cord blood sample

source_name: cord blood 52


title: gingival tissue, obese 10

city: London

first: Anastasia

middle: Z.

last: Kalea

address: 5 University Street

department: Centre for Cardiovascular Genetics

institute: UCL Institute of Cardiovascular Science

description: miRNA expression in gingival tissue biopsies

hyb_protocol: The Affymetrix Fluidics protocol (FS450_0003) was followed for hybridization, washing, and scanning of the slides using the GeneChip Scanner 3000.

scan_protocol: Affymetrix miRNA QC tools were used for data normalization and background correction. This was done using RMA (Robust Multi-array Average) and DABG (Detection Above Background) methods to down-weigh the poorly performing probes and to detect the P-value for each probe set

data_processing: Data analysis was done using Partek 6.6 software

source_name: human gingival tissue, obese

label_protocol: FlashTag Biotin RNA Labeling Kit for Affymetrix GeneChip miRNA arrays (Genisphere, PA, USA) was used to label 500ng of total RNA by the addition of polyA-polymerase, following the manufacturer’s instructions.

extract_protocol: mirVana™ miRNA Isolation Kit (Ambion®, TX, USA) following the manufacturer’s instructions

tag: weight

value: obese


title: gingival tissue, obese 8


title: Thalassiosira_T=2h_rep1


title: Thalassiosira_T=1h_rep1


title: gingival tissue, obese 7


title: gingival tissue, obese 9


title: Thalassiosira_T=0.5h_rep2

source_name: Thalassiosira, Si-plus, 0.5h


title: genomic DNA from cord blood 50

description: normal cord blood sample

source_name: cord blood 50


title: N-16

description: sample name: 08-29740N

source_name: normal mucosa-16


title: gingival tissue, obese 6


title: N-15

description: sample name: 08-29075N

source_name: normal mucosa-15


title: genomic DNA from cord blood 53

description: normal cord blood sample

source_name: cord blood 53


title: Thalassiosira_T=0.5h_rep1


title: N-17

description: sample name: 08-39721N

source_name: normal mucosa-17


title: genomic DNA from cord blood 49

description: normal cord blood sample

source_name: cord blood 49


title: gingival tissue, obese 5


title: N-13

description: sample name: 08-15457N

source_name: normal mucosa-13


title: gingival tissue, obese 4


title: genomic DNA from cord blood 48

description: normal cord blood sample

source_name: cord blood 48


title: Thalassiosira_T=0.25h_rep2

source_name: Thalassiosira, Si-plus, 0.25h


title: N-14

description: sample name: 08-23789N

source_name: normal mucosa-14


title: genomic DNA from cord blood 47

description: normal cord blood sample

source_name: cord blood 47


title: genomic DNA from cord blood 72

description: normal cord blood sample

source_name: cord blood 72


title: Thalassiosira_T=0.25h_rep1


title: N-12

description: sample name: 08-07305N

source_name: normal mucosa-12


title: genomic DNA from cord blood 46

description: normal cord blood sample

source_name: cord blood 46


title: gingival tissue, obese 1


title: gingival tissue, obese 3


title: genomic DNA from cord blood 45

description: normal cord blood sample

source_name: cord blood 45


title: genomic DNA from cord blood 44

description: normal cord blood sample

source_name: cord blood 44


title: N-10

description: sample name: 08-04760N

source_name: normal mucosa-10


title: Thalassiosira_T=-0.25h_rep2

source_name: Thalassiosira, Reference sample, -0.25h

value: Reference


title: gingival tissue, obese 2

source_name: human gingival tissue, obese


title: Thalassiosira_T=-0.25h_rep1


title: N-11

description: sample name: 08-06979N

source_name: normal mucosa-11


title: genomic DNA from cord blood 43

description: normal cord blood sample

source_name: cord blood 43


title: Thalassiosira_Si-depletion_T=72h_rep2

source_name: Thalassiosira, Si-depletion, 72h

value: Silicon shift-down


title: Thalassiosira_Si-depletion_T=72h_rep1


title: genomic DNA from cord blood 42

description: normal cord blood sample

source_name: cord blood 42


title: N-9

description: sample name: 07-42862N

source_name: normal mucosa-9

value: colorectal carcinoma


title: Thalassiosira_Si-depletion_T=7.5h_rep2

source_name: Thalassiosira, Si-depletion, 7.5h


title: genomic DNA from cord blood 41

description: normal cord blood sample

source_name: cord blood 41


title: gingival tissue, normal weight 10

source_name: human gingival tissue, normal weight

value: normal weight


title: genomic DNA from cord blood 40

description: normal cord blood sample

source_name: cord blood 40


title: Thalassiosira_Si-depletion_T=4h_rep2

source_name: Thalassiosira, Si-depletion, 4h


title: Thalassiosira_Si-depletion_T=7.5h_rep1


title: N-7

description: sample name: 07-31446N

source_name: normal mucosa-7

value: stageIII


title: gingival tissue, normal weight 7


title: Thalassiosira_Si-depletion_T=4h_rep1


title: gingival tissue, normal weight 6


title: gingival tissue, normal weight 8


title: N-8

description: sample name: 07-41576N

source_name: normal mucosa-8


title: Thalassiosira_Si-depletion_T=2h_rep2

source_name: Thalassiosira, Si-depletion, 2h


title: Thalassiosira_Si-depletion_T=2h_rep1


title: gingival tissue, normal weight 5


title: gingival tissue, normal weight 9


title: genomic DNA from cord blood 39

description: normal cord blood sample

source_name: cord blood 39


title: N-5

description: sample name: 07-15174N

source_name: normal mucosa-5

value: male


title: gingival tissue, normal weight 4


title: N-3

description: sample name: 07-05689N

source_name: normal mucosa-3


title: N-2

description: sample name: 06-34696N

source_name: normal mucosa-2


title: gingival tissue, normal weight 3


title: genomic DNA from cord blood 36

description: normal cord blood sample

source_name: cord blood 36


title: genomic DNA from cord blood 37

description: normal cord blood sample

source_name: cord blood 37


title: genomic DNA from cord blood 35

description: normal cord blood sample

source_name: cord blood 35


title: N-6

description: sample name: 07-21601N

source_name: normal mucosa-6


title: N-4

description: sample name: 07-13626N

source_name: normal mucosa-4


title: genomic DNA from cord blood 38

description: normal cord blood sample

source_name: cord blood 38


title: genomic DNA from cord blood 34

description: normal cord blood sample

source_name: cord blood 34


title: Thalassiosira_Si-depletion_T=1h_rep2

source_name: Thalassiosira, Si-depletion, 1h


title: genomic DNA from cord blood 33

description: normal cord blood sample

source_name: cord blood 33


title: genomic DNA from cord blood 30

description: normal cord blood sample

source_name: cord blood 30


title: Thalassiosira_Si-depletion_T=1h_rep1


title: gingival tissue, normal weight 2

source_name: human gingival tissue, normal weight


title: genomic DNA from cord blood 32

description: normal cord blood sample

source_name: cord blood 32


title: Thalassiosira_Si-depletion_T=0.33h_rep1

source_name: Thalassiosira, Si-depletion, 0.33h


title: gingival tissue, normal weight 1


title: N-1

description: sample name: 06-14028N

source_name: normal mucosa-1


title: T13_2 h

city: Bunkyo-ku

first: Shizu

last: Aikawa

state: Tokyo

address: 7-3-1 Hongo

country: Japan

institute: The University of Tokyo

description: Gene expression data from uteri treated with T13 for 2 h.

hyb_protocol: 3 ug of labeled DNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA (quantile) using Affymetrix default analysis settings.

organism: Mus musculus

source_name: T13-treated pseudopregnant uteri for 2 h

label_protocol: Amplified sense-strand DNA products were synthesized by the Ambion WT Expression Kit, and were fragmented and labeled by the WT Terminal Labeling and Controls Kit.

growth_protocol: 8-12-wk-old WT mice (ICR background) were housed in climate-controlled (25C) pathogen-free facilities with a 12 h light-dark cycle, with free access to standard diet (CE2; CLEA Japan) and water.

extract_protocol: Total RNA was purified using a GenElute Mammalian Total RNA Miniprep kit (Sigma-Aldrich) , and the quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: 5 µl/horn of T13 solution (1 mM) or 0.01% BSA-PBS was injected into the uterine cavity adjacent to the ovary on 3.5 dpc of pseudopregnancy.

value: ICR

tag: age

value: 8-12 weeks

tag: injected with

value: lysophosphatidic acid receptor 3 agonist (T13)

value: 2 hr after the injection

value: pseudopregnant uteri


title: genomic DNA from cord blood 31

description: normal cord blood sample

source_name: cord blood 31

tag: cohort

value: Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS)

tag: tissue


title: Thalassiosira_Si-depletion_T=0.33h_rep2


title: genomic DNA from cord blood 29

description: normal cord blood sample

source_name: cord blood 29


title: vehicle_2 h

description: Gene expression data from uteri treated with vehicle for 2 h.

source_name: vehicle-treated pseudopregnant uteri for 2 h

tag: strain

value: vehicle


title: vehicle_1 h

description: Gene expression data from uteri treated with vehicle for 1 h.

source_name: vehicle-treated pseudopregnant uteri for 1 h

value: 1 hr after the injection


title: genomic DNA from cord blood 28

description: normal cord blood sample

source_name: cord blood 28


title: T13_1 h

description: Gene expression data from uteri treated with T13 for 1 h.

source_name: T13-treated pseudopregnant uteri for 1 h


title: Thalassiosira_T=-2h_rep2

source_name: Thalassiosira, Reference sample, -2h


title: Thalassiosira_T=-2h_rep1


title: genomic DNA from cord blood 27

description: normal cord blood sample

source_name: cord blood 27


title: genomic DNA from cord blood 24

description: normal cord blood sample

source_name: cord blood 24


title: T13_0.5 h

description: Gene expression data from uteri treated with T13 for 0.5 h.

source_name: T13-treated pseudopregnant uteri for 0.5 h

value: 0.5 hr after the injection


title: genomic DNA from cord blood 26

description: normal cord blood sample

source_name: cord blood 26

value: cord blood


title: vehicle_0.5 h

description: Gene expression data from uteri treated with vehicle for 0.5 h.

source_name: vehicle-treated pseudopregnant uteri for 0.5 h


title: genomic DNA from cord blood 21

description: normal cord blood sample

source_name: cord blood 21


title: genomic DNA from cord blood 25

description: normal cord blood sample

source_name: cord blood 25


title: genomic DNA from cord blood 22

description: normal cord blood sample

source_name: cord blood 22


title: mouse_heart_sham_28day_rep2

city: Taipei city

first: Yao-Ming

last: CHANG

address: No.128, Academia Rd. Nangang Dist.

country: Taiwan

institute: Academia Sinica

hyb_protocol: The labelled miRNAs were hybridized to the Mouse & Rat miRNA OneArray® with Phalanx hybridization buffer using OneArray® Hybridization Chamber. After 16 hrs hybridization, non-specific binding targets were washed away.

scan_protocol: The slides were scanned using a DNA Microarray Scanner (Model 4000B, Molecular Devices, Sunnyvale, CA, USA). The Cy5 fluorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).

data_processing: The miRNAs with flags < 0 within repeated probes and all chips were filtered out first. Then, the intensity values from repeated probes within one chip were combined by median. Then the combined values were normalized by a quantile normalized method within technical replicate. The processed data were provided by Phalanx Biotech Group, Taiwan.

source_name: heart, left ventricle

label_protocol: Fluorescent targets were prepared from 2.5 µg total RNA samples using miRNA ULSTM Labeling Kit (Kreatech Diagnostics. USA).

growth_protocol: Mouse were kept under specific pathogen-free conditions, and all procedures performed were approved by the Institutional Animal Care and Use Committee of Academia Sinica, Taiwan.

extract_protocol: Total RNA was extracted using the TRIzol® Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. The concentration and purity of the RNA was measured by NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific). Purity was checked by the ratio of the OD260/OD280 and OD260/OD230. The quality of total RNA was accessed using Agilent 2100 Bioanalyzer (Aglient Technologies, Santa Clara, CA, USA).

treatment_protocol: Eight-week-old adult male mice (C57BL/6J) weighing 20–25 g were anaesthetized (vaporized 1% isoflurane) and subjected to pressure overload by transverse aortic banding (TAB) .

value: heart, left ventricle

tag: condition

value: Sham 28day

tag: Sex


title: genomic DNA from cord blood 19

description: normal cord blood sample

source_name: cord blood 19


title: genomic DNA from cord blood 18

description: normal cord blood sample

source_name: cord blood 18


title: mouse_heart_sham_28day

hyb_protocol: The labelled RNAs were then hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization, non-specific binding targets were washed away.

scan_protocol: The slides were scanned using a DNA microarray Scanner (Model G2505C, Agilent Technologies). The Cy 5 Fluorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).

data_processing: For each array, the intensities were firstly normalized by median scaling normalization method, then taken the average of repeated data from the same sample (the processed data were provided by Phalanx Biotech Group, Taiwan). The whole data for a probe were removed if the intensity values were negative or less than one in any of the five time points.

source_name: heart, left ventricle, sham surgery, 28day

label_protocol: Fluorescent RNA targets were prepared from 1 µg total RNA samples using OneArray® Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dye (GE Healthcare).


title: mouse_heart_TAB_28day

source_name: heart, left ventricle, TAB surgery, 28day

value: TAB 28day


title: genomic DNA from cord blood 20

description: normal cord blood sample

source_name: cord blood 20


title: mouse_heart_sham_7day_rep2

value: Sham 7day


title: mouse_heart_TAB_14day

source_name: heart, left ventricle, TAB surgery, 14day

value: TAB 15day


title: mouse_heart_TAB_7day

source_name: heart, left ventricle, TAB surgery, 7day

value: TAB 7day


title: mouse_heart_sham_14day

source_name: heart, left ventricle, sham surgery, 14day

value: Sham 14day

value: male


title: genomic DNA from cord blood 17

description: normal cord blood sample

source_name: cord blood 17


title: mouse_heart_sham_7day

source_name: heart, left ventricle, sham surgery, 7day


title: genomic DNA from cord blood 23

description: normal cord blood sample

source_name: cord blood 23


title: genomic DNA from cord blood 16

description: normal cord blood sample

source_name: cord blood 16


title: mouse_heart_sham_5day

source_name: heart, left ventricle, sham surgery, 5day

value: Sham 5day


title: genomic DNA from cord blood 13

description: normal cord blood sample

source_name: cord blood 13


title: mouse_heart_TAB_5day

source_name: heart, left ventricle, TAB surgery, 5day

value: TAB 5day


title: mouse_heart_sham_7day_rep1


title: mouse_heart_sham_14day_rep1


title: genomic DNA from cord blood 14

description: normal cord blood sample

source_name: cord blood 14


title: mouse_heart_sham_14day_rep2

source_name: heart, left ventricle


title: mouse_heart_sham_3day

source_name: heart, left ventricle, sham surgery, 3day

value: Sham 3day


title: genomic DNA from cord blood 12

description: normal cord blood sample

source_name: cord blood 12


title: mouse_heart_sham_28day_rep1


title: mouse_heart_TAB_3day

source_name: heart, left ventricle, TAB surgery, 3day

value: TAB 3day


title: mouse_heart_sham_5day_rep2


title: genomic DNA from cord blood 15

description: normal cord blood sample

source_name: cord blood 15

value: Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS)


title: genomic DNA from cord blood 8

description: normal cord blood sample

source_name: cord blood 8


title: genomic DNA from cord blood 9

description: normal cord blood sample

source_name: cord blood 9


title: mouse_heart_TAB_14day_rep2


title: genomic DNA from cord blood 5

description: normal cord blood sample

source_name: cord blood 5


title: mouse_heart_TAB_14day_rep1


title: mouse_heart_TAB_7day_rep1


title: genomic DNA from cord blood 7

description: normal cord blood sample

source_name: cord blood 7


title: mouse_heart_TAB_5day_rep1


title: genomic DNA from cord blood 1

description: normal cord blood sample

source_name: cord blood 1


title: mouse_heart_sham_3day_rep2


title: mouse_heart_TAB_28day_rep2


title: genomic DNA from cord blood 10

description: normal cord blood sample

source_name: cord blood 10


title: mouse_heart_sham_3day_rep1


title: mouse_heart_TAB_5day_rep2


title: genomic DNA from cord blood 11

description: normal cord blood sample

source_name: cord blood 11


title: mouse_heart_TAB_3day_rep2


title: genomic DNA from cord blood 4

description: normal cord blood sample

source_name: cord blood 4


title: genomic DNA from cord blood 6

description: normal cord blood sample

source_name: cord blood 6


title: mouse_heart_TAB_28day_rep1


title: genomic DNA from cord blood 3

description: normal cord blood sample

source_name: cord blood 3


title: genomic DNA from cord blood 2

description: normal cord blood sample

source_name: cord blood 2


title: mouse_heart_TAB_7day_rep2


title: mouse_heart_TAB_3day_rep1


title: pseudopregnant uteri_36hr_vehicle

description: Gene expression in pseudopregnant uteri 36 hr after vehicle injection

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit protocol. Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: uterus

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: 8-12-wk-old WT mice (ICR background) were housed in climate-controlled (25 oC) pathogen-free facilities with a 12 h light-dark cycle, with free access to standard diet (CE2; CLEA Japan) and water. ）

value: ICR


title: ExVivoLV_DM_rep1_miRNA

city: Sapporo

first: Masaya

last: Tanno

department: Department of Cardiovascular, Renal and Metabolic Medicine

institute: Sapporo Medical University

description:
Diabetes
Sample name: OLETF1
micro RNA
Cardiac cells

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions.
For the normalization it uses the value of U6, a housekeeping gene.
Target miRNA signals normalized to the housekeeping genes 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
normalized data file reports normalized signal (against housekeeping genes).
Fold Change file reports test/control (i.e., Diabetes/Non-diabetes) ratios.

label: SYBR Green

organism: Rattus norvegicus

source_name: Left ventricular tissue of DM rat, replicate 1

label_protocol: The PCR was run in a 7900HT Fast Real-Time PCR System (Applied Biosystems, Foster City, CA), and miRNA expression was calculated by comparative delta Ct analysis. U6 snRNA (Applied Biosystems, Foster City, CA) was used as an endogenous control.

extract_protocol: RNA of the rat heart was isolated using a mirVana miRNA isolation kit (Ambion, Austin, TX) and was reverse-transcribed using the miRNA reverse transcription kit in combination with stem-loop Megaplex primer pool (Applied Biosystems, Foster City, CA).

value: OLETF

tag: disease state

value: diabetes

value: heart

tag: tissue compartment

value: left ventricle


title: ExVivoLV_DM_rep2_miRNA

description:
Diabetes
Sample name: OLETF2
micro RNA
Cardiac cells

source_name: Left ventricular tissue of DM rat, replicate 2


title: pseudopregnant uteri_24hr_vehicle

description: Gene expression in pseudopregnant uteri 24 hr after vehicle injection


title: pseudopregnant uteri_30hr_vehicle

description: Gene expression in pseudopregnant uteri 30 hr after vehicle injection


title: ExVivoLV_nonDM_rep3_miRNA

description:
Non-diabetes
Sample name: LETO4
micro RNA
Cardiac cells

source_name: Left ventricular tissue of non-DM rat, replicate 3

value: LETO

value: healthy control


title: Galactose pMEF (SeV)

city: Fukuoka

first: Takumi

last: Koshiba

address: 744 Motooka, Nishi-ku

institute: Faculty of Science, Kyushu University

description: Gene expression profile of SeV-infected pMEF cultured in galactose medium

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of four samples were normalized by the quantile algorithm with the Bioconductor.

source_name: galactose-cultured MEF, SeV infection

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Primary MEFs were cultured in DMEM (non glucose; Gibco) supplemented with either 10 mM glucose or 10 mM galactose for the nutrients.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: cell line

value: Primary embryonic fibroblast

tag: culture condition

value: galactose-cultured

tag: infection

value: SeV


title: Glucose pMEF

description: Gene expression profile of pMEF cultured in glucose medium (control)

source_name: glucose-cultured MEF

value: glucose-cultured

value: control


title: pseudopregnant uteri_36hr_T13

description: Gene expression in pseudopregnant uteri 36 hr after injection of LPA3 agonist


title: pseudopregnant uteri_30hr_T13

description: Gene expression in pseudopregnant uteri 30 hr after injection of LPA3 agonist


title: ExVivoLV_nonDM_rep2_miRNA

description:
Non-diabetes
Sample name: LETO3
micro RNA
Cardiac cells

source_name: Left ventricular tissue of non-DM rat, replicate 2


title: ExVivoLV_DM_rep3_miRNA

description:
Diabetes
Sample name: OLETF3
micro RNA
Cardiac cells

source_name: Left ventricular tissue of DM rat, replicate 3


title: Galactose pMEF

description: Gene expression profile of pMEF cultured in galactose medium (control)

source_name: galactose-cultured MEF


title: copt5 2 Cu 1uM

status: Public on May 30 2017

city: Burjassot

first: Angela

last: Carrió-Seguí

state: Valencia

address: Dr. Moliner 50

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Valencia

description: ko 2 B

hyb_protocol: Hybridization protocol was performed by the technical service in the IBMCP (Politecnic University of Valencia) according to the manufacturer protocol of 4x44 Agilent microarray system

scan_protocol: Samples were scanned by an Axon Instruments Genepix 4000B

data_processing: Results obtained were processed by Genespring GX software academic license

label: Ko 2 B

organism: Arabidopsis thaliana

source_name: ko copt5_Cu 1 uM

label_protocol: Label protocol was performed by the technical service in the IBMCP (Politecnic University of Valencia) according to the manufacturer protocol of Agilent microarray system

growth_protocol: Arabidopsis thaliana columbia 0  as wt and copt5-2 mutant (knockout mutant T-DNA insertion) seeds were grown during 7 days. The growth medium was 1/2 MS, supplemented by Cu 1uM in the control conditions and by BCS 100uM for the treatment, in order to generate severe Cu defficiency. Light conditions were DHLC(12/12) and the material was collected after 12 hours of light. 3 biological replicates with 4 samples of each one were collected (in total 12 samples).

extract_protocol: Quiagen RNeasy Plant Mini Kit was employed to obtain total RNA from samples studied. The extraction protocol followed the manufacturer instructions

tag: ecotype background

value: columbia 0

tag: genotype/variation

value: copt5-2 knockout mutant

value: 7 days

value: whole seedlings

tag: growth condition

value: 1/2 MS + 1uM Cu (control condition)


title: Glucose pMEF (SeV)

description: Gene expression profile of SeV-infected pMEF cultured in glucose medium

source_name: glucose-cultured MEF, SeV infection


title: copt5 3 Cu 1uM

description: ko 3 B

label: Ko 3 B


title: copt5 2 BCS 100uM

description: ko 2 A

label: Ko 2 A

source_name: ko copt5_BCS 100 uM

value: 1/2 MS + 100uM BCS  (treatment condition)


title: Wt 2 Cu 1uM

description: wt 2 B

label: Wt 2 B

source_name: Wild type_Cu1 uM

value: wild type


title: Wt 3 Cu 1uM

description: wt 3 B

label: Wt 3 B


title: ExVivoLV_nonDM_rep1_miRNA

description:
Non-diabetes
Sample name: LETO2
micro RNA
Cardiac cells

source_name: Left ventricular tissue of non-DM rat, replicate 1


title: Wt 1 Cu 1uM

description: wt 1 B

label: Wt 1 B

source_name: Wild type_Cu 1 uM


title: Wt 3 BCS 100uM

description: wt 3 A

label: Wt 3 A

source_name: Wild type_BCS100 uM


title: copt5 3 BCS 100uM

description: ko 3 A

label: Ko 3 A


title: pseudopregnant uteri_24hr_T13

description: Gene expression in pseudopregnant uteri 24 hr after injection of LPA3 agonist

value: ICR


title: Wt 2 BCS 100uM

description: wt 2 A

label: Wt 2 A


title: copt5 1 Cu 1uM

description: ko 1 B

label: Ko 1 B


title: copt5 1 BCS 100uM

description: ko 1 A

label: Ko 1 A


title: Wt 1 BCS 100uM

description: wt 1 A

label: Wt 1 A


title: mouse_heart_sham_5day_rep1

source_name: heart, left ventricle

value: heart, left ventricle

value: Sham 5day

value: male


title: 757_Col_KO_rpl_3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression from colon from aged SIRT1 iKO mice

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNA was fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: Aged SIRT1 iKO, colon

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: Mice were maintained on normal chow diet

extract_protocol: TRIzol reagent, followed by RNA clean up using the Qiagen RNA easy mini kit with on-column DNAseI treatment

treatment_protocol: No special treatment

tag: gender

value: 24 months

value: colon

tag: diet

value: chow diet

value: SIRT1 iKO


title: 757_Col_KO_rpl_2

tag: age


title: 735_Y_KO_rpl_3

description: Gene expression from ileum from young SIRT1 iKO mice

source_name: Young SIRT1 iKO, ileum

value: 6-8 weeks

value: ileum


title: 757_Col_KO_rpl_4


title: 757_Col_Flox_rpl_4

description: Gene expression from colon from aged Flox control mice

source_name: Aged Flox control, colon

value: Flox control


title: 757_Col_Flox_rpl_1


title: 735_O_Flox_rpl_1

description: Gene expression from ileum from aged Flox control mice

source_name: Aged Flox control, ileum


title: 735_Y_KO_rpl_2


title: 735_O_KO_rpl_3

description: Gene expression from ileum from aged SIRT1 iKO mice

source_name: Aged SIRT1 iKO, ileum


title: 735_O_KO_rpl_1


title: 735_Y_Flox_rpl_3

description: Gene expression from ileum from young Flox control mice

source_name: Young Flox control, ileum


title: 735_O_KO_rpl_2


title: 735_Y_KO_rpl_4


title: 15dpc WT gb 4

city: Tokyo

first: AIsa

last: Ozawa

address: Yayoi 1-1-1,Bunkyo-ku

institute: The university of Tokyo

hyb_protocol: RNA samples were hybridized to Affymetrix Mouse 430 2.0 DNA microarray chips using the GeneChip® Hybridization Oven 640 (Affymetrix,Clara, CA). Washing and staining of the hybridized chips were conducted using the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: Chips were scanned using the Affymetrix GeneChip® Scanner 3000 (Affymetrix) with autoloader.

data_processing:
Data Processing using AltAnalyze Software(ver 2.0.9). The default recommended settings by Altanalyze was used to analyze the data
Gene expression values are calculated using constitutive probesets in AltAnalyze ver 2.0.9

source_name: gallbladder in wildtype mouse embryo

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified by spectrophotometry (nano drop 2000 ThermoScientific) and quality was verified using spectrophotometry (nano drop 2000 Thermo Scientific).

value: gall bladder

tag: gestational stage

value: wildtype

value: day 15 of pregnancy


title: 757_Col_Flox_rpl_3


title: 15dpc Sox17+/- gb 4

source_name: gallbladder in sox17+/- mouse embryo


title: 757_Col_KO_rpl_1


title: 735_O_Flox_rpl_3


title: 735_O_KO_rpl_4


title: 735_O_Flox_rpl_4


title: 735_Y_KO_rpl_1


title: 735_Y_Flox_rpl_4


title: 735_Y_Flox_rpl_1


title: 735_Y_Flox_rpl_2


title: genomic DNA from medulloblastoma_NMB906

status: Public on May 29 2017

city: Newcastle upon Tyne

first: Ed

last: Schwalbe

address: Ellison Place

department: Applied Sciences

institute: Northumbria University

description: medulloblastoma 426

hyb_protocol: According to the manufacturer’s instructions

scan_protocol: Illumina iScan System, according to the manufacturer’s instructions

data_processing: Arrays were processed using the R package minfi. Beta values were reported after functional normalisation. Intensity values were calculated without background subtraction and normalized to internal controls.

source_name: genomic DNA from medulloblastoma

extract_protocol: Extraction of DNA from tumor samples was carried out using Qiagen Allprep DNA/RNA/Protein Mini kit (Fresh Frozen) and Qiagen QIAamp DNA FFPE Tissue Kit (FFPE)

tag: sample type

value: medulloblastoma

value: primary medulloblastoma

value: M

tag: age (yrs)

tag: pathology

value: CLA


title: 15dpc Sox17+/- gb 3

tag: tissue

tag: strain


title: genomic DNA from medulloblastoma_PNET350080

description: medulloblastoma 417

label_protocol: According to the manufacturer’s instructions

tag: disease state


title: genomic DNA from medulloblastoma_PNET350120

description: medulloblastoma 419


title: 15dpc Sox17+/- gb 2

value: ICR


title: genomic DNA from medulloblastoma_PNET30193

description: medulloblastoma 412

value: F

value: LCA


title: 15dpc WT gb 3


title: genomic DNA from medulloblastoma_PNET350241

description: medulloblastoma 424


title: genomic DNA from medulloblastoma_PNET350091

description: medulloblastoma 418


title: 15dpc WT cd 2

source_name: cysticduct in wildtype mouse embryo

value: cystic duct


title: genomic DNA from medulloblastoma_PNET30131

description: medulloblastoma 408


title: genomic DNA from medulloblastoma_NMB93

description: medulloblastoma 397


title: genomic DNA from medulloblastoma_PNET30009

description: medulloblastoma 399

value: NOS


title: 15dpc WT cd 1


title: genomic DNA from medulloblastoma_PNET30035

description: medulloblastoma 403


title: 15dpc Sox17+/- gb 1


title: genomic DNA from medulloblastoma_PNET350049

description: medulloblastoma 416


title: genomic DNA from medulloblastoma_NMB94

description: medulloblastoma 398


title: genomic DNA from medulloblastoma_NMB869

description: medulloblastoma 378


title: genomic DNA from medulloblastoma_PNET30032

description: medulloblastoma 402


title: genomic DNA from medulloblastoma_NMB858

description: medulloblastoma 373


title: genomic DNA from medulloblastoma_NMB874

description: medulloblastoma 382


title: genomic DNA from medulloblastoma_NMB810

description: medulloblastoma 364


title: genomic DNA from medulloblastoma_NMB808

description: medulloblastoma 362


title: genomic DNA from medulloblastoma_NMB806

description: medulloblastoma 360

value: DN


title: genomic DNA from medulloblastoma_NMB866

description: medulloblastoma 375


title: genomic DNA from medulloblastoma_NMB873

description: medulloblastoma 381


title: genomic DNA from medulloblastoma_NMB795

description: medulloblastoma 350


title: genomic DNA from medulloblastoma_NMB791

description: medulloblastoma 347


title: genomic DNA from medulloblastoma_NMB759

description: medulloblastoma 322


title: genomic DNA from medulloblastoma_NMB79

description: medulloblastoma 346


title: genomic DNA from medulloblastoma_NMB870

description: medulloblastoma 379


title: genomic DNA from medulloblastoma_NMB763

description: medulloblastoma 326


title: genomic DNA from medulloblastoma_NMB757

description: medulloblastoma 320


title: 15dpc WT gb 1


title: genomic DNA from medulloblastoma_NMB831

description: medulloblastoma 371


title: genomic DNA from medulloblastoma_NMB81

description: medulloblastoma 363


title: 15dpc WT gb 2


title: genomic DNA from medulloblastoma_NMB798

description: medulloblastoma 352


title: genomic DNA from medulloblastoma_NMB730

description: medulloblastoma 300


title: genomic DNA from medulloblastoma_NMB803

description: medulloblastoma 357


title: genomic DNA from medulloblastoma_NMB823

description: medulloblastoma 368


title: genomic DNA from medulloblastoma_NMB788

description: medulloblastoma 345


title: genomic DNA from medulloblastoma_NMB724

description: medulloblastoma 295


title: genomic DNA from medulloblastoma_NMB756

description: medulloblastoma 319


title: genomic DNA from medulloblastoma_NMB717

description: medulloblastoma 290


title: genomic DNA from medulloblastoma_NMB740

description: medulloblastoma 309


title: genomic DNA from medulloblastoma_NMB690

description: medulloblastoma 279


title: genomic DNA from medulloblastoma_NMB711

description: medulloblastoma 285


title: genomic DNA from medulloblastoma_NMB726

description: medulloblastoma 297


title: genomic DNA from medulloblastoma_NMB743

description: medulloblastoma 312


title: genomic DNA from medulloblastoma_NMB745

description: medulloblastoma 313


title: genomic DNA from medulloblastoma_NMB675

description: medulloblastoma 273


title: genomic DNA from medulloblastoma_NMB674

description: medulloblastoma 272


title: genomic DNA from medulloblastoma_NMB673

description: medulloblastoma 271


title: genomic DNA from medulloblastoma_NMB720

description: medulloblastoma 293


title: genomic DNA from medulloblastoma_NMB712

description: medulloblastoma 286


title: genomic DNA from medulloblastoma_NMB719

description: medulloblastoma 292


title: genomic DNA from medulloblastoma_NMB662

description: medulloblastoma 265


title: genomic DNA from medulloblastoma_NMB738

description: medulloblastoma 307


title: genomic DNA from medulloblastoma_NMB651

description: medulloblastoma 263

value: MBEN


title: genomic DNA from medulloblastoma_NMB667

description: medulloblastoma 267


title: genomic DNA from medulloblastoma_NMB645

description: medulloblastoma 259


title: genomic DNA from medulloblastoma_NMB732

description: medulloblastoma 301


title: genomic DNA from medulloblastoma_NMB708

description: medulloblastoma 283


title: genomic DNA from medulloblastoma_NMB765

description: medulloblastoma 328


title: genomic DNA from medulloblastoma_NMB649

description: medulloblastoma 262


title: genomic DNA from medulloblastoma_NMB63

description: medulloblastoma 252


title: genomic DNA from medulloblastoma_NMB713

description: medulloblastoma 287


title: genomic DNA from medulloblastoma_NMB608

description: medulloblastoma 237


title: genomic DNA from medulloblastoma_NMB707

description: medulloblastoma 282


title: genomic DNA from medulloblastoma_NMB594

description: medulloblastoma 232


title: genomic DNA from medulloblastoma_NMB706

description: medulloblastoma 281


title: genomic DNA from medulloblastoma_NMB676

description: medulloblastoma 274


title: genomic DNA from medulloblastoma_NMB64

description: medulloblastoma 258


title: genomic DNA from medulloblastoma_NMB546

description: medulloblastoma 215


title: genomic DNA from medulloblastoma_NMB553

description: medulloblastoma 219


title: genomic DNA from medulloblastoma_NMB537

description: medulloblastoma 213


title: genomic DNA from medulloblastoma_NMB555

description: medulloblastoma 221


title: genomic DNA from medulloblastoma_NMB549

description: medulloblastoma 217


title: genomic DNA from medulloblastoma_NMB617

description: medulloblastoma 243


title: genomic DNA from medulloblastoma_NMB502

description: medulloblastoma 200


title: genomic DNA from medulloblastoma_NMB497

description: medulloblastoma 197


title: genomic DNA from medulloblastoma_NMB496

description: medulloblastoma 196


title: genomic DNA from medulloblastoma_NMB621

description: medulloblastoma 247


title: genomic DNA from medulloblastoma_NMB59

description: medulloblastoma 229


title: genomic DNA from medulloblastoma_NMB583

description: medulloblastoma 227


title: genomic DNA from medulloblastoma_NMB560

description: medulloblastoma 222


title: genomic DNA from medulloblastoma_NMB486

description: medulloblastoma 189


title: genomic DNA from medulloblastoma_NMB670

description: medulloblastoma 269


title: genomic DNA from medulloblastoma_NMB612

description: medulloblastoma 240


title: genomic DNA from medulloblastoma_NMB580

description: medulloblastoma 225


title: genomic DNA from medulloblastoma_NMB485

description: medulloblastoma 188


title: genomic DNA from medulloblastoma_NMB495

description: medulloblastoma 195


title: genomic DNA from medulloblastoma_NMB482

description: medulloblastoma 185


title: genomic DNA from medulloblastoma_NMB619

description: medulloblastoma 245


title: genomic DNA from medulloblastoma_NMB548

description: medulloblastoma 216


title: genomic DNA from medulloblastoma_NMB476

description: medulloblastoma 182


title: genomic DNA from medulloblastoma_NMB483

description: medulloblastoma 186


title: genomic DNA from medulloblastoma_NMB462

description: medulloblastoma 176


title: genomic DNA from medulloblastoma_NMB625

description: medulloblastoma 249


title: genomic DNA from medulloblastoma_NMB49

description: medulloblastoma 191


title: genomic DNA from medulloblastoma_NMB554

description: medulloblastoma 220


title: genomic DNA from medulloblastoma_NMB498

description: medulloblastoma 198


title: genomic DNA from medulloblastoma_NMB441

description: medulloblastoma 169


title: genomic DNA from medulloblastoma_NMB436

description: medulloblastoma 164


title: genomic DNA from medulloblastoma_NMB471

description: medulloblastoma 180


title: genomic DNA from medulloblastoma_NMB479

description: medulloblastoma 184


title: genomic DNA from medulloblastoma_NMB406

description: medulloblastoma 146


title: genomic DNA from medulloblastoma_NMB477

description: medulloblastoma 183


title: genomic DNA from medulloblastoma_NMB409

description: medulloblastoma 148


title: genomic DNA from medulloblastoma_NMB460

description: medulloblastoma 175


title: genomic DNA from medulloblastoma_NMB474

description: medulloblastoma 181


title: genomic DNA from medulloblastoma_NMB380

description: medulloblastoma 129


title: genomic DNA from medulloblastoma_NMB465

description: medulloblastoma 178


title: genomic DNA from medulloblastoma_NMB440

description: medulloblastoma 168


title: genomic DNA from medulloblastoma_NMB439

description: medulloblastoma 167


title: genomic DNA from medulloblastoma_NMB414

description: medulloblastoma 152


title: genomic DNA from medulloblastoma_NMB466

description: medulloblastoma 179


title: genomic DNA from medulloblastoma_NMB445

description: medulloblastoma 171


title: genomic DNA from medulloblastoma_NMB437

description: medulloblastoma 165


title: genomic DNA from medulloblastoma_NMB359

description: medulloblastoma 109


title: genomic DNA from medulloblastoma_NMB363

description: medulloblastoma 113


title: genomic DNA from medulloblastoma_NMB347

description: medulloblastoma 106


title: genomic DNA from medulloblastoma_NMB382

description: medulloblastoma 131


title: genomic DNA from medulloblastoma_NMB379

description: medulloblastoma 128


title: genomic DNA from medulloblastoma_NMB386

description: medulloblastoma 135


title: genomic DNA from medulloblastoma_NMB417

description: medulloblastoma 155


title: genomic DNA from medulloblastoma_NMB413

description: medulloblastoma 151


title: genomic DNA from medulloblastoma_NMB370

description: medulloblastoma 120


title: genomic DNA from medulloblastoma_NMB371

description: medulloblastoma 121


title: genomic DNA from medulloblastoma_NMB32

description: medulloblastoma 90


title: genomic DNA from medulloblastoma_NMB367

description: medulloblastoma 117


title: genomic DNA from medulloblastoma_NMB435

description: medulloblastoma 163


title: genomic DNA from medulloblastoma_NMB269

description: medulloblastoma 77


title: genomic DNA from medulloblastoma_NMB341

description: medulloblastoma 102


title: genomic DNA from medulloblastoma_NMB400

description: medulloblastoma 142


title: genomic DNA from medulloblastoma_NMB345

description: medulloblastoma 104


title: genomic DNA from medulloblastoma_NMB33

description: medulloblastoma 97


title: genomic DNA from medulloblastoma_NMB324

description: medulloblastoma 92


title: genomic DNA from medulloblastoma_NMB272

description: medulloblastoma 78


title: genomic DNA from medulloblastoma_NMB328

description: medulloblastoma 95


title: genomic DNA from medulloblastoma_NMB364

description: medulloblastoma 114


title: genomic DNA from medulloblastoma_NMB191

description: medulloblastoma 59


title: genomic DNA from medulloblastoma_NMB325

description: medulloblastoma 93


title: genomic DNA from medulloblastoma_NMB139

description: medulloblastoma 21


title: genomic DNA from medulloblastoma_NMB143

description: medulloblastoma 25


title: genomic DNA from medulloblastoma_NMB156

description: medulloblastoma 34


title: genomic DNA from medulloblastoma_NMB264

description: medulloblastoma 74


title: genomic DNA from medulloblastoma_NMB252

description: medulloblastoma 67


title: genomic DNA from medulloblastoma_NMB253

description: medulloblastoma 68


title: genomic DNA from medulloblastoma_NMB135

description: medulloblastoma 18


title: genomic DNA from medulloblastoma_NMB254

description: medulloblastoma 69


title: genomic DNA from medulloblastoma_NMB168

description: medulloblastoma 37


title: genomic DNA from medulloblastoma_NMB278

description: medulloblastoma 81


title: genomic DNA from medulloblastoma_NMB141

description: medulloblastoma 23


title: genomic DNA from medulloblastoma_NMB138

description: medulloblastoma 20


title: genomic DNA from medulloblastoma_NMB123

description: medulloblastoma 9


title: genomic DNA from medulloblastoma_NMB200

description: medulloblastoma 62


title: genomic DNA from medulloblastoma_NMB119

description: medulloblastoma 8


title: genomic DNA from medulloblastoma_NMB118

description: medulloblastoma 7


title: genomic DNA from medulloblastoma_NMB116

description: medulloblastoma 6


title: genomic DNA from medulloblastoma_NMB131

description: medulloblastoma 15


title: genomic DNA from medulloblastoma_NMB128

description: medulloblastoma 13


title: genomic DNA from medulloblastoma_NMB181

description: medulloblastoma 49


title: 19+ sorted_ Normal Control_ rep_ 2_gene_expression

city: New Delhi

first: Ritu

last: Gupta

state: Delhi

address: Dr. B.R.A.IRCH, Ansari Nagar

department: Laboratory Oncology

country: India

institute: All India Institute of Medical Sciences, New Delhi

description:
NC3
Gene expression data

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene expression array v2 (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with GE Wash buffer 2 at 37°C (Agilent).

scan_protocol: After washing, slides were scanned immediately on the Agilent DNA Microarray Scanner (G2565C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Age-matched pooled healthy Controls

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input  labelling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the mirVana total RNA isolation kit (Thermofisher Scientific, MA, USA) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: disease status

value: Healthy

value: whole blood

tag: cell type

value: 19+ sorted cells


title: CLL_Mutated_rep9_gene_expression

description:
S25
Gene expression data

source_name: IGHV Mutated

value: CLL

tag: ighv status

value: mutated

value: mononuclear cells

tag: rai stage

value: II

value: Female


title: CLL_Mutated_rep10_gene_expression

description:
S26
Gene expression data

value: Male


title: CLL_Mutated_rep8_gene_expression

description:
S24
Gene expression data

value: I


title: CLL_Unmutated_rep10_gene_expression

description:
S17
Gene expression data

source_name: IGHV Unmutated

value: wildtype


title: genomic DNA from medulloblastoma_NMB258

description: medulloblastoma 72

value: medulloblastoma

value: primary medulloblastoma

value: M

value: CLA


title: genomic DNA from medulloblastoma_NMB115

description: medulloblastoma 5


title: CLL_Mutated_rep6_gene_expression

description:
S22
Gene expression data


title: CLL_Mutated_rep5_gene_expression

description:
S21
Gene expression data


title: CLL_Mutated_rep3_gene_expression

description:
S19
Gene expression data


title: CLL_Unmutated_rep7_gene_expression

description:
S13
Gene expression data


title: CLL_Unmutated_rep11_gene_expression

description:
S18
Gene expression data


title: CLL_Mutated_rep4_gene_expression

description:
S20
Gene expression data


title: CLL_Unmutated_rep4_gene_expression

description:
S5
Gene expression data


title: genomic DNA from medulloblastoma_PNET30019

description: medulloblastoma 401


title: CLL_Unmutated_rep5_gene_expression

description:
S6
Gene expression data


title: CLL_Unmutated_rep9_gene_expression

description:
S16
Gene expression data


title: CLL_Unmutated_rep8_methylation

description:
S13
Human DNA Methylation Microarray 244k

hyb_protocol: Nine mg each of Cy3 labelled input DNA (Specific activity>25) and Cy5 labelled immunoprecipitated DNA (Specific activity>20)  alongwith Cot-1 DNA, 10X aCGH blocking agent and 2XHI-RPM hybridisation buffer was incubated at 98° and 37°C for 3 and 30 minutes respectively. Finally, 490ml of the sample mixture was hybridized on a human DNA Methylation Microarray 1x244k slide (G4495A) at 67°C for 40 hours in a rotating hybridisation oven (Agilent). After hybridisation, slides were washed sequentially in Oligo aCGH/ChIP-on-Chip wash buffer 1 and 2  (maintained at 37°C) for 5 and 1 minute respectively.

scan_protocol: After washing, slides were scanned immediately on the Agilent DNA Microarray Scanner (G2565C) using two color scan setting for 1x244K array slides (Scan Area 61x21.6 mm, Scan resolution 3um).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0 (Agilent) using default parameters (protocol ChIP_11 and Grid: 023795_D_F_20091014) to obtain background subtracted and spatially detrended Processed Signal intensities.  Log-ratio data for each probe was normalized based on the Tm values.

label: Cyanine 5

source_name: IGHV Unmutated_Immunoprecipitated DNA

label_protocol: Six mg of genomic DNA was digested with MseI restriction enzyme (New England Biolabs Inc., Ipswich, MA, USA). One fraction (1mg) of the restriction digested DNA was processed further for immunoprecipitation (labelled with anti-5 methyl cytidine antibody (Abcam, Cambridge, UK) overnight at 4°C and immunoprecipitated with protein A agarose beads (Invitrogen, Carlsbad, CA, USA), and another fraction (250ng) was used as the input DNA. Both immunoprecipitated  DNA and input DNA (only MseI digested DNA) was purified using phenol-chloroform:isoamyl alcohol (25:24:1); and amplified using whole genome amplification kit (Sigma Aldrich, St. Louis, MO, USA). One mg of Input as well as IP DNA was labelled with Cy3- and Cy5-dUTP respectively by SureTag DNA Labelling kit (Agilent Technologies, Santa Clara, CA, USA,).  Dye incorporation and DNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Genomic DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany). The  yield and purity of DNA was assessed using Nano Drop 1000 (Thermo Scientific, Waltham, MA) and  integrity was confirmed by agarose gel electrophoresis.

value: Whole blood

source_name: IGHV Unmutated_input DNA


title: CLL_Unmutated_rep9_methylation

description:
S14
Human DNA Methylation Microarray 244k


title: CLL_Unmutated_rep3_gene_expression

description:
S4
Gene expression data


title: 19+ sorted_Normal Control_ rep_ 1_gene_expression

description:
NC2
Gene expression data


title: genomic DNA from medulloblastoma_NMB113

description: medulloblastoma 4


title: CLL_Mutated_rep7_gene_expression

description:
S23
Gene expression data


title: CLL_Mutated_rep1_gene_expression

description:
S10
Gene expression data


title: CLL_Unmutated_rep1_gene_expression

description:
S2
Gene expression data


title: 19+ sorted_Normal Control_ rep_ 3_methylation

description:
NC3
Human DNA Methylation Microarray 244k

source_name: Age matched healthy Pooled control_Immunoprecipitated DNA

value: healthy

source_name: Age matched healthy controls_input DNA


title: CLL_Mutated_rep5_methylation

description:
S11
Human DNA Methylation Microarray 244k

source_name: IGHV Mutated_Immunoprecipitated DNA

source_name: IGHV Mutated_input DNA


title: CLL_Mutated_rep2_gene_expression

description:
S11
Gene expression data


title: CLL_Unmutated_rep6_gene_expression

description:
S12
Gene expression data


title: CLL_Mutated_rep1_methylation

description:
S7
Human DNA Methylation Microarray 244k


title: Control rat5

city: Beijing

first: Hui

last: Yang

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

country: China

institute: China National Center for Food Safety Risk Assessment (CFSA)

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Control

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: male

tag: sample group

value: normal diet control without NMBA treatment

value: Esophageal epithelium


title: NMBA rat3

source_name: NMBA

value: NMBA treatment plus normal diet


title: NMBA rat2


title: CLL_Unmutated_rep2_gene_expression

description:
S3
Gene expression data

value: CLL

value: whole blood


title: NMBA rat1


title: CLL_Unmutated_rep6_methylation

description:
S6
Human DNA Methylation Microarray 244k

value: mononuclear cells

value: II


title: CLL_Unmutated_rep5_methylation

description:
S5
Human DNA Methylation Microarray 244k

value: Female


title: 19+ sorted_Normal Control_ rep_ 1_methylation

description:
NC1
Human DNA Methylation Microarray 244k

value: 19+ sorted cells


title: 19+ sorted_ Normal Control_ rep_ 2_methylation

description:
NC2
Human DNA Methylation Microarray 244k


title: Control rat4


title: CLL_Unmutated_rep4_methylation

description:
S4
Human DNA Methylation Microarray 244k

value: wildtype

value: I


title: NMBA rat4


title: CLL_Unmutated_rep7_methylation

description:
S12
Human DNA Methylation Microarray 244k

value: Male


title: NMBA+Gamma enriched-T rat3

source_name: NMBA+Gamma enriched-T

value: NMBA plus gamma enriched-tocopherol intervention


title: CLL_Unmutated_rep1_methylation

description:
S1
Human DNA Methylation Microarray 244k


title: Control rat3


title: Control rat2


title: CLL_Mutated_rep4_methylation

description:
S10
Human DNA Methylation Microarray 244k

value: mutated


title: NMBA+Gamma enriched-T rat4


title: NMBA+Gamma enriched-T rat1


title: NMBA+Delta-T rat5

source_name: NMBA+Delta-T

value: NMBA plus Delta-tocopherol intervention


title: NMBA rat5


title: CLL_Unmutated_rep2_methylation

description:
S2
Human DNA Methylation Microarray 244k

value: Whole blood


title: NMBA+Gamma enriched-T rat5

value: male


title: CLL_Mutated_rep2_methylation

description:
S8
Human DNA Methylation Microarray 244k


title: Control rat1

value: normal diet control without NMBA treatment


title: CLL_Unmutated_rep3_methylation

description:
S3
Human DNA Methylation Microarray 244k


title: CLL_Mutated_rep3_methylation

description:
S9
Human DNA Methylation Microarray 244k


title: NMBA+Delta-T rat4

value: Esophageal epithelium


title: NMBA+Delta-T rat1


title: NMBA+Gamma enriched-T rat2


title: NMBA+Delta-T rat3


title: NMBA+Delta-T rat2


title: NMBA+Alpha-T rat4

source_name: NMBA+Alpha-T

value: NMBA plus Alpha-tocopherol intervention


title: NMBA+Alpha-T rat5


title: NMBA+Alpha-T rat1


title: MDA-MB-231 treated to resistance (TTR), replicate 1

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

description: MDA-MB-231_TTR_1_LD020112plus125_untreated.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 1.1 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed and normalized by using Affymetrix Power Tools (apt-probeset-summarize) with RMA.

source_name: MDA-MB-231 treated to resistance (TTR)

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

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

tag: cell line

tag: treated

value: to resistance (TTR)


title: MDA-MB-231 treated to resistance (TTR), replicate 2

description: MDA-MB-231_TTR_2_LD020612plus125_untreated.CEL


title: NMBA+Alpha-T rat2

tag: gender


title: MDA-MB-231 treated to resistance (TTR) with TRAIL, replicate 2

description: MDA-MB-231_TTR_TRAIL_2_LD020612plus125_TRAIL100ng_per_ml_2h.CEL

value: to resistance (TTR) with TRAIL


title: MDA-MB-231 treated to resistance (TTR), replicate 3

description: MDA-MB-231_TTR_3_LD020812plus125_untreated.CEL


title: NMBA+Alpha-T rat3


title: MDA-MB-231 treated to resistance (TTR) with TRAIL, replicate 1

description: MDA-MB-231_TTR_TRAIL_1_LD020112plus125_TRAIL100ng_per_ml_2h.CEL


title: MDA-MB-231 treated with TRAIL, replicate 3

description: MDA-MB-231_TRAIL_3_LD020812minus125_TRAIL100ng_per_ml_2h.CEL

source_name: MDA-MB-231 treated with TRAIL

value: with TRAIL


title: MDA-MB-231 untreated, replicate 3

description: MDA-MB-231_Parental_3_LD020812minus125_untreated.CEL

source_name: MDA-MB-231 untreated

value: none (baseline before treatment)


title: MDA-MB-231 treated with TRAIL, replicate 2

description: MDA-MB-231_TRAIL_2_LD020612minus125_TRAIL100ng_per_ml_2h.CEL


title: MDA-MB-231 treated to resistance (TTR) with TRAIL, replicate 3

description: MDA-MB-231_TTR_TRAIL_3_LD020812plus125_TRAIL100ng_per_ml_2h.CEL


title: MDA-MB-231 treated with TRAIL, replicate 1

description: MDA-MB-231_TRAIL_1_LD020112minus125_TRAIL100ng_per_ml_2h.CEL


title: MDA-MB-231 untreated, replicate 1

description: MDA-MB-231_Parental_1_LD20112minus125_untreated.CEL


title: MDA-MB-231 untreated, replicate 2

description: MDA-MB-231_Parental_2_LD020612minus125_untreated.CEL


title: Homo sapiens Small cell lung carcinoma cells NCIH446 siRNA control_cy5

status: Public on May 27 2017

first: Shi

last: Juan

address: 5 Dong Dan San Tiao

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College

description:
This sample is of Homo sapiens gastric carcinoma SGC-7901 transfected with siRNA agianst MTA2 (MTA2-homo-556: Sense：5'-3' CAGCCUGGCUGAUAGUAAUTT, Antisense：5'-3' AUUACUAUCAGCCAGGCUGTT; MTA2-homo-2364:Sense：5'-3' GCACCAAUGAGCCUAUUGUTT, Antisense：5'-3' ACAAUAGGCUCAUUGGUGCTT; MTA2-homo-409:Sense：5'-3' GGUGGGAGAUUACGUCUAUTT, Antisense：5'-3' AUAGACGUAAUCUCCCACCTT)
1--2.gpr

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

data_processing: Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

source_name: gastric cancer cell line SGC-7901

label_protocol: Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit; 4) Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).

growth_protocol: Homo sapiens Small cell lung carcinoma cells NCIH446  was grown to Logarithmic phase phase (5% CO2,at 37°C ) in RPMI1640 (Gibco, Eggenstein, Germany) supplemented with 10% (vol) fetal bovine serum (10106078, Gibco) and 100U/ml penicillin,transfected with siRNA control 20nmol/ml for 48 h

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Homo sapiens Small cell lung carcinoma cells NCIH446 was grown to Logarithmic phase phase (5% CO2,at 37°C ) in RPMI1640 (Gibco, Eggenstein, Germany) supplemented with 10% (vol) fetal bovine serum (10106078, Gibco) and 1% (vol) penicillin (15140114, Gibco) ,transfected with siRNA negative control or siRNAs against  Follitin1 for 48h.

value: Small cell lung carcinoma


title: Homo sapiens Small cell lung carcinoma cells NCIH446 siRNA against Follitin1_cy3

description:
This sample is of Homo sapiens gastric carcinoma SGC-7901 transfected with vector(pCDH-CMV-MCS-EF1-GreenPuro-CD511B-1, SBI, )
3--4.gpr

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).


title: Homo sapiens Small cell lung carcinoma cells NCIH446 siRNA control_cy3

description:
This sample is of Homo sapiens gastric carcinoma SGC-7901 transfected with siRNA normal control (Sense：5'-3'UUCUCC GAA CGU GUC ACGUTT, Antisense：5'-3'ACG UGA CAC GUU CGG AGA ATT). It is the control group
1--2.gpr


title: sub-lethal heat treated SMMC-7721 Cell Replicate 2

city: Chongqing

first: qingsong

last: deng

state: Chongqing

address: Gaotanyan, NO.30

department: hepatobiliary surgery

institute: Southwest Hospital, Third Military Medical University

description:
raw data file:
C2 vs. S2.txt
Biological replicate 2 of 3. sub-lethal heat treated cells

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by lowess normalization.

source_name: sub-lethal heat treated SMMC-7721 Cell

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: Human SMMC-7721 HCC cells were maintained in high-glucose Dulbecco’s modiﬁed Eagle’s medium (DMEM) (GIBCO, Invitrogen) supplemented with 10% fetal bovine serum (FBS) (GIBCO, Invitrogen, Australia) and 1% penicillin-streptomycin (GIBCO, Invitrogen) at 37°C in a 5% CO2 atmosphere.

treatment_protocol: SMMC-7721 cells were sub-lethally heated (50°C) for 10 min. Heat treatments were carried out by sealing the culture bottle with Parafilm, and submerging the plates in a water bath (HH·W21·600S, Shanghai, China) set at 50°C and returned to the incubation chamber (SERIES II WATER JACKET, Thermo Scientific) for 24 h at 37°C. Three independent experiments were performed.

value: SMMC-7721 cells (TCHu 52)

value: hepatocellular carcinoma (HCC) cells

tag: passage

tag: treated with

value: sub-lethal heat


title: Control SMMC-7721 Cell Replicate 1

description:
raw data file:
C1 vs. S1.txt
Biological replicate 1 of 3. control untreated cells

source_name: SMMC-7721 cells

value: none (untreated control)


title: sub-lethal heat treated SMMC-7721 Cell Replicate 1

description:
raw data file:
C1 vs. S1.txt
Biological replicate 1 of 3. sub-lethal heat treated cells


title: Homo sapiens Small cell lung carcinoma cells NCIH446 siRNA against Follitin1_cy5

description:
This sample is of Homo sapiens gastric carcinoma SGC-7901 transfected with vector
3--4.gpr


title: Control SMMC-7721 Cell Replicate 3

description:
raw data file:
C3 vs. S3.txt
Biological replicate 3 of 3. control untreated cells


title: sub-lethal heat treated SMMC-7721 Cell Replicate 3

description:
raw data file:
C3 vs. S3.txt
Biological replicate 3 of 3. sub-lethal heat treated cells


title: AD-MSC-replicate 2

status: Public on May 26 2017

city: Indianapolis

first: Leni

last: Moldovan

state: IN

address: 980 W Walnut St., Rm. C422

department: Ophthalmology

institute: Indiana University

hyb_protocol: Fluidics Station 450, standard protocol for Gene ST 100-Format arrays (FS450_0002).

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G.

data_processing: Partek Genomics Suite v.6.16.0419, and Affymetrix Expression Console + Affymetrix Transcriptome Analysis Console v.3.

organism: Equus caballus

source_name: Adipose tissue, MSCs, untreated (control)

label_protocol: NuGEN Encore Biotin module, standard protocol.

growth_protocol: MSCs were isolated using Ficoll-paque and plated on uncoated, plastic, flat bottom, 6-well plates. They were grown in a 1:1 mix of Ham's F-12 (Lonza, Basel, Switzerland) and low-glucose DMEM (Gibco®, Carlsbad, California) supplemented with 15% fetal bovine serum (FBS) (Thermo Scientific, Waltham, Massachusetts) and Gibco® antibiotic-antimycotic solution. After 96 hours, non-adherent cells were removed, and the remaining cells were used for RNA extraction.

extract_protocol: Qiagen RNeasy Mini standard protocol. 100 ng total RNA were used for microarrays (processed with Ovation® RNA Amplification System V2).

treatment_protocol: Horses were treated by electroacupuncture, and blood for microarray analysis was collected after 2 hrs. Control horses (for BM-MSC and AD-MSC isolation) received no treatment.

value: Tailhead fat

value: Adipose tissue-derived mesenchymal stem cells (AD-MSC)

tag: treatment


title: BM-MSC-replicate 1

description: Horse 1

source_name: Bone marrow, MSCs, untreated (control)

value: Bone marrow

value: Bone marrow-derived mesenchymal stem cells (BM-MSC)


title: EA-ADSC-replicate 1

description: Horse R1

source_name: Peripheral blood, MSCs, electroacupuncture

value: Blood mononuclear cells

value: Peripheral blood-derived mesenchymal cells (EA-ADSC), mobilized by electroacupuncture

value: electroacupuncture (EA)


title: EA-ADSC-replicate 2

description: Horse Ap2


title: AD-MSC-replicate 1


title: Control SMMC-7721 Cell Replicate 2

description:
raw data file:
C2 vs. S2.txt
Biological replicate 2 of 3. control untreated cells


title: AD-MSC-replicate 3


title: BM-MSC-replicate 2

description: Horse 2


title: Adjacent non-tumor tissue, 37

city: Singapore

first: Surya Pavan

last: Yenamandra

address: 30, Biopolis street, #07-01 Matrix

country: Singapore

institute: Bioinformatics Institute

description: Sample name: ANTT37

hyb_protocol: Illumina HumanHT-12 v4 Expression BeadChip arrays using Illumina standard protocol.

scan_protocol: BeadChips were scanned using the Illumina BeadArray Reader and the BeadScan Software (Illumina).

data_processing: Raw data was obtained via the GenomeStudio; data have been normalized using the RSN method from R-package lumi.

label: Biotin

source_name: adjacent non-tumor tissue

label_protocol: 500 ng of RNA from each sample were reverse transcribed into cDNA and thereby labeled with biotin-UTP following manufacturer protocols.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: diagnosis

value: hepatocellular carcinoma (HCC)

tag: patient id

value: adjacent non-tumor liver tissue


title: Adjacent non-tumor tissue, 23

description: Sample name: ANTT23


title: EA-ADSC-replicate 3

description: Horse Am3


title: Adjacent non-tumor tissue, 82

description: Sample name: ANTT82


title: Adjacent non-tumor tissue, 102

description: Sample name: ANTT102


title: BM-MSC-replicate 3

description: Horse 3


title: Adjacent non-tumor tissue, 14

description: Sample name: ANTT14


title: CLL_Unmutated_rep8_gene_expression

description:
S15
Gene expression data

source_name: IGHV Unmutated

value: CLL

value: wildtype

value: whole blood

value: mononuclear cells

value: I

value: Female

tag: age


title: Adjacent non-tumor tissue, 72

description: Sample name: ANTT72

tag: tissue


title: Adjacent non-tumor tissue, 70

description: Sample name: ANTT70


title: Adjacent non-tumor tissue, 4

description: Sample name: ANTT4


title: Adjacent non-tumor tissue, 11

description: Sample name: ANTT11


title: Adjacent non-tumor tissue, 84

description: Sample name: ANTT84


title: Adjacent non-tumor tissue, 47

description: Sample name: ANTT47


title: Adjacent non-tumor tissue, 31

description: Sample name: ANTT31


title: Adjacent non-tumor tissue, 34

description: Sample name: ANTT34


title: Adjacent non-tumor tissue, 103

description: Sample name: ANTT103


title: Adjacent non-tumor tissue, 36

description: Sample name: ANTT36


title: Adjacent non-tumor tissue, 26

description: Sample name: ANTT26


title: Adjacent non-tumor tissue, 22

description: Sample name: ANTT22


title: Adjacent non-tumor tissue, 3

description: Sample name: ANTT3


title: Adjacent non-tumor tissue, 7

description: Sample name: ANTT7


title: Adjacent non-tumor tissue, 32

description: Sample name: ANTT32


title: Adjacent non-tumor tissue, 5

description: Sample name: ANTT5


title: Adjacent non-tumor tissue, 99

description: Sample name: ANTT99


title: Adjacent non-tumor tissue, 98

description: Sample name: ANTT98


title: Adjacent non-tumor tissue, 6

description: Sample name: ANTT6


title: Adjacent non-tumor tissue, 97

description: Sample name: ANTT97


title: Adjacent non-tumor tissue, 78

description: Sample name: ANTT78


title: Adjacent non-tumor tissue, 16

description: Sample name: ANTT16


title: Adjacent non-tumor tissue, 40

description: Sample name: ANTT40


title: Adjacent non-tumor tissue, 76

description: Sample name: ANTT76


title: Adjacent non-tumor tissue, 18

description: Sample name: ANTT18


title: Adjacent non-tumor tissue, 57

description: Sample name: ANTT57


title: Adjacent non-tumor tissue, 88

description: Sample name: ANTT88