title: bronchial gland (A)

description:
SAMPLE 13
replicate 1

value: bronchial gland


title: Stim1Cd4 mouse 1

status: Public on Mar 17 2015

type: RNA

city: New York City

first: Stefan

last: Feske

state: NY

address: 550 First Avenue

department: Pathology

country: USA

institute: New York University

description: RMA expression value derived from Expression Console software

hyb_protocol: Biotin-labeled amplified aRNA was prepared and hybridized to 1.0 Eon expression chips  (Affymetrix) according to the manufacturer’s protocols

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

data_processing:
The values in the CHP sample data tables were derived from the Expression Console Software (Affymetrix) by performing a gene-level normalization and signal summarization on the raw CEL files (gene-level analysis).
Data were further analyzed and visualized using TCA software (Affymetrix) and IPA pathway analysis software (Qiagen). Probesets were defined using a treshold with  p<0.05 and FC >1.5 or  <-1.5.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: Stim1 deficient mouse (Stim1CD4)

growth_protocol: CD4+ T cells were isolated from the spleens of WT mice using a negative selection kit (STEMCELL Technologies) and stimulated with 0.5 µg/ml plate-bound anti-CD3 and 1 µg/ml anti-CD28 antibodies (BioXCess) and cultured in the presence  or absence of 2.5 ng/ml TGF-β (Peprotech)

extract_protocol: Total RNA was isolated using the RNeasy micro RNA isolation kit (Quiagen)

treatment_protocol: For the generation of  Thn cells (non-polarizing conditions), CD4+ T cells were stimulated  for 48h with 0.5 µg/ml anti-CD3 and 1µg/ml anti-CD28. For the generation of inducible T regulatory cells (iTreg), CD4+ T cells were stimulated for 48h with 0.5 µg/ml anti-CD3 and 1.0 µg/ml anti-CD28 in the presence of 2.5 ng/ml TGF-β.

tag: genotype/variation

value: STIM1 deficient CD4+ T cells

tag: treatment

value: stimulation with aCD3/aCD28+TGFbeta (48)


title: glomerulus (B)

city: Osaka

first: Kosuke

last: Endo

address: 5-7-1 Fujishirodai, Suita

department: Dept. of Genomic Medicine

country: Japan

institute: National Cerebral and Cardiovascular Center

description:
SAMPLE 17
replicate 1

scan_protocol: The ABI Prism 7900 HT Sequence Detection System (Applied Biosystems) was used for amplification and detection.

data_processing: Ct values were obtained from the amplification plot using the SDS software (Applied Biosystems). U6 was used as endogenous control and DCt defined by the formula (Ct of the specific miRNAs - average Ct of the endogenous control U6 in the sample).

label: FAM

organism: Rattus norvegicus

source_name: cell

label_protocol: ABI TaqMan Human MicroRNA Array kit (Card B; Applied Biosystems, CA, USA) according to the manufacturer’s instructions.

extract_protocol: Total RNA isolated by TRIzol reagent for tissue samples and mirVana PARIS Kit for LMD samples.

tag: strain

value: Sprague-Dawley

tag: age

value: 4 weeks

tag: tissue/cell type

value: glomerulus

tag: pre-amp

value: 12 cycles


title: small intestine (A)

description:
SAMPLE 12
replicate 1

source_name: Tissue

label_protocol: ABI TaqMan Human MicroRNA Array kit (Card A; Applied Biosystems, CA, USA) according to the manufacturer’s instructions.

value: small intestine

value: no


title: Stim1Cd4 Thn mouse 2

label_protocol: Biotin-labeled amplified aRNA was prepared and hybridized to 1.0 Eon expression chips  (Affymetrix) according to the manufacturer’s protocols

value: stimulation with aCD3/aCD28 (48h)


title: Wt Thn mouse 2

source_name: Wt mouse

value: WT CD4+ T cells


title: Stim1Cd4 Thn mouse 1


title: Stim1Cd4 Thn mouse 3


title: HD non-classical 1

city: Bethesda

first: Baoying

last: Liu

address: 9000 Rockville Pike

institute: NEI

description: Sample 3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Genechip human genome U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip scanner 3000 operated by Affymetrix GeneChip Operating Software, version 1.4 (GCOS 1.4).

data_processing:
GeneSpring software GX 7.3.1 (Agilent Technologies) or R package limma (version 3.23.6)
data processing was performed in two groups; [1] HD intermediate, classical and non-classical samples (total 12 samples) [2] HD intermediate and P intermediate samples (total 9 samples).
For group [1], values (raw intensity) were determined by using GeneSpring software GX 7.3.1 (Agilent Technologies) and the normalization algorithm is RMA.
For group [2], RMA function in Limma (version 3.23.6) was used to do the following:
1. Probe specific correction of the PM probes using a model based on observed intensity being the sum of signal and noise 2. Normalization of corrected PM probes using quantile normalization (Bolstad et al., 2003) 3. Calculation of Expression measure using median polish.
Reference of Limma:
Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3.

label: biotin

organism: Homo sapiens

source_name: human non-classical monocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (MessageAmp™ II-Biotin Enhanced Kit).

growth_protocol: PBMCs were purified and then flow cytometry was used to sort 3 monocyte subsets

extract_protocol: RNeasy (QIAGEN) was used to purify total RNA according to the manufacturer's instructions.

treatment_protocol: No treatment

tag: subject status

value: healthy donor

tag: subject id

tag: tissue

value: human peripheral monocytes

tag: tissue subtype

value: non-classical monocyte subset


title: HD classical 1

description: Sample 2

source_name: human classical monocytes

value: classical monocyte subset


title: Wt Thn mouse 3


title: Wt Thn mouse 1


title: spleen (A)

description:
SAMPLE 11
replicate 1

value: spleen


title: proximal tubule (B)

description:
SAMPLE 16
replicate 1

value: proximal tubule


title: heart (A)

description:
SAMPLE 9
replicate 1

value: heart


title: skeletal muscle (A)

description:
SAMPLE 10
replicate 1

value: skeletal muscle


title: mammary gland (B)

description:
SAMPLE 14
replicate 1

value: mammary gland


title: liver (A)

description:
SAMPLE 8
replicate 1

value: Sprague-Dawley

value: liver


title: bile duct (A)

description:
SAMPLE 7
replicate 1

value: 4 weeks

value: bile duct


title: bronchial gland (B)

description:
SAMPLE 13
replicate 1

value: bronchial gland

value: 12 cycles


title: small intestine (B)

description:
SAMPLE 12
replicate 1

value: small intestine

value: no


title: lung (A)

description:
SAMPLE 6
replicate 1

value: lung


title: HD intermediate 1

description: Sample 1

source_name: human intermediate monocytes

value: healthy donor

value: human peripheral monocytes

value: intermediate monocyte subset


title: lacrimal gland (A)

description:
SAMPLE 5
replicate 1

value: lacrimal gland


title: 50 weeks old mice 4

city: Shinagawa

first: Atsushi

last: Yamada

state: Tokyo

address: 1-5-8 Hatanodai

department: School of Dentistry

institute: Showa University

description: SAMPLE 10

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Mouse sabmandibular gland

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.


title: 50 weeks old mice 6

description: SAMPLE 12


title: 50 weeks old mice 3

description: SAMPLE 9


title: prostate (B)

description:
SAMPLE 4
replicate 1

value: prostate


title: intestinal villus (B)

description:
SAMPLE 15
replicate 1

value: intestinal villus


title: prostate (A)

description:
SAMPLE 4
replicate 1


title: salivary gland (A)

description:
SAMPLE 3
replicate 1

value: salivary gland


title: 8 weeks old mice 6

description: SAMPLE 6


title: 50 weeks old mice 1

description: SAMPLE 7


title: lacrimal gland (B)

description:
SAMPLE 5
replicate 1


title: 50 weeks old mice 5

description: SAMPLE 11


title: 50 weeks old mice 2

description: SAMPLE 8


title: 8 weeks old mice 4

description: SAMPLE 4


title: 8 weeks old mice 5

description: SAMPLE 5


title: salivary gland (B)

description:
SAMPLE 3
replicate 1


title: pancreas (A)

description:
SAMPLE 2
replicate 1

value: pancreas


title: bile duct (B)

description:
SAMPLE 7
replicate 1

value: Sprague-Dawley


title: kidney (A)

description:
SAMPLE 1
replicate 1

value: kidney


title: pancreas (B)

description:
SAMPLE 2
replicate 1

value: 4 weeks


title: 8 weeks old mice 3

description: SAMPLE 3


title: 8 weeks old mice 2

description: SAMPLE 2


title: 8 weeks old mice 1

description: SAMPLE 1


title: Calu.1.9585NF.MonocultureMix (A161)

status: Public on Mar 16 2015

city: Vienna

first: Andreas

last: Wernitznig

address: Dr.-Boehringer-Gasse 5-11

department: Oncology - Pharmacology

country: Austria

institute: Boehringer Ingelheim

description: Sample name: 7497_A161_20130205

hyb_protocol: Hybridization solution was prepared using the Affymetrix HWS Kit (Affymetrix, P/N 900720) according to NuGEN´ Applause WT Amp Plus System User Guide. The final concentration of cDNA was between 18 and 23 ng/μl. Hybridization was performed on Affymetrix GeneChips Exon 1.0 for 18+/-2 h at 45°C and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix).

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix)

data_processing: RMA normalized data using the Affy Package in R 2.14/Bioconductor and alternative CDF huex10stv2hsrefseq 16.1.0 from Brainarray

source_name: Calu.1.9585NF, monocultureMix

label_protocol: NuGEN’s Encore Biotin Module (NuGEN, 4200-12) was used to fragment 4 to 5 μg cDNA followed by Biotin-labeling according to the manufacturer’s instructions.

growth_protocol: For mono-cultures 2e6 tumor or FB cells were seeded in a 100 mm dish (Corning, 35300) with a total volume of 10 ml of RPMI medium supplemented with 10% FBS and Pen/Strep. Co-cultures were prepared with 2e6 cells for each cell type per dish.

extract_protocol: not applicable

treatment_protocol: not applicable

tag: tumor cell line

tag: fibroblast line

tag: growth type

value: MonocultureMix

tag: sampleID


title: Calu.1.9585CAF.MonocultureMix (A164)

description: Sample name: 7497_A164_20130205

source_name: Calu.1.9585CAF, monocultureMix


title: Calu.1.9585CAF.MonocultureMix (A163)

description: Sample name: 7497_A163_20130205


title: Calu.1.HDF.MonocultureMix (A156)

description: Sample name: 7497_A156_20130205

source_name: Calu.1.HDF, monocultureMix

value: HDF


title: Calu.1.9585NF.MonocultureMix (A162)

description: Sample name: 7497_A162_20130205


title: Calu.1.9585CAF.Cocultured (A152)

description: Sample name: 7497_A152_20130205

source_name: Calu.1.9585CAF, coculture

value: Cocultured


title: Calu.1.WI.38.MonocultureMix (A159)

description: Sample name: 7497_A159_20130205

source_name: Calu.1.WI.38, monocultureMix


title: Calu.1.9585CAF.MonocultureMix (A165)

description: Sample name: 7497_A165_20130205


title: Calu.1.9585CAF.Cocultured (A151)

description: Sample name: 7497_A151_20130205


title: Calu.1.9585NF.Cocultured (A148)

description: Sample name: 7497_A148_20130205

source_name: Calu.1.9585NF, coculture


title: Calu.1.9585NF.Cocultured (A149)

description: Sample name: 7497_A149_20130205


title: Calu.1.HDF.MonocultureMix (A155)

description: Sample name: 7497_A155_20130205


title: Calu.1.HDF.Cocultured (A143)

description: Sample name: 7497_A143_20130205

source_name: Calu.1.HDF, coculture


title: Calu.1.WI.38.Cocultured (A146)

description: Sample name: 7497_A146_20130205

source_name: Calu.1.WI.38, coculture


title: Calu.1.HDF.Cocultured (A144)

description: Sample name: 7497_A144_20130205


title: Calu.1.HDF.Cocultured (A142)

description: Sample name: 7497_A142_20130205


title: Calu.1.9585NF.Cocultured (A150)

description: Sample name: 7497_A150_20130205


title: Calu.1.WI.38.Cocultured (A145)

description: Sample name: 7497_A145_20130205


title: Calu.1.WI.38.MonocultureMix (A157)

description: Sample name: 7497_A157_20130205


title: Calu.1.WI.38.Cocultured (A147)

description: Sample name: 7497_A147_20130205


title: Calu.1.WI.38.MonocultureMix (A158)

description: Sample name: 7497_A158_20130205


title: Calu.1.9585NF.MonocultureMix (A160)

description: Sample name: 7497_A160_20130205


title: Calu.1.9585CAF.Cocultured (A153)

description: Sample name: 7497_A153_20130205


title: HD intermediate 1 [re-analysis]

description: Sample 1 [re-analysis]


title: Calu.1.HDF.MonocultureMix (A154)

description: Sample name: 7497_A154_20130205


title: HD intermediate 4 [re-analysis]

description: Sample 10 [re-analysis]


title: NCI.H1437.9585NF.MonocultureMix (A138)

description: Sample name: 7496_A138_20130201

source_name: NCI.H1437.9585NF, monocultureMix


title: NCI.H1437.9585CAF.MonocultureMix (A139)

description: Sample name: 7496_A139_20130201

source_name: NCI.H1437.9585CAF, monocultureMix


title: NCI.H1437.9585NF.MonocultureMix (A137)

description: Sample name: 7496_A137_20130201


title: NCI.H1437.9585CAF.MonocultureMix (A141)

description: Sample name: 7496_A141_20130201


title: NCI.H1437.9585CAF.MonocultureMix (A140)

description: Sample name: 7496_A140_20130201


title: NCI.H1437.WI.38.MonocultureMix (A134)

description: Sample name: 7496_A134_20130201

source_name: NCI.H1437.WI.38, monocultureMix


title: NCI.H1437.HDF.MonocultureMix (A132)

description: Sample name: 7496_A132_20130201

source_name: NCI.H1437.HDF, monocultureMix


title: NCI.H1437.HDF.MonocultureMix (A130)

description: Sample name: 7496_A130_20130201


title: NCI.H1437.9585NF.MonocultureMix (A136)

description: Sample name: 7496_A136_20130201


title: NCI.H1437.WI.38.MonocultureMix (A135)

description: Sample name: 7496_A135_20130201


title: NCI.H1437.9585CAF.Cocultured (A129)

description: Sample name: 7496_A129_20130201

source_name: NCI.H1437.9585CAF, coculture


title: NCI.H1437.HDF.MonocultureMix (A131)

description: Sample name: 7496_A131_20130201


title: NCI.H1437.9585NF.Cocultured (A126)

description: Sample name: 7496_A126_20130201

source_name: NCI.H1437.9585NF, coculture


title: NCI.H1437.9585NF.Cocultured (A124)

description: Sample name: 7496_A124_20130201


title: NCI.H1437.WI.38.Cocultured (A121)

description: Sample name: 7496_A121_20130201

source_name: NCI.H1437.WI.38, coculture


title: NCI.H1437.WI.38.Cocultured (A123)

description: Sample name: 7496_A123_20130201


title: 9585CAF.Monocultured (A116)

description: Sample name: 7461_A116_20130206

source_name: 9585CAF, monoculture

value: Monocultured


title: NCI.H1437.WI.38.Cocultured (A122)

description: Sample name: 7496_A122_20130201


title: NCI.H1437.WI.38.MonocultureMix (A133)

description: Sample name: 7496_A133_20130201


title: NCI.H1437.9585CAF.Cocultured (A128)

description: Sample name: 7496_A128_20130201


title: NCI.H1437.HDF.Cocultured (A118)

description: Sample name: 7496_A118_20130201

source_name: NCI.H1437.HDF, coculture


title: 9585CAF.Monocultured (A117)

description: Sample name: 7461_A117_20130206


title: NCI.H1437.9585NF.Cocultured (A125)

description: Sample name: 7496_A125_20130201


title: NCI.H1437.HDF.Cocultured (A119)

description: Sample name: 7496_A119_20130201


title: NCI.H1437.9585CAF.Cocultured (A127)

description: Sample name: 7496_A127_20130201


title: NCI.H1437.HDF.Cocultured (A120)

description: Sample name: 7496_A120_20130201


title: 9585NF.Monocultured (A113)

description: Sample name: 7461_A113_20130206

source_name: 9585NF, monoculture


title: 9585CAF.Monocultured (A115)

description: Sample name: 7461_A115_20130206


title: 9585NF.Monocultured (A114)

description: Sample name: 7461_A114_20130206


title: WI.38.Monocultured (A110)

description: Sample name: 7461_A110_20130206

source_name: WI.38, monoculture


title: WI.38.Monocultured (A111)

description: Sample name: 7461_A111_20130206


title: WI.38.Monocultured (A109)

description: Sample name: 7461_A109_20130206


title: HDF.Monocultured (A106)

description: Sample name: 7461_A106_20130206

source_name: HDF, monoculture


title: 9585NF.Monocultured (A112)

description: Sample name: 7461_A112_20130206


title: Calu.1.Monocultured (A104)

description: Sample name: 7461_A104_20130206

source_name: Calu.1, monoculture


title: HDF.Monocultured (A107)

description: Sample name: 7461_A107_20130206


title: HDF.Monocultured (A108)

description: Sample name: 7461_A108_20130206


title: NCI.H1437.Monocultured (A102)

description: Sample name: 7461_A102_20130206

source_name: NCI.H1437, monoculture


title: Calu.1.Monocultured (A103)

description: Sample name: 7461_A103_20130206


title: NCI.H1437.Monocultured (A100)

description: Sample name: 7461_A100_20130206


title: NCI.H1437.Monocultured (A101)

description: Sample name: 7461_A101_20130206


title: Derivative can1/CAN1 diploid YKO clone pool treated with 15 microgram per ml zeocin

type: genomic

city: Warszawa

first: Adrianna

last: Skoneczna

address: Pawinskiego 5A

department: Laboratory of Mutagenesis and DNA Repair

country: Poland

institute: Institute of Biochemistry and Biophysics

hyb_protocol: Hybridization to   Four PCR labeling reactions were used for single hybridization: UPTAGs and DNTAGs from the first DNA sample labeled with Cy3 and UPTAGs and DNTAGs from the second DNA sample labeled with Cy5. 50 μl each of two UPTAG reactions were mixed with 40 μl of 250mM U1 primer and 40 μl of 250mM U2 primer to block the common primer sequences on the labeled strand. Likewise, 50 μl each of two DNTAG reactions were mixed with 40 μl of 250mM D1 primer and 40 μl of 250mM D2 primer. Both mixes were incubated for 2-3' in 95-100°C, then put on ice for 2'. The mixes were then combined, 36 ml 3 M sodium acetate pH 5.4 and 840 ml 95% EtOH were added and the probe was put into liquid nitrogen bath for 2' to precipitate DNA. Probe was spun down 15' at top speed in a microcentrifuge. Small violet precipitate should be visible at this point. Probe pellet was washed with 80% EtOH, air dried and dissolved in 7.5μl of water. Dissolved probe was incubated for 5' in 75°C and added to hybridization solution containing 110 ml 1 x SSTE (1 M NaCl, 10 mM Tris, pH 7.5, 0.5% Triton X-100), 1 ml each of 5nM Cy3-G and Cy5-G gridline primers and 0.22 ml 0.5 M DTT prewarmed to 42°C. Hybridization probe was mixed gently to avoid generating foam and kept at 42°C until the microarray slide is ready. Gasket slide (Agilent) was put into hybridization chamber (Agilent), probes in hybridization solution were pipetted onto each well of the gasket and covered with Agilent custom-made Barcode  microarray slide. Hybridization chamber was closed, rotated slowly to moisten microarray slide with the hybridization mix without producing excessive air bubbles and put into hybridization oven for 16 hours, 42°C, 10 RPM.    Microarray washing  Washing was done in Falcon tubes in three dilutions of 20x SSPE (3 M NaCl, 200 mM NaH2PO4, 50 mM EDTA pH 7.4). Hybridization chamber was opened, microarray-gasket sandwich was dropped into first wash solution (6x SSPE + 0.05% Triton X100) and separated. Gasket slide was removed and the microarray slide was washed by rocking the Falcon tube several times. Slide was transferred into the second wash solution (1x SSPE) and washing was repeated. Final wash was done in 0.06x SSPE. The slide was taken out from the final wash solution with the slow steady move to allow its hydrophobic surface to repel the solution without leaving droplets.

scan_protocol: After washing the slides were immediately scanned using Axon GenePix 4000B scanner (Molecular Devices, USA) at 5mm and 100% laser power. PMT gain was adjusted individually (between 600 and 800 volts) to get optimal images. Feature extraction was done using GenePix Pro 6.1 (Molecular Devices, USA) using separate GAL files for DN-TAG and UP-TAG blocks. The GAL files are submitted together with raw data files.

data_processing: The LogRatio data from all replicates of each comparison, which includes the data for DN-TAGs and UP-TAGs were ratio-normalized, averaged and the statistical significance was calculated. Since the LogRatio data for each gene in the Matrix Table are the average of both DN-TAG and UP-TAG datasets, the IDs of both DN-TAG and UP-TAG probes are included in the Matrix Table.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Derivative, can1delta/CAN1 Yeast knock-out collection diploid clone pool

label_protocol: Sequences of primers used for labeling blocking and hybridization:  D1 – CGGTGTCGGTCTCGTAG  D2 – ATCGATGAATTCGAGCTCG  U1 – GATGTCCACGAGGTCTCT  U2 – CGTACGCTGCAGGTCGAC  Cy3-U3 – 5’-Cy3-GTCGACCTGCAGCGTACG  Cy5-U3 – 5’-Cy5-GTCGACCTGCAGCGTACG  Cy3-D3 – 5’-Cy3-CGAGCTCGAATTCATCGAT  Cy5-D3 – 5’-Cy5-CGAGCTCGAATTCATCGAT  Cy3-G – 5’-Cy3-GGATACACTGACCAGCTACGATGAT  Cy5-G – 5’-Cy5-GGATACACTGACCAGCTACGATGAT    PCR labeling  Each PCR reaction for UPTAG or DNTAG labeling contained in a final volume of 100 μl: 2.5 U of BIOTOOL polymerase (BIOMOL), 10 μl 10x Reaction Buffer, 10 μl 2mM dNTP mix, 150 ng genomic DNA and 10 μl of one of these 5 µM primer mixes: U1+Cy3-U3, U1+Cy5-U3, D1+Cy3-D3, D1+Cy5-D3. Each reaction mix was split into two 50 ml aliquots kept in separate tubes. The reaction was started with 3' of melting at 94°C followed by 30 cycles of PCR reaction (94°C 15 - 50°C 15 - 72°C 30) followed by 3' incubation at 72°C. After reaction the aliquots of reaction mixes were recombined and the labeled probes were stored frozen in the dark until use.

growth_protocol: The pool of Saccharomyces cerevisiae diploid strains from Yeast Knock-out collection (Open Biosystems), specifically homozygous diploid strains for non-essential genes (HD) and heterozygous strains for essential genes (ESS), or alternatively the heterozygous CAN1/can1::LEU2 derivative pool of these described above (HDC and ESSC respectively) was grown at 28°C with agitation in YPD medium to the log phase (2*107cell per ml). Then cells were mock-treated or zeocin was added to final concentration 5 µg per ml or 15 µg per ml. After one hour further incubation, in the dark, cells were washed with sterile 0.9% NaCl and plated on SC plates. After 2 day-incubation at 28°C colonies were washed out, and aliquots of 109 cells were taken for genomic DNA preparation for subsequent barcode labeling.

extract_protocol: 10^9 cells were thawed, resuspended in 0.5 ml of 1 M Sorbitol/0.1 M EDTA and 20μl of 2.5 mg per ml zymolyase 100T solution was added. The suspension was mixed well and incubated 1 hour in 37°C with occasional mixing by inverting of tube. Spheroplasted cells were spun down in microcentrifuge at top speed for 1', resuspended in 0.5ml 10 mM Tris 50 mM EDTA buffer and 50µl of 10% SDS was added to the suspension. Tube content was mixed very delicately by inverting and the tube and was incubated for 1 hour in 65°C. After adding 200 µl of 5 M potassium acetate tube was mixed vigorously and immediately put on ice for 1 hour. Tube was spun in the microfuge at top speed at 4°C for 15', supernatant (~ 750 µl) was transfered to a new tube. Genomic DNA was precipitated by adding equal volume (~750 µl) of isopropanol and gentle mixing by inverting the tube. Precipitate was spun at top speed at 4°C for 5', DNA pellet was washed with 80% EtOH and dried by leaving open tube on the bench at RT for 5-10'. Dried DNA sample was dissolved in 400 µl of 10mM Tris-HCl buffer pH 8.0. To clean up DNA solution of RNA 5 µl of 10 mg per ml of RNase A was added and the mixture was incubated at 37°C for 30'. DNA sample was then extracted with 400 µl of phenol pH 8.0. Aqueous phase was transferred to Phase Lock Gel tube (Eppendorf) and centrifuged in the microfuge at top speed for 10 min to get rid of phenol residues. Aqueous phase was transferred to a new tube and DNA was precipitated by the addition of 40 µl of 3 M sodium acetate pH 5.4 and 1 ml of 100% EtOH followed by gentle mixing by inverting the tube. After leaving the tube for several minutes at room temperature DNA precipitate was spun in the microfuge at top speed at 4°C for 10', washed with 80% EtOH, air dried and resuspend in 100 µl of 10mM Tris-HCl buffer pH 8.0. Concentration of the genomic DNA was determined using NanoDrop spectrophotometer. The quality of the DNA preparation was estimated by resolving 3 µl of the solution on 1% agarose gel. The entire genomic DNA preparation should run as one discrete band appearing larger than 20 kb in size. For labeling procedure genomic DNA was diluted to 100ng/μl.

treatment_protocol: One hour incubation in YPD medium supplemented with 5 µg per ml or 15 µg per ml zeocin.

value: mock

value: 15 microgram per ml zeocin


title: Calu.1.Monocultured (A105)

description: Sample name: 7461_A105_20130206


title: Original diploid YKO clone pool treated with 5 microgram per ml zeocin

source_name: Original Yeast knock-out collection diploid clone pool

value: 5 microgram per ml zeocin


title: Original diploid YKO clone pool treated with 15 microgram per ml zeocin


title: Derivative can1/CAN1 diploid YKO clone pool treated with 5 microgram per ml zeocin


title: Control_HF_12hr vs TGFb_HF_12hr_rep2

city: Bangalore

first: Neeraj

last: KUMAR

address: Indian Institute of Science Bangalore

department: MRDG

country: India

institute: Indian Institute of Science Bangalore

hyb_protocol: 750 ng of labelled cRNA each from treated and untreated were mixed with blocking agent and fragmentation buffer followd by incubation at 65 °C for 30 min. This is followed by addition of 55 ul of 2x GEx Hybridization Buffer HI-RPM to stop the fragmentation reaction. Later 100 ul of the above mix were added to each array.

scan_protocol: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

data_processing: Limma package was used for back ground correction and normalization.forground median and background median values were used for both R and G for background correction and normalization.log2(R/G) background subtracted and loess normalized value are given in data matrix value for all arrays.

source_name: untreated HFhTERT cells after 12hr

label_protocol: 200 ng of RNA each from untreated and treated samples were used. Labeling of the RNA was done using the Low RNA Input Linear Amplification Kit (Agilent Technologies, USA). Briefly 200 ng of RNA was reverse transcribed using T7promoter attached Oligo-dT primers at 40 °C for 2 hrs followed by 65 °C for 15 min. This cDNA were transcribed using T7 polymerase with respective labelled nucleotides at 40 °C for 2hrs. This synthesized labelled cRNA were purified using RNeasy mini column.

growth_protocol: All the three cell-lines hFhTERT, hFhTERT-LTgRAS and HT1080 cell-lines were maintained in DMEM (Sigma-Aldrich, USA) supplemented with 10% fetal bovine serum (Certified grade, Invitrogen corporation, USA), 100 units/mL penicillin and 100µg/mL streptomycin (Invitrogen Life Sciences, USA) at 37°C in a humidified chamber with 5% CO2.

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

treatment_protocol: For treatments, both the cell-lines were serum starved for 24 hr and treated with 5 ng/ ml of TGF-beta1 (R&D systems, USA) for 1 hr, 4 hr and 12 hrs. RNA isolated from untreated cells at each timepoint served as controls

tag: cell type

value: Human immortal foreskin fibroblasts

tag: cell line

value: HFhTERT

source_name: HFhTERT cells after 12hr of TGF-beta treatment


title: Control_HF_12hr vs TGFb_HF_12hr_rep1


title: Control_LTgRAS_12hr vsTGF-b_LTgRAS_12hr_2

source_name: untreated hFhTERT-LTgRAS cells after 12hr

value: HFhTERT-LTgRAS

value: Human immortal foreskin fibroblasts transformed with SV 40 large T antigen and activated RAS


title: Control_LTgRAS_4hr vsTGF-b_LTgRAS_4hr_2

source_name: untreated hFhTERT-LTgRAS cells after 4hr


title: Control_HF_4hr vs TGFb_HF_4hr_rep2

source_name: untreated HFhTERT cells after 4hr

source_name: HFhTERT cells after 4hr of TGF-beta treatment


title: Str sc lamot 4

city: Groton

first: Thomas

middle: A

last: Lanz

state: CT

address: Eastern Point Rd

department: Multi-Omics & Biomarkers

institute: Pfizer

description: STR R14

hyb_protocol: Five (5) ug of fragmented, biotin-labeled cDNA was hybridized to Affymetrix Rat Genome 230 2.0 Gene Chips for 18 hours, then washed/stained according to manufacturer's recommendations using the Affymetrix 450 fluidics station.

scan_protocol: Gene chips were scanned using an Affymetrix 3000 array scanner.

data_processing: R version 2.7.2 was used with midas2 version 1.16 for  Robust Multi-Array Average (RMA) normalization.

source_name: Striatum Lamotrigine

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Trizol extraction of total RNA was performed.

value: SD

tag: treated with

value: Lamotrigine (30 mg/kg)

tag: time point

value: after 21 days of constant drug delivery

value: Snap-frozen microdissected mouse brain region

value: Striatum


title: Control_LTgRAS_12hr vsTGF-b_LTgRAS_12hr_1


title: Str sc lamot 5

description: STR R9


title: Control_LTgRAS_1hr vsTGF-b_LTgRAS_1hr_2

source_name: untreated hFhTERT-LTgRAS cells after 1hr


title: Control_LTgRAS_4hr vsTGF-b_LTgRAS_4hr_1


title: Control_LTgRAS_1hr vsTGF-b_LTgRAS_1hr_1


title: Control_HT_4hr vsTGF-b_HT_4hr_rep2

source_name: untreated HT1080 cells after 4hr

value: Fibrosarcoma

source_name: HT1080 cells after 4hr of TGF-beta treatment


title: Control_HT_4hr vsTGF-b_HT_4hr_rep1


title: Control_HT_12hr vsTGF-b_HT_12hr_rep2

source_name: untreated HT1080 cells after 12hr

source_name: HT1080 cells after 12hr of TGF-beta treatment


title: Control_HT_12hr vsTGF-b_HT_12hr_rep1


title: Control_HF_4hr vs TGFb_HF_4hr_rep1


title: Str sc lamot 1

description: STR R10


title: Str chow veh 5

source_name: Striatum veh for LiCl

value: Vehicle (for LiCl)


title: Control_HT_1hr vsTGF-b_HT_1hr_rep2

source_name: untreated HT1080 cells after 1hr

source_name: HT1080 cells after 1hr of TGF-beta treatment


title: Str sc lamot 3

description: STR R13


title: Str sc lamot 2

description: STR R11


title: Control_HF_1hr vs TGFb_HF_1hr_rep1

source_name: untreated HFhTERT cells after 1hr

source_name: HFhTERT cells after 1hr of TGF-beta treatment


title: Control_HT_1hr vsTGF-b_HT_1hr_rep1


title: Klotho-wild type, replicate 3

city: Cincinnati

first: Elaine

middle: Emily

last: Wirrig

state: Ohio

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from 6 week old Klotho-wild type mice

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 18 hr at 45C on the GeneChip mouse genome 430 2.0 Array using the GeneChip hybridization oven 640 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol FS450-0004.

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

data_processing:
Gene expression levels were measured using the GeneChip Operating Software (Affymetrix). The array data was normalized using the robust multi-array average (RMA) algorithm and statistical analysis of the data was performed using GeneSpring GX 7.3 software (Agilent Technologies).
CEL files represent data generated using GeneChip Operating software. Matrix values represent data generated using Mas5.

source_name: Aortic roots from 3 klotho-wild type mice at 6-6.5 weeks of age.

label_protocol: cRNA was synthesized using the WT- Ovation Pico RNA amplification system version 1.0 (NuGEN) and labeled using the FL- Ovation cDNA Biotin Module V2 (NuGEN).

growth_protocol: Aortic roots were manually dissected from wild type and klotho-deficient mice at 6.0 to 6.5 weeks of age

extract_protocol: RNA was extracted using Trizol reagent and following the manufacturer's protocol.

treatment_protocol: The aortic root, consisting of the aortic valve leaflets, valve annulus, and a portin of the ascending aortic wall were manually dissected from animals aged 6.0-6.5 weeks. Three specimens were pooled to make 1 biological replicate.

value: Aortic root

value: C57BL/6J albino

tag: genotype

value: Klotho homozygous wild type


title: Klotho-wild type, replicate 2

tag: strain


title: Str chow veh 3


title: Klotho-wild type, replicate 1

tag: age


title: Str chow veh 4


title: Str chow veh 2


title: Str sc veh 1

description: STR R25

source_name: Striatum veh for Lam

value: Vehicle (for lamotrigine)


title: Str chow veh 1


title: Klotho-deficient, replicate 2

description: Gene expression data from 6 week old Klotho-deficient mice

source_name: Aortic roots from 3 klotho-deficient mice at 6-6.5 weeks of age.

value: Klotho homozygous mutant


title: Str sc veh 2

description: STR R26


title: Str LiCl 5

source_name: Striatum lithium

value: Lithium chloride (0.2% in chow)


title: Str sc veh 3

description: STR R27


title: Str sc veh 4

description: STR R28


title: Str LiCl 4


title: Str LiCl 1


title: Str LiCl 3


title: Str sc veh 5

description: STR R29


title: aorta-20m_rep5

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

description: reanalysis of GSM1230900

hyb_protocol: After fragmentation labelled cRNA was hybridized to Agilent SurePrint G3 Mouse GE 8x60k Microarrays for 17 h at 65 °C

scan_protocol: Samples were scanned as described in the manufacturers protocol. Signal intensities on 20 bit tiff images were calculated by Feature Extraction software (FE, Vers. 10.7.1.1; Agilent Technologies).

data_processing: Data analyses were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probe signal intensities were quantile normalized across all samples to reduce inter-array variability (Bolstad et al., 2003). Input data pre-processing was concluded by baseline transformation to the median of all samples.

source_name: aorta, 20 months

label_protocol: Synthesis of cDNA and subsequent fluorescent labelling of cRNA was performed on six replicates of each experimental condition (adult and old mice) according to the manufacturers protocol (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and incorporation of Cy3-CTP into nascent cRNA.

extract_protocol: The descending aorta was flushed thoroughly with ice-cold phosphate-buffered saline (PBS), through the left ventricle of the heart, cleaned of periadventitial fat and connective tissues, and snap-frozen in liquid nitrogen and stored at -80 °C. Extraction of total RNA from the tissue was followed with Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany). Total RNA from 6 individual mice of each group was treated with DNase I to remove residual genomic DNA. Total RNA preparations were checked for RNA integrity by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). All samples showed common high quality RNA Integrity Numbers (RIN 9.0-9.6) and RNA was quantified by photometric Nanodrop measurement.

treatment_protocol: Male C57BL/6 mice were obtained from Janvier (Saint Berthevin, France) and kept one week in the local animal house for acclimatization. Mice were aged  20 months and standard rodent chow was fed ad libitum. Mice were treated with 1g/L NaNO3 dissolved in the drinking water for 8 weeks.

tag: agent

value: control

tag: gender

value: male

value: 20 months

value: aorta


title: Str LiCl 2

value: SD


title: aorta-20m_rep1

description: reanalysis of GSM1230896


title: aorta-20m-NO3_rep4

source_name: aorta, 20 months, NaNO3 supplemented


title: aorta-20m_rep2

description: reanalysis of GSM1230897


title: aorta-20m_rep6

description: reanalysis of GSM1230901


title: aorta-20m_rep4

description: reanalysis of GSM1230899


title: Ctx sc lamot 4

description: PFC R14

source_name: Cortex Lamotrigine

value: Lamotrigine (30 mg/kg)

value: cortex


title: aorta-20m-NO3_rep5


title: aorta-20m-NO3_rep2


title: Klotho-deficient, replicate 1


title: aorta-20m_rep3

description: reanalysis of GSM1230898


title: aorta-20m-NO3_rep3


title: Klotho-deficient, replicate 3


title: Ctx sc lamot 5

description: PFC R9

value: after 21 days of constant drug delivery

value: Snap-frozen microdissected mouse brain region


title: Ctx sc lamot 1

description: PFC R10


title: Ctx chow veh 1

source_name: Cortex veh for LiCl


title: Ctx chow veh 4


title: Ctx sc lamot 2

description: PFC R11


title: WT_3

city: Vancouver

first: Jiamin

last: Chen

state: BC

department: OvCaRe

country: Canada

institute: bc cancer agency

description: Gene expression after 108 hours

hyb_protocol: Samples were hybridized on Agilent SurePrint G3 Mouse GE 8x60K Microarray (Design ID 028005) according to manufacturer's instructions.

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution.

data_processing: Data were processed with Agilent Feature Extraction 11.0.1.1.

source_name: DKO172 cells, expressing WT, replicate 3

label_protocol: An input of 100ng of total RNA was used to generate Cyanine-3 labeled cRNA following Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0.

growth_protocol: DKO172 cells were maintained at DMEM/F12 with 10%FBS.

extract_protocol: RNA was extracted using the Qiagen miRNeasy according to manufacturer's instructions.RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: DKO172 cells were transfected with 2ug of pLD-hygro-EnVM vectors expressing DICER1 WT, D1709N, G1809R, or GFP control. The cells were harvested after 24 hours and re-plated into P60 plates. Cells were then selected with 300ug/ml hygromycin for 84 hours.

value: Female

value: DKO172 (derived from a fallopian tumor)

tag: genotype/variation

value: expressing WT


title: Ctx sc veh 3

description: PFC R27

source_name: Cortex veh for Lam


title: Ctx sc veh 5

description: PFC R29


title: Ctx chow veh 5

value: Vehicle (for LiCl)


title: GFP_2

description: Gene expression after 108 hours

source_name: DKO172 cells, expressing GFP, replicate 2

value: expressing GFP


title: Ctx chow veh 2


title: Ctx sc veh 2

description: PFC R26

value: Vehicle (for lamotrigine)


title: GFP_1

description: Gene expression after 108 hours

source_name: DKO172 cells, expressing GFP, replicate 1


title: Ctx LiCl 5

source_name: Cortex lithium


title: Ctx chow veh 3


title: Puf4 Pumilio Domain Knockout Replicate 5

city: Stanford

first: Greg

last: Hogan

state: CA

address: 259 Campus Drive

institute: Stanford University / HHMI

hyb_protocol: Labeled cDNA from an experimental and wild-type sample were mixed (27 µL total) along with 6 µL of 20X SSC (1X SSC is 150 mM NaCl, 15 mM sodium citrate at pH 7.0), 2 µL of Qiagen buffer EB (10 mM Tris-HCl, pH 8.5), 3 µL of 10 µg/µL polyA RNA (Sigma P4303), 1 µL of 1 M Hepes-NaOH pH 7.0, and 1 µL of 10% SDS.  This 40 µL probe mixture was heated at 95°C for 2 minutes then centrifuged for 5 minutes.  Arrays were post-processed on the day of hybridization.  Arrays were rehydrated by placing slides face down over 50 mL of 0.5X SSC in a humidity chamber (Sigma H6644) for 30 minutes.  Arrays were then snapped dried on a 70-80°C inverted heat block for 5 seconds.  For N. crassa arrays, the DNA was crosslinked to the slide using 600 millijoules of UV energy in a Stratalinker.  The aminosilane surface was blocked by incubation for 35 minutes in a solution of 5X SSC, 1% SDS, and 1% w/v of Blocking Reagent (Roche 11096176001) at 60°C.  Arrays were washed twice in high-quality water for 2 minutes at room temperature then dried by centrifugation Probe mixture containing labeled cDNA was hybridized to post-processed microarrays using the MAUI hybridization system (BioMicro) at 65°C for ~16 hours.

scan_protocol: The MAUI mixer was removed from the microarray while submerged in a warm solution of 2X SSC and 0.01% SDS.  The array was then placed in a 2X SSC solution at room temperature until all arrays were ready for washing.  Arrays were washed with 2X SSC and 0.05% SDS at 65°C for 5 minutes with agitation, then at room temperature with agitation in 2X SSC for 1 minute, another 2X SSC wash for 2 minutes, 1X SSC for 2 minutes, and 0.2X SSC for 2 minutes.  The arrays were dried by centrifugation in a low-ozone environment. Microarrays were scanned using an AxonScanner 4000B and GenePix 6.0 software (Molecular Devices).  PMT levels were set to maximize signal in each channel and only saturate a few spots.

data_processing: Spots were located using the GenePix software with some manual adjustment and flagging.  Spots were then auto-flagged as bad if they met any of the following criteria: greater than 10% of the spot pixels were saturated in either channel, the spot contained 12 pixels or less, the R2 for the fit between Cy5 (red) and Cy3 (green) pixel intensities was less than 0.6, or if in either channel the signal intensity minus the local background is less than three times the standard deviation of the local background. Array data were exported in a GenePix Results file (.gpr) and further processed and analyzed within the R statistical environment.  After data were loaded into R, a spot was filtered if signal intensity was not 2x over background in both channels for N. crassa gene expression experiments.  For features passing flagging and filtering, we calculated the ratio between the experiment and reference channels as log2(red signal - red background)/(green signal - green background)).  Log2 ratio data for each experiment were mean centered and then replicate spots on the array were averaged.

organism: Neurospora crassa

source_name: mycelium from partial knockout strain of puf4 (NCU01775.2)

label_protocol: 15 µg of RNA was used in each reverse transcription reaction  RNA was reverse transcribed in the presence of 5-(3-Aminoallyl)-dUTP.  13.8 µL of sample RNA plus water was mixed with 1 µL of control RNA (Ambion AM1780) and 2 µL of N9 and dT20VN primers (each at 2.5 µg/µL).  This mixture was heated to 70°C for 2 minutes then cooled to 4°C.  6 µL of 5x 1st Strand Buffer, 1.2 µL of 25x dNTP/aminoallyl-dUTP mix (Ambion AM8439), 3 µL of 0.1 M DTT, 1 µL SuperaseIn (Ambion AM2696), and 2 µL of Superscript III  (Invitrogen 18080-085) was added as a 13.2 µL master mix, and reverse transcription performed at 42°C for 2 hours.  RNA was then hydrolyzed by addition of 15 µL of 1 M NaOH  and heating to 70°C for 15 minutes.  The sample was neutralized by addition of 15 µL of 1 M HCl and 10 µL of sodium acetate pH 5.2.  cDNA was purified using the Qiagen MinElute kit and eluted off the column with 20 µL of 10 mM sodium phosphate pH 8.5.  Experimental sample cDNA was labeled with Cy5 dye while cDNA made from the wild-type strain was labeled with Cy3 dye (GE Healthcare Life Science RPN5661).  A tube of NHS-monoester Cy dye was resuspended in 60 µL of DMSO then 20 µL was used for each appropriate sample.  Coupling was performed at room temperature in the dark for 1-2 hours.  The labeling reaction was quenched by addition of 9 µL of 3 M hydroxylamine and incubation for 15 minutes.  Labeled cDNA was purified using the Qiagen MinElute kit.

growth_protocol: Conidia were extracted in water from N. crassa strains streaked onto 3 mL agar slants made with Vogel's Medium with 2% sucrose and grown for 7-10 days at room temperature with constant exposure to indoor light.  An estimate of conidia concentration was made by taking a sample, diluting 1:40 into water, and measuring the optical density at 530 nm.  An OD530 of 0.25 is approximately 108 conidia/mL in the undiluted sample.  Conidia were added to a final concentration of 106 conidia per mL into 25 mL of Vogel's Medium with 2% glucose as the carbon source.  Cultures were shaken at 200 rpm in a 30°C  incubator with lights on.  After 8 hours ~100% exhibited hyphal growth with the bulk of germ tube lengths between 50 and 400 µm.  At this point mycelia were collected by vacuum filtration.  Material was scraped from the filter and placed into tubes containing 0.5 mL of buffer AE (50 mM sodium acetate, 10 mM EDTA), 33.3 µL of 25% SDS, and 0.5 mL of acid phenol:chloroform pH 4.5 (Ambion AM9720) then inverted to mix and flash frozen in liquid nitrogen.

extract_protocol: RNA was isolated by the method of hot acid phenol/chloroform extraction.  Samples were placed at 65°C in a thermomixer shaking at 1400 rpm for 10 minutes, vortexed for 10 seconds, then placed back in thermomixer for another 5 minutes.   Samples were cooled on ice for 5 minutes, then spun down at 12,000 rpm in a microcentrifuge for 15 minutes.  The aqueous phase was extracted and placed into a 2 mL phase-lock gel tube.  Two more extractions with acid phenol:chlorofom were performed, followed by an extraction with chloroform.  RNA was precipitated by adding 1/10th volume of 3M sodium acetate, mixing, then adding 1 volume of isopropanol.  Samples were mixed and placed at -20°C for at least an hour.  Samples were spun down for 20 minutes at top speed in a microcentrifuge.  The RNA pellet was washed with ice-cold 75% ethanol then air dried for 10 minutes before being resuspended in 100 µL of water.  RNA yields were ~250 µg.

value: Puf4 Pumilio Domain Knockout

organism: Neurospora crassa OR74A

source_name: mycelium from wild-type strain 74-OR23-1VA

value: wild-type


title: G1809R_1

description: Gene expression after 108 hours

source_name: DKO172 cells, expressing G1809R, replicate 1

value: expressing G1809R


title: Ctx sc veh 1

description: PFC R25


title: GFP_3

description: Gene expression after 108 hours

source_name: DKO172 cells, expressing GFP, replicate 3


title: WT_2

description: Gene expression after 108 hours

source_name: DKO172 cells, expressing WT, replicate 2


title: Ctx sc veh 4

description: PFC R28


title: Ctx sc lamot 3

description: PFC R13


title: WT_1

description: Gene expression after 108 hours

source_name: DKO172 cells, expressing WT, replicate 1


title: D1709N_3

description: Gene expression after 108 hours

source_name: DKO172 cells, expressing D1709N, replicate 3

value: expressing D1709N


title: G1809R_2

description: Gene expression after 108 hours

source_name: DKO172 cells, expressing G1809R, replicate 2


title: G1809R_3

description: Gene expression after 108 hours

source_name: DKO172 cells, expressing G1809R, replicate 3


title: aorta-20m-NO3_rep1

source_name: aorta, 20 months, NaNO3 supplemented

value: male

value: 20 months


title: D1709N_1

description: Gene expression after 108 hours

source_name: DKO172 cells, expressing D1709N, replicate 1


title: Control_HF_1hr vs TGFb_HF_1hr_rep2

source_name: untreated HFhTERT cells after 1hr

value: Human immortal foreskin fibroblasts

value: HFhTERT

source_name: HFhTERT cells after 1hr of TGF-beta treatment


title: D1709N_2

description: Gene expression after 108 hours

source_name: DKO172 cells, expressing D1709N, replicate 2


title: Puf4 Pumilio Domain Knockout Replicate 4


title: Ctx LiCl 3

value: SD

value: Lithium chloride (0.2% in chow)

value: cortex


title: Puf4 Pumilio Domain Knockout Replicate 1


title: Puf4 Pumilio Domain Knockout Replicate 2


title: Puf4 N-terminal Knockout Replicate 5

source_name: mycelium from partial knockout strain of puf4 (NCU01774.2)

value: Puf4 N-terminal Knockout


title: Puf4 N-terminal Knockout Replicate 1


title: Hip sc lamot 5

description: HPC R9

source_name: Hipp Lamotrigine

value: Lamotrigine (30 mg/kg)

value: after 21 days of constant drug delivery

value: Snap-frozen microdissected mouse brain region

value: hippocampus


title: Ctx LiCl 4

source_name: Cortex lithium


title: Puf4 N-terminal Knockout Replicate 2


title: Puf8 Knockout Replicate 2

source_name: mycelium from knockout strain of puf8 (NCU01760.2)

value: Puf8 Knockout


title: Puf4 N-terminal Knockout Replicate 3

source_name: mycelium from wild-type strain 74-OR23-1VA


title: Hip sc lamot 3

description: HPC R13


title: Hip chow veh 4

source_name: Hipp veh for LiCl

value: Vehicle (for LiCl)


title: Hip sc lamot 4

description: HPC R14


title: Puf8 Knockout Replicate 4

value: wild-type


title: Puf8 Knockout Replicate 3


title: Puf8 Knockout Replicate 1


title: Puf4 Pumilio Domain Knockout Replicate 3

source_name: mycelium from partial knockout strain of puf4 (NCU01775.2)

value: Puf4 Pumilio Domain Knockout


title: Hip chow veh 1


title: Hip sc lamot 1

description: HPC R10


title: Hip chow veh 3


title: Hip sc lamot 2

description: HPC R11


title: Puf8 Knockout Replicate 5


title: Ctx LiCl 1


title: Ctx LiCl 2


title: Puf3 Knockout Replicate 4

source_name: mycelium from knockout strain of puf3 (NCU06511.2)

value: Puf3 Knockout


title: Puf3 Knockout Replicate 5


title: Hip sc veh 3

description: HPC R27

source_name: Hipp veh for Lam

value: Vehicle (for lamotrigine)


title: Hip chow veh 2


title: Hip sc veh 4

description: HPC R28


title: Hip sc veh 5

description: HPC R29


title: Puf3 Knockout Replicate 3


title: Hip sc veh 1

description: HPC R25


title: Hip sc veh 2

description: HPC R26


title: Hip LiCl 5

source_name: Hipp lithium


title: Hip LiCl 4


title: striatum risp 4

description: 57 STR

source_name: str risperidone

value: Risperidone 5 mg/kg/d

value: Striatum


title: striatum veh 3

description: 34 STR

source_name: str vehicle

value: vehicle


title: Hip LiCl 2

value: SD


title: striatum veh 1

description: 32 STR


title: striatum risp 5

description: 60 STR


title: striatum veh 5

description: 36 STR


title: striatum veh 2

description: 33 STR


title: Hip LiCl 3

value: Lithium chloride (0.2% in chow)


title: striatum risp 3

description: 56 STR


title: striatum hal 5

description: 50 STR

source_name: str haldol

value: Haloperidol 0.25 mg/kg/d


title: striatum risp 2

description: 54 STR


title: striatum hal 4

description: 49 STR


title: striatum hal 3

description: 46 STR


title: hippocampus veh 5

description: 36 HPC

source_name: hip vehicle

value: Hippocampus


title: striatum veh 4

description: 35 STR


title: striatum hal 2

description: 42 STR


title: Puf3 Knockout Replicate 2


title: striatum risp 1

description: 52 STR


title: hippocampus veh 4

description: 35 HPC


title: Hip LiCl 1


title: striatum hal 1

description: 41 STR


title: Puf3 Knockout Replicate 1


title: hippocampus veh 3

description: 34 HPC


title: hippocampus veh 1

description: 32 HPC


title: hippocampus veh 2

description: 33 HPC


title: hippocampus risp 5

description: 60 HPC

source_name: hip risperidone


title: hippocampus hal 5

description: 50 HPC

source_name: hip haldol


title: hippocampus hal 1

description: 41 HPC


title: hippocampus risp 1

description: 52 HPC


title: cortex veh 4

description: 35 fCTX

source_name: ctx vehicle

value: Frontal cortex


title: hippocampus hal 2

description: 42 HPC

value: after 21 days of constant drug delivery


title: hippocampus risp 3

description: 56 HPC

value: Snap-frozen microdissected mouse brain region


title: hippocampus risp 2

description: 54 HPC


title: cortex veh 1

description: 32 fCTX


title: cortex risp 1

description: 52 fCTX

source_name: ctx risperidone


title: cortex veh 2

description: 33 fCTX


title: hippocampus hal 3

description: 46 HPC


title: cortex hal 1

description: 41 fCTX

source_name: ctx haldol


title: hippocampus risp 4

description: 57 HPC


title: ID8_peritoneal cavity selected_rep2

city: Dallas

first: yun

last: lian

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description:
ID8-M2
replicate 2
Total RNA, including microRNA

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

source_name: Mouse ovarian cancer cell line_ peritoneal cavity selected

growth_protocol: Ovarian epithelial papillary serous adenocarcinoma cell line ID8  and in vivo selected  ID8-M were cultured in high-glucose Dulbecco’s modified Eagle’s medium (DMEM, GIBCO, Grand Island, NY) supplemented with 4% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin, 5 μg/ml insulin, 5 μg/ml transferrin and 5 ng/ml sodium selenite at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol: miRNeasy Mini Kit (Qiagen) was used to extract Total RNAs according to following instructions:   1. Homogenize cultured cells with 1 ml of “Qiazol” and incubate for 5 min at room temperature;  2. Add 200 ul of chloroform and cap tube securely, vortex vigorously for 15 s, incubate for 2-3 min at room temperature;  3. Centrifuge for 15 min at 14,000 g at 4°C;  4. Transfer the upper aqueous phase to a new collection tube (Avoid transferring any Interphase), add 1.5 volumes of 100% ethanol, and mix thoroughly by shaking;  5. Pipet up to 700 ul sample, including any precipitate, into an RNeasy Mini column in a 2 ml collection tube. Close the lid and centrifuge at ≥ 8000 g for 15s at room temperature;  6. Discard the flow-through;  7. Repeat step 5 using the remainder of the sample;  8. Add 700 ul Buffer RWT to the RNeasy Mini column. Close the lid, and centrifuge for 15 s at ≥ 8000 g. Discard the flow-through;  9. Pipet 500 ul Buffer RPE onto the RNeasy Mini column. Close the lid, and centrifuge for 15 s at ≥8000 g. Discard the flow-through;  10. Add 500 ul Buffer RPE to the RNeasy Mini column. Close the lid, and centrifuge for 2 min at ≥8000 g;  11.  Place the RNeasy Mini column into a new 2 ml collection tube, centrifuge at full speed (17,000 g) for 1 min to further dry the membrane. Then open the lid, remove the additional liquid on the walls using pippet;  12. Transfer the RNeasy Mini column to a new 1.5 ml collection tube. Pipet 30 ul RNase-free water directly onto the RNeasy Mini column membrane. Close the lid, and centrifuge for 1 min at ≥8000 g to elute.

value: female

value: ovary

value: In vivo-selected ID8 ovarian cancer cells

tag: chip #

tag: position on chip

value: E


title: cortex risp 2

description: 54 fCTX

tag: tissue

tag: tissue subtype


title: hippocampus hal 4

description: 49 HPC


title: cortex risp 4

description: 57 fCTX


title: cortex veh 5

description: 36 fCTX


title: cortex hal 2

description: 42 fCTX


title: cortex hal 4

description: 49 fCTX


title: cortex risp 3

description: 56 fCTX


title: cortex hal 3

description: 46 fCTX


title: cortex veh 3

description: 34 fCTX


title: cortex hal 5

description: 50 fCTX


title: cortex risp 5

description: 60 fCTX


title: ID8_peritoneal cavity selected_rep3

description:
ID8-M3
replicate 3
Total RNA, including microRNA

value: F


title: ID8_peritoneal cavity selected_rep1

description:
ID8-M1
replicate 1
Total RNA, including microRNA

value: D


title: ID8_parental_rep2

description:
ID8-2
replicate 2
Total RNA, including microRNA

source_name: Mouse ovarian cancer cell line

value: Ovarian epithelial papillary serous adenocarcinoma cell line ID8

value: B


title: ID8_parental_rep3

description:
ID8-3
replicate 3
Total RNA, including microRNA

value: C


title: CONTROL-2

city: New York

first: Richard

middle: Mark

last: White

address: 1275 York Avenue MB 424

department: Cancer Biology & Genetics

institute: Memorial Sloan Kettering Cancer Center

description: Control

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: Affymetrix Gene Console, followed by GenePattern analysis

source_name: control CD34 cells

label_protocol: Standard Affymetrix protocol.

growth_protocol: Human CD34+ cells treated in culture

extract_protocol: Trizol RNA prep

treatment_protocol: Purified mANGPTL2 (experimental group) or vehicle (PBS) was added to cultured cells (in triplicates) at 1ug/ml for 1 hour prior to RNA harvest

value: CD34+ cells

value: control


title: Hip chow veh 5

source_name: Hipp veh for LiCl

value: SD

value: Vehicle (for LiCl)

value: hippocampus


title: S. cerevisiae Puf3 replicate 1

hyb_protocol: Labeled cDNA from an experimental and wild-type sample were mixed (27 µL total) along with 6 µL of 20X SSC (1X SSC is 150 mM NaCl, 15 mM sodium citrate at pH 7.0), 2 µL of Qiagen buffer EB (10 mM Tris-HCl, pH 8.5), 3 µL of 10 µg/µL polyA RNA (Sigma P4303), 1 µL of 1 M Hepes-NaOH pH 7.0, and 1 µL of 10% SDS.  This 40 µL probe mixture was heated at 95°C for 2 minutes then centrifuged for 5 minutes.  Arrays were post-processed on the day of hybridization.  Arrays were rehydrated by placing slides face down over 50 mL of 0.5X SSC in a humidity chamber (Sigma H6644) for 30 minutes.  Arrays were then snapped dried on a 70-80°C inverted heat block for 5 seconds.  For S. cerevisiae arrays, the epoxysilane surface of the slides was blocked by incubation in a solution of 1 M Tris-HCl pH 9.0, 100 mM ethanolamine, and 0.1% SDS for 20 minutes at 50°C.  Arrays were washed twice in high-quality water for 1 minute then dried by centrifugation. Probe mixture containing labeled cDNA was hybridized to post-processed microarrays using the MAUI hybridization system (BioMicro) at 65°C for ~16 hours.

data_processing: Spots were located using the GenePix software with some manual adjustment and flagging.  Spots were then auto-flagged as bad if they met any of the following criteria: greater than 10% of the spot pixels were saturated in either channel, the spot contained 12 pixels or less, the R2 for the fit between Cy5 (red) and Cy3 (green) pixel intensities was less than 0.6, or if in either channel the signal intensity minus the local background is less than three times the standard deviation of the local background. Array data were exported in a GenePix Results file (.gpr) and further processed and analyzed within the R statistical environment.  After data were loaded into R, a spot was filtered if signal intensity was not 1.5x over background for S. cerevisiae affinity purifications.  For features passing flagging and filtering, we calculated the ratio between the experiment and reference channels as log2(red signal - red background)/(green signal - green background)).  Log2 ratio data for each experiment were mean centered and then replicate spots on the array were averaged.

source_name: N. crassa Puf3-TAP expressed in p413ADH in GHY002

label_protocol: Two-thirds of the affinity purification sample RNA (~0.5-2 µg) was used for reverse transcription, while 12 µL (~8-10 µg) of depleted supernatant (reference) RNA was used. RNA was reverse transcribed in the presence of 5-(3-Aminoallyl)-dUTP.  13.8 µL of sample RNA plus water was mixed with 1 µL of control RNA (Ambion AM1780) and 2 µL of N9 and dT20VN primers (each at 2.5 µg/µL).  This mixture was heated to 70°C for 2 minutes then cooled to 4°C.  6 µL of 5x 1st Strand Buffer, 1.2 µL of 25x dNTP/aminoallyl-dUTP mix (Ambion AM8439), 3 µL of 0.1 M DTT, 1 µL SuperaseIn (Ambion AM2696), and 2 µL of Superscript III  (Invitrogen 18080-085) was added as a 13.2 µL master mix, and reverse transcription performed at 42°C for 2 hours.  RNA was then hydrolyzed by addition of 15 µL of 1 M NaOH  and heating to 70°C for 15 minutes.  The sample was neutralized by addition of 15 µL of 1 M HCl and 10 µL of sodium acetate pH 5.2.  cDNA was purified using the Qiagen MinElute kit and eluted off the column with 20 µL of 10 mM sodium phosphate pH 8.5.  Experimental sample cDNA was labeled with Cy5 dye while cDNA made from the wild-type strain was labeled with Cy3 dye (GE Healthcare Life Science RPN5661).  A tube of NHS-monoester Cy dye was resuspended in 60 µL of DMSO then 20 µL was used for each appropriate sample.  Coupling was performed at room temperature in the dark for 1-2 hours.  The labeling reaction was quenched by addition of 9 µL of 3 M hydroxylamine and incubation for 15 minutes.  Labeled cDNA was purified using the Qiagen MinElute kit.

growth_protocol: Yeast were grown as 250 mL cultures in SD -His (+His for GHY002 alone) media to mid-log phase (OD600 of 0.6-0.9).  Cells were collected by centrifugation at 5,000xg, and cell pellets were chilled on ice.  The cell pellet was washed twice in 5 mL of ice-cold buffer A (50 mM Hepes-KOH pH 8.0, 140 mM KCl, 1.8 mM MgCl2, 0.1% NP-40 alternative, and 0.2 mg/mL heparin). The cell pellet was resuspended in 0.5 mL of  buffer B (buffer A plus 1 µg/mL pepstatin and leupeptin, 2.5 µg/mL aprotinin, 1 mM PMSF, 0.5 mM DTT, and 100 units/mL Murine RNase Inhibitor (NEB M0314)).  Cells were lysed using 0.65 mL of glass beads (Biospec 11079105) and a Beadbeater (Biospec) for four 1 minute cycles with 1 minute on ice between cycles. Beads were removed by centrifugation at 1,000xg, and the lysate was cleared by centrifugation at 8,000xg for 5 minutes at 4°C. The supernatant was extracted, and the total protein concentration was adjusted to 15 mg/mL by dilution with buffer B.

extract_protocol: RNA was isolated from affinity purification samples and the depleted supernatants.  35 µL of 10% SDS (1% final) and 7 µL of 0.5 M EDTA (10mM final) was added to each sample, and samples were adjusted to 350 µL total with water. RNA was purified by extractions with hot acid phenol:chloroform, phenol:chloroform, and chloroform alone.  For the depleted supernatants, RNA from 100 µL of the final aqueous phase was then purified using Qiagen RNeasy columns by adding 1/10th volume sodium acetate, mixing with 5 volumes of Qiagen buffer PB, loading onto the column, washing with buffer PE, and eluting off the column with 50 µL of warm water.  For the affinity purification samples, RNA from the aqueous phase was isopropanol precipitated, washed with 75% ethanol, dried, and resuspended in 20 µL of water.

treatment_protocol: Magnetic beads were prepared for use in Protein A purification. Rabbit IgG (Calbiochem 401590) was made free of detectable RNase activity by spin column purification (Sartorius VS-ARAMAXIK) then biotinylated (Pierce 21329) and bound to Dynabeads MyOne Streptavidin C1 magnetic beads (Invitrogen 65002). 100 µg of biotinylated-IgG and 250 µL of magnetic beads was used for each affinity purification. Lysate (1 mL at 15 mg/mL) was added to beads after its buffer was removed. Lysate and beads were mixed for 2 hours at 4°C.  100 uL of depleted supernatant was saved for reference RNA. The beads were washed 1x with 1.5 mL of buffer B for 15 minutes and 3x with 1.5 mL of buffer C (buffer B plus 10% glycerol) for 15 minutes at 4°C then resuspended in 300 µL of buffer C and flash frozen in liquid nitrogen.

tag: affinity purification

source_name: depleted supernant RNA from N. crassa Puf3-TAP


title: 52755

city: Philadelphia

first: Andy

last: Minn

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

hyb_protocol: Samples were hybridized to GeneChip Mouse Gene 1.0 or 2.0 ST Arrays (Affymetrix) in a GeneChip Hyb Oven 640 (Affymetrix) for 16 hours at 45C. Arrays were washed and stained using the GeneChip Hyb, Wash and Stain kit (Affymetrix) with a GeneChip Fluidics Station 450 (Affymetrix) according to standard protocol.

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix), and image processing was performed using AGCC version 3.1.

data_processing: Affymetrix CEL files for all samples were processed using the RMA method as implemented in the oligo R package. Probe annotations were provided by the mogene10sttranscriptcluster.db or mogene20sttranscriptcluster.db R package. Data were z-score transformed and probe intensities mapping to the same gene symbol were averaged. After median centering, genes common to both array types were kept. Batch effects were corrected using ComBat from the sva R package.

source_name: B16-F10 tumor

label_protocol: Microarray target preparation from total RNA was done using Ambion WT Expression Kit from Life Technologies following standard Affymetrix protocol. Sense strand cDNA was fragmented and labeled using Genechip WT Terminal Labeling Kit from Affymetrix.

growth_protocol: B16-F10 was purchased from ATCC. Cell lines were cultured at 37º C in DMEM supplemented with 10% FBS, 100 U/ml penicillin and 100 ug/ml streptomycin, 2 mM L-glutamine. All cell lines were determined to be free of Mycoplasma and common mouse pathogens.

extract_protocol: Total RNA extraction using Qiagen RNEasy

treatment_protocol: For B16-F10 melanoma, 5x10e4 cells were mixed with an equal volume of Matrigel and subcutaneously injected on the right flank of C57BL/6 mice on day 0 and the left flank on day 2. The right flank tumor site was irradiated with 20 Gy on day 8. A blocking antibody to CTLA4 (9H10) was given on days 5, 8 and 11.

tag: subline

value: sensitive


title: 52757


title: CONTROL-1

description: Control


title: N. crassa Puf3 Replicate 3

source_name: S. cerevisiae Puf3-TAP

value: S. cerevisiae Puf3-TAP

source_name: depleted supernant RNA from S. cerevisiae Puf3-TAP


title: 45820


title: S. cerevisiae Puf3 replicate 3

value: N. crassa Puf3-TAP expressed in p413ADH in GHY002

value: depleted supernant RNA from N. crassa Puf3-TAP


title: Mock from 5Δpufs strain Replicate 3

source_name: 5Δpufs his4-539::HIS4 his3::HPH (named GHY002)

source_name: depleted supernant RNA from mock

value: depleted supernant RNA from mock


title: ANGPTL2-1HR-3

description: CD34+ cells treated with ANGPTL2 (1ug/ml) for 1 hour

source_name: ANGPTL2 treated CD34 cells


title: 52759

value: Res 499

value: resistant


title: Mock from 5Δpufs strain Replicate 2

value: 5Δpufs his4-539::HIS4 his3::HPH (named GHY002)


title: ANGPTL2-1HR-1


title: ANGPTL2-1HR-2


title: CONTROL-3

description: Control


title: 52758


title: 52756


title: 52761


title: 52760


title: 52763


title: ID8_parental_rep1

description:
ID8-1
replicate 1
Total RNA, including microRNA

value: female

value: ovary

value: A


title: S. cerevisiae Puf3 replicate 2


title: 52762


title: 45821

value: Res 177


title: 52750


title: N. crassa Puf3 Replicate 1

value: depleted supernant RNA from S. cerevisiae Puf3-TAP


title: N. crassa Puf3 Replicate 2


title: CD115+.CELls_WT_rep4

description: gene expression after 4 weeks of feeding a Western type diet

hyb_protocol: Biotin labeled cDNA was hybridized to Affymetrix Mouse Gene 2.0 ST Gene Expression Microarrays for 18h at 45 °C, stained by strepatavidin/phycoerythrin conjugate and scanned as described in the manufacturers´ protocol (GeneChip Whole Transcript (WT) Sense Labeling Assay User Manual, Affymetrix, Inc.)

scan_protocol: Gene ChIP Scanner 3000 7G (Affymetrix Inc.); AGCC (Vers. 3.3)

data_processing:
Tissue specific data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probeset were summarized by GeneSprings´ ExonRMA16 algorithm after quantile normalization of probe level signal intensities across all samples to reduce inter-array variability. Input data pre-processing was concluded by baseline transformation to the median of all samples.
probe group file: MoGene-2_0-st.pgf
meta-probeset file: MoGene-2_0-st.mps

source_name: isolated peripheral blood CD115+.CELls

label_protocol: Synthesis of cDNA and subsequent biotin labeling was performed according to the manufacturers´ protocol (Ovation Pico WTA System V2 / Encore Biotin Module, NuGEN Inc.). Briefly, 1 ng of total RNA was converted to cDNA, followed by isothermal amplification, fragmentation and biotin labeling of cDNA

extract_protocol: Samples of aorta with perivascular adipose tissue were homogenised and CD115+ circulating.CELls were  isolated from peripheral blood after Ficoll centrifugation by using the CD115 MicroBead Kit (Miltenyi) according to the manufacturer`s protocol. Extraction of RNA from aortas and CD115+.CELls was then performed using the RNeasy Microarray Tissue Kit (Qiagen) according to the manufacturer`s instructions.

treatment_protocol: Male ApoE/LTbR double-deficient mice and their respective ApoE-deficient littermate controls were fed a Western type diet for 4 weeks starting at 8 weeks of age followed by isolation of aorta and CD115+.CELls (Miltenyi) from peripheral blood of apoE-/- and apoE-/-LTbR-/- mice

value: ApoE deficient

tag: input for rna preparation

value: RNA prep from pool of two littermate samples

value: male

value: 12 weeks


title: CD115+.CELls_KO_rep2

value: ApoE/LTbR-double deficient

value: RNA prep from single sample


title: CD115+.CELls_WT_rep1


title: aorta_WT_rep4

source_name: aorta


title: CD115+.CELls_KO_rep3


title: aorta_WT_rep3


title: aorta_WT_rep2


title: Mock from 5Δpufs strain Replicate 1


title: CN AML patient 11 Dg

first: Rotraud

last: Wieser

address: Waehringer Guertel 18-20

department: Clinic of Medicine I

institute: Medical University of Vienna

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA

source_name: peripheral blood sample from the time of diagnosis of AML

label_protocol: Affymetrix standard protocol

growth_protocol: Ficoll purified, vitally frozen primary patient samples

extract_protocol: RNeasy (Quiagen)

tag: Sex

value: m

tag: fab type

tag: wbc/dg

tag: % blasts pb/dg

tag: response

value: CR

tag: wbc/r

tag: % blasts pb/r

tag: months from dg to r

tag: os


title: CN AML patient 11 R

source_name: peripheral blood sample from relapsed AML

tag: age


title: CN AML patient 9 R


title: CN AML patient 9 Dg


title: CD115+.CELls_KO_rep1

tag: genotype

tag: gender


title: CN AML patient 10 R


title: aorta_WT_rep1


title: CD115+.CELls_WT_rep3


title: aorta_KO_rep3


title: follicular phase isthmus epithelial cells animal #3

city: Lexington

first: Phillip

middle: J

last: Bridges

state: KY

address: 206 WP Garrigus Building

department: Animal and Food Sciences

institute: University of Kentucky

description: Gene expression data from heifer oviducts

hyb_protocol: Following fragmentation, 10 µg of labeled cRNA was hybridized to Affymetrix Bovine Genome Array for 16 hr at 45°C using the gene chips in the GeneChip Hybridization Oven 640, using 1 chip per RNA sample. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were stained with R-Phycoerythrin Streotavidin, followed by an antibody solution and a second R-Physcoerythrin Streptavidin solution, with all lquid handling performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G GeneChip Scanner (GCS) with AGCC software (Command Console).

data_processing: The raw data were collected with the GeneChip Operating Software (GCOS, version 1.2). The expression intensity values from the software (i.e., the .cel files) were imported into Partek Genomics Suite software (version 6.4; Partek Inc., St. Louis, MO, USA). The algorithm of Robust Multichip Averaging were further converted into expression values via the algorithms of Quantile normalization of different chips and then Median Polish summarization of multiple probes.

organism: Bos taurus

label_protocol: Biotinylated cRNA were prepared from 3 µg of total RNA according to Affymetrix protocol. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA, USA) and oligo(dT)24 primers. Bio-labeled cRNA was prepared by cDNA in vitro transcription biotinylated UTP.

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

treatment_protocol: Normally cycling Angus heifers were assigned to either luteal phase (LP, high progesterone, n=3) or follicular phase (FP, high estradiol, n=3) groups.  Heifers in the LP group were killed between day 11 and 12 after ovulation.  Heifers in the FP group were treated with 25 mg PGF2α (Lutalyse, Pfizer, NY) at 8 pm on day 6 after ovulation and killed 36 h later.  Cycle stage was confirmed by ultrasonography as described in the overall design above.

tag: tissue

value: isthmus epithelial cells

tag: stage of estrous cycle

value: Follicular phase


title: aorta_KO_rep4


title: CN AML patient 10 Dg


title: follicular phase ampulla epithelial cells animal #1

value: ampulla epithelial cells


title: aorta_KO_rep1


title: follicular phase ampulla epithelial cells animal #2


title: CN AML patient 8 R

value: f


title: follicular phase isthmus epithelial cells animal #2


title: aorta_KO_rep2


title: 52764

value: Res 499

value: resistant


title: CN AML patient 7 Dg

value: PR


title: CN AML patient 7 R


title: luteal phase isthmus epithelial cells animal #1

value: Luteal phase


title: CN AML patient 8 Dg


title: follicular phase isthmus epithelial cells animal #1


title: luteal phase ampulla epithelial cells animal #1


title: CN AML patient 5 R


title: 52754

value: Res 177


title: luteal phase isthmus epithelial cells animal #3


title: CN AML patient 5 Dg


title: CN AML patient 6 R


title: CN AML patient 2 R


title: CN AML patient 3 R


title: luteal phase ampulla epithelial cells animal #3


title: CN AML patient 3 Dg


title: follicular phase ampulla epithelial cells animal #3


title: luteal phase ampulla epithelial cells animal #2


title: luteal phase isthmus epithelial cells animal #2


title: CN AML patient 2 Dg


title: CN AML patient 6 Dg


title: CN AML patient 1 R


title: LoVo-OxPt_rep2

status: Public on Mar 15 2015

city: Frederiksberg C

first: Niels

middle: Frank

last: Jensen

address: Dyrlaegevej 88, 1.

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

description:
GE_23
Gene expression of cell line growing in drug-free medium

hyb_protocol: Cy3-labeled cRNA was hybridized to Agilent Human Gene Expression Microarrays (G4112F).

scan_protocol: Microarrays were scanned using an Agilent DNA Microarray scanner (Agilent Technologies).

data_processing: Microarray data processing was performed in R (www.r-project.org) using the Bioconductor bioinformatics software package (www.bioconductor.org). Data (gProcessedSignals) were loaded into R using the Limma package and normalized between arrays using quantile normalization. Probes were collapsed taking the median and expression values were log2 transformed.

source_name: LoVo cell line, oxaliplatin resistant, replicate 2

label_protocol: Total RNA was separately converted into cDNA through reverse transcription, thereafter cRNA was transcribed with T7 RNA Polymerase. Labeled cRNA was coupled to a Cyanine 3-CTP fluorescent dye using the One-Color Microarray-Based Gene Expression Analysis, Low Input Quick Amp Labeling (version 6.5 protocol) (Agilent Technologies).

growth_protocol: Three parental cell lines (HCT116, HT29 and LoVo) were exposed in vitro to gradually increasing concentrations of oxaliplatin or SN-38 for about nine months. Before cell harvest, parental and drug-resistant cell lines were cultured in drug-free growth medium (RPMI1640+Glutamax supplemented with 10% fetal bovine serum, Invitrogen) for two to three weeks.

extract_protocol: RNA was purified from each cell line in independent triplicates (three different passages). Following a wash with cold PBS, TRIzol Reagent (Invitrogen) was added and the cells were lysed on ice. The lysate was frozen at -80˚C for later purification of RNA. RNA was purified according to the manufacturer’s instructions with minor modifications (centrifugation for 4500 x g, with centrifugation times of 20 min for the phase separation and 15 min for the RNA precipitation).

value: Cell line, colon cancer derived

tag: cell line

value: LoVo

tag: treatment

value: Oxaliplatin


title: CN AML patient 4 Dg


title: LoVo-SN38_rep2

description:
GE_26
Gene expression of cell line growing in drug-free medium

source_name: LoVo cell line, SN-38 resistant, replicate 2

value: SN-38 (irinotecan active metabolite)


title: LoVo_rep3

description:
GE_21
Gene expression of cell line growing in drug-free medium

source_name: LoVo cell line, parental, replicate 3

value: No drug (control parental cell line)


title: LoVo-SN38_rep3

description:
GE_27
Gene expression of cell line growing in drug-free medium

source_name: LoVo cell line, SN-38 resistant, replicate 3


title: LoVo-SN38_rep1

description:
GE_25
Gene expression of cell line growing in drug-free medium

source_name: LoVo cell line, SN-38 resistant, replicate 1


title: LoVo-OxPt_rep1

description:
GE_22
Gene expression of cell line growing in drug-free medium

source_name: LoVo cell line, oxaliplatin resistant, replicate 1


title: LoVo_rep2

description:
GE_20
Gene expression of cell line growing in drug-free medium

source_name: LoVo cell line, parental, replicate 2


title: LoVo-OxPt_rep3

description:
GE_24
Gene expression of cell line growing in drug-free medium

source_name: LoVo cell line, oxaliplatin resistant, replicate 3


title: HT29-SN38_rep2

description:
GE_17
Gene expression of cell line growing in drug-free medium

source_name: HT29 cell line, SN-38 resistant, replicate 2


title: HT29-SN38_rep3

description:
GE_18
Gene expression of cell line growing in drug-free medium

source_name: HT29 cell line, SN-38 resistant, replicate 3


title: HT29-SN38_rep1

description:
GE_16
Gene expression of cell line growing in drug-free medium

source_name: HT29 cell line, SN-38 resistant, replicate 1


title: CN AML patient 4 R


title: HT29-OxPt_rep2

description:
GE_14
Gene expression of cell line growing in drug-free medium

source_name: HT29 cell line, oxaliplatin resistant, replicate 2


title: HT29-OxPt_rep1

description:
GE_13
Gene expression of cell line growing in drug-free medium

source_name: HT29 cell line, oxaliplatin resistant, replicate 1


title: HCT116-OxPt_rep1

description:
GE_04
Gene expression of cell line growing in drug-free medium

source_name: HCT116 cell line, oxaliplatin resistant, replicate 1


title: HCT116-SN38_rep2

description:
GE_08
Gene expression of cell line growing in drug-free medium

source_name: HCT116 cell line, SN-38 resistant, replicate 2


title: HT29_rep3

description:
GE_12
Gene expression of cell line growing in drug-free medium

source_name: HT29 cell line, parental, replicate 3


title: HCT116-SN38_rep3

description:
GE_09
Gene expression of cell line growing in drug-free medium

source_name: HCT116 cell line, SN-38 resistant, replicate 3


title: HCT116-OxPt_rep2

description:
GE_05
Gene expression of cell line growing in drug-free medium

source_name: HCT116 cell line, oxaliplatin resistant, replicate 2


title: LoVo_rep1

description:
GE_19
Gene expression of cell line growing in drug-free medium

source_name: LoVo cell line, parental, replicate 1


title: HT29_rep2

description:
GE_11
Gene expression of cell line growing in drug-free medium

source_name: HT29 cell line, parental, replicate 2


title: HT29-OxPt_rep3

description:
GE_15
Gene expression of cell line growing in drug-free medium

source_name: HT29 cell line, oxaliplatin resistant, replicate 3


title: HCT116_rep1

description:
GE_01
Gene expression of cell line growing in drug-free medium

source_name: HCT116 cell line, parental, replicate 1


title: HT29_rep1

description:
GE_10
Gene expression of cell line growing in drug-free medium

source_name: HT29 cell line, parental, replicate 1


title: HCT116-OxPt_rep3

description:
GE_06
Gene expression of cell line growing in drug-free medium

source_name: HCT116 cell line, oxaliplatin resistant, replicate 3


title: HCT116-SN38_rep1

description:
GE_07
Gene expression of cell line growing in drug-free medium

source_name: HCT116 cell line, SN-38 resistant, replicate 1


title: HCT116_rep2

description:
GE_02
Gene expression of cell line growing in drug-free medium

source_name: HCT116 cell line, parental, replicate 2


title: MCF7_PRB_vehicle_6h, rep3

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description:
pSG5.PRB.EtOH.3
Replicate 3 of 3.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were filtered and any probes with a detection P-value higher than 0.05 were removed. The data were then normalized using log2 transformation and quantile normalization with R using the lumi Bioconductor package.

source_name: MCF7 cells stably expressing PRB vector, treated with ethanol vehicle, for 6 hours

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

growth_protocol: Samples were grown in complete medium (MEM, 5% FBS, 1% NEAA, 1% pen/strep, 6ng/ml insulin, 200 ug/ml G418) before 1 day starvation in IMEM medium, then treated in IMEM medium for 6 hr.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Samples were treated in IMEM medium, with or without 10e-7 M estradiol for 6 hr.

tag: parental cell line

tag: tissue derivation

value: breast cancer

tag: stable vector integration

value: ethanol vehicle

tag: time point

value: 6 hr


title: MCF7_PRB_vehicle_6h, rep2

description:
pSG5.PRB.EtOH.2
Replicate 2 of 3.


title: MCF7_vector_E2_6h, rep1

description:
pSG5.E2.1
Replicate 1 of 3.

source_name: MCF7 cells stably expressing plasmid vector, treated with estradiol, for 6 hours

value: estradiol 10e-7 M


title: MCF7_PRB_E2_6h, rep1

description:
pSG5.PRB.E2.1
Replicate 1 of 3.

source_name: MCF7 cells stably expressing PRB vector, treated with estradiol, for 6 hours


title: MCF7_vector_E2_6h, rep2

description:
pSG5.E2.2
Replicate 2 of 3.


title: HCT116_rep3

description:
GE_03
Gene expression of cell line growing in drug-free medium

source_name: HCT116 cell line, parental, replicate 3


title: MCF7_PRB_vehicle_6h, rep1

description:
pSG5.PRB.EtOH.1
Replicate 1 of 3.


title: MCF7_PRB_E2_6h, rep3

description:
pSG5.PRB.E2.3
Replicate 3 of 3.


title: CN AML patient 1 Dg

source_name: peripheral blood sample from the time of diagnosis of AML

tag: Sex

value: m

tag: fab type

tag: wbc/dg

tag: % blasts pb/dg

value: CR


title: MCF7_vector_vehicle_6h, rep2

description:
pSG5.EtOH.2
Replicate 2 of 3.

source_name: MCF7 cells stably expressing plasmid vector, treated with ethanol vehicle, for 6 hours


title: MCF7_vector_vehicle_6h, rep3

description:
pSG5.EtOH.3
Replicate 3 of 3.


title: MCF7_PRB_E2_6h, rep2

description:
pSG5.PRB.E2.2
Replicate 2 of 3.


title: MCF7_vector_E2_6h, rep3

description:
pSG5.E2.3
Replicate 3 of 3.


title: 11F2

status: Public on Mar 14 2015

city: Chiba

first: Makiko

last: Mochizuki-Kashio

address: 1-8-1 Inohana

institute: Chiba University

description: Gene expression in Ezh2 KO LSK cells at 9-12 months post-transplantation

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Cre-Ert;Ezh2fl/fl MDS

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.02 ug RNA using the One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling), ver6.0 (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: sorted CD45.2 LSK cells from BM cell.

extract_protocol: RNA was prepared using TRIZOL LS following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain

tag: disease

value: MDS

tag: time period

value: 9-12 months post-transplantation


title: 10F5_2nd_002

source_name: Cre-Ert;Ezh2fl/fl not determinded

tag: genotype

value: not determined


title: 11F5

source_name: Cre-Ert;Ezh2fl/fl MDS/MPN(CMMoL)

value: MDS/MPN


title: 9-12Mo_Wild

description: Gene expression in Wt LSK cells at 9-12 months post-transplantation

source_name: Cre-Ert Aged

value: Cre-Ert

value: no


title: 9-12Mo_Ezh2 deletion

source_name: Cre-Ert;Ezh2fl/fl　Aged


title: 3Mo_Ezh2 deletion

description: Gene expression in Ezh2 KO LSK cells at 3 months post-transplantation

value: 3 months post-transplantation


title: MCF7_vector_vehicle_6h, rep1

description:
pSG5.EtOH.1
Replicate 1 of 3.


title: 9F2

source_name: Cre-Ert;Ezh2fl/fl MDS/MPN


title: 10F14


title: HUVEC In-6h biological rep2

city: Tokyo

first: Mari

last: Katsura

address: 2-11-16 Yayoi, Bunkyo-ku

department: Isotope Science Center

institute: The University of Tokyo

hyb_protocol: Following fragmentation, 11 μg of aRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multi-array Analysis (RMA) method. The gene set probes were using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: HUVEC

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip 3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: Human umbilical vein endothelial cell (HUVEC) from sixth to twelfth passages was grown in endothelial cell basal medium-2 (EBM-2) (Lonza) with 5% fetal bovine serum (FBS).

extract_protocol: Total RNA was extracted with RNeasy Micro Kits.

treatment_protocol: After confluence medium was replaced with that containing 0.5% FBS to synchronize for sixteen hours. Then they were exposed to chronic radiation for 72h. .

tag: radiation time

tag: method

value: Internal

tag: experimental date


title: CD34+ hematopoietic progenitors of polycythemia vera - biological replicate 7

city: Belgrade

first: Vladan

middle: Predrag

last: Cokic

address: Dr Subotica 4

country: Serbia

institute: Institute for Medical Research

description:
PV 7
Polycythemia vera 7

hyb_protocol: For hybridization, 36 μl hybridization mixture [26 μl cDNA mixture, 1 μl (10 μg) COT-1 DNA, 1 μl (8-10 μg) poly(dA), 1 μl yeast tRNA (4 μg), 6 μl 20X SSC and 1 μl 10% SDS] was pre-heated at 100oC for 2 minutes and cooled for 1 minute. Total volume of probe was added on the array and covered with cover slip. Slides are placed in hybridization chamber and 20µl water was added to the slide, and incubated overnight at 65oC.  Slides were then washed for 2 minutes each in 2X SSC, 1X SSC and 0.1X SSC and spin-dried.

scan_protocol: Microarray slides were scanned in both Cy3 (532nm) and Cy5 (635nm) channels using Axon GenePix 4000B scanner (Axon Instruments, Inc., Foster City, CA) with a 10-micron resolution. Scanned microarray images were exported as TIFF files to GenePix Pro 3.0 software for image analysis. The raw images were collected at 16-bit/pixel resolutions with 0 to 65,535 count dynamic range.

data_processing:
The area surrounding each spot image was used to calculate a local background and subtracted from each spot before the Cy5:Cy3 ratio calculation. The average of the total Cy3 and Cy5 signal gave a ratio that was used to normalize the signals. Spots with confidence interval of 99 (≥ 2 fold) with at least 150-fluorescence intensity for both channel and 30 μm spot size were considered as good quality spots for analysis. For advanced data analysis, gpr and jpeg files were imported into microarray database, and normalized by mAdb software provided by NIH Center for Information Technology (http://nciarray.nci.nih.gov/).
We have used the normalization method (Linear & Lowess) to normalize the data and then the Welch T test (comparison mean for single group test);
Default Ratio: ChanB/ChanA (Cy5/Cy3) Signal calculation: Mean Intensity minus Median Background Any Features designated Control were excluded.
Normalization method: Local Mean Across Element Signal Intensity (LOESS)
Spot Filter Options: Include Spots not flagged BAD or Not Found AND Target diameter >= 20 um AND Target diameter <= 300 um AND Both Chan A and Chan B Signal >= 200
Data was extracted and aligned by the Inventory Well ID Within array multiple occurrences of Well ID were reduced to a single instance by selecting the one with the strongest signal (Chan A + Chan B) Note: For all GenePix results from Axon scanned arrays Chan A is CY3 and Chan B is CY5.
Then the gene list was analyzed by GOFFA library for functional characterization of the overexpressed genes. The same gene list was copied and analyzed in Ingenuity for functional characterization. Ingenuity Pathways Analysis is a software application that enables identification of the biological mechanisms, pathways and functions most relevant to the genes of interest [www.ingenuity.com].
Each microarray experiment was globally normalized to make the median value of the log2-ratio equal to zero. The normalization process corrects for dye bias, photo multiplier tube voltage imbalance, and variations between channels in the amounts of the labeled cDNA probes hybridized. The data files representing the differentially expressed genes were then created.

source_name: Peripheral blood CD34+

label_protocol: Labeled cDNA probes were produced: 5 μg of tRNA was incubated at 70oC for 5 minutes along with 1 μl of aminoallyl-oligo dT primer and quickly chilled for 3 minutes. Then, 2 μl 10X first strand buffer, 1.5 μl SSII enzyme (Stratagene, La Jolla, CA), 1.5 μl 20X aminoallyl dUTP and 2 μl of 0.1M DTT were added and incubated for 90 minutes at 42oC. After incubation, volume of the reaction mixture was raised to 60 μl with 40 μl of DEPC water. cDNA was purified by the MinElute column (Qiagen). 300 μl of Binding buffer PB was added to the coupled cDNA, and the mixture applied to the MinElute column, and centrifuged for 1minute at 10.000 rpm.  After discharging the flow-through, 600 μl of washing buffer PE was added to the column, and centrifuged for 1 minute at 10.000 rpm. The flow-through was discharged and the washing repeated. Then the columns were placed into a fresh eppendorf tube and 15 μl elution buffer added to the membrane, incubated for 1 minute at room temperature, centrifuged for 1 minute at 10.000 rpm and probe collected. The probe was dried in speed-vac for 16 minutes. Finally, 5 μl of 2X coupling buffer and 5 μl Cy3 and Cy5 dye (GE Healthcare Bio-Sciences Corp., Piscataway, NJ) were mixed into the control (huURNA) and experimental cDNAs (huES cell-derived) respectively and incubated at room temperature in dark for 90 minutes. After incubation, the volume was raised to 60 μl by 50 μl DEPC water and then cDNA was purified by the MinElute column and eluted with 13 μl elution buffer by centrifugation.

growth_protocol: CD34+ hematopoietic progenitors are isolated from peripheral blood by immunomagnetic separation, while granulocytes are isolated after lymphoprep application

extract_protocol: we used the RNeasy protocol for isolation of total RNA (tRNA) from erythroid progenitor cells (Qiagen, Valencia, CA) according to the manufacturer's instructions

treatment_protocol: Immunomagnetic separation

tag: subject condition

value: Polycythemia vera (PV)

tag: cell type

value: CD34+ hematopoietic progenitors

source_name: Total human universal RNA (HuURNA)

tag: sample type

value: reference

tag: sample source

value: isolated from a collection of adult human tissues to represent a broad range of expressed genes from both male and female donors (BD Biosciences, Palo Alto, CA)


title: HUVEC NT, biological rep2

value: Non


title: CD34+ hematopoietic progenitors of primary myelofibrosis - biological replicate 1

description:
PMF 1
Primary myelofibrosis JAK2+ 1

value: Primary myelofibrosis JAK2+


title: 3Mo_Wild

description: Gene expression in WT LSK cells at 3 months post-transplantation

source_name: Cre-Ert


title: CD34+ hematopoietic progenitors of chronic myelogenous leukemia - biological replicate 7

description:
CML 7
Chronic myelogenous leukemia 7

value: Chronic myelogenous leukemia


title: CD34+ hematopoietic progenitors of chronic myelogenous leukemia - biological replicate 6

description:
CML 6
Chronic myelogenous leukemia 6


title: CD34+ hematopoietic progenitors of chronic myelogenous leukemia - biological replicate 5

description:
CML 5
Chronic myelogenous leukemia 5


title: CD34+ hematopoietic progenitors of normal controls - biological replicate 6

description:
Control 6
Healthy donor 6

value: Healthy donor


title: HUVEC In-1h, biological rep2


title: 10F7


title: HUVEC In-3h, biological rep1


title: Granulocytes of normal controls - biological replicate 10

description:
Control 10
Healthy donor 10

source_name: Peripheral blood granulocytes

value: Granulocytes


title: HUVEC In-3h, biological rep2


title: Granulocytes of normal controls - biological replicate 9

description:
Control 9
Healthy donor 9


title: HUVEC NT, biological rep1


title: Granulocytes of normal controls - biological replicate 8

description:
Control 8
Healthy donor 8


title: Granulocytes of normal controls - biological replicate 7

description:
Control 7
Healthy donor 7


title: HUVEC In-1h, biological rep1


title: HUVEC In-6h biological rep1


title: CD34+ hematopoietic progenitors of normal controls - biological replicate 5

description:
Control 5
Healthy donor 5


title: CD34+ hematopoietic progenitors of normal controls - biological replicate 4

description:
Control 4
Healthy donor 4


title: CD34+ hematopoietic progenitors of normal controls - biological replicate 3

description:
Control 3
Healthy donor 3


title: U937_EVI1 TPA replicate 3

city: Vienna

hyb_protocol: 12.5 µg of fragmented and labeled aRNA were hybridized to Affymetrix Human Affymetrix GeneChip Human Genome U133 plus 2.0 arrays for 16 h at 45 °C in a GeneChip hybridization oven 640.

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

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using the RMA algorithm (Irizarry et al., 2003) in the Affymetrix GeneChip Expression Console v1.3 software.

source_name: U937_EVI1 cells, 24 h TPA treatment

label_protocol: The Affymetrix GeneChip 3’ IVT Express Protocol was used for the preparation of biotinylated amplified RNA (aRNA) from 250ng of total RNA.

growth_protocol: RPMI 10% FCS 1% Penicillin-Streptomycin-Glutamin

extract_protocol: RNeasy (Qiagen)

treatment_protocol: Logarithmically growing cells were treated with TPA (50 ng/ml) or an equivalent amount of solvent (EtOH) for 24 h

tag: cell line

tag: protocol

value: EVI1 expression vector

tag: agent

value: TPA


title: U937_vec TPA replicate 3

source_name: U937_vec cells, 24 h TPA treatment

value: empty vector


title: CD34+ hematopoietic progenitors of normal controls - biological replicate 1

description:
Control 1
Healthy donor 1


title: Granulocytes of chronic myelogenous leukemia - biological replicate 8

description:
CML 8
Chronic myelogenous leukemia 8


title: U937_EVI1 EtOH replicate 3

source_name: U937_EVI1 cells, 24 h EtOH treatment

value: EtOH


title: U937_vec EtOH replicate 2

source_name: U937_vec cells, 24 h EtOH treatment


title: U937_EVI1 TPA replicate 2


title: U937_vec EtOH replicate 3


title: CD34+ hematopoietic progenitors of chronic myelogenous leukemia - biological replicate 3

description:
CML 3
Chronic myelogenous leukemia 3


title: U937_EVI1 EtOH replicate 2


title: CD34+ hematopoietic progenitors of chronic myelogenous leukemia - biological replicate 4

description:
CML 4
Chronic myelogenous leukemia 4


title: U937_EVI1 TPA replicate 1


title: U937_vec TPA replicate 2


title: CD34+ hematopoietic progenitors of chronic myelogenous leukemia - biological replicate 2

description:
CML 2
Chronic myelogenous leukemia 2


title: Granulocytes of chronic myelogenous leukemia - biological replicate 9

description:
CML 9
Chronic myelogenous leukemia 9


title: CD34+ hematopoietic progenitors of chronic myelogenous leukemia - biological replicate 1

description:
CML 1
Chronic myelogenous leukemia 1


title: U937_vec TPA replicate 1


title: Granulocytes of primary myelofibrosis - biological replicate 7

description:
PMF 7
Primary myelofibrosis JAK2- 7

value: Primary myelofibrosis JAK2-


title: Granulocytes of primary myelofibrosis - biological replicate 6

description:
PMF 6
Primary myelofibrosis JAK2+ 6


title: CD34+ hematopoietic progenitors of normal controls - biological replicate 2

description:
Control 2
Healthy donor 2


title: U937_EVI1 EtOH replicate 1


title: U937_vec EtOH replicate 1