title: expt.773 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.773 extraction4_array1 channel_1

value: embryo-derived cell-line

value: late embryonic stage


title: expt.815 extraction2_array1

status: Public on Mar 09 2011

type: genomic

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: channel ch1 is input DNA;

hyb_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

scan_protocol: Standard Affymetrix Array Scanning Protocol was used

data_processing: M-value normalization protocol. The log-intensity ratio values (M-values) are calculated for all perfect match (PM) probes as log2(ChIP intensity) - log2(input intensity). The M values are then shifted so that the mean is equal to 0.

label: biotin

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: expt.815 extraction2_array1 channel_1

extract_protocol:
1. Grow cell cultures in large T-flasks (175-225cm2) to a density of~5x106 cells/ml. Combine the content of 2-3 flasks in one. Immediately proceed with the following steps.   2. Add 37% formaldehyde (Sigma) to final concentration 1.8% directly to the culture incubate for 10min at 250C on a rotating or rocking platform.   3. Stop reaction by adding 1.25M glycine pH 7.0 to each culture to the final concentration of 125mM. Mix well, within next 5 min aliquot cell suspension into 50ml falcon tubes and accumulate them on ice.   4. Pellet fixed cells by spinning for 2? at 1500g, +40C. Use swinging bucket rotor.   5. Resuspend each pellet in 5ml of sterile 1xPBS, pool suspensions together.   6. Pellet the cells by spinning for 2? at 1500g, +40C.   7. Resuspend the cells in 10ml of ChIP wash A solution. Transfer suspension to a new 15ml Falcon tube. Wash fixed cells for 10min at +40C using rotating wheel. Pellet as above.   8. Thoroughly resuspend fixed cells in 10ml of  ChIP wash B solution, wash for 10min at +40C. Use rotating wheel.
After treatment with formaldehyde, Drosophila tissue culture cells were lysed with SDS and sonication (on ice) in the presence of protease inhibitors.  The resulting chromatin was treated with non-ionic detergents at physiological concentrations of monovalent cations.  Ribonucleic acid was removed by RNAse A, and the DNA was purified using SDS, proteinase K, and organic extraction, followed by ethanol precipitation.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C.   2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin.   3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel.   4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel.   5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C.   6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C.   7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C.   8. Transfer samples at +650C, incubate 6h.   9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution).  10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h.  11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH  12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C.  13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).

tag: cell line

tag: tissue

tag: developmental stage

tag: genotype

value: se/e

tag: Sex

value: Female


title: ASH1-Cy5 labeled (2)

status: Public on Mar 10 2011

type: RNA

city: Stanford

first: Dan

last: Klass

state: CA

address: 259 Campus Drive Beckman Rm 439

department: Biochemistry

country: USA

institute: Stanford University

description:
Simple annotation: mRNA vs Total RNA Comparison, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78600.gif

hyb_protocol: not provided

scan_protocol: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Total mRNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Total mRNA

source_name: ASH1 IVT mRNA


title: SLE-215_Fresh_Neutro

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: Fresh neutrophils isolated from this SLE patient

hyb_protocol: Hybridize 6-Sample Beadchip

scan_protocol: SentrixScanVersion 2.3.0.13

data_processing: The data were analyzed using BeadStudio version 1.5.1.3 using the average chip normalization method.

organism: Homo sapiens

source_name: Neutrophils from SLE Patient

label_protocol: Biotynlated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion.

extract_protocol: RNeasy Mini

tag: cell type

value: Neutrophil

tag: disease state

value: SLE

tag: age

tag: gender

value: F

tag: race

value: Hispanic

tag: treatment


title: salinity root 1

city: Tsukuba

first: Hiroshi

last: Mizuno

address: 2-1-2 Kannondai

department: Genome and Biodiversity Research

country: Japan

hyb_protocol: DNA microarrays were hybridized for 16 h with 825 ng of Cy3- and Cy5-labeled probes from salinity-stressed plants or unstressed plants.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Lowess normalized raw signal intensities for all probe sets from each array were extracted by using GeneSpring (GX10) software.Parts of the signals were removed for further analysis if they were not positive, significant, or above background levels.

organism: Oryza sativa

source_name: Nipponbare

label_protocol: 400 ng of total RNAs was used for Cy3- or Cy5-labeled probes.The labeling, hybridization experiments and array scanning were performed at an open laboratory run by the DNA Bank of the National Institute of Agrobiological Sciences.

growth_protocol: Seeds of rice (Oryza sativa L. ‘Nipponbare’) were germinated at 28 °C in a sterilized germination tray. The seedlings had been grown for 7 days at 28 °C.

extract_protocol: Total RNA was extracted by using an RNeasy Plant kit (Qiagen). RNA quality was calculated with a Bioanalyzer 2100 algorithm (Agilent Technologies); high-quality (RNA Integrity Number >8) RNA was used.

treatment_protocol: After 1 h of exposure to 150 mM NaCl solution, roots and shoots were collected and immediately frozen in liquid nitrogen.

value: root

tag: hour

tag: cultivar

value: Nipponbare


title: expt.596 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.596 extraction4_array1 channel_1

label_protocol: 1. Prehybridize array for 1 hr in 200ml of 1xMES-Triton at 450C with 45 rpm rotation.   2. Incubate hybridization cocktail for 10min at 1000C then 10min at 450C. Spin at max speed for 3 min at RT. Transfer the supernatant to new tube. Spin for 3 more minutes use 200ml of resulted supernatant for hybridization.   3. Hybridize 18hr at 450C with 45 rpm rotation.   4. Use fluidics station EukGE-WS2v4 protocol (Affymetrix) for washing and staining.

value: dorsal mesothoracic disc

value: third instar larval stage

value: Male


title: H158_Fresh_Neutro

description: Fresh neutrophils isolated from this healthy donor

source_name: Neutrophils from Healthy control

value: control

value: M

value: Caucasian


title: salinity shoot 1

institute: National Institute of Agrobiological Sciences

value: shoot


title: ASH1-Cy3 labeled (2)

description:
Simple annotation: mRNA vs Total RNA Comparison, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78601.gif

value: ASH1 IVT mRNA

tag: experiment


title: expt.597 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.597 extraction2_array1 channel_1


title: SLE-216_Fresh_Neutro


title: expt.112 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.112 extraction2_array1 channel_1

value: embryo-derived cell-line

value: late embryonic stage


title: expt.814 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.814 extraction4_array1 channel_1

value: se/e

value: Female


title: P19_undifferentiation_rep2

city: Nomi

first: Hitoshi

last: Suzuki

state: Ishikawa

address: 1-1 Asahidai

department: CNMT

institute: JAIST

description: Day 00

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the Kanazawa Medical University.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
RMA expression value derived from Expression Console software; core-exon analysis
program-name = Expression Console
affymetrix-algorithm-name = plier-exon-core : dabg
affymetrix-algorithm-version = 2.0
Probe group file used in analysis = MoEx-1_0-st-v1.r2.pgf

organism: Mus musculus

source_name: P19 cell, undifferentiation, Day 0

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: cells were culture in alpha-MEM with 10% FBS under the 5% CO2 condition. cells were treated with 1 µM RA by aggregation culture for 4 days, and were cultured additional 3 days for neuright growth

extract_protocol: total RNA was isolated from P19 cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

value: embryonic carcinoma (EC) P19 cell line

tag: agent

value: untreated

tag: time

value: Day 0

value: P19 cell, undifferentiation


title: SLE-214_Fresh_Neutro

value: Neutrophil

value: SLE

value: F

value: Hispanic


title: expt.774 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.774 extraction2_array1 channel_1

tag: cell line

value: Male


title: expt.111 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.111 extraction4_array1 channel_1

tag: tissue


title: expt.289 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.289 extraction2_array1 channel_1

value: dorsal mesothoracic disc

tag: developmental stage

value: third instar larval stage


title: expt.453 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.453 extraction2_array1 channel_1


title: expt.724 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.724 extraction4_array1 channel_1


title: expt.290 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.290 extraction2_array1 channel_1

tag: genotype


title: expt.291 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.291 extraction4_array1 channel_1

tag: Sex


title: expt.288 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.288 extraction4_array1 channel_1


title: expt.812 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.812 extraction4_array1 channel_1


title: expt.813 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.813 extraction2_array1 channel_1


title: P19_undifferentiation_rep1

description: Day 0


title: P19_neuronal_rep1

description: Day 7

source_name: P19 neuronal cell, Day 7

value: retinoic acid (RA)

value: Day 7

value: P19 neuronal cell


title: expt.289 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.289 extraction4_array1 channel_1


title: P19_earlyglial_rep2

description: Day 010

source_name: P19 early glial cell, Day 10

value: Day 10

value: P19 early glial cell


title: expt.288 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.288 extraction2_array1 channel_1


title: expt.566 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.566 extraction4_array1 channel_1

value: embryo-derived cell-line

value: late embryonic stage


title: expt.644 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.644 extraction2_array1 channel_1


title: salinity shoot 2

source_name: Nipponbare

value: shoot

value: Nipponbare


title: expt.823 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.823 extraction4_array1 channel_1

value: CNS-derived cell-line

value: y v f mal

value: Unknown


title: 8D hippocampus_transcription_low_LGABN_20080829 2

type: mixed

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

institute: McGill University

description: comparison of hippocampus RNA expression in offspring of low and high LGABN mothers

hyb_protocol: All the steps of hybridization and washing were performed following the Agilent protocol for chip-on-chip analysis.

scan_protocol: Scanning was performed using the Agilent Technologies Scanner G2505B.

data_processing: The value is background subtracted and log2R quantile normalized.

organism: Rattus norvegicus

label_protocol: At least 825ng of purified sample Cy3-labelled cDNA was hybridized along with the identical amount of purified Cy5-labelled genomic DNA of the sample subject or vice versa. Yeast tRNA and Cot-1 DNA were added to the hybridization mix to minimize cross-hybridization between repetitive elements.

growth_protocol: days 1-22 with mother; days 23-90 with same-sex, same-litter group

extract_protocol: Whole brains were removed from 90-day-old (adult) male High and Low LG adult offspring by rapid decapitation <1 min after removal from the home cage. The hippocampal tissue was dissected, snap-frozen on dry ice, and stored at -80.  cDNA was generated from a starting amount of 1-2ug of RNA using random hexamer primers.  Genomic DNA was sonicated on ice for a total of 3 min, using 5 sec pulses with 15 sec resting times to fragment the DNA to between 200 bp and 700 bp, as verified subsequently on a 1.5% agarose gel.

tag: frequency of maternal licking/grooming and arched-back nursing

value: low

tag: frequency maternal licking/grooming and arched-back nursing


title: salinity root 2

value: root


title: 8D hippocampus_transcription_low_LGABN_20080829 1


title: expt.671 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.671 extraction4_array1 channel_1


title: 4B hippocampus_transcription_high_LGABN_20080829 2

value: high


title: expt.565 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.565 extraction2_array1 channel_1

value: Male


title: 4AH hippocampus_transcription_high_LGABN_20080821 1


title: 8A hippocampus_transcription_low_LGABN_20080829 1


title: 4AH hippocampus_transcription_high_LGABN_20080821 2


title: expt.671 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.671 extraction2_array1 channel_1

value: third instar larval stage


title: 30A hippocampus_transcription_high_LGABN_20080829 2


title: 2AH hippocampus_transcription_low_LGABN_20080821 2


title: 4B hippocampus_transcription_high_LGABN_20080829 1


title: 30A hippocampus_transcription_high_LGABN_20080829 1


title: 8A hippocampus_transcription_low_LGABN_20080829 2


title: 12A hippocampus_transcription_high_LGABN_20080829 2


title: 10A hippocampus_transcription_low_LGABN_20080829 1


title: 12A hippocampus_transcription_high_LGABN_20080829 1


title: 2AH hippocampus_transcription_low_LGABN_20080821 1


title: expt.822 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.822 extraction2_array1 channel_1


title: 10A hippocampus_transcription_low_LGABN_20080829 2


title: 8 hippocampus_medip_low_LGABN_20080319 3

description: comparison of hippocampus DNA methylation and H3K9 acetylation in offspring of low and high LGABN mothers

label_protocol: 2ug of each of the input and bound fractions were labeled for the microarray hybridization.Cy3-dUTP and Cy5-dUTP (Perkin Elmer) were used to label the input and the bound fractions respectively. Cot-1 DNA was added to the hybridization mix to minimize cross-hybridization between repetitive element.

extract_protocol: Whole brains were removed from 90-day-old (adult) male High and Low LG adult offspring by rapid decapitation <1 min after removal from the home cage. The hippocampal tissue was dissected, snap-frozen on dry ice, and stored at -80. For H3K9 acetylation experiments, adult male High and Low LG adult offspring were perfused transcardially with ice-cold 0.9% saline followed by 4% paraformaldehyde after which whole brains were removed by rapid decapitation. Hippocampal tissue was dissected and stored overnight in 4% paraformaldehyde prior to freezing at -80.  DNA (2.g) was sonicated on ice for a total of 3 min, using 5 sec pulses with 15 sec resting times to fragment the DNA to between 200 bp and 700 bp, as verified subsequently on a 1.5% agarose gel. After denaturing, 1/10th of the each sample was removed as input DNA. The remainder of the sample was then precleared with sepharose beads, bound to anti-5 methylcytosine antibody (Calbiochem), washed, and eluted. PCR was performed to assess relative enrichment of an unmethylated plasmid DNA (GFP) versus an invitro methylated plasmid DNA (Luciferase). Samples were PCR purified (Genescript), quantified by nanodrop, and for each sample 100ng of input and immunoprecipitated DNA were subject to whole genome amplification (Sigma). Samples were again quantified to assess the results of WGA, and then labeled with Cy3 (Input) or Cy5 (mDIP) prior to hybridization to the microarray. Chromatin was immunoprecipitated using rabbit polyclonal anti-acetyl-histone H3 Lysine 9 antibody (Upstate Cell Signaling Solutions, Waltham, MA). One-tenth of the lysate was kept to quantify the amount of DNA present in different samples before immunoprecipitation (input). 5ul of the input and bound fractions were amplified using the Whole Genome Amplification kit (Sigma) to obtain a sufficient amount for labeling. The amplified DNA was purified with the PCR purification kit (Genscript).

tag: chip antibody

value: anti-5 methylcytosine antibody


title: 4 hippocampus_medip_high_LGABN_20080319 2


title: 4 hippocampus_medip_high_LGABN_20080319 1


title: 8 hippocampus_medip_low_LGABN_20080319 2


title: 4 hippocampus_medip_high_LGABN_20080319 3


title: 31 hippocampus_medip_high_LGABN_20080319 3


title: 8 hippocampus_medip_low_LGABN_20080319 1


title: 31 hippocampus_medip_high_LGABN_20080319 1


title: expt.936 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.936 extraction4_array1 channel_1


title: Chimp 3 liver at week 24

city: San Antonio

first: Bernadette

last: Guerra

state: Texas

department: Virology and Immunology

institute: Southwest Foundation for Biomedical Research

description: Gene expression data from chimpanzee liver at week 24 during an HAV infection.

hyb_protocol: Genome Explorations performed the hybridization.

scan_protocol: Genome Explorations performed the scanning.

data_processing: The data were analyzed with GCOS Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250.

organism: Pan troglodytes

source_name: liver, HAV infection, week 24

label_protocol: RNA was sent to Genome Explorations for labeling.

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

treatment_protocol: Chimpanzees were infected by intravenous challenge with the HM175 strain of HAV.

value: liver

value: hepatitis A virus (HAV) infection

tag: treatment duration

value: week 24

tag: chimpanzee identifier


title: Chimp 2 liver at week 26

description: Gene expression data from chimpanzee liver at week 26 during an HAV infection.

source_name: liver, HAV infection, week 26

value: week 26


title: P19_earlyglial_rep1

description: Day 10

value: embryonic carcinoma (EC) P19 cell line

value: retinoic acid (RA)

value: Day 10

tag: cell type

value: P19 early glial cell


title: 2 hippocampus_medip_low_LGABN_20080319 1


title: Chimp 3 liver at week 7

description: Gene expression data from chimpanzee liver at week 7 during an HAV infection.

source_name: liver, HAV infection, week 7

tag: treatment

value: week 7


title: Chimp 2 liver at week 14

description: Gene expression data from chimpanzee liver at week 14 during an HAV infection.

source_name: liver, HAV infection, week 14

value: week 14


title: Chimp 2 liver at week 4

description: Gene expression data from chimpanzee liver at week 4 during an HAV infection.

source_name: liver, HAV infection, week 4

value: week 4


title: 30 hippocampus_medip_high_LGABN_20080319 1


title: 2 hippocampus_medip_low_LGABN_20080319 2

value: low


title: 30 hippocampus_medip_high_LGABN_20080319 3


title: 120 hippocampus_h3k9acetylation_low_LGABN_20080820 2

value: rabbit polyclonal anti-acetyl-histone H3 Lysine 9 antibody


title: 31 hippocampus_medip_high_LGABN_20080319 2

value: high


title: 132 hippocampus_h3k9acetylation_low_LGABN_20080820 3


title: Chimp 2 liver at week 6

description: Gene expression data from chimpanzee liver at week 6 during an HAV infection.

source_name: liver, HAV infection, week 6

value: week 6


title: 120 hippocampus_h3k9acetylation_low_LGABN_20080820 3


title: Chimp 2 liver at week -6

description: Gene expression data from chimpanzee liver 6 weeks before HAV infection.

source_name: liver, baseline week -6

value: week -6


title: Chimp 3 liver at week 36

description: Gene expression data from chimpanzee liver at week 36 during an HAV infection.

source_name: liver, HAV infection, week 36

value: week 36


title: 132 hippocampus_h3k9acetylation_low_LGABN_20080820 2


title: 120 hippocampus_h3k9acetylation_low_LGABN_20080820 1


title: Chimp 2 liver at week 10

description: Gene expression data from chimpanzee liver at week 10 during an HAV infection.

source_name: liver, HAV infection, week 10

value: liver

value: week 10


title: Chimp 2 liver at week -12

description: Gene expression data from chimpanzee liver 12 weeks before HAV infection.

source_name: liver, baseline week -12

value: week -12


title: Chimp 2 liver at week 1

description: Gene expression data from chimpanzee liver at week 1 during an HAV infection.

source_name: liver, HAV infection, week 1

value: hepatitis A virus (HAV) infection

value: week 1


title: 2 hippocampus_medip_low_LGABN_20080319 3

value: anti-5 methylcytosine antibody


title: 30 hippocampus_medip_high_LGABN_20080319 2


title: Chimp 2 liver at week 3

description: Gene expression data from chimpanzee liver at week 3 during an HAV infection.

source_name: liver, HAV infection, week 3

value: week 3


title: 110B hippocampus_h3k9acetylation_high_LGABN_20080820 1


title: Chimp 2 liver at week 2

description: Gene expression data from chimpanzee liver at week 2 during an HAV infection.

source_name: liver, HAV infection, week 2

value: week 2


title: Chimp 2 liver at day 2

description: Gene expression data from chimpanzee liver at day 2 during an HAV infection.

source_name: liver, HAV infection, day 2

value: day 2


title: Chimp 3 liver at week 4


title: 110B hippocampus_h3k9acetylation_high_LGABN_20080820 2


title: 110B hippocampus_h3k9acetylation_high_LGABN_20080820 3


title: Chimp 1 liver at week 27

description: Gene expression data from chimpanzee liver at week 27 during an HAV infection.

source_name: liver, HAV infection, week 27

value: week 27


title: expt.566 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.566 extraction4_array1 channel_1

value: embryo-derived cell-line

value: late embryonic stage

value: Male


title: 132 hippocampus_h3k9acetylation_low_LGABN_20080820 1

value: rabbit polyclonal anti-acetyl-histone H3 Lysine 9 antibody

value: low


title: 110A hippocampus_h3k9acetylation_high_LGABN_20080820 2

value: high


title: 109 hippocampus_h3k9acetylation_low_LGABN_20080820 1


title: 110A hippocampus_h3k9acetylation_high_LGABN_20080820 3


title: 109 hippocampus_h3k9acetylation_low_LGABN_20080820 2


title: Chimp 1 liver at week 2


title: expt.773 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.773 extraction2_array1 channel_1


title: Chimp 1 liver at week 6

value: week 6


title: expt.774 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.774 extraction4_array1 channel_1


title: Chimp 1 liver at week 39

description: Gene expression data from chimpanzee liver at week 39 during an HAV infection.

source_name: liver, HAV infection, week 39

value: liver

value: week 39


title: Chimp 1 liver at week 10

value: week 10


title: expt.565 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.565 extraction2_array1 channel_1


title: Chimp 1 liver at week 1

value: hepatitis A virus (HAV) infection


title: 109 hippocampus_h3k9acetylation_low_LGABN_20080820 3

description: comparison of hippocampus DNA methylation and H3K9 acetylation in offspring of low and high LGABN mothers


title: 102 hippocampus_h3k9acetylation_high_LGABN_20080820 1


title: expt.391 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.391 extraction4_array1 channel_1

value: CNS-derived cell-line

value: third instar larval stage

value: y v f mal

value: Unknown


title: expt.423 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.423 extraction2_array1 channel_1


title: Chimp 1 liver at week 4

source_name: liver, HAV infection, week 4

value: week 4


title: expt.846 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.846 extraction4_array1 channel_1


title: expt.847 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.847 extraction2_array1 channel_1


title: 110A hippocampus_h3k9acetylation_high_LGABN_20080820 1


title: Chimp 1 liver at day 2

value: day 2


title: 10 hippocampus_medip_low_LGABN_20080319 2

value: anti-5 methylcytosine antibody


title: 102 hippocampus_h3k9acetylation_high_LGABN_20080820 2


title: 10 hippocampus_medip_low_LGABN_20080319 1


title: expt.530 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.530 extraction2_array1 channel_1

value: embryo-derived cell-line

value: late embryonic stage


title: expt.531 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.531 extraction4_array1 channel_1

value: Male


title: brain_72h_mouse38

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

country: Netherlands

institute: Amsterdam UMC

description: Common-reference sample was a pool of equal amounts of RNA from all the samples investigated, including additional samples from 5 mice that were fasted for 48 hours supplemented with vitamin B complex after 24 and 36 hours of fasting.

hyb_protocol: The microarrays were hybridized overnight with 200 µl hybridization mixture, consisting of 50 µl Cy3-and Cy5-labeled aRNA , 100 µl Formamide and 50 µl 4 x RPK0325 MicroArray Hybridization Buffer (Amersham Pharmacia Biosciences, Piscataway, NJ, USA) at 37°C and washed in an Automated Slide Processor (Amersham Pharmacia Biosciences, Piscataway, NJ, USA)

scan_protocol: Scanned on an Agilent G2565AA scanner. Spot intensities were quantified as artifact removed densities, using Array Vision software (version 6.0)

data_processing: Estimated foreground and background signals were extracted from the ArrayVision files. Quality control was performed on the raw data; two arrays did not pass our quality criteria because of spatial artifacts and one array (from liver and clustering with brain) was excluded from further analysis. Background correction was performed by using the normexp method (Bioconductor package limma) to adjust the foreground signal without introducing negative values. Resulting log-ratios were normalized per array by using print-tip loess. Control probes were downweighted to zero in the normalization step. The oligo library was re-annotated by aligning each oligo to the Ensembl assembly using a BLAT/BLAST search. If no hit was found, oligos were blasted to a set of sequences containing Refseq RNAs (version 22) and UniGene clusters (version 163) that could not be aligned with the genome. Using information from NCBI Refseq and Unigene identifierss were linked to an Entrez gene ID. These Entrez gene IDs were used as input for the Bioconductor package AnnBuilder, with which a annotation data package was created.

source_name: brain, 72 hours fasting, mouse 38

label_protocol: 1,5 µg of total RNA was amplified using the Amino Allyl MessageAmp aRNA kit (Ambion, Austin, Texas, USA), and labeled with Cy5 (experimental samples) and Cy3 (common reference) reactive dye according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from each of the frozen organs of eight animals per experimental group with TRIzol reagent (Invitrogen, Breda, The Netherlands), followed by a repeated phenol-chloroform extraction, LiCl precipitation, and additional purification using the RNeasy Mini Kit (Qiagen Benelux, Venlo, The Netherlands). The RNA quality was assessed using the RNA 6000 Nano LabChip® Kit in an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, USA). All samples had intact bands corresponding to 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had an RNA integrity number (RIN) > 8. Five out of eight animals per group were chosen based on the best RNA quality across all 5 tissues, so that the RNAs used in this study all originated from the same 5 mice per time point.

tag: strain

value: FVB

tag: mouse

value: brain

tag: timepoint

source_name: reference pool

value: reference pool


title: expt.1113 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1113 extraction4_array1 channel_1

value: se/e

value: Female


title: brain_72h_mouse35

source_name: brain, 72 hours fasting, mouse 35


title: Chimp 1 liver at week -14

description: Gene expression data from chimpanzee liver 14 weeks before HAV infection.

source_name: liver, baseline week -14

value: liver

value: week -14


title: brain_12h_mouse14

source_name: brain, 12 hours fasting, mouse 14


title: brain_72h_mouse36

source_name: brain, 72 hours fasting, mouse 36


title: brain_48h_mouse30

source_name: brain, 48 hours fasting, mouse 30


title: 10 hippocampus_medip_low_LGABN_20080319 3

value: low


title: expt.1114 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1114 extraction2_array1 channel_1


title: brain_72h_mouse40

source_name: brain, 72 hours fasting, mouse 40


title: expt.288 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.288 extraction4_array1 channel_1

value: dorsal mesothoracic disc

value: third instar larval stage


title: brain_12h_mouse12

source_name: brain, 12 hours fasting, mouse 12


title: expt.289 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.289 extraction2_array1 channel_1


title: expt.935 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.935 extraction4_array1 channel_1

value: CNS-derived cell-line

value: y v f mal

value: Unknown


title: Chimp 1 liver at week -6

source_name: liver, baseline week -6

value: week -6


title: expt.936 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.936 extraction2_array1 channel_1


title: brain_24h_mouse20

source_name: brain, 24 hours fasting, mouse 20


title: brain_48h_mouse54

source_name: brain, 48 hours fasting, mouse 54


title: brain_48h_mouse55

source_name: brain, 48 hours fasting, mouse 55

source_name: reference pool


title: expt.530 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.530 extraction2_array1 channel_1

value: embryo-derived cell-line


title: brain_12h_mouse13

source_name: brain, 12 hours fasting, mouse 13


title: expt.531 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.531 extraction4_array1 channel_1

value: late embryonic stage


title: brain_72h_mouse33

source_name: brain, 72 hours fasting, mouse 33


title: brain_48h_mouse32

source_name: brain, 48 hours fasting, mouse 32


title: brain_48h_mouse31

source_name: brain, 48 hours fasting, mouse 31


title: expt.291 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.291 extraction4_array1 channel_1


title: muscle_48h_mouse32

source_name: muscle, 48 hours fasting, mouse 32

value: muscle


title: 102 hippocampus_h3k9acetylation_high_LGABN_20080820 3

value: rabbit polyclonal anti-acetyl-histone H3 Lysine 9 antibody

value: high


title: brain_12h_mouse10

source_name: brain, 12 hours fasting, mouse 10

value: FVB

value: brain

value: reference pool


title: expt.290 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.290 extraction2_array1 channel_1

value: se/e

value: Female


title: muscle_48h_mouse30

source_name: muscle, 48 hours fasting, mouse 30


title: muscle_48h_mouse55

source_name: muscle, 48 hours fasting, mouse 55


title: brain_24h_mouse17

source_name: brain, 24 hours fasting, mouse 17


title: brain_24h_mouse19

source_name: brain, 24 hours fasting, mouse 19


title: brain_0h_mouse1

source_name: brain, 0 hours fasting, mouse 1


title: brain_0h_mouse2

source_name: brain, 0 hours fasting, mouse 2


title: brain_0h_mouse6

source_name: brain, 0 hours fasting, mouse 6

source_name: reference pool


title: muscle_48h_mouse54

source_name: muscle, 48 hours fasting, mouse 54


title: muscle_72h_mouse38

source_name: muscle, 72 hours fasting, mouse 38


title: brain_0h_mouse3

source_name: brain, 0 hours fasting, mouse 3


title: brain_24h_mouse21

source_name: brain, 24 hours fasting, mouse 21


title: expt.289 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.289 extraction4_array1 channel_1

value: Male


title: expt.288 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.288 extraction2_array1 channel_1

value: dorsal mesothoracic disc


title: muscle_72h_mouse35

source_name: muscle, 72 hours fasting, mouse 35


title: muscle_72h_mouse36

source_name: muscle, 72 hours fasting, mouse 36


title: expt.814 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.814 extraction4_array1 channel_1


title: brain_0h_mouse5

source_name: brain, 0 hours fasting, mouse 5


title: muscle_72h_mouse33

source_name: muscle, 72 hours fasting, mouse 33


title: brain_12h_mouse11

source_name: brain, 12 hours fasting, mouse 11


title: muscle_72h_mouse40

source_name: muscle, 72 hours fasting, mouse 40


title: muscle_48h_mouse31

source_name: muscle, 48 hours fasting, mouse 31


title: muscle_24h_mouse18

source_name: muscle, 24 hours fasting, mouse 18


title: muscle_24h_mouse20

source_name: muscle, 24 hours fasting, mouse 20


title: expt.815 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.815 extraction2_array1 channel_1


title: muscle_24h_mouse17

source_name: muscle, 24 hours fasting, mouse 17

source_name: reference pool


title: expt.596 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.596 extraction4_array1 channel_1

value: third instar larval stage


title: muscle_24h_mouse19

source_name: muscle, 24 hours fasting, mouse 19


title: expt.597 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.597 extraction2_array1 channel_1


title: expt.812 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.812 extraction4_array1 channel_1


title: expt.813 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.813 extraction2_array1 channel_1


title: expt.289 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.289 extraction4_array1 channel_1


title: expt.288 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.288 extraction2_array1 channel_1


title: muscle_24h_mouse21

source_name: muscle, 24 hours fasting, mouse 21


title: expt.670 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.670 extraction4_array1 channel_1


title: muscle_0h_mouse5

source_name: muscle, 0 hours fasting, mouse 5


title: expt.644 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.644 extraction2_array1 channel_1


title: muscle_12h_mouse13

source_name: muscle, 12 hours fasting, mouse 13


title: expt.671 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.671 extraction4_array1 channel_1

value: CNS-derived cell-line


title: expt.405 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.405 extraction2_array1 channel_1

value: y v f mal


title: muscle_0h_mouse1

source_name: muscle, 0 hours fasting, mouse 1


title: kidney_72h_mouse40

source_name: kidney, 72 hours fasting, mouse 40

value: kidney


title: muscle_12h_mouse14

source_name: muscle, 12 hours fasting, mouse 14

source_name: reference pool


title: kidney_72h_mouse35

source_name: kidney, 72 hours fasting, mouse 35


title: kidney_48h_mouse54

source_name: kidney, 48 hours fasting, mouse 54


title: kidney_48h_mouse31

source_name: kidney, 48 hours fasting, mouse 31


title: muscle_12h_mouse10

source_name: muscle, 12 hours fasting, mouse 10


title: muscle_12h_mouse11

source_name: muscle, 12 hours fasting, mouse 11


title: kidney_48h_mouse32

source_name: kidney, 48 hours fasting, mouse 32


title: kidney_12h_mouse12

source_name: kidney, 12 hours fasting, mouse 12


title: muscle_0h_mouse2

source_name: muscle, 0 hours fasting, mouse 2


title: muscle_0h_mouse6

source_name: muscle, 0 hours fasting, mouse 6


title: kidney_12h_mouse14

source_name: kidney, 12 hours fasting, mouse 14


title: expt.904 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.904 extraction2_array1 channel_1


title: kidney_12h_mouse10

source_name: kidney, 12 hours fasting, mouse 10


title: kidney_24h_mouse19

source_name: kidney, 24 hours fasting, mouse 19


title: kidney_48h_mouse30

source_name: kidney, 48 hours fasting, mouse 30


title: kidney_12h_mouse13

source_name: kidney, 12 hours fasting, mouse 13


title: kidney_48h_mouse55

source_name: kidney, 48 hours fasting, mouse 55


title: expt.815 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.815 extraction4_array1 channel_1


title: kidney_24h_mouse17

source_name: kidney, 24 hours fasting, mouse 17

source_name: reference pool


title: kidney_0h_mouse2

source_name: kidney, 0 hours fasting, mouse 2


title: kidney_0h_mouse5

source_name: kidney, 0 hours fasting, mouse 5


title: muscle_0h_mouse3

source_name: muscle, 0 hours fasting, mouse 3


title: kidney_24h_mouse18

source_name: kidney, 24 hours fasting, mouse 18


title: kidney_24h_mouse20

source_name: kidney, 24 hours fasting, mouse 20


title: expt.814 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.814 extraction2_array1 channel_1


title: kidney_72h_mouse38

source_name: kidney, 72 hours fasting, mouse 38


title: kidney_72h_mouse33

source_name: kidney, 72 hours fasting, mouse 33


title: expt.320 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.320 extraction2_array1 channel_1


title: expt.774 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.774 extraction4_array1 channel_1


title: expt.773 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.773 extraction2_array1 channel_1


title: expt.404 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.404 extraction4_array1 channel_1


title: kidney_72h_mouse36

source_name: kidney, 72 hours fasting, mouse 36


title: kidney_0h_mouse3

source_name: kidney, 0 hours fasting, mouse 3


title: expt.847 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.847 extraction4_array1 channel_1


title: expt.846 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.846 extraction2_array1 channel_1


title: kidney_0h_mouse1

source_name: kidney, 0 hours fasting, mouse 1

source_name: reference pool


title: kidney_12h_mouse11

source_name: kidney, 12 hours fasting, mouse 11


title: intestine_72h_mouse40

source_name: intestine, 72 hours fasting, mouse 40

value: intestine


title: expt.531 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.531 extraction4_array1 channel_1

value: embryo-derived cell-line


title: muscle_12h_mouse12

source_name: muscle, 12 hours fasting, mouse 12


title: intestine_48h_mouse54

source_name: intestine, 48 hours fasting, mouse 54


title: intestine_72h_mouse33

source_name: intestine, 72 hours fasting, mouse 33


title: kidney_0h_mouse6

source_name: kidney, 0 hours fasting, mouse 6


title: intestine_48h_mouse55

source_name: intestine, 48 hours fasting, mouse 55


title: intestine_72h_mouse36

source_name: intestine, 72 hours fasting, mouse 36


title: expt.530 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.530 extraction2_array1 channel_1

value: late embryonic stage


title: intestine_24h_mouse21

source_name: intestine, 24 hours fasting, mouse 21


title: intestine_24h_mouse20

source_name: intestine, 24 hours fasting, mouse 20


title: intestine_12h_mouse12

source_name: intestine, 12 hours fasting, mouse 12


title: expt.905 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.905 extraction4_array1 channel_1


title: intestine_12h_mouse13

source_name: intestine, 12 hours fasting, mouse 13


title: intestine_72h_mouse35

source_name: intestine, 72 hours fasting, mouse 35


title: intestine_24h_mouse19

source_name: intestine, 24 hours fasting, mouse 19

source_name: reference pool


title: intestine_48h_mouse32

source_name: intestine, 48 hours fasting, mouse 32


title: intestine_12h_mouse10

source_name: intestine, 12 hours fasting, mouse 10


title: intestine_12h_mouse11

source_name: intestine, 12 hours fasting, mouse 11


title: intestine_48h_mouse30

source_name: intestine, 48 hours fasting, mouse 30


title: expt.935 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.935 extraction4_array1 channel_1

value: Unknown


title: intestine_24h_mouse18

source_name: intestine, 24 hours fasting, mouse 18


title: intestine_0h_mouse6

source_name: intestine, 0 hours fasting, mouse 6


title: intestine_0h_mouse5

source_name: intestine, 0 hours fasting, mouse 5


title: intestine_24h_mouse17

source_name: intestine, 24 hours fasting, mouse 17


title: expt.936 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.936 extraction2_array1 channel_1


title: expt.846 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.846 extraction4_array1 channel_1


title: intestine_72h_mouse38

source_name: intestine, 72 hours fasting, mouse 38


title: expt.813 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.813 extraction2_array1 channel_1


title: expt.1113 extraction4_array1

description: channel ch1 is input DNA;

source_name: expt.1113 extraction4_array1 channel_1


title: expt.847 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.847 extraction2_array1 channel_1


title: intestine_48h_mouse31

source_name: intestine, 48 hours fasting, mouse 31


title: expt.1114 extraction2_array1

description: channel ch1 is input DNA;

source_name: expt.1114 extraction2_array1 channel_1


title: intestine_0h_mouse1

source_name: intestine, 0 hours fasting, mouse 1

source_name: reference pool


title: intestine_0h_mouse2

source_name: intestine, 0 hours fasting, mouse 2


title: intestine_0h_mouse3

source_name: intestine, 0 hours fasting, mouse 3


title: liver_72h_mouse40

source_name: liver, 72 hours fasting, mouse 40

value: liver


title: liver_24h_mouse20

source_name: liver, 24 hours fasting, mouse 20


title: liver_24h_mouse21

source_name: liver, 24 hours fasting, mouse 21


title: liver_72h_mouse35

source_name: liver, 72 hours fasting, mouse 35


title: liver_72h_mouse36

source_name: liver, 72 hours fasting, mouse 36


title: NORM_10_normal

status: Public on Mar 08 2011

city: Tromsø

first: Chris

last: Fenton

address: Thor Knutsen vg 6

department: Microarray

country: Norway

institute: UITO

description: Hy3TM-labeled samples and a Hy5TM-labelled reference RNA sample

hyb_protocol: The hybridization was performed according to the miRCURYTM LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria)

scan_protocol: The miCURYTM LNA Array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent technologies Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery Inc., USA).

data_processing: The quantified signals were background corrected with offset value 10 and normalized using the global Lowess (Locally Weighted Scatterplot Smoothing) regression algorithm. Many rows were deleted because they did were not present in 80% of all the total samples. That is if over 20% of a row was flagged as non viable by the scanner the data row was removed. Criteria included signal/noise greater than 2.5, and well formed circular spot.

source_name: normal

label_protocol: Total RNA (700ng) from sample and reference was labelled with Hy3TM and Hy5TM fluorescent label using the miRCURYTm LNA Array power labelling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: twenty formalin-fixed and paraffin-embedded (FFPE) tumor tissue samples were obtained from patients diagnosed with stage I-IIIA at the University Hospital of Northern Norway (UNN) and Nordland Central Hospital (NLCH)

extract_protocol: RNA was isolated from the collected core samples by using the Recover All™ Total Nucleic Acid Isolation Kit for FFPE Tissues (Ambion, Austin, TX), according to the manufacturer’s instructions, with some minor adjustments. Xylene treatment was increased from 3 min to 8 min, and protease treatment was increased from 3 hrs to approximately 20 hrs. RNA quality and quantity was assessed by using the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE) and further verified by an Agilent 2100 Bioanalyzer profil

treatment_protocol: Four sample cores, each 0.6mm in diameter, from viable tumor areas from each tumor and normal specimen were taken and pooled prior to RNA isolation in order to obtain a representative sample of each patient

value: lung

tag: disease status

value: normal control

source_name: common ref pool (samples s1 to s30)

tag: reference

value: common ref pool (samples s1 to s30)


title: liver_48h_mouse54

source_name: liver, 48 hours fasting, mouse 54

value: FVB

value: reference pool


title: liver_24h_mouse17

source_name: liver, 24 hours fasting, mouse 17


title: liver_48h_mouse32

source_name: liver, 48 hours fasting, mouse 32


title: liver_72h_mouse33

source_name: liver, 72 hours fasting, mouse 33


title: liver_72h_mouse38

source_name: liver, 72 hours fasting, mouse 38


title: intestine_12h_mouse14

source_name: intestine, 12 hours fasting, mouse 14


title: liver_48h_mouse55

source_name: liver, 48 hours fasting, mouse 55


title: liver_48h_mouse30

source_name: liver, 48 hours fasting, mouse 30

source_name: reference pool


title: liver_24h_mouse18

source_name: liver, 24 hours fasting, mouse 18


title: liver_12h_mouse13

source_name: liver, 12 hours fasting, mouse 13


title: liver_24h_mouse19

source_name: liver, 24 hours fasting, mouse 19


title: NORM_09_normal


title: liver_48h_mouse31

source_name: liver, 48 hours fasting, mouse 31


title: liver_0h_mouse5

source_name: liver, 0 hours fasting, mouse 5


title: NORM_08_normal


title: liver_12h_mouse12

source_name: liver, 12 hours fasting, mouse 12


title: liver_0h_mouse3

source_name: liver, 0 hours fasting, mouse 3


title: liver_12h_mouse10

source_name: liver, 12 hours fasting, mouse 10


title: liver_12h_mouse14

source_name: liver, 12 hours fasting, mouse 14


title: liver_0h_mouse6

source_name: liver, 0 hours fasting, mouse 6


title: NORM_07_normal

source_name: normal

source_name: common ref pool (samples s1 to s30)


title: NORM_06_normal


title: NORM_05_normal


title: NORM_04_normal


title: NSCLC_13_late

source_name: late

value: NSCLC patient

tag: survival (months)

tag: age

tag: dead


title: NSCLC_14_late

tag: tissue


title: NSCLC_15_late


title: NSCLC_17_late


title: NSCLC_16_late


title: NSCLC_20_late


title: NORM_02_normal


title: NSCLC_19_late


title: NORM_01_normal


title: NSCLC_18_late


title: NORM_03_normal


title: NSCLC_12_late


title: liver_0h_mouse2

source_name: liver, 0 hours fasting, mouse 2


title: NSCLC_09_early

source_name: early


title: NSCLS_11_late


title: NSCLC_10_early


title: liver_0h_mouse1

source_name: liver, 0 hours fasting, mouse 1


title: NSCLC_03_early


title: NSCLC_04_early


title: NSCLC_02_early


title: NSCLC_01_early


title: NSCLC_05_early


title: NSCLC_08_early


title: NSCLC_06_early


title: Zebrafish exposed to Estrogen 3 (17b-estradiol; 10mM final concentration and ICI 1uM final concentration)

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

description: replicate 3

hyb_protocol: The arrays were hybridized following the strategies described in. A minimum of three good hybridizations were selected for the analysis.

scan_protocol: The signal intensities of Cy5 and Cy3 dyes in each spot and the local background were measured using the GenePix 4000B microarray scanner (Axon Instruments, USA) to calculate the net intensity of each spot for analysis.

data_processing:
Compugen microarray set (Compugen, USA) containing 16,416 oligonucleotide probes representing zebrafish genes was used in this study. Briefly, the oligonucleotide probes were spotted onto poly-L-lysine coated microscope slides using a custom-built DNA microarrayer and post-processed following the standard procedures previously described.
Microarray data from GenePix image analysis software (i.e gpr files) were subjected to Lowess normalization. There were 4 control (ethanol controls) samples, 3 samples treated with E2 and 3 samples treated with E2 and ICI in the normalized data, respectively. The good arrays were selected based on scatter plot analysis.
Significance Analysis of Microarrays (SAM) was used to identify the prominent signals for the two kinds of treatments as previously described. To boost the power of the test, we applied 3-class SAM on the whole array by excluding spots with more than 6 missing values. As a result, 1610 out of 16416 genes were selected at q-value <8%. Subsequently, estrogen-responsive genes were identified by analyzing the expression values for the samples treated with E2 and E2+ICI with respect to control samples using 2-class SAM. The genes selected following this analysis displayed between 2- to 130-fold differential expressions. A cluster of 715 up-regulated genes were identified which showed significant up regulation in E2. These genes displayed decreased expression both in the Control and E2+ICI compared to their level of expression in E2. Similarly, another cluster of 376 genes (down-regulated group) were identified which displayed significantly reduced expression in E2 compared to control and E2+ICI. Hence, the genes selected by the above analysis are estrogen-responsive and are sensitive to E2 and ICI. Datasets extracted using the above statistical analysis were clustered and visualized as previously described.

organism: Danio rerio

source_name: Zebrafish exposed to Estrogen (17b-estradiol; 10mM final concentration and ICI 1uM final concentration)

label_protocol: Sample and reference RNA were reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively, to fluorescently label the target cDNAs.

extract_protocol: Total RNA was extracted from individual frozen fish belonging to control and experimental samples (ethanol control, E2 and E2+ICI treated). Frozen samples were homogenized to a crude powder form in a pre-cooled mortar and pestle.   Partially homogenized sample was transferred to a pre-cooled sterile graduated falcon tube containing appropriate amount of Trizol reagent (Invitrogen, USA) and homogenized completely using a motorized homogenizer.  Total RNA was extracted from the samples using Trizol reagent according to manufacturer’s instructions. Subsequently RNA was purified using Qiagen column and the quality was evaluated using gel electrophoresis

treatment_protocol:
A batch of healthy adult males were exposed to the medium containing 17β-estradiol (E2; Sigma-Aldrich; 10 nM final concentration) and an equal number of males were exposed to the medium containing a combination of E2 (10 nM) and ICI 182,780 (Tocris Cookson) (1 µM final concentration). Control fishes (males) were maintained in water containing 0.01% (v/v) ethanol (ethanol control; ethanol was used to dissolve E2 and ICI). The final ethanol concentration in the control was similar to those in medium with E2 or E2 and ICI.
Minimum 3 replicates were maintained for each treatment. Control and experimental animals were maintained in their respective medium for 96 hours and the medium was changed every day during the course of the experiment. Upon completion of the experiment at 96 hours, the fish were snapped frozen in liquid nitrogen and stored at -80°C for subsequent analysis.

tag: treatment group

value: E2ICI treatment

source_name: Reference (control)

value: reference


title: NSCLC_07_early


title: Zebrafish exposed to Estrogen 1 (17b-estradiol; 10mM final concentration and ICI 1uM final concentration)

description: replicate 1


title: Zebrafish exposed to Estrogen 2 (17b-estradiol; 10mM final concentration and ICI 1uM final concentration)

description: replicate 2


title: Zebrafish exposed to Estrogen 1 (17b-estradiol; 10mM final concentration)

description: replicate 1

source_name: Zebrafish exposed to Estrogen (17b-estradiol; 10mM final concentration)

value: E2 treatment


title: Zebrafish exposed to Estrogen 3 (17b-estradiol; 10mM final concentration)

description: replicate 3


title: Zebrafish control 1 (ethanol control 0.01%v/v)

description: replicate 1

source_name: Zebrafish control (ethanol control 0.01%v/v)

value: Control


title: Zebrafish exposed to Estrogen 2 (17b-estradiol; 10mM final concentration)

description: replicate 2


title: Zebrafish control 2 (ethanol control 0.01%v/v)

description: replicate 2


title: Zebrafish control 4 (ethanol control 0.01%v/v)

description: replicate 4


title: Zebrafish control 3 (ethanol control 0.01%v/v)

description: replicate 3


title: Day 13 embryo_in vivo_biological rep3

first: Jai Prakash

last: Mehta

address: Veterinary Science Center, University College Dublin

department: UCD School of Agriculture, Food Science & Veterinary Medicine

country: Ireland

institute: University College Dublin, Ireland

description: Gene expression data from Day 13 embryos

hyb_protocol: 10 μg of fragmented cRNA were hybridized to the GeneChip® Bovine Genome Array. Each sample was added to a hybridization solution containing 100 mM 2-(N-morpholino) ethanesulfonic acid, 1 M Na+, and 20 mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 μg/ml. Hybridization was performed for 16 h at 45ºC. Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix).

scan_protocol: Each array was scanned at 1.56 μm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix).

data_processing: The raw data intensity files were read into R (http://www.r-project.org/) and preprocessed using functions of the Affymetrix and Gene Chip Robust Multi-array Average (GCRMA) packages of the BioConductor project (http://www.bioconductor.org/) (Gentleman et al Genome Biology 2004). Identification of differentially expressed genes from Day 7 and Day 13 embryos was achieved using the Limma package employing linear modeling and an empirical Bayes framework to shrink the variance of measurements on each probe set. A modified t-test was carried out and P-values were adjusted for multiple testing using the Benjamini and Hochberg false discovery rate method. Lists of differentially expressed genes were selected on the basis of an adjusted P-value of <0.05.

organism: Bos taurus

source_name: Day 13 bovine conceptuses derived from in vivo produced blastocysts

label_protocol: cDNA was synthesized from 75 ng of total RNA using Two-cycle target labeling and control reagents (Affymetrix, Santa Clara, CA) to produce biotin labeled cRNA.

growth_protocol: Day 7 bovine blastocysts were produced in vitro or in vivo. A proportion of embryos were snap frozen on Day 7 for analysis while the remainder were transferred to synchronized recipient heifers and recovered at Day 13 and snap frozen for analysis.

extract_protocol: Trizol was used to extract total RNA from embryos according to the manufacturer´s instruction.

value: Day 13 embryo


title: ENK_myeloma_patient_19

city: Little Rock

first: Tarun

middle: Kumar

last: Garg

state: AR

address: 4301 W Markham St

department: Myeloma Institute for Research and Therapy

institute: University of Arkansas for Medical Sciences

description:
MM_ENK_19
Gene expression data from myeloma patient expanded NK cells

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45ºC on HG-U133plus 2.0 gene chip microarrays (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.  Scanned images were processed using the GCOS v1.4 software.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: enriched expanded natural killer cells from myeloma patient

label_protocol: Biotinylated cRNA were prepared according to the New GeneChip 3 IVT Labeling Kit protocol from 500 ng of total RNA (The New GeneChip® IVT Labeling Kit: Optimized Protocol for Improved Results, 2004, Affymetrix).

growth_protocol:
Expansion Protocol: Peripheral Blood was centrifuged over Ficoll-Paque PLUS (Amersham Biosciences, Piscataway, NJ). PBMCs were harvested and washed in RPMI1640 (Invitrogen, Carlsbad, CA) containing 10% fetal bovine serum (FBS) (Invitrogen). PBMCs from the donor and myeloma patient were co-cultured with irradiated (100 gray) K562-mb15-41BBL cells at a ratio of 1.5:1 in RPMI 1640 + 10% FBS + 300 IU/ml of IL-2 (Prometheus, San Diego, CA). One half the media was changed every other day with fresh media containing IL2. The cells were collected on day 10. The number of viable cells was based on counts using trypan blue exclusion.
NK Enrichment Protocol:  NK cells were isolated from fresh PBMCs from healthy donors using customized NK cell enrichment kit (catalog # 19055) from Stem Cell Technologies Inc. (Vancouver, BC). In brief, 10x107 cells were incubated with 200μl enrichment cocktail for 10-15 minutes at room temperature. Magnetic microparticles/nanoparticles were added to the cells and incubated for 10 minutes. Cell suspension was then placed into the EasySep® Magnet for 5 minutes. The magnetically labeled unwanted cells remained bound inside the original tube. Unlabeled NK cell fraction was collected into a new tube. Purity and viability of enriched NK fraction was assessed by trypan blue exclusion and flow cytometry analysis for NK cell surface markers. A similar process was performed for the enrichment of ENK cells from expanded cells.  For NK/ENK enrichment from myeloma patients, 10μl CD138TAC was added to the enrichment cocktail to remove any myeloma cell contaminants.

extract_protocol: Total RNA was extracted from ~95% purified NK/ENK cells (2-5M cells) using the Qiagen RNeasy® Mini Kit (Qiagen, Catalog # 74104) as per instructions. The samples were eluted in RNase free water and quantitated using a NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc. Wilmington, DE).

tag: individual

value: Myeloma patient 19

value: natural killer cells

tag: nkc state

value: expanded


title: Day 13 embryo_in vitro_biological rep3

source_name: Day 13 bovine conceptuses derived from in vitro produced blastocysts


title: Day 13 embryo_in vivo_biological rep2


title: NK_myeloma_patient_18

description:
MM_NK_18
Gene expression data from myeloma patient non-expanded NK cells

source_name: enriched non-expanded natural killer cells from myeloma patient

value: Myeloma patient 18

value: non-expanded


title: NK_myeloma_patient_20

description:
MM_NK_20
Gene expression data from myeloma patient non-expanded NK cells

value: Myeloma patient 20


title: Day 13 embryo_in vivo_biological rep1


title: ENK_myeloma_patient_17

description:
MM_ENK_17
Gene expression data from myeloma patient expanded NK cells

value: Myeloma patient 17


title: ENK_myeloma_patient_15

description:
MM_ENK_15
Gene expression data from myeloma patient expanded NK cells

value: Myeloma patient 15


title: ENK_myeloma_patient_24

description:
MM_ENK_24
Gene expression data from myeloma patient expanded NK cells

value: Myeloma patient 24


title: Day 7 embryo_in vivo_biological rep3

description: Gene expression data from Day 7 embryos

source_name: Day 7 in vivo produced bovine blastocysts

value: Day 7 embryo


title: ENK_myeloma_patient_16

description:
MM_ENK_16
Gene expression data from myeloma patient expanded NK cells

value: Myeloma patient 16


title: ENK_myeloma_patient_20

description:
MM_ENK_20
Gene expression data from myeloma patient expanded NK cells


title: ENK_myeloma_patient_18

description:
MM_ENK_18
Gene expression data from myeloma patient expanded NK cells


title: NK_myeloma_patient_19

description:
MM_NK_19
Gene expression data from myeloma patient non-expanded NK cells


title: NK_myeloma_patient_24

description:
MM_NK_24
Gene expression data from myeloma patient non-expanded NK cells


title: ENK_myeloma_patient_14

description:
MM_ENK_14
Gene expression data from myeloma patient expanded NK cells

value: Myeloma patient 14


title: Day 13 embryo_in vitro_biological rep2


title: NK_myeloma_patient_17

description:
MM_NK_17
Gene expression data from myeloma patient non-expanded NK cells


title: Pineal_CT22_L_rep1

city: Tokyo

first: Yoshitaka

last: Fukada

address: Hongo 7-3-1

institute: The University of Tokyo

hyb_protocol: Twenty micrograms of biotinylated cRNA was hybridized to GeneChip Chicken Genome Array for 16 h at 45°C. The arrays were washed and stained by using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned by the Affymetrix Model 3000 scanner.

data_processing: The scanned array image was processed by GeneChip Operating Software Version 1.4 (Affymetrix) to calculate the signal intensity data for each probe set.

organism: Gallus gallus

source_name: Chicken pineal gland, CT22, light

label_protocol: Nine micrograms of total RNA from 6 pineal glands was used to synthesize biotinylated cRNA by using Affymetrix GeneChip one-cycle cDNA synthesis kit and IVT labeling kit (Affymetrix).

growth_protocol: 12-h light/12-h dark cycle-entrained chicks were transferred to constant darkness for a day.

extract_protocol: Total RNA was prepared from the isolated pineal glands by using TRIZOL reagent (Invitrogen).

treatment_protocol: The animals were exposed to light for 1 h from CT (circadian time) 6 (representing subjective day), CT14 (early subjective night) or CT22 (late subjective night). Control animals were kept in the dark without light pulse.

tag: gender

value: male

value: pineal gland

value: 8 days

tag: time

value: light


title: Pineal_CT22_D_rep2

source_name: Chicken pineal gland, CT22, dark

value: dark


title: Day 7 embryo_in vivo_biological rep2

description: Gene expression data from Day 7 embryos


title: Day 7 embryo_in vitro_biological rep2

description: Gene expression data from Day 7 embryos

source_name: Day 7 in vitro produced bovine blastocysts


title: Day 7 embryo_in vitro_biological rep1

description: Gene expression data from Day 7 embryos


title: NK_myeloma_patient_15

description:
MM_NK_15
Gene expression data from myeloma patient non-expanded NK cells


title: Day 13 embryo_in vitro_biological rep1

value: Day 13 embryo


title: Pineal_CT22_L_rep2


title: Pineal_CT14_D_rep2

source_name: Chicken pineal gland, CT14, dark


title: Pineal_CT14_L_rep2

source_name: Chicken pineal gland, CT14, light


title: Pineal_CT14_D_rep1


title: NK_myeloma_patient_16

description:
MM_NK_16
Gene expression data from myeloma patient non-expanded NK cells

value: natural killer cells


title: Pineal_CT6_D_rep1

source_name: Chicken pineal gland, CT6, dark


title: Pineal_CT22_D_rep1


title: Pineal_CT6_L_rep1

source_name: Chicken pineal gland, CT6, light


title: Pineal_CT14_L_rep1


title: NK_myeloma_patient_14

description:
MM_NK_14
Gene expression data from myeloma patient non-expanded NK cells


title: Day 7 embryo_in vitro_biological rep3

description: Gene expression data from Day 7 embryos


title: Day 7 embryo_in vivo_biological rep1

description: Gene expression data from Day 7 embryos


title: SF3b155 knock-down siRNA 5 replicate 3 Dye-Swap

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

description: Mean foreground and background intensities were extracted from the red (Cy5) and green (Cy3) channels for every spot on the microarray. The background intensities are used to correct the foreground intensities for local variation on the array surface, resulting in corrected red and green intensities.

hyb_protocol: Slides were hybridized following manufacturer protocol, with the exception that we hybridized 6 micrograms of each amplified cRNA sample and the Agilent hybridization oven was set to 60ºC.

scan_protocol: Fluorescent images were obtained using the G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings and 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Molecular Devices, www.moleculardevices.com).

data_processing: Raw data were processed using SAPO (http://bioinfo.ciberehd.org/SAP.ang.htm) and CGEM (http://bioinfo.ciberehd.org/CGEM.ang.html) alternative splicing analysis tools, obtaining lowess normalized log2ratios.

source_name: SF3b155 siRNA 5 knock-down in HeLa cell line replicate 3

label_protocol: Sample was labeled using the Quick-Amp labeling kit, no dye (Agilent 5190-0447) and cyanine 5-CTP and cyanine 3-CTP (Perkin-Elmer NEL580, NEL581). Purified using Quiagen RNeasy mini kit. Quality control assessed by Agilent Bioanalyzer 2100.

growth_protocol: HeLa cells were grown in complete media (DMEM + 10% FBS + penicillin/streptomycin).

extract_protocol:
RNeasy mini kit (QUIAGEN, cat.no. 74104) and DNase treated on-column with DNase RNase-free (QUIAGEN, cat no. 79254)
Quality assesment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.

treatment_protocol: HeLa cells were plated the day before transfection in 100 mm plates in DMEM 10%FBS without antibiotics. Cells at 80% confluency were transfected with 50 nM SF3b155 siRNA oligonucleotides (oligo 5: 5’-CCCUGUGGCAUUGCUUAAUGAUAU-3’) using Lipofectamine 2000 (Cat. No. 11668-500, Invitrogen) in optimem media (Invitrogen). 24 h after transfection, the media was replaced. Cells were harvested after 72 hours after transfection.

tag: transfection

value: SF3b155 5 siRNA oligo

tag: cell line

value: HeLa

source_name: HeLa siRNA control of trasfection replicate 3

treatment_protocol: HeLa cells were plated the day before transfection in 100 mm plates in DMEM 10%FBS without antibiotics. Cells at 80% confluency were transfected with either 50 nM scrambled RNA using Lipofectamine 2000 (Cat. No. 11668-500, Invitrogen) in optimem media (Invitrogen). 24 h after transfection, the media was replaced. Cells were harvested after 72 hours after transfection.

value: scrambled oligo


title: SF3b155 knock-down siRNA 5 replicate 1 Dye-swap

source_name: SF3b155 siRNA 5 knock-down in HeLa cell line replicate 1

source_name: HeLa siRNA control of trasfection replicate 1


title: Pineal_CT6_L_rep2

tag: treatment


title: SF3b155 knock-down siRNA 5 replicate 4

source_name: SF3b155 siRNA 5 knock-down in HeLa cell line replicate 4

source_name: HeLa siRNA control of trasfection replicate 4


title: SF3b155 knock-down siRNA 5 replicate 4 Dye-Swap


title: SF3b155 knock-down siRNA 5 replicate 3


title: Pineal_CT6_D_rep2


title: SF3b155 knock-down siRNA 3 replicate 4 Dye-Swap

source_name: SF3b155 siRNA 3 knock-down in HeLa cell line replicate 4

treatment_protocol: HeLa cells were plated the day before transfection in 100 mm plates in DMEM 10%FBS without antibiotics. Cells at 80% confluency were transfected with 50 nM SF3b155 siRNA oligonucleotide (oligo 3: 5’-GACAGCAGAUUUGCUGGAUACGUGA-3') using Lipofectamine 2000 (Cat. No. 11668-500, Invitrogen) in optimem media (Invitrogen). 24 h after transfection, the media was replaced. Cells were harvested after 72 hours after transfection.

value: SF3b155 3 siRNA oligo

treatment_protocol: HeLa cells were plated the day before transfection in 100 mm plates in DMEM 10%FBS without antibiotics. Cells at 80% confluency were transfected with 50 nM scrambled RNA using Lipofectamine 2000 (Cat. No. 11668-500, Invitrogen) in optimem media (Invitrogen). 24 h after transfection, the media was replaced. Cells were harvested after 72 hours after transfection.


title: 5B1 melanoma cell line-miR-30d- treated-sample repeat 1

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

hyb_protocol: 10 micrograms of cRNA generated by the IVT procedure was hybridized for 16 hr to the Affymetrix array according to the manufacturer's manual. Genechips® were processed using protocol EukGE_WS2v4 450 for Genechip® fluidics station 450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring GX11 program. No further adjustments were made to the data in the table.

source_name: Total RNA of  50nM miR-30d-transfected cells for 48h

label_protocol: 100 ng of total cellular RNA was converted to cDNA/cRNA and labeled using the Affymetrix 3'IVT Express Kit.

growth_protocol: human melanoma cell lines (4L or 5B1) weregrown in RPMI supplemented with 5% FBS.

extract_protocol: Total RNA was extracted using RNeasy micro-elute columns (QIAGEN), according to manufacturer's instructions.

treatment_protocol: 250,000 human melanoma cell lines (4L or 5B1) were transiently transfected ,using lipofectamine, with 50nM of scrambled or miR-30d oligos for 48 hours

tag: cell type

value: human melanoma cell line 5B1

value: 50nM miR-30d-transfected for 48h


title: SF3b155 knock-down siRNA 3 replicate 2

source_name: SF3b155 siRNA 3 knock-down in HeLa cell line replicate 2

source_name: HeLa siRNA control of trasfection replicate 2

value: scrambled oligo.


title: 5B1 melanoma cell line-miR-30d- treated-sample repeat 2


title: Spliceostatin treatment replicate 3 Dye-Swap

data_processing: Raw data were processed using SAPO (http://bioinfo.ciberehd.org/SAP.ang.htm) and CGEM (http://bioinfo.ciberehd.org/CGEM.ang.html) alternative splicing analysis tools.

source_name: HeLa spliceostatin treatment replicate 3

growth_protocol: Cells were grown in a 6-well plate with DMEM glutamax (Invitrogen 61965-059) in the presence of 10% serum and penicillin/streptomycin until 80% confluence.

extract_protocol:
RNeasy mini kit (QUIAGEN, cat.no. 74104) and DNase treated on-column with DNase RNase-free
Quality assesment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.

treatment_protocol: Before treatment, media was removed, cell were washed twice with 1 ml 1X PBS, added 1 ml DMEM without serum and antibiotics and treat the cells with spliceostatin 100 ng/ml  for three hours.

tag: agent

value: spliceostatin

source_name: HeLa methanol treatment replicate 3

extract_protocol:
RNeasy mini kit (QUIAGEN, cat.no. 74104)
Quality assesment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.

treatment_protocol: Before treatment, media was removed, cell were washed twice with 1 ml 1X PBS, added 1 ml DMEM without serum and antibiotics and treat the cells with methanol for three hours.

value: methanol


title: SF3b155 knock-down siRNA 3 replicate 2 Dye-Swap


title: Spliceostatin treatment replicate 3B Dye-Swap

source_name: HeLa spliceostatin treatment replicate 3B

source_name: HeLa methanol treatment replicate 3B


title: 4L melanoma cell line-scrambled-treated-sample repeat 1

source_name: Total RNA of  50nM scrambled-transfected cells for 48h

value: human melanoma cell line 4L

value: 50nM scrambled-transfected for 48h


title: 4L melanoma cell line-miR-30d- treated-sample repeat 2


title: SF3b155 knock-down siRNA 3 replicate 1 Dye-Swap

source_name: SF3b155 siRNA 3 knock-down in HeLa cell line replicate 1


title: 5B1 melanoma cell line-scrambled-treated-sample repeat 2


title: 4L melanoma cell line-scrambled-treated-sample repeat 2


title: 4L melanoma cell line-miR-30d-treated-sample repeat 1


title: SF3b155 knock-down siRNA 3 replicate 4


title: treatment: Post-vernalized - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: The 2nd leaf was harvested from plants that had been vernalized for 49 days and then grown in normal glasshouse conditions until the 3 leaf stage. All samples were harvested at the same time of day.

hyb_protocol: Affymetrix (AGRF)

scan_protocol: Affymetrix (AGRF)

data_processing: The MAS5.0 Normalization is performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org). The target value is 500 for all cases. The code was developed using R2.4.1, Bioconductor 1.9, and simpleaffy 2.8.0. The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html. The normalization scripts are available from the PLEXdb team by request.

organism: Hordeum vulgare

source_name: adult leaf (treatment: Post-vernalized)

label_protocol: Affymetrix (AGRF)

extract_protocol: Pine tree extraction method (Chang et al 1993)

value: Post-vernalized

tag: germplasm name

value: sonja

tag: organism part

value: po:0006340 adult leaf

tag: development stage

value: PO:0007106 LP.03 three leaves visible

tag: growth media

value: peat/perlite/soil


title: treatment: Non-vernalized - rep3 [BB95]

description: The 2nd leaf was harvested from non-vernalized plants that had been grown to the 3 leaf stage. All samples were harvested at the same time.

source_name: adult leaf (treatment: Non-vernalized)

value: Non-vernalized


title: 5B1 melanoma cell line -scrambled-treated-sample repeat 1


title: treatment: Non-vernalized - rep1 [BB95]


title: treatment: Post-vernalized - rep2


title: Spliceostatin treatment replicate 1 Dye-Swap

source_name: HeLa spliceostatin treatment replicate 1

source_name: HeLa methanol treatment replicate 1


title: Site 8 YSK2_reps3

city: changsha

first: xueduan

last: liu

address: lushan south road

country: China

institute: central south university

description: Each gene was spotted on the arrays in four replicates. A total of 320 spot data for control were already eliminated from the whole 4608 spot data on the array.

hyb_protocol: All hybridizations were carried out in triplicate. The hybridization solution contained 3× standard saline citrate (SSC) (1× SSC contained 150 mM NaCl and 15 mM trisodium citrate), 1ug of unlabeled herring sperm DNA (Promega, Madison, WI, USA), 0.30% SDS, and 50% formamide in a total volume of 15uL. To avoid bubbles, the hybridization solution was deposited directly onto the microarrays. The microarray (probe-side down) was placed on the coverslip (22 × 22 mm) and then into a hybridization chamber (Corning® hybridization chamber; Corning, Acton, MA, USA). Fifteen microliters of 3× SSC were dispensed into the hydration wells on each side of the microarray slide, and hybridization was carried out for 12–15 h. The hybridization was carried out at 50°C. Following hybridization, the arrays were washed with 1×SSC, 0.2% SDS and 0.1× SSC, and 0.2% SDS for 5 min each at ambient temperature and then with 0.1×SSC for 30 s (ambient temperature) prior to being air dried in the dark.

scan_protocol: The microarrays were scanned with a GenePix 4000B Array Scanner (AXON instruments, Inc, U.S.A).The emitted fluorescent signal was detected by a photomultiplier tube (PMT) at 570 nm (Cy3). The scanned images were saved as 16-bit TIFF files, and each spot was quantified by using GenePix Pro 6.0 software (AXON instruments, Inc, USA).

data_processing: A grid of individual circles defining the location of each DNA spot on the array was superimposed on the image to designate each fluorescent spot to be quantified. The mean signal intensity was determined for each spot. The local background signal was subtracted automatically from the hybridization signal of each separate spot also computed for each spot to discriminate true signals from noise. The SNR ratio was also calculated based on the following formula: SNR=(signal intensity – background)/standard deviation of background, in which the background measurement refers to the local spot background intensity and the standard deviation of background was calculated across all pixels measured by the ImaGene software. The SNRs from four replicate data sets were then averaged to represent the SNR for a particular probe. A commonly accepted criterion for the minimum signal (threshold) that can be accurately quantified is SNR ? 2. Spots that appeared to be lower than the threshold value were removed from the data set.

organism: unidentified microorganism

source_name: acid mine drainages microorganism

label_protocol: For genomic DNA labeling, 5µg genomic DNA was denatured by boiling for 2 min and immediately chilled to ice. The labeling reaction mixture contained denatured genomic DNA, 1.5 ug of random hexamers (Gibco BRL, Gaithersburg, Md.); 1u EcoPol buffer (New England Biolabs, Beverly, Mass.); 50 uM dATP, dTTP, and dGTP; 20 uM dCTP; 10 uM Cy3-dCTP (Amersham Pharmacia Biotech, Piscataway, N.J.); 2.5 mM dithiothreitol; and 10 U of the large Klenow fragment of DNA polymerase I (Invitrogen, U.S. A). The reaction mixture was incubated at 37°C for 3 h, then heat treated in a 100°C heating block for 3 min, and chilled in ice. Labeled target DNA was purified with a QIAquick PCR purification column according to the manufacturer’s instructions. Finally, the labeled DNA was resuspended in an appropriate volume of distilled water.

growth_protocol: Twenty three water samples (150 L for each sample) were obtained from the depth of 0-10 cm from the surface of the acid mine drainages in Dexing and Yingshankang.

extract_protocol: 5 g filters were mixed with 13.5 ml of DNA extraction buffer (100 mM Tris-HCl [pH 8.0], 100 mM sodium EDTA [pH = 8.0], 100 mM sodium phosphate [pH = 8.0], 1.5 M NaCl, 1% CTAB) and 100 ml of proteinase K (10 mg/ml) in Oakridge tubes by horizontal shaking at 225 rpm for 30 min at 37°C. After the shaking treatment, 1.5 ml of 20% SDS was added, and the samples were incubated in a 65°C water bath for 2 h with gentle end-over-end inversions every 15 to 20 min. The supernatants were collected after centrifugation at 6,000 × g for 10 min at room temperature and transferred into 50-ml centrifuge tubes. The pellets were extracted two more times by adding 4.5 ml of the extraction buffer and 0.5 ml of 20% SDS, vortexing for 10 s, incubating at 65°C for 10 min, and centrifuging as before. Supernatants from the three cycles of extractions were combined and mixed with an equal volume of chloroform isoamyl alcohol (24:1, vol/vol). The aqueous phase was recovered by centrifugation and precipitated with 0.6 volume of isopropanol at room temperature for 1h. The pellet of crude nucleic acids was obtained by centrifugation at 16,000 × g for 20 min at room temperature, washed with cold 70% ethanol, and resuspended in sterile deionized water, to give a final volume of 500 µl.

treatment_protocol: All water samples were filtered through a 0.2-µm nylon filter and the biomass on the filters was then immediately transferred to a bottle and kept in a cooler at approximately 0-4°C. The cooled biomass was then transferred to the laboratory and stored in -20°C walk-in freezer prior to molecular analysis.

tag: location

value: Yingshankang


title: Site 9 YSK3_reps2


title: Site 6 KZX_reps2

value: Dexing


title: Site 7 YSK1_reps3


title: Site 5 FKBZ_reps2


title: treatment: Post-vernalized - rep1


title: Spliceostatin treatment replicate 2

source_name: HeLa spliceostatin treatment replicate 2

value: HeLa

source_name: HeLa methanol treatment replicate 2


title: treatment: 1 day post-vernalized - rep1

description: Whole seedlings (minus seedcoat) (4cm coleoptile) grown in the dark for 1 day at normal growth temperatures after 49 days vernalization treatment. All samples were harvested at midday.

source_name: whole plant (treatment: 1 day post-vernalized)

value: 1 day post-vernalized

value: po:0000003 whole plant

value: UD:0000051 vegetative

value: Whatman filter paper


title: Site 4 ZJ_reps3


title: Spliceostatin treatment replicate 2B

source_name: HeLa spliceostatin treatment replicate 2B

value: spliceostatin

source_name: HeLa methanol treatment replicate 2B


title: treatment: 1 day post-vernalized - rep3


title: treatment: 1 day post-vernalized - rep2


title: treatment: Vernalized - rep3

description: Whole seedlings (minus seedcoat) (4cm coleoptile) grown in the dark, vernalized for 49 days. All samples were harvested at midday.

source_name: whole plant (treatment: Vernalized)

value: Vernalized


title: Spliceostatin treatment replicate 3

source_name: HeLa spliceostatin treatment replicate 3

value: methanol


title: SF3b155 knock-down siRNA 3 replicate 1

value: SF3b155 3 siRNA oligo

source_name: HeLa siRNA control of trasfection replicate 1

value: scrambled oligo


title: Site 2 YTW_reps2


title: Site 3 DWT_reps2


title: treatment: Vernalized - rep1

value: sonja


title: Spliceostatin treatment replicate 1

source_name: HeLa methanol treatment Replicate 1


title: treatment: Short-term cold - rep2

description: Whole seedlings (minus seedcoat) (4cm coleoptile) grown in the dark after 1 day cold treatment (4 degrees Celsius). All samples were harvested at midday.

source_name: whole plant (treatment: Short-term cold)

value: Short-term cold


title: Spliceostatin treatment replicate 2 Dye-Swap


title: treatment: Vernalized - rep2


title: treatment: Non-vernalized - rep1

description: Non-vernalized whole seedlings (minus seedcoat) (4cm coleoptile) grown in the dark. All samples were harvested at midday.

source_name: whole plant (treatment: Non-vernalized)


title: treatment: Non-vernalized - rep2


title: treatment: Short-term cold - rep3


title: Site 1 SLS_reps4

hyb_protocol: All hybridizations were carried out in triplicate. The hybridization solution contained 3× standard saline citrate (SSC) (1× SSC contained 150 mM NaCl and 15 mM trisodium citrate), 1?g of unlabeled herring sperm DNA (Promega, Madison, WI, USA), 0.30% SDS, and 50% formamide in a total volume of 15?L. To avoid bubbles, the hybridization solution was deposited directly onto the microarrays. The microarray (probe-side down) was placed on the coverslip (22 × 22 mm) and then into a hybridization chamber (Corning® hybridization chamber; Corning, Acton, MA, USA). Fifteen microliters of 3× SSC were dispensed into the hydration wells on each side of the microarray slide, and hybridization was carried out for 12–15 h. The hybridization was carried out at 50°C. Following hybridization, the arrays were washed with 1×SSC, 0.2% SDS and 0.1× SSC, and 0.2% SDS for 5 min each at ambient temperature and then with 0.1×SSC for 30 s (ambient temperature) prior to being air dried in the dark.

label_protocol: For genomic DNA labeling, 5µg genomic DNA was denatured by boiling for 2 min and immediately chilled to ice. The labeling reaction mixture contained denatured genomic DNA, 1.5 ?g of random hexamers (Gibco BRL, Gaithersburg, Md.); 1? EcoPol buffer (New England Biolabs, Beverly, Mass.); 50 ?M dATP, dTTP, and dGTP; 20 ?M dCTP; 10 ?M Cy3-dCTP (Amersham Pharmacia Biotech, Piscataway, N.J.); 2.5 mM dithiothreitol; and 10 U of the large Klenow fragment of DNA polymerase I (Invitrogen, U.S. A). The reaction mixture was incubated at 37°C for 3 h, then heat treated in a 100°C heating block for 3 min, and chilled in ice. Labeled target DNA was purified with a QIAquick PCR purification column according to the manufacturer’s instructions. Finally, the labeled DNA was resuspended in an appropriate volume of distilled water.


title: treatment: Short-term cold - rep1


title: treatment: Non-vernalized - rep3


title: ATCC 1015 rep3

status: Public on Mar 07 2011

city: Kgs. Lyngby

first: Mikael

middle: R

last: Andersen

address: Søltofts plads, bygn 223

department: BioCentrum-DTU

country: Denmark

institute: Technical University of Denmark

description: Strain: ATCC 1015, Growth: Exponential phase

hyb_protocol: Standard Affymetrix GeneChip Expression Analysis protocol

scan_protocol: The array was washed and stained using a GeneChip Fluidics Station FS-400, and scanned on an Agilent GeneArray Scanner 3000

data_processing: Affymetrix CEL-data files were preprocessed using the statistical language and environment R version 2.5.1. The probe intensities were normalised for background using the robust multiarray average (RMA) method using only perfect match (PM) probes. Normalization was performed subsequently using the quantiles algorithm. Gene expression values were calculated from the PM probes with the medianpolish summary method. All statistical preprocessing methods were used by invoking them through the affy package.

organism: Aspergillus niger

source_name: A. niger ATCC 1015 mycelium grown on a glucose medium

label_protocol: Affymetrix GeneChip Expression Analysis Technical Manual

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Mini Kit(QIAGEN Nordic, Ballerup, Denmark), according to the protocol for isolation of total RNA from plant and fungi

tag: Strain

value: ATCC 1015

tag: Growth

value: Exponential phase


title: Wild Type MAECs: 1103ZG0005

city: Nashville

first: Xinghua

last: Lin

state: Tennessee

address: 1005 D. B. Todd Jr. Blvd

department: Physiology

institute: Meharry Medical College

hyb_protocol: Affymetrix standard protocol was used.

scan_protocol: GeneChips were scanned using GeneArray Scanner 3000 and analyzed with the Affymetrix GeneChip Command Console.

data_processing: The data were analyzed and normalized with Affymetrix Expression Console software (program-version: 1.1.2800.19935, affymetrix-algorithm-name = rma-gene-default).

source_name: Wild Type MAECs: 1103ZG0005

label_protocol: Affymetrix standard protocol was used.

growth_protocol: MAECs grown to 80% confluence in six-well plates were made quiescent in serum-free DMEM for 12 h and then cultured in 10% FBS DMEM for 12 h.

extract_protocol: Total RNA was extracted with Trizol® reagent and purified by Rneasy Mini kit.

value: mouse aorta endothelial cells

tag: genotype/variation

value: Wild type

tag: strain


title: ATCC 1015 rep1


title: Wild Type MAECs: 1103ZG0001

source_name: Wild Type MAECs: 1103ZG0001


title: CBS 513.88 rep2

description: Strain: CBS 513.88, Growth: Exponential phase

source_name: A. niger CBS 513.88 mycelium grown on a glucose medium


title: CBS 513.88 rep3


title: hcatTg MAECs: 1103ZG0006

source_name: hcatTg MAECs: 1103ZG0006

value: hcatTg


title: hcatTg MAECs: 1103ZG0002

source_name: hcatTg MAECs: 1103ZG0002


title: ATCC 1015 rep2


title: CBS 513.88 rep1


title: huvecs_controltransfected_48h_2

city: Freiburg

first: Sebastian

last: Grundmann

address: Hugstetter Str. 55

country: Germany

institute: University Hospital Freiburg

description: Human umbilical vein endothelial cells (HUVECs) were isolated from donated umbilical cords, pooled from two donors and cultivated up to passage 5.

hyb_protocol: 1.65 µg of Cy3-labelled cRNA were fragmented according to the manufacturer´s instructions, and 1.5 µg of fragmented cRNA hybridized to an Agilent 4x44K array. Hybridization conditions: 65°C, 10 rpm, 17 h; in an Agilent hybridization oven

scan_protocol: Agilent arrays were washed using Agilent´s gene expression wash buffer 1 and 2 according to Agilent´s instructions. Scanning was performed using an Agilent DNA microarray Scanner and Agilent´s Scan Control Software (version A.8.3.1).

data_processing: Primary data analysis was performed using Agilent´s Feature Extraction Software (version 10.5.1.1) using default parameters (protocol GE1_105_Dec08) to obtain background subtracted and spatially detrended green Processed Signal intensities.

source_name: human umbilical cord endothelials cells

label_protocol: Kit: Quick Amp Labeling Kit, One Color (#5190-0442), using 200 ng of total RNA as starting material, according to the manufacturer´s instructions (Manual .One-color microarray-based gene expression analysis“, version 5.5, February 2007). cRNA synthesis was regarded successful provided that .1.65 µg of cRNA with a Cy3-incorporation rate .8.0 pmol/µg cRNA were synthesized.

extract_protocol: Total RNA was isolated from HUVECs 48h after transfection with TRIzol (Invitrogen) according to the manufacturers instructions.

treatment_protocol: For transfection with pre-miR microRNA precursor molecules (all Ambion), cells were cultured to 70% confluence and transfected with 8nM pre-miR-100 or anti-miR-100 oligonucleotides using Lipofectamin RNAiMax (Invitrogen) according to the manufacturers instructions.

tag: tissue

value: human umbilical cord

value: endothelials cells

tag: cell passage

tag: genome/variation

value: control transfected


title: huvecs_mir100transfected_48h_2

treatment_protocol: For transfection with pre-miR microRNA precursor molecules or anti-miR miRNA-inhibitors (all Ambion), cells were cultured to 70% confluence and transfected with 8nM pre-miR-100 or anti-miR-100 oligonucleotides using Lipofectamin RNAiMax (Invitrogen) according to the manufacturers instructions.

value: mir100 transfected


title: huvecs_mir100transfected_48h_1


title: huvecs_controltransfected_48h_1


title: HBL100 Aza Biological Replicate 2 (Expression)

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Standard Illumina Hybridisation Protocols

scan_protocol: Standard Illuminina Scanning Protocols

data_processing: Data were background subtracted and normalised using Illumina Genome Studio (average normalisation).  Data were then exported from Genome Studio and analysed using R.  Submitted data are those exported from Genome Studio.

source_name: Human Cancer Cell Line

label_protocol: RNA was amplified and biotinylated using an Illumina® TotalPrep™ RNA Amplification Kit

growth_protocol: Standard culture conditions

extract_protocol: Total RNA was isolated using Trizol and standard molecular biology protocols

treatment_protocol: 1µM 5'-aza-2'-deoxycytidine, refreshed every 24hrs, for a total of 72 h.

value: breast


title: HBL100 Aza Biological Replicate 1 (Expression)


title: HBL100 Control Biological Replicate 1 (Expression)

value: untreated


title: BT20 Control Biological Replicate 2 (Expression)


title: MCF7 Aza Biological Replicate 2 (Expression)


title: HBL100 Control Biological Replicate 2 (Expression)


title: MCF7 Control Biological Replicate 2 (Expression)


title: BT20 Control Biological Replicate 1 (Expression)


title: BT20 Aza Biological Replicate 1 (Expression)


title: BT20 Aza Biological Replicate 2 (Expression)


title: MCF7 Aza Biological Replicate 1 (Expression)


title: MCF7 Control Biological Replicate 1 (Expression)


title: HCT116wt Aza Biological Replicate 1 (Expression)

value: colon

value: wild type HCT116


title: HCT116wt Aza Biological Replicate 2 (Expression)


title: SF3b155 knock-down siRNA 5 replicate 1

source_name: SF3b155 siRNA 5 knock-down in HeLa cell line replicate 1

tag: transfection

value: SF3b155 5 siRNA oligo

value: HeLa


title: K54

city: Cambridge

first: Bernardo

last: Lemos

state: MA

address: 16 Divinity Avenue, Room 2105

institute: Harvard University

description: Biological replicate

hyb_protocol: 3DNA procedure

scan_protocol: Scanned on an Axon 4000B scanner. Images were quantified using Genepix.

data_processing: LOESS normalized, VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: Total RNA from male flies.

label_protocol: 3DNA procedure

extract_protocol: TriZol procedure

tag: genotype

tag: sex

value: male

tag: age

value: 2 days old


title: F74

description: Biological replicate


title: HCT116dko Control Biological Replicate 2 (Expression)

tag: cell line

value: DNA methyltransferase deficient HCT116 cells

tag: agent


title: treatment: Non-vernalized - rep2 [BB95]

source_name: adult leaf (treatment: Non-vernalized)

tag: treatment

value: Non-vernalized

tag: germplasm name

value: sonja

tag: organism part

value: po:0006340 adult leaf

value: PO:0007106 LP.03 three leaves visible

value: peat/perlite/soil


title: HCT116dko Control Biological Replicate 1 (Expression)


title: F75

description: Biological replicate


title: F76

description: Biological replicate


title: HCT116wt Control Biological Replicate 1 (Expression)


title: K53

description: Biological replicate


title: Primary Breast Tumour AP (Methylation)

data_processing: Data were exported from Illumina Genome Studio (BeadStudio Methylation Analysis Module) and analysed using R.  Submitted data are those exported from Genome Studio.

label: Cy3 and Cy5

source_name: Human Breast Tumour Sample

label_protocol: Genomic DNA (500 ng) from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo research Corporation, Orange, US) before being amplified and enzymatically fragmented (standard Illumina protocols)

extract_protocol: Genomic DNA was extracted using standard molecular biology protocols (pK digestion, phenol-chloroform extraction and ethanol precipitation)

value: Primary Breast Tumour

value: Fresh Frozen Primary Breast Tumour  Sample


title: F77

description: Biological replicate


title: Primary Breast Tumour AT (Methylation)


title: F79

description: Biological replicate


title: F78

description: Biological replicate


title: Primary Breast Tumour AO (Methylation)


title: F81

description: Biological replicate


title: Primary Breast Tumour AU (Methylation)


title: Primary Breast Tumour AN (Methylation)


title: HCT116wt Control Biological Replicate 2 (Expression)


title: Primary Breast Tumour AR (Methylation)


title: Primary Breast Tumour AK (Methylation)