title: Monozygotic Twin Bulls brother Sperm DNA methylation analysis H vs. h

city: Quebec city

first: Habib

last: Shojaei Saadi

state: Quebec

address: 2440 bl hochelaga, pavillon inaf

country: Canada

institute: Laval University

description: Dye-Swap

hyb_protocol: Hybridizations were performed according to the microarray manufacturer's instructions (Agilent Technologies, Santa Clara, USA). Briefly, 1 µg of labeled sample (in 40 µL) was mixed with 158 µL of hybridization master mix containing 25 µL of bovine Cot-1 DNA (1.0 mg/mL, Bovine Hybloc competitor DNA, Applied Genetics Laboratories, Melbourne, FL, USA), 2.6 µL of Agilent 100x Blocking Agent and 130 µL of Agilent 2x HI-RPM Hybridization Buffer (Agilent Technologies, Santa Clara, USA). Samples were held at 95 °C for 3 min and at 37 °C for 30 min followed by addition of 65 µL of Agilent-CGHBlock (final volume 260 µL). The samples were loaded onto the microarray and hybridization was carried out in a hybridization oven (Shel Lab, Cornelius, OR, USA) for 40 h at 65 °C and 20 rpm. Washing was carried out according to the microarray manufacturer's instructions

scan_protocol: Slides were scanned with the PowerScanner (Tecan, Männedorf, Switzerland)

data_processing: Intensity values were obtained from slide images using the Array-Pro Analyzer 6.3 software (MediaCybernetics, Bethesda, MD, USA). Raw intensities were subjected to within-array normalization(loess) followed by between-array normalization (quantile) using the limma library from Bioconductor.

organism: Bos taurus

source_name: Sperm

label_protocol: Comparable DNA inputs (10 ng) were used for all sperm samples. For quality control purposes, all samples were spiked with a mixture of six synthetic DNA constructs all bearing an MseI restriction site at each end. One pair of constructs was designed for each methyl-sensitive restriction enzyme (HpaII, HinP1I and Aci1I) to be used in the fragment selection process. For each pair, one control DNA fragment was methylated in vitro using CpG methyltransferase M.SssI (New England Biolabs, Ipswich, MA, USA). The difference between the extents of cleavage obtained with each pair was used to calculate cleavage efficiency. Residual MseI sites within the fragments were measured after processing to determine the extent of genomic fragmentation. Sample (in 30 µL of phosphate buffered saline) plus 0.5 µL of bovine serum albumin (New England Biolabs, Ipswich, MA, USA), 5 µL of 10X Buffer 4 (New England Biolabs, Ipswich, MA, USA) and 28 µL of DNAse/RNAse free water were divided into two equal fractions and fragmented using 10 U of MseI restriction enzyme (New England Biolabs, Ipswich, MA, USA) and incubated for 16 h at 37 °C following enzyme inactivation (heating to 65 °C for 20 min). The two fractions were combined and DNA was concentrated by ethanol precipitation following addition of 1 µL of linear acrylamide solution (5 mg/mL, Ambion, Austin, TX, USA) as carrier and 5 µL of sodium acetate buffer (3 M, pH 5.5, Ambion Inc., Austin, TX, USA). The pellet was washed twice with 70 % ethanol and air-dried before dissolution in 5 µL of DNAse/RNAse free water. Adaptors were ligated as described previously (Klein et al. , 1999) to the fragment cohesive ends left by MseI. Briefly, 0.5 µL of 100 µM stock solution of each primer (MseLig 21: 5’-AGT GGG ATT CCG CAT GCT AGT-3’, MseLig 12: 5’-TAA CTA GCA TGC-3’, IDT DNA, Coralville, IA, USA), 0.5 µL of One-Phor-All plus Buffer (Pharmacia Biotech, Piscataway, NJ) and 1.5 µL of nuclease-free water were added to the sample. Annealing was begun at 65 °C and the temperature was ramped at 1 °C/min down to 15 °C. T4 DNA ligase (5 units, Boehringer Mannheim) and 10 nmol of ATP were added and the reaction mixture was held at 15 °C for 16 h. The ligated sample was triple-cleaved with FastDigest™ methyl-sensitive restriction endonucleases (MSRE) HpaII (C/CGG), HinP1I (GC/GC), Aci1I (C/CGC) from Fermentas Thermo Fisher Scientific, Waltham, MA, USA. A first cleavage in 50 µL including 10 µL of sample, 0.5 µL of HpaII, 0.5 µL of HinP1I, 5 µL of 10X FastDigest buffer and 34 µL of nuclease-free water was performed at 37 °C for 12 h. A second cleavage was performed by adding 0.5 µL of Aci1I, 5 µL of 10X FastDigest buffer and 44.5 µL of nuclease-free water and incubating at 37 °C for 4 h, followed by thermal inactivation at 85 °C for 10 min. Amplicon specificity was determined from the shape of the melting curve and the difference in threshold cycle (Δ Ct) between methylated and unprotected templates was used to calculate cleavage efficiency. The DNA samples were then precipitated in ethanol, washed and dissolved in 10 µL of nuclease-free water. Selective amplification of methylated fragments was performed using two rounds of ligation-mediated PCR (LM-PCR) as described previously (Klein et al., 1999), with some modifications. The first LM-PCR amplification was carried out in 50 µL using 10 µL of sample to which 0.5 µL of primer solution (MseLig12 and MseLig21, 100 µM) was added, 0.5 µL of One-Phor-All plus Buffer (Pharmacia Biotech, Piscataway, NJ), 3 µL of 10X Ex Taq™ buffer without Mg2+ (TaKaRa, Madison, WI, USA), 1 µL (5 U) of Ex Taq™ enzyme (TaKaRa, Madison, WI, USA), 3 µL of MgCl2 (25 mM), 8 µL of dNTP (2.5 mM ), and 23.5 µL of nuclease-free water. The mixture was then subjected to thermal cycling as follows: 94 °C (40 sec), 57 °C (30 sec) and 72 °C (1 min 15 sec) for 15 cycles; 94 °C (40 sec), 57 °C (30 sec) and 72 °C (1 min, 45 sec) for 34 cycles; and 94 °C (40 sec), 57 °C (30 sec) and 72 °C (5 min) for the final cycle. The PCR products were resolved on 1 % agarose gel to assess the quality. Samples DNA content was quantified using the NanoDrop ND-1000 spectrophotometer before proceeding to the next enrichment round. To obtain sufficient DNA for downstream processing, three PCR reactions were carried out using 0.75 µL aliquots from the first LM PCR, to which 0.75 µL of MseLig21 primer (100 µM ) was added, plus 5 µL of 10X Buffer 1 (Roche/Boehringer Mannheim, Expand Long Template), 4 µL of dNTPs (2.5 mM ), 0.8 µL of Expand Long Template Enzyme Mix (Roche/ Boehringer Mannheim) and 38.7 µL of nuclease-free water. The following four-step programs were used: 94 °C (60 sec), 65 °C (30 sec), and 72 °C (2 min) for 1 cycle; 94 °C (40 sec), 65 °C (30 sec) and 72 °C (90 sec) for14 cycles; 94 °C (40 sec), 65 °C (30 sec) and 72 °C (2 min) for 9 cycles and 72 °C (5 min) as the final cycle. The quality and concentration of DNA were evaluated as described above. The amplified product from the second LM-PCR was first purified using a QIAquick PCR Purification Kit (Qiagen, Chatsworth, CA, USA) according to the manufacturer's instructions with minor modifications. Final elution volume was 41.5 µL, of which 1.5 µL was used for quantification by absorbance measurement. The rest was divided in two separate 20 µL aliquots. Adaptors were removed by digestion for 16 h at 37 °C with 5 U of MseI (New England Biolabs, Ipswich, MA, USA). The mixture also contained 0.5 µL of bovine serum albumin (New England Biolabs, Ipswich, MA, USA), 5 µL of 10X Buffer 4 (New England Biolabs, Ipswich, MA, USA), and 24 µL of nuclease-free water. The reaction was terminating by heating for 20 min at 65 °C. The sample was then purified using a QIAquick PCR Purification Kit (Qiagen, Chatsworth, CA, USA), eluted in 23.5 µL of nuclease-free water and quantified by absorbance. For each sample, 2.5 µg of DNA was labeled using the Universal Linkage System (ULS) labeling kit (Kreatech Biotechnology, Amsterdam, Netherlands) according to the manufacturer's instructions with minor modifications: 1 µL of Cy-ULS dye was added per 1 µg of genomic DNA adjusted with 10X labeling buffer. The labelling mixture was then held for 30 min at 85 °C in a thermocycler, followed by 3 min on ice. Non-reacted ULS-Cy3/5 was removed by purification using a QIAquick PCR Purification Kit and samples were eluted in 23.5 µL nuclease-free water. A 1.5 µL aliquot was used to determine DNA concentration and dye incorporation using the ND-1000 NanoDrop.

growth_protocol: Four pairs of MZ twin bulls were generated by embryo splitting at morula stage and transferred to different recipient cows and reared in different environments. The MZ twin pairs were born either the same day or a maximum of three days from each other. After puberty these bulls were put in service for progeny testing. Frozen straws of the collected semen were used for analyses. The age (in months) at collection of the MZ twin pairs were respectively: Pair #1: 41 and 28; Pair #2: 59 and 51; Pair #3: 13 and 13; Pair #4: 15 and 14 months old.

extract_protocol: High quality intact gDNA was extracted from these semen samples using a protocol developed in-house. A single straw containing ~5 x 107 sperm was diluted with 1 ml phosphate-buffered saline, pH 7•4 containing 2% SDS in a 1•5 ml microcentrifuge tube and then vortexed (5 sec) followed by centrifugation at 15,500 x g for 5 min to pellet the sperm. The supernatant was discarded completely and 450 µL lysis buffer (10 mM Tris pH 8•0, 10mM EDTA pH 8•0, 1.5% SDS, 100 mM NaCl) were added followed by the addition of 30 µL 1M dithiothreitol (DTT), and 20 µL Proteinase K solution (20 mg/ml). The sperm solution was placed in an incubator at 56 °C (Inkubator 1000, Heidolph, Schwabach, Germany) with an integrated orbital shaker (155 rpm, Unimax 1010, Heidolph) for 12-16 h. Following incubation, 160 µL of saturated NaCl solution were added and the mixture was vortexed 3X for 5 sec. The solution was then centrifuged for 10 min at 15,500 x g. The supernatant from the liquid pellet was carefully removed and transferred to a 2 ml microtube. One ml of chilled (4˚C) ethanol was added and gently mixed by hand shaking (15-20 times) to allow the extracted gDNA to precipitate and collected by centrifugation at 13,500 rpm for 15 min at 4˚C. The supernatant was discarded and the gDNA pellet was washed with 500 µL 70% ethanol and centrifuged at 13,500 rpm for 5 min at 4˚C. After discarding the supernatant, a final wash was done by adding 200 µL 50% ethanol and centrifuging at 13,500 rpm 5 min at 4˚C. The purified extracted bovine sperm gDNA was resuspended in 100 µL of TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8•0) or nuclease-free water. The quality and purity of the extracted gDNA were tested on Nanodrop ND100 (Thermo Scientific, Wilmington, DE) and the integrity of gDNA was assessed by running the samples on 0.5% agarose gel at 45 volts for 2 h.

tag: cell type

value: sperm

tag: sample type

value: Twin 4H

value: Twin 4h


title: BA11 sample #128

status: Public on Dec 31 2015

type: RNA

city: Pittsburgh

first: Etienne

last: Sibille

state: PA

address: 450 Technology Drive, Suite 231

department: Psychiatry

country: USA

institute: University of Pittsburgh

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials: • Heat the hybridization cocktail to 99°C for 5 minutes in a heat block • Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation • Transfer the hybridization cocktail that has been heated at 99°C, to a 45°C heat block for 5 minutes • Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture • Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube • Place probe array into the hybridization oven, set to 45°C • To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm • Hybridize for 16 hours • During the latter part of the 16-hour hybridization, proceed to the GeneChip® Expression Wash, Stain and Scan User Manual, P/N 702731, to prepare reagents for the washing and staining steps required immediately after completion of hybridization

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G

data_processing: All samples were analyzed using the Affymetrix Human Gene 1.1 ST microarray platform. Gene expression values were corrected, quantile-normalized, and log2-transformed via Affymetrix Expression Console software (build 1.2.1.20) using RMA algorithm. A total of 33,297 probe sets were available on each array; only those probe sets with annotated gene symbols were selected (20,237 gene symbols). If a gene was represented by multiple probe sets, the one with the largest intensity interquartile region was selected to represent that gene. Microarray data for each brain region were analyzed separately.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Brain prefrontal cortex, broadman areas 11

label_protocol: According to standard affymetrix protocol: • 10ul  Purified cDNA10ul • DEPC H2O • 4ul  10x IVT Labeling Buffer • 12ul  IVT Labeling NTP mix • 4ul  IVT Labeling Enzyme mix - Incubate at 37C 16 hour in an incubating oven or thermal cycler with heated lid to avoid condensation. - Purify labeled cRNA generated from either IVT labeling reaction using RNeasy RNA Purification Mini kit (Qiagen) using the RNA Cleanup Protocol according to manufacturers instructions. - Quantitate Biotin labeled cRNA using 260nm/280nm spectrophotometric assay.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from frozen samples stored in TRIzol (Invitrogen, Carlsbad, Calif.) and processed for microarray analysis according to the microarray manufacturer’s protocol (Affymetrix, Santa Clara, Calif.)

treatment_protocol: not applicable

tag: tissue

value: brain

tag: age

tag: pmi

tag: ph

tag: rin

tag: Sex

value: F

tag: race

value: W

tag: tod


title: Monozygotic Twin Bulls brother Sperm DNA methylation analysis e vs. E dye-swap

type: genomic

middle: A.

description: Dye-Swap

molecule: genomic DNA

value: Twin 3e

value: Twin 3E


title: KMCH control 2

city: Mainz

first: Jens

middle: U.

last: Marquardt

address: Langenbeckstrasse 1

department: Department of Medicine I

country: Germany

institute: University of Mainz

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: We used Illumina Genome Studio for the Quantile data normalization (standard pipeline).

source_name: Hepatoma cell line

label_protocol: Illumina protocol

growth_protocol: Human hepatoma cells were cultured with DMEM and 10% FCS

extract_protocol: Qiagen Rneasy Kit

treatment_protocol: 72h of treatment with 25uM of curcmumin

tag: cell line

value: KMCH

tag: agent


title: Monozygotic Twin Bulls brother Sperm DNA methylation analysis h vs. H dye-swap

description: Dye-Swap


title: BA11 sample #125


title: D9 combined with ADR rep1

city: Singpapore

first: Xia

last: Jiang

address: 60 Biopolis Street, #02-01, Genome, Singapore

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genome Studio

source_name: AML cell line TF-1a

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

growth_protocol: TF-1a cells were cultured in RPMI 1640 (Invitrogen) medium supplemented with 10% Fetal Bovine Serum (FBS) and 1% Penicillin Streptomycin (PS). TF-1a cells were maintained at 37 °C with 5% CO2.

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.

treatment_protocol: TF-1a cells before and after Ara-C (50 nM) or ADR (50 nM) treatment or co-treated with D9 (100 nM) for 72 hours were harvested for RNA isolation and genome-wide transcription profilling.

tag: treatment

value: co-treated with D9 and ADR for 72 hours


title: KMCH control 1


title: plasma of control

city: Beijing

first: Qinghua

last: Cui

address: 38 Xueyuan Road

country: China

institute: Peking University

hyb_protocol: The labeled cRNAs were hybridized onto the Mouse LncRNA Array v2.0 (8 x 60K, Arraystar).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

organism: Mus musculus

source_name: mouse plasma of control

label_protocol: The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: Plasma

value: Male


title: LCL_truncating6

city: Madrid

first: Tereza

last: Vaclova

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics

country: Spain

institute: CNIO - Spanish National Cancer Research Centre

description: miRNA expression at basal conditions

hyb_protocol: Total RNA was hybridized on LNA based miRNA microarrays 7th generation (miRNAs from miRBase Release 19.0; GAL File used for identification of miRNAs was created on 2013-02-21, 11:09). Labeled RNA was hybridized to miRCURY LNA™ microRNA Arrays over 16 hours at 56ºC using Agilent Hybridization chambers SureHyb and a rotating oven.

scan_protocol: Arrays were washed, dried and scanned with Agilent G2565AA Microarray Scanner System (Agilent Technologies). Fluorescence intensities on scanned images were measured with Agilent Feature Extraction software, version 10.7 (Agilent Technologies), using a modified Exiqon protocol.

data_processing: The raw data were extracted from scanned slides with Feature Extraction software (Agilent; version 10.7). The microarray background correction was performed using normexp method and normalization between arrays was carried out via quantiles method in R statistical software (version 2.13.0). Human miRNAs were filtered and replicate probes were merged by their mean profile.

source_name: LCL, truncating BRCA1

label_protocol: 300 ng of RNA was CIP treated and Hy3-labeled using miRCURY LNA™ microRNA Hi-Power Labeling Kit (Exiqon)

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer´s instructions. Ten million cells from each LCL was used for RNA isolation. RNA quality and quantity was determined using LabChip technology on an Agilent 2100 BioAnalyser (Agilent Technologies).

value: lymphoblastoid cell line

tag: genotype/variation

value: truncating BRCA1

tag: gender

value: female


title: BA11 sample #124

value: M


title: ADR rep1

value: treated with ADR at 50 nM for 72 hours


title: D9 combined with Ara-C rep1

value: co-treated with D9 and Ara-C for 72 hours


title: Monozygotic Twin Bulls brother Sperm DNA methylation analysis E vs. e

description: Dye-Swap

value: sperm


title: Monozygotic Twin Bulls brother Sperm DNA methylation analysis B vs. b dye-swap

description: Dye-Swap

value: Twin 2b

value: Twin 2B


title: LCL_truncating5

description: miRNA expression at basal conditions


title: Monozygotic Twin Bulls brother Sperm DNA methylation analysis B vs. b

description: Dye-Swap


title: LCL_truncating4

description: miRNA expression at basal conditions


title: LCL_truncating3

description: miRNA expression at basal conditions


title: LCL_truncating2

description: miRNA expression at basal conditions


title: BA11 sample #143

value: brain


title: LCL_truncating1

description: miRNA expression at basal conditions


title: Monozygotic Twin Bulls brother Sperm DNA methylation analysis A vs. a dye-swap

description: Dye-Swap

value: Twin 1a

value: Twin 1A


title: BA11 sample #123

value: F

value: W


title: Ara-C rep1

value: treated with Ara-C at 50 nM for 72 hours


title: BA11 sample #122

value: B


title: BA11 sample #121


title: BA11 sample #120


title: LCL_missense4

description: miRNA expression at basal conditions

source_name: LCL, missense BRCA1

value: missense BRCA1


title: untreated ctrl rep1

value: untreated


title: D9 rep1

value: treated with D9 at 100 nM for 72 hours


title: BA11 sample #118


title: MOLM-14 D9 1 μM 48h rep1

source_name: human AML cell lines

growth_protocol: These AML cell lines were cultured in either RPMI 1640 or IMDM (Invitrogen) medium supplemented with 10 or 20% Fetal Bovine Serum (FBS) and 1% Penicillin Streptomycin (PS). The culture medium for TF-1 cell line was supplemented with10% FBS, PS and 5 ng/ml of IL-3 (R&D). All cells were maintained at 37 °C with 5% CO2.

treatment_protocol: These AML cells lines were treated with D9 at 1 or 5 μM for 48h prior to harvesting

value: treated with D9 at 1 μM for 48h


title: LCL_missense3

description: miRNA expression at basal conditions

value: lymphoblastoid cell line

value: female


title: MOLM-14 D9 5 μM 48h rep1

value: treated with D9 at 5 μM for 48h


title: LCL_missense5

description: miRNA expression at basal conditions


title: BA11 sample #119


title: MV-4-11 ctrl 48h rep1


title: MV-4-11 D9 1 μM 48h rep1


title: LCL_missense2

description: miRNA expression at basal conditions


title: MOLM-14 ctrl 48h rep1


title: BA11 sample #115

value: M


title: LCL_missense1

description: miRNA expression at basal conditions


title: LCL_WT6

description: miRNA expression at basal conditions

source_name: LCL, WT BRCA1

value: WT BRCA1


title: Monozygotic Twin Bulls brother Sperm DNA methylation analysis A vs. a

description: Dye-Swap

value: sperm


title: LCL_WT5

description: miRNA expression at basal conditions


title: LCL_WT4

description: miRNA expression at basal conditions


title: BA11 sample #117

value: brain


title: KG-1a D9 5 μM 48h rep1


title: BA11 sample #114


title: BA11 sample #116


title: BA11 sample #113


title: KG-1a ctrl 48h rep1


title: LCL_WT3

description: miRNA expression at basal conditions


title: BA11 sample #110


title: BA11 sample #112


title: KG-1a D9 1 μM 48h rep1


title: BA11 sample #109


title: LCL_WT2

description: miRNA expression at basal conditions


title: BA11 sample #111


title: Mono-Mac-1 D9 5 μM 48h rep1


title: LCL_WT1

description: miRNA expression at basal conditions


title: BA11 sample #106


title: TF-1 D9 5 μM 48h rep1


title: Mono-Mac-1 ctrl 48h rep1


title: BA11 sample #108


title: THP-1 ctrl 48h rep1


title: BA11 sample #107


title: SK-N-BE(2) treated for 8h with 1 uM compound 8148_30880

city: Beerse

first: Steven

last: Osselaer

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica NV

hyb_protocol: Target hybridization was processed on the GeneTitan® Instrument according to the instructions provided in the User Guide for Expression Array Plates (P/N 702933).

scan_protocol: Plate scan was processed on the GeneTitan® Instrument according to the instructions provided in the User Guide for Expression Array Plates (P/N 702933). Images were analyzed using the GeneChip® Command Console Software (AGCC), (Affymetrix).

data_processing: The data were analyzed using R 3.0.1, affy package version 1.34.0 & 1.38.1, farms package version 1.12.0 and Entrez based alternative CDF version 15.1.0 for probeset annotation

label_protocol: All microarray related steps for target preparation including  amplification of total RNA and  labeling were carried out as described in the GeneChip®3’ IVT, Express Kit User Manual , (Affymetrix 2004).

growth_protocol: Neuroblastoma SK-N-BE(2) cells (ATCC CRL-2271) were cultured using a modified 1:1 mixture of Dulbecco's Modified Eagle's Medium and F12 Medium, DMEM/HAMF12 (Composition: 500 ml DMEM/HAMF12 (31331), 28 ml FBS (heat inactivated, New Zealand origin), 5 ml SOL B, 5.7 ml NEAA, 8.5 ml HEPES, 5.7 ml L-Glutamine)., complemented with fetal bovine serum to a final concentration of 5%. Cells were grown in 175cm² culture flasks at 37°C under 5% CO2 and split at 80% confluence every 3 to 4 days.

extract_protocol: Cells were lysed using RLT buffer (Qiagen) and RNA extracted with the RNeasy 96 kit (p/n 74181 Qiagen).

treatment_protocol: SK-N-BE(2) cells were incubated with compound 8 h. DMSO was used as negative control.


title: BA11 sample #104


title: TF-1 ctrl 48h rep1


title: Mono-Mac-1 D9 1 μM 48h rep1


title: THP-1 D9 1 μM 48h rep1


title: BA11 sample #102


title: SK-N-BE(2) treated for 8h with DMSO_30863

value: DMSO


title: BA11 sample #105


title: RAS_ER_SNAI1_LA_2

city: Lyon

first: Anne

last: Wierinckx

state: select a state

address: 8, av Rockefeller

country: France

institute: University Lyon1

description:
7509352146_K
human mammary epithelial cells, immortalized with hTERT and transduced with inducible form of RASG12V and SNAI1 in low adherence conditions

data_processing: The data were normalised using quantile normalisation with GenomeStudio 2011.1 with Gene Expression module v1.9 from Illumina

growth_protocol: cells were grown in DMEM/HAMF12 medium supplemented with penicillin/streptomycin, L-glutamin, 10% fetal bovine serum, 10ng/ml hEGF, 0.2µg/ml cortisone and 10µg/ml insulin or in specified medium  containing 3mM glucose and 0.5mM glutamine.

extract_protocol: Total RNAs were extract with the Qiagen RNeasy minikit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Immortalized human mammary epithelial cells (HMEC-hTERT cells)

tag: transduced with

value: inducible form of RASG12V and SNAI1

tag: culture media

value: Low adherence/3mM glucose 0.5mM glutamine


title: THP-1 D9 5 μM 48h rep1


title: BA11 sample #100

value: W


title: BA11 sample #103

value: F


title: SK-N-BE(2) treated for 8h with DMSO_30871


title: RAS_ER_SNAI2_LA_2

description:
7509352146_L
human mammary epithelial cells, immortalized with hTERT and transduced with inducible form of RASG12V and SNAI2 in low adherence conditions

tag: cell type

value: inducible form of RASG12V and SNAI2


title: BA11 sample #101


title: LnCap treated for 8h with DMSO_30931

source_name: LnCap

growth_protocol: Human prostate (LnCaP cells, ATCC CRL-1740) were cultured using modified ATCC-formulated RPMI-1640 Medium, Catalog No. 30-2001 (Composition: 500 ml RPMI 1640 , 5.7 ml L-glutamine 2mM, 57 ml FBS (not heat inactivated), 5.7 ml Gentamycine (50 µg/ml)), complemented with fetal bovine serum to a final concentration of 10% and with 1% of L-glutamine and Gentamycine. Cells were grown in 175cm² culture flasks at 37°C under 5% CO2 and split at 80% confluence every 3 to 4 days.

treatment_protocol: LNCaP cells were incubated with compound 8 h. DMSO was used as negative control.

value: LnCap


title: LnCap treated for 8h with DMSO_30939


title: SK-N-BE(2) treated for 8h with DMSO_30879


title: LnCap treated for 8h with 1 uM compound 8148_30940


title: TF-1 D9 1 μM 48h rep1


title: BA11 sample #99

value: B


title: RAS_ER_LA_PF

description:
7509352146_J
human mammary epithelial cells, immortalized with hTERT and transduced with inducible form of RASG12V in low adherence conditions

value: inducible form of RASG12V


title: RAS_ER_SNAI1_LA

description:
7509352146_H
human mammary epithelial cells, immortalized with hTERT and transduced with inducible form of RASG12V and SNAI1 in low adherence conditions


title: RAS_ER_SNAI2_LA

description:
7509352146_I
human mammary epithelial cells, immortalized with hTERT and transduced with inducible form of RASG12V and SNAI2 in low adherence conditions


title: LnCap treated for 8h with DMSO_30923


title: BA11 sample #97


title: HepG2 treated for 8h with 1 uM compound 8148_33832

growth_protocol: Hepatocarcinoma (HepG2 cells, ATCC HB-8065) were cultured using modified Minimum Essential Medium, GIBCO 31095 (Composition: 500 ml MEM (GIBCO 31095), 57 ml FBS (heat inactivated), 5.7 ml L-glutamine, 5.7 ml NA-pyruvaat, 5.7 ml NEAA (100x), 10 ml NaHCO3  7.5%, 0.57 ml gentamycine (50 mg/ml)), complemented with fetal bovine serum to a final concentration of 10%. Cells were grown in 175cm² culture flasks at 37°C under 5% CO2 and split at 80% confluence every 3 to 4 days.

treatment_protocol: HepG2 cells were incubated with compound 8 h. DMSO was used as negative control.


title: HepG2 treated for 8h with DMSO_33831


title: RAS_ER_SNAI2_2

description:
7509352146_F
human mammary epithelial cells, immortalized with hTERT and transduced with inducible form of RASG12V and SNAI2

value: DMEM with 3mM glucose 0.5 mM Glutamine


title: RAS_ER_LA

description:
7509352146_G
human mammary epithelial cells, immortalized with hTERT and transduced with inducible form of RASG12V in low adherence conditions


title: BA11 sample #94


title: RAS_ER_SNAI1_2

description:
7509352146_E
human mammary epithelial cells, immortalized with hTERT and transduced with inducible form of RASG12V and SNAI1


title: HepG2 treated for 8h with DMSO_33823


title: RAS_ER_SNAI2

description:
7509352146_C
human mammary epithelial cells, immortalized with hTERT and transduced with inducible form of RASG12V and SNAI2


title: HepG2 treated for 8h with DMSO_33815


title: BA11 sample #96


title: BA11 sample #98


title: RAS_ER_SNAI1

description:
7509352146_B
human mammary epithelial cells, immortalized with hTERT and transduced with inducible form of RASG12V and SNAI1


title: BA11 sample #95


title: BA11 sample #93


title: BA11 sample #90


title: BA11 sample #91


title: RAS_ER_2

description:
7509352146_D
human mammary epithelial cells, immortalized with hTERT and transduced with inducible form of RASG12V


title: HMEChTert_Snail2_3_GlucRed

description:
6991001014_K
human mammary epithelial cells, immortalized with hTERT and transduced with SNAI2 and maintained 16h in DMEM with 3mM glucose 0.5mM glutamine


title: HMEChTert_Snail3_3_GlucRed

description:
6991001014_L
human mammary epithelial cells, immortalized with hTERT and transduced with SNAI3 and and maintained 16h in DMEM with 3mM glucose 0.5mM glutamine


title: BA11 sample #89


title: RAS_ER

description:
7509352146_A
human mammary epithelial cells, immortalized with hTERT and transduced with inducible form of RASG12V


title: BA11 sample #92


title: BA11 sample #86


title: HMEChTert_Snail1_3_GlucRed

description:
6991001014_J
human mammary epithelial cells, immortalized with hTERT and transduced with SNAI1 and maintained 16h in DMEM with 3mM glucose 0.5mM glutamine


title: HMEChTert-Control_3_GlucRed

description:
6991001014_I
human mammary epithelial cells, immortalized with hTERT, and maintained 16h in DMEM with 3mM glucose 0.5mM glutamine

source_name: HMEChTert-Control


title: HMEChTert_Snail2_3_MEMred

description:
6991001014_G
human mammary epithelial cells, immortalized with hTERT and transduced with SNAI2, and maintained 16h in MEM

value: MEM


title: BA11 sample #88

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole


title: HMEChTert_Snail3_3_MEMred

description:
6991001014_H
human mammary epithelial cells, immortalized with hTERT and transduced with SNAI3, and maintained 16h in MEM


title: HMEChTert_Snail1_3_MEMred

description:
6991001014_F
human mammary epithelial cells, immortalized with hTERT, transduced with SNAI1 and maintained 16h in MEM


title: BA11 sample #87


title: BA11 sample #84


title: HMEChTert-Control_3_MEMred

description:
6991001014_E
human mammary epithelial cells, immortalized with hTERT and maintained 16h in MEM


title: BA11 sample #85


title: HMEChTert_Snail2_3

description:
6991001014_C
human mammary epithelial cells, immortalized with hTERT and transduced with SNAI2


title: BA11 sample #83


title: BA11 sample #80


title: HMEChTert_Snail3_3

description:
6991001014_D
human mammary epithelial cells, immortalized with hTERT and transduced with SNAI3


title: BA11 sample #81


title: BA11 sample #79


title: HMEChTert-Control_3

description:
6991001014_A
human mammary epithelial cells, immortalized with hTERT


title: BA11 sample #82


title: DOK(2)

city: Zhunan Miaoli County

first: Chia

middle: Huei

last: Lee

address: 35, Keyan Rd.

department: National Institute of Cancer Research

country: Taiwan

institute: Taiwan National Health Research Institute

description: replicate 2

data_processing: Data analysis was performed with GeneSpring GX software (Agilent Technologies). Arrays with less than 50% detected probes were excluded. Quantile normalisation was performed.

source_name: dysplasitc oral keratinocyte derived from a heavy smoker with OSC

label_protocol: 500ng total RNA was converted into cDNA using biotinylated random nonamers, oligodeoxythymidine 18 primers and Illumina-supplied reagents, according to Illumina manufacturer's instructions.

extract_protocol: Total RNA was isolated using an RNeasy mini kit (Qiagen) according to the manufacturer's instruction.

value: male

value: oral keratinocyte

tag: status

value: Dysplastic

tag: smoking

value: Yes


title: BA11 sample #78

tag: tissue

value: brain

tag: age

value: M


title: BA11 sample #77

tag: pmi

tag: ph


title: DOK(1)

description: replicate 1


title: BA11 sample #75

tag: rin

tag: Sex


title: HOK(2)

description: replicate 2

source_name: normal human oral keratinocyte

value: Healthy

value: No


title: BA11 sample #76

tag: race

tag: tod


title: PHH_berberine_2hr_donor 3

city: Taipei

first: Ting-fang

last: Lo

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Institute of Biological Chemistry

institute: Academia Sinica

description: miRNA expression after berberine chloride treatment for 4 hr

hyb_protocol: Standard Agilent miRNA microarray system  hybridization protocol

scan_protocol: Microarrays were scanned following the Agilent microarray scanner protocol, and the image analysis and quantitation were performed by the Agilent Feature Extraction software

data_processing: The data were normalised using quantile normalization with by GeneSpring GX.

source_name: primary human hepatocytess from donor 3, berberine chloride , 2 hr

label_protocol: Agilent's miRNA microarray system V2.2 miRNA with Complete Labeling and Hyb Kit according to the manufacture’s protocol

growth_protocol: The primary human hepatocytes (induction qualified human plateable cryopreserved hepatocytes, HMCPIS) from Caucasian donors were purchased from Invitrogen and cultured following the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using TRIZOL reagent (Invitrogen) according to the manufacture’s protocol. The total RNA quantity was measured using a NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies). The total RNA quality and integrity were assayed by Agilent 2100 bioanalyzer with RNA 6000 nano kit (Agilent Technologies).

treatment_protocol: A 50 mM stock solution of Berberine chloride (Sigma-Aldrich) was prepared in DMSO. Cells were treated with 40 M berberine chloride or 0.08% DMSO as control. Comparing miRNA profiles of 40 M berberine-treated PHHs to those of control cells sampled after 2  hours treatment

value: primary human hepatocytes


title: BA11 sample #74

value: W


title: HOK(1)

description: replicate 1


title: PHH_berberine_2hr_donor 2

source_name: primary human hepatocytes from donor 2, berberine chloride , 2 hr


title: PHH_control_2hr_donor 2

description: miRNA expression after 0.08% DMSO treatment for 4hr

source_name: primary human hepatocytes from donor 2, 0.08% DMSO, 2 hr


title: PHH_control_2hr_donor 3

source_name: primary human hepatocytes from donor 3, 0.08% DMSO, 2 hr


title: BA11 sample #72


title: BA11 sample #71


title: PHH_berberine_2hr_donor 1

description: miRNA expression after berberine chloride treatment for 2hr

source_name: primary human hepatocytes from donor 1, berberine chloride , 2 hr


title: PHH_control_2hr_donor 1

description: miRNA expression after 0.08% DMSO treatment for 2hr

source_name: primary human hepatocytes from donor 1, 0.08% DMSO, 2 hr


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #90]

city: Bologna

first: Carolina

last: Terragna

address: Via Massarenti, 9

department: Department of Experimental, Diagnostic and Specialty Medicine - DIMES

country: Italy

institute: Institute of Hematology "L.A.Seràgnoli"

description: Hybridized to Affymetrix Genome-Wide Human SNP 6.0 Array

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G.

data_processing: The array image was acquired using Affymetrix Command Console, version 4.0. Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Affymetrix Genotyping Console, version 4.0, software. Nexus, version 7.5 (BioDiscovery) was employed to perform CNAs comparisons; inferred copy number states were derived from segmentation algorithm implemented in Nexus.

source_name: CD138+ cell fractions obtained from MM patients' BM

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from CD138+ plasma cells obtained from bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

treatment_protocol: Pre-treatment plasma cells (PC) were purified from mononuclear bone marrow cells obtained by Ficoll-Hypaque density gradient centrifugation using anti-CD138 micro beads on an AutoMacs Magnetic Cell Separator (MACS system, Miltenyi Biotec, Auburn, CA). CD138+ cell fractions were than stored at -80°C in guanidium thiocyanate, until use.

tag: patient id

value: MM patient #90

tag: disease state

value: Multiple Myeloma

tag: tumor stage

value: diagnosis

tag: response to vtd therapy

value: nCR

value: mononuclear bone marrow cells

tag: cell subtype

value: CD138+ cell fractions


title: BA11 sample #70

source_name: Brain prefrontal cortex, broadman areas 11


title: HMEChTert_Snail1_3

description:
6991001014_B
human mammary epithelial cells, immortalized with hTERT and transduced with SNAI1

value: Immortalized human mammary epithelial cells (HMEC-hTERT cells)

tag: transduced with

tag: culture media


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #27]

value: MM patient #27

tag: cell type


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #310]

value: MM patient #310

value: VGPR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #324]

value: MM patient #324


title: BA11 sample #68

value: brain


title: BA11 sample #69

value: M


title: BA11 sample #73


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #296]

value: MM patient #296

value: MR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #96]

value: MM patient #96

value: PR


title: BA11 sample #65

value: W


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #413]

value: MM patient #413

value: Multiple Myeloma

value: CR


title: BA11 sample #64


title: BA11 sample #67


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #242]

value: MM patient #242

value: diagnosis

value: mononuclear bone marrow cells


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #459]

value: MM patient #459

value: CD138+ cell fractions


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #207]

value: MM patient #207


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #271]

value: MM patient #271

value: NR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #2]

value: MM patient #2


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #206]

value: MM patient #206


title: BA11 sample #63

value: brain

value: M


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #241]

value: MM patient #241

value: PR


title: BA11 sample #61

value: W


title: BA11 sample #66


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #225]

value: MM patient #225

value: Multiple Myeloma


title: BA11 sample #62


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #139]

value: MM patient #139


title: BA11 sample #60


title: BA11 sample #56


title: BA11 sample #57


title: BA11 sample #58


title: BA11 sample #59


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #164]

value: MM patient #164

value: diagnosis

value: CR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #179]

value: MM patient #179

value: mononuclear bone marrow cells

value: CD138+ cell fractions


title: BA11 sample #55


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #195]

value: MM patient #195

value: VGPR


title: BA11 sample #52


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #135]

value: MM patient #135

value: NR


title: BA11 sample #53

value: brain

value: M


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #138]

value: MM patient #138

value: PR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #169]

value: MM patient #169


title: BA11 sample #51

value: F

value: W


title: BA11 sample #54

value: B


title: BA11 sample #50


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #115]

value: MM patient #115

value: Multiple Myeloma

value: diagnosis


title: BA11 sample #49


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #465]

value: MM patient #465

tag: hh cluster

value: mononuclear bone marrow cells


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #311]

value: MM patient #311

value: CD138+ cell fractions


title: GRO Mex67-5 t40 on filter V8-L1-x

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing: Raw image quantization with background subtraction. This experiment is a single repeat. No elaborated data were generated.

organism: Saccharomyces cerevisiae S288C

source_name: mex67-5 40 min at 37ºC

label_protocol: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were permeabilized with 20 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.

growth_protocol: Cells were grown in YPD at 26ºC to 0.5 OD600. At that time cells were shifted to 37ºC to induce Mex67 protein inactivation and recovered after, 0, 5,20,40, 60 and 150 min.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

tag: time point (min)

tag: genotype/variation


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #105]

value: MM patient #105

value: nCR


title: GRO Mex67-5 t150 on filter V8-L1-x

source_name: mex67-5 150 min at 37ºC


title: GRO Mex67-5 t60 on filter V8-L1-x

source_name: mex67-5 60 min at 37ºC


title: BA11 sample #48

tag: tissue

value: brain

tag: age

tag: pmi


title: BA11 sample #47

tag: ph

tag: rin

tag: Sex

value: M


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #104]

tag: patient id

value: MM patient #104

value: VGPR


title: GRO Mex67-5 t20 on filter V8-L1-x

source_name: mex67-5 20 min at 37ºC


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #278]

value: MM patient #278

tag: disease state

value: PR


title: BA11 sample #45

tag: race

value: W

tag: tod


title: BA11 sample #46

value: F


title: GRO Mex67-5 t0 on filter V8-L1-x

source_name: mex67-5 at 26ºC


title: GRO Mex67-5 t5 on filter V8-L1-x

source_name: mex67-5 5 min at 37ºC


title: BA11 sample #44


title: cDNA wt-SAC3 YPD

description: mRNA Amount: Processed data of cDNA triplicate experiment, [mRNA/cell volume] adjusted and Median Absolut Deviation normalized.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times.

data_processing: Raw image quantization with background subtracted and Median Absolute Desviation normalization of each triplicate.

organism: Saccharomyces cerevisiae

source_name: Wild type cells grown in YPD to exponential phase.

growth_protocol: Exponential growth in YPD at 28ºC.

tag: strain

value: BY4741 wild type


title: BA11 sample #42


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #11]

value: MM patient #11

value: Multiple Myeloma

tag: tumor stage

tag: cell subtype

tag: response to vtd therapy


title: cDNA sac3NM YPD

source_name: sac3NM cells grown in YPD to exponential phase

value: sac3N+M mutant lacking C-terminal part. Background BY4741


title: BA11 sample #41

value: B


title: cDNA sac3 YPD

source_name: sac3Δ cells grown in YPD to exponential phase

value: sac3Δ deletion mutant background BY4741


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #161]

value: MM patient #161

value: diagnosis

tag: hh cluster

tag: cell type

value: mononuclear bone marrow cells

value: CD138+ cell fractions


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #403]

value: MM patient #403


title: GRO sus1 YPD

description: nascent Transcriptional Rate: Processed data of Genomic Run On triplicate experiment, Median Absolut Deviation normalized.

source_name: sus1Δ cells grown in YPD to exponential phase

value: sus1Δ deletion mutant background BY4741


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #136]

value: MM patient #136

value: CR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #341]

value: MM patient #341

value: PR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #457]

value: MM patient #457

value: MR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #111]

value: MM patient #111

value: VGPR


title: BA11 sample #40

value: brain

value: M

value: W


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #315]

value: MM patient #315

value: Multiple Myeloma


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #273]

value: MM patient #273

value: diagnosis

value: mononuclear bone marrow cells


title: BA11 sample #43


title: BA11 sample #38

value: F

value: B


title: GRO sac3 YPD

value: sac3Δ deletion mutant background BY4741


title: GRO wt-SAC3 & SUS1 YPD

value: BY4741 wild type


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #321]

value: MM patient #321

value: CD138+ cell fractions


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #93]

value: MM patient #93

value: SD


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #359]

value: MM patient #359

value: PR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #277]

value: MM patient #277

value: VGPR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #261]

value: MM patient #261


title: BA11 sample #36

value: brain

value: M

value: W


title: BA11 sample #37


title: BA11 sample #35


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #48]

value: MM patient #48

value: Multiple Myeloma

value: diagnosis

value: mononuclear bone marrow cells


title: BA11 sample #39


title: PHH_berberine_8hr_donor 3

description: gene expression after berberine chloride treatment for 8hr

hyb_protocol: Agilent one color microarray-based gene gexpreesion analysis v4  hybridization protocol

source_name: primary human hepatocytess from donor 3, berberine chloride , 8 hr

label_protocol: Agilent's low input quick Amp Labeling Kit according to the manufacture’s protocol

treatment_protocol: A 50 mM stock solution of Berberine chloride (Sigma-Aldrich) was prepared in DMSO. Cells were treated with 40 M berberine chloride or 0.08% DMSO as control. Comparing miRNA profiles of 40 M berberine-treated PHHs to those of control cells sampled after 2, 4, and 8  hours treatment

value: primary human hepatocytes


title: GRO sac3NM YPD

value: sac3N+M mutant lacking C-terminal part. Background BY4741


title: PHH_control_8hr_donor 3

description: gene expression after 0.08% DMSO treatment for 8hr

source_name: primary human hepatocytes from donor 3, 0.08% DMSO, 8 hr


title: BA11 sample #33

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole

value: B


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #272]

value: MM patient #272

value: CD138+ cell fractions


title: BA11 sample #34

value: F


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #246]

value: MM patient #246

value: PR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #238]

value: MM patient #238

value: VGPR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #155]

value: MM patient #155

value: CR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #228]

value: MM patient #228


title: PHH_berberine_8hr_donor 2

source_name: primary human hepatocytes from donor 2, berberine chloride , 8 hr


title: PHH_berberine_8hr_donor 1

source_name: primary human hepatocytes from donor 1, berberine chloride , 8 hr


title: BA11 sample #32

value: brain

value: M

value: W


title: BA11 sample #30


title: BA11 sample #31


title: PHH_control_8hr_donor 1

source_name: primary human hepatocytes from donor 1, 0.08% DMSO, 8 hr


title: BA11 sample #29


title: BA11 sample #28


title: PHH_control_4hr_donor 3

description: gene expression after 0.08% DMSO treatment for 4hr

source_name: primary human hepatocytes from donor 3, 0.08% DMSO, 4 hr


title: PHH_berberine_4hr_donor 2

description: gene expression after berberine chloride treatment for 4hr

source_name: primary human hepatocytes from donor 2, berberine chloride , 4 hr


title: PHH_berberine_4hr_donor 3

source_name: primary human hepatocytess from donor 3, berberine chloride , 4 hr


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #116]

source_name: CD138+ cell fractions obtained from MM patients' BM

value: MM patient #116

value: Multiple Myeloma

value: diagnosis

value: mononuclear bone marrow cells

value: SD


title: BA11 sample #27

source_name: Brain prefrontal cortex, broadman areas 11


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #134]

value: MM patient #134

value: CD138+ cell fractions


title: PHH_control_4hr_donor 2

source_name: primary human hepatocytes from donor 2, 0.08% DMSO, 4 hr

value: primary human hepatocytes


title: BA11 sample #26


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #23]

value: MM patient #23

value: PR


title: BA11 sample #24


title: BA11 sample #25


title: PHH_berberine_2hr_donor 3

description: gene expression after berberine chloride treatment for 2hr

source_name: primary human hepatocytess from donor 3, berberine chloride , 2 hr


title: PHH_control_4hr_donor 1

source_name: primary human hepatocytes from donor 1, 0.08% DMSO, 4 hr


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #199]

value: MM patient #199


title: PHH_control_2hr_donor 3

description: gene expression after 0.08% DMSO treatment for 2hr

source_name: primary human hepatocytes from donor 3, 0.08% DMSO, 2 hr


title: BA11 sample #23


title: BA11 sample #22


title: PHH_berberine_2hr_donor 2

source_name: primary human hepatocytes from donor 2, berberine chloride , 2 hr


title: BA11 sample #21


title: PHH_berberine_4hr_donor 1

source_name: primary human hepatocytes from donor 1, berberine chloride , 4 hr


title: BA11 sample #20


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #350]

value: MM patient #350

value: VGPR


title: BA11 sample #19

value: F

value: B


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #109]

value: MM patient #109


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #396]

value: MM patient #396


title: PHH_control_2hr_donor 2

source_name: primary human hepatocytes from donor 2, 0.08% DMSO, 2 hr


title: PHH_berberine_2hr_donor 1

source_name: primary human hepatocytes from donor 1, berberine chloride , 2 hr


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #12]

value: MM patient #12


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #98]

value: MM patient #98

value: Multiple Myeloma


title: PHH_control_2hr_donor 1

source_name: primary human hepatocytes from donor 1, 0.08% DMSO, 2 hr


title: BA11 sample #18

value: brain

value: M

value: W


title: BA11 sample #17


title: PHH_control_8hr_donor 2

source_name: primary human hepatocytes from donor 2, 0.08% DMSO, 8 hr


title: L3

city: suzhou

first: Jian

last: Pan

address: Jingde road 303

department: Department of Hematology and Oncology

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Microarray Scanner (G2505B)

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that at least 3 out of 15 samples had flagged as “Present” or “Marginal” were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs were identified through fold change (FC) filtering. Differentially expressed lncRNAs and mRNAs with statistical significance (as determined by two-tailed student’s t-test < 0.05) were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1).

source_name: Bone marrow specimens were obtained at the time of diagnosis during routine clinical assessment of  pediatric patients with AML

extract_protocol: Briefly, RNA purified from total RNA after removal of rRNA was amplified and transcribed into fluorescent cRNA and cDNA was labeled and hybridized to the Human LncRNA Array v2.0 (8660 K, Arraystar). 30,586 LncRNAs and 26,109coding transcripts which collected from the most authoritative databases such as RefSeq, UCSC Knowngenes, Ensembl and many related literatures can be detected by the microarray.

treatment_protocol: Bone marrow specimens were obtained at the time of diagnosis during routine clinical assessment of 3 pediatric patients with AML, who presented at the Department of Hematology and Oncology, Children's Hospital of Soochow University between 2000 and 2011. Additionally, bone marrow samples from 3 healthy donors were analyzed as controls.Bone marrow mononuclear cells (BMNCs) were isolated using Ficoll solution within 2 h after bone marrow samples harvested and subjected for the extraction of total RNA. Human LncRNA Array analysis was performed by KangChen Bio-tech, Shanghai P.R. China.  Briefly, RNA purified from total RNA after removal of rRNA was amplified and transcribed into fluorescent cRNA and cDNA was labeled and hybridized to the Human LncRNA Array v3.0 (8660 K, Arraystar). 30,586 LncRNAs and 26,109 coding transcripts which collected from the most authoritative databases such as RefSeq, UCSC, Knowngenes, Ensembl and many related literatures can be detected by the microarray.

tag: diagnosis

value: AML

value: mononuclear cells

value: bone marrow


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #188]

value: MM patient #188

value: diagnosis

value: mononuclear bone marrow cells

value: CD138+ cell fractions

value: PR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #14]

value: MM patient #14


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #477]

value: MM patient #477


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #422]

value: MM patient #422

value: NR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #262]

value: MM patient #262

value: nCR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #9]

value: MM patient #9

value: Multiple Myeloma

value: MR


title: BA11 sample #16

tag: tissue

value: brain

value: M

value: W


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #127]

value: MM patient #127

value: VGPR


title: BA11 sample #14

tag: age


title: C3

institute: Children's Hospital of Soochow University

source_name: Bone marrow specimens were obtained from healthy donors

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

value: normal (healthy)

value: mononuclear cells

value: bone marrow


title: C2


title: BA11 sample #15

tag: pmi

value: F


title: C1


title: BA11 sample #12

tag: ph


title: BA11 sample #11

tag: rin

value: B


title: L2

value: AML


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #431]

value: MM patient #431

value: diagnosis

value: mononuclear bone marrow cells

value: CD138+ cell fractions

value: PR


title: BA11 sample #9

tag: Sex


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #173]

tag: patient id

value: MM patient #173

value: Multiple Myeloma


title: L1


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #71]

value: MM patient #71

tag: disease state


title: BA11 sample #8

value: brain

value: M

tag: race

value: W


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #196]

value: MM patient #196

value: VGPR


title: old_c514 (CN)

city: Boston

first: Björn

last: Chapuy

state: MA

address: 450 Brookline Ave.

department: Medical Onology

institute: Dana-Farber Cancer Institute

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_H11_41202

hyb_protocol: Following fragmentation, biotinylated PCR fragments were hybridized overnight according to the Affymetrix protocol.

scan_protocol: GCS3000 (Affymetrix)

data_processing:
Copy number values were inferred from raw CEL files with a GenePattern pipeline which runs the following modules: SNPFileCreator, CopyNumberInference, RemoveCopyNumberOutliers, DivideByNormals and Quality Control.
input_to_gistic.seg.txt: Segmented copy number file containing all of the 41 samples and addtionally 180 primary DLBCLs previously deposited at GEO under the accesison number GSE34171 from Monti and Chapuy et al. Cancer Cell 2012.

source_name: fresh frozen tumor sample

label_protocol: PCR products were labeled with a single biotin according to the Affymetrix protocol.

extract_protocol: For total RNA, frozen tissue sections were homogenized in Trizol and RNA was extracted according to standard protocols. For high molecular weight genomic DNA,  frozen tissue sections were homogenized in 1 ml of G2-buffer supplemented with 2 ml RNase (Qiagen). Subsequently, DNA was extracted  using the genomic buffer kit with 20/G genomic-tips (Qiagen) following the manufacturer's recommendations.

treatment_protocol: 10-20 x 20mm sections from frozen tumor specimens from newly diagnosed previously untreated diffuse large B-cell lymphomas and peripheral blood lymphocytes from normal donors were directly transferred to extraction buffers.

tag: type

value: primary DLBCL


title: BA11 sample #7

tag: tod


title: BA11 sample #6


title: old_c506 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_H06_41122


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #110]

value: MM patient #110

tag: tumor stage


title: BA11 sample #4

value: B


title: BA11 sample #13


title: BA11 sample #5

value: F


title: BA11 sample #3


title: old_c503 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_H04_41090


title: old_c502 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_H03_41074


title: old_c504 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_H05_41106


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #85]

value: MM patient #85

tag: cell subtype


title: old_c501 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_H02_41058


title: BA11 sample #1


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #342]

value: MM patient #342

value: diagnosis

tag: response to vtd therapy

value: nCR


title: BA47 sample #210

source_name: Brain prefrontal cortex, broadman areas 47


title: BA11 sample #2


title: BA11 sample #10


title: old_c497 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G12_41216


title: old_c495 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G10_41184


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #185]

value: MM patient #185

tag: hh cluster

value: mononuclear bone marrow cells

value: CD138+ cell fractions


title: BA47 sample #207


title: BA47 sample #208


title: old_c494 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G09_41168


title: BA47 sample #206


title: BA47 sample #205


title: old_c496 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G11_41200


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #407]

value: MM patient #407

value: Multiple Myeloma

tag: cell type


title: old_c491 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G06_41120


title: BA47 sample #203

value: brain

value: M


title: BA47 sample #204


title: old_c490 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G05_41104


title: old_c486 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G04_41088


title: BA47 sample #202

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole

value: W


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #375]

value: MM patient #375

value: CR


title: old_c484 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G02_41056

value: primary DLBCL


title: BA47 sample #201


title: BA47 sample #200


title: old_c482 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F12_41214


title: old_c481 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F10_41182


title: old_c479 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F09_41166


title: BA47 sample #199


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #73]

value: MM patient #73


title: old_c478 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F08_41150


title: BA47 sample #198


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #208]

value: MM patient #208

value: VGPR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #189]

value: MM patient #189

value: PR


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #32]

value: MM patient #32

value: diagnosis


title: BA47 sample #196


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #70]

value: MM patient #70

value: mononuclear bone marrow cells


title: BA47 sample #194


title: old_c477 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F07_41134


title: old_c476 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F06_41118


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #402]

value: MM patient #402

value: CD138+ cell fractions


title: BA47 sample #209

value: brain


title: BA47 sample #195

value: M


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #25]

value: MM patient #25

value: Multiple Myeloma

value: nCR


title: old_c475 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F05_41102

value: primary DLBCL


title: old_c498 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_H01_41042


title: old_c474 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F04_41086


title: BA47 sample #191

value: F

value: W


title: BA47 sample #193


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #204]

value: MM patient #204

value: VGPR


title: BA47 sample #192


title: old_c472 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F02_41054


title: old_c460 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F03_41070


title: old_c471 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_F01_41038


title: BA47 sample #190


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #376]

value: MM patient #376

value: PR


title: old_c470 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E12_41212


title: old_c469 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E11_41196


title: BA47 sample #189


title: old_c468 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E10_41180


title: old_c467 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E09_41164


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #205]

value: MM patient #205

value: diagnosis

value: CR


title: old_c466 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E08_41148


title: BA47 sample #197

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole


title: BA47 sample #188


title: old_c465 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E07_41132


title: old_c464 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E06_41116


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #175]

value: MM patient #175

value: mononuclear bone marrow cells


title: BA47 sample #186

value: brain


title: old_c462 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E05_41100


title: old_c461 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E04_41084


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #201]

value: MM patient #201

value: CD138+ cell fractions


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #64]

value: MM patient #64

value: Multiple Myeloma


title: old_c473 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E03_41068

value: primary DLBCL


title: old_c458 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_E02_41052


title: old_c453 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D11_41194


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #313]

value: MM patient #313


title: Multiple Myeloma patient, diagnosis, rep 1 [MM patient #22]

value: MM patient #22


title: BA47 sample #182

value: M

value: W


title: BA47 sample #183

value: B


title: old_c450 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D08_41146


title: old_c449 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D07_41130


title: old_c448 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D06_41114


title: old_c447 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D05_41098


title: BA47 sample #185


title: old_c445 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D04_41082


title: old_c443 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D03_41066


title: old_c438 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D01_41034


title: BA47 sample #181


title: old_c451 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_D09_41162


title: BA47 sample #187

value: F


title: BA47 sample #177


title: old_c492 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_G08_41152


title: old_c437 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C12_41208


title: BA47 sample #179

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole


title: BA47 sample #176


title: BA47 sample #178


title: old_c436 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C11_41192


title: BA47 sample #180


title: BA47 sample #171


title: BA47 sample #184


title: BA47 sample #172


title: BA47 sample #173


title: BA47 sample #174


title: BA47 sample #175


title: BA47 sample #169


title: old_c433 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C09_41160


title: BA47 sample #167


title: old_c430 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C07_41128


title: old_c429 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C06_41112


title: old_c432 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C08_41144


title: old_c428 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C05_41096


title: BA47 sample #166


title: old_c426 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C04_41080


title: old_c425 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C03_41064


title: BA47 sample #164


title: BA47 sample #165


title: old_c404 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B09_41158


title: old_c407 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B10_41174


title: old_c408 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B11_41190


title: BA47 sample #168


title: BA47 sample #163


title: old_c304 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B06_41110


title: old_c300 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B05_41094


title: BA47 sample #161


title: BA47 sample #162


title: BA47 sample #159


title: old_c291 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B03_41062


title: BA47 sample #158


title: old_c411 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B12_41206


title: BA47 sample #156


title: BA47 sample #157


title: BA47 sample #153


title: BA47 sample #154


title: old_c287 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B02_41046


title: BA47 sample #152

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole


title: old_c422 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_C02_41048


title: old_c307 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B07_41126


title: BA47 sample #170


title: BA47 sample #149


title: BA47 sample #160


title: BA47 sample #155


title: BA47 sample #150


title: BA47 sample #148


title: old_c295 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B04_41078


title: old_c268 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A11_41188


title: old_c274 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A12_41204


title: old_c261 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A09_41156


title: BA47 sample #147


title: old_c251 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A06_41108


title: BA47 sample #146


title: BA47 sample #145


title: old_c242 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A04_41076


title: old_c250 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A05_41092


title: old_c254 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A07_41124


title: old_c277 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_B01_41030


title: old_c239 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A03_41060


title: old_c230 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A02_41044


title: Lymphoma_P11_Dx (CN)

description: MYOID_g_Kuni2newsamples_GenomeWideSNP_6_H10_41784


title: old_c267 (CN)

description: ZAPPY_g_Kuni_1_OMMM581_GenomeWideSNP_6_A10_41172


title: c_D_1158 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_H10_609544


title: c_D_1051 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_H03_609548


title: c_D_1048 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_H07_609672


title: BA47 sample #142

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole


title: BA47 sample #151


title: BA47 sample #143


title: BA47 sample #140


title: BA47 sample #144


title: BA47 sample #141


title: BA47 sample #138


title: BA47 sample #139


title: BA47 sample #135


title: BA47 sample #137


title: c_D_1103 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_G10_609622


title: BA47 sample #136


title: c_D_1049 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_G01_609606


title: BA47 sample #134


title: c_D_1130 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_F05_609650


title: c_D_1151 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_G05_609600


title: c_D_1108 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_G04_609576


title: c_D_1004 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_F02_609646


title: BA47 sample #133


title: c_D_1054 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_H01_609694


title: c_D_1129 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_E08_609638


title: c_D_1152 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_E06_609608


title: BA47 sample #131


title: c_D_1109 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_E04_609538


title: BA47 sample #132


title: BA47 sample #130


title: BA47 sample #128


title: BA47 sample #125


title: BA47 sample #127


title: BA47 sample #126


title: c_D_1046 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_C12_609588


title: c_D_1053 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_D05_609560


title: c_D_1135 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_D12_609590


title: c_D_1124 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_D10_609676


title: BA47 sample #129


title: c_D_1127 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_C06_609712


title: c_D_1112 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_C08_609680


title: c_D_1118 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_B11_609534


title: c_D_1153 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_B10_609714


title: BA47 sample #124

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole


title: BA47 sample #122


title: BA47 sample #120


title: BA47 sample #121


title: BA47 sample #117


title: BA47 sample #116


title: BA47 sample #118


title: BA47 sample #114


title: c_D_1043 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_A12_609586


title: BA47 sample #123


title: c_D_1025 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_H08_566346


title: BA47 sample #119


title: c_D_1106 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_C04_609698


title: BA47 sample #115


title: c_D_1047 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_A08_609596


title: c_D_1134 (CN)

description: LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_A07_609592


title: c_D_1041 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_G11_566358


title: c_D_1029 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_G09_566512


title: c_D_1050 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_H02_566404


title: BA47 sample #112


title: BA47 sample #111


title: BA47 sample #110


title: BA47 sample #113


title: BA47 sample #109


title: BA47 sample #107


title: BA47 sample #108


title: c_D_1017 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_G02_566506


title: BA47 sample #105


title: c_D_1020 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_F07_566334


title: c_D_1027 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_F06_566382


title: c_D_1019 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_F10_566430


title: c_D_1012 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_G08_566338


title: c_D_1036 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_F03_566380


title: c_D_1030 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_E12_566518


title: c_D_1023 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_E09_566348


title: c_D_1010 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_G06_566424


title: c_D_1008 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_E04_566456


title: c_D_1034 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_D12_566356


title: c_D_1005 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_F02_566410


title: c_D_1002 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_D11_566344


title: c_D_1028 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_D10_566386


title: BA47 sample #102

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole


title: BA47 sample #101


title: BA47 sample #106


title: BA47 sample #99


title: BA47 sample #98


title: BA47 sample #95


title: BA47 sample #93


title: BA47 sample #94


title: c_D_1006 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_D01_566500


title: c_D_1001 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_B08_566408


title: c_D_1016 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_C08_566398


title: c_D_1039 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_D02_566520


title: BA47 sample #104


title: c_D_1032 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_A10_566480


title: BA47 sample #103


title: BA47 sample #96


title: c_D_1035 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_A11_566370


title: BA47 sample #100


title: c_D_1003 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_D07_566388


title: c_D_1037 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_A05_566444


title: BA47 sample #97


title: BA47 sample #91


title: c_D_1022 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_A04_566454


title: BA47 sample #90


title: BA47 sample #88


title: BA47 sample #87


title: BA47 sample #89


title: BA47 sample #86


title: BA47 sample #92


title: BA47 sample #84


title: Lymphoma_P09_Dx (CN)

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_D09_40970


title: BA47 sample #85


title: c_D_1024 (CN)

description: HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_A03_566342


title: Lymphoma_P10_Dx (CN)

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_D12_41018


title: Lymphoma_P08_Dx (CN)

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_D06_40922


title: Lymphoma_P07_Dx (CN)

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_D04_40890


title: BA47 sample #81


title: Lymphoma_P03_Dx (CN)

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_C12_41016


title: Lymphoma_P02_Dx (CN)

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_C10_40984


title: BA47 sample #83

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole


title: BA47 sample #82


title: c_D_1166 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_G05_609800


title: c_D_1164 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_G03_609836


title: c_D_1163 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_G02_609752


title: c_D_1162 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_G01_609754


title: BA47 sample #77


title: c_D_1159 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_F10_609758


title: BA47 sample #76


title: BA47 sample #78


title: BA47 sample #74


title: Lymphoma_P04_Dx (CN)

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_D02_40858


title: BA47 sample #80


title: BA47 sample #75


title: BA47 sample #79


title: c_D_1155 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_F06_609786


title: c_D_1156 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_F07_609882


title: BA47 sample #73


title: c_D_1154 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_F05_609740


title: BA47 sample #72


title: Lymphoma_P01_Dx (CN)

description: FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_C08_40952


title: BA47 sample #71


title: BA47 sample #69


title: c_D_1132 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E11_609730


title: c_D_1147 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E10_609732


title: c_D_1145 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E08_609858


title: BA47 sample #68


title: BA47 sample #70


title: c_D_1140 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E04_609818


title: c_D_1144 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E07_609794


title: c_D_1150 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_F01_609808


title: BA47 sample #65

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole


title: BA47 sample #63


title: BA47 sample #64


title: BA47 sample #67


title: BA47 sample #66


title: c_D_1141 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E05_609756


title: c_D_1138 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E02_609764


title: c_D_1149 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E12_609724


title: BA47 sample #60


title: c_D_1136 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E01_609742


title: c_D_1146 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E09_609788


title: BA47 sample #61


title: BA47 sample #62


title: BA47 sample #56


title: BA47 sample #57


title: BA47 sample #59


title: BA47 sample #58


title: c_D_1139 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E03_609912


title: c_D_1131 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_D08_609908


title: c_D_1133 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_D10_609722


title: BA47 sample #55


title: c_D_1128 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_D05_609782


title: c_D_1125 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_D02_609826


title: c_D_1126 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_D03_609896


title: BA47 sample #54


title: c_D_1121 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_C10_609892


title: BA47 sample #53


title: BA47 sample #50


title: BA47 sample #52


title: c_D_1119 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_C08_609852


title: c_D_1114 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_C04_609816


title: Deletion_XRS2

city: Bangalore

first: Malathi

last: Srinivasan

state: Karnataka

address: Allalasandra, GKVK Post, Bellary Road

department: Lipidomic Center

country: India

institute: Central Food Technological Research Institute

description:
Stationary Phase cells
5(x2)

hyb_protocol: The labeled cRNA samples were hybridized on to a Agilent Platform Custom Saccharomyces cerevisiae 8x15k designed by Genotypic Technology Private Limited (AMADID: 016333) 600ng of cy3 labeled samples were  fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Agilent Microarray Scanner G2505C at 5 micron resolution.

data_processing: Images were quantified using Feature Extraction Software (Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version 11.0 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift (Gene based Analysis was performed)

source_name: Saccharomyces cerevisiae

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse transcription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: synthetic minimal medium (SM) (6.7g/L of Yeast Nitrogen Base (Difco), 1.92 g/L of Yeast Synthetic Drop-out (Sigma) and 2% Dextrose

extract_protocol: RNA was extracted using the TRIzol (Invitrogen) method with glass beads (Sigma, 425-600um, Cat #G8772) for homogenization following the manufacturer's recommendations.

tag: genotype


title: c_D_1120 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_C09_609864


title: BA47 sample #51

tag: tissue


title: c_D_1142 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_E06_609900


title: BA47 sample #48

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole

tag: age


title: BA47 sample #49

tag: pmi


title: c_D_1110 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_B12_609886


title: BA47 sample #45

tag: ph


title: c_D_1113 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_C03_609894


title: AAR of Ysa1 deleted cells-2

city: MIAOLI COUNTY

first: GUNN-GUANG

last: LIOU

state: TAIWAN

address: 35 KEYAN ROAD, JHUNAN TOWN

department: INSTITUTE OF MOLECULAR AND GENOMIC MEDICINE

institute: NATIONAL HEALTH RESEARCH INSTITUTES

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., following their standard operating protocol.(NG_Chip-chip_Guide_v6p2)

scan_protocol: The protocol for scanning one-color NimbleGen arrays with a GenePix 4000B Scanner and associated software Genepix6.0. (NimbleGen_ChIP_Users_Guide_v3p1)

data_processing:
Images were aligned and quantified using NimbleScan software  (V2.4) (Roche NimbleGen) which produced .pair reports of raw data and converted to ratio of Cy5 vs cy3
normalized log2 ratio of Sir3 or of Sir2 immunoprecipitated or AAR affinity-precipitated DNA, respectively, to input DNA

source_name: ysa1 deleted_AAR affinity-precipitated DNA

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol.(NG_Chip-chip_Guide_v6p2)

extract_protocol: Myc-antibody (for Sir3), Sir2-antibody and AAR individually coupled resins were incubated with cell lysate at 4°C overnight. Beads were then washed once with cell lysis buffer (50 mM Hepes-KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 0.5% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, and protease inhibitors), twice with 50 mM Hepes-KOH pH 7.5, 250 mM NaCl, 1 mM EDTA, 0.25% Triton X-100, 0.1% sodium deoxycholate, 0.05% SDS, and protease inhibitors, twice with 10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 0.5% NP40, 0.5% sodium deoxycholate, and 1 mM EDTA, twice with 10 mM Tris-HCl pH 8.0, 0.25 M LiCl and 1 mM EDTA, and once with TE (10 mM Tris-HCl pH 8.0 and 1 mM EDTA pH 8.0) at room temperature. Beads were eluted by incubating with 100 μl of 50 mM Tris-HCl pH 8.0, 10 mM EDTA, and 1% SDS at 65°C for 15 minutes. Elute was transferred to a fresh tube and pooled with a final bead wash of 150 μl TE with 0.67% SDS. For input DNA, 200 μl TE with 1% SDS was added to 50 μl cell lysate extract. To reverse the cross-links, all samples were incubated at 65°C overnight, combined with 250 μl TE, 5 μg glycogen, and 100 mg proteinase K, and incubated at 37°C for 2 h. After adding 55 μl of 4 M LiCl, samples were extracted once with phenol/chloroform and once with chloroform. The remaining associated DNA was precipitated by the addition of 400 mM LiCl, and 2 volumes of ethanol, washed with 75% ethanol, air dried, and resuspended in 50 μl TE with RNase A (20 mg/ml for input DNA and 2 mg/ml for affinity-precipitated DNA) and incubated at 37°C for 1 hour

tag: genotype/variation

value: Ysa1 deleted

source_name: input DNA


title: BA47 sample #44

tag: rin

tag: Sex


title: BA47 sample #47


title: BA47 sample #46


title: c_D_1111 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_C01_609884


title: BA47 sample #43


title: c_D_1107 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_B09_609728


title: BA47 sample #41


title: BA47 sample #42


title: c_D_1105 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_B07_609760


title: AAR of wild-type cells-1

source_name: WT_AAR affinity-precipitated DNA

value: wild-type


title: Sir2 of Ysa1 deleted cells-2

source_name: ysa1 deleted_Sir2 ChIP-DNA

tag: chip antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: BA47 sample #40

tag: race

tag: tod


title: c_D_1026 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_B02_609748

tag: type


title: AAR of Ysa1 deleted cells-1


title: Oocytes_single sample_RiboAmp_2

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

hyb_protocol: For the Arcturus RAHSP samples, each hybridization mixture contained 825 ng of “test RNA” and 825 ng “reference RNA”. For the NuGEN WTOOD samples, each hybridization mixture contained 3 µg of “test cDNA” and 3 µg “reference cDNA”. The hybridization mixture was prepared according to the Two-Color Microarray-Based Gene Expression Analysis protocol. Labeling and array hybridization of the NuGEN WTOOD samples was performed according to the NuGEN recommendations51. The RNA/cDNA was hybridized for 17 hours at 65°C and 10 rpm. Afterwards, the slides were washed and scanned in an ozone-free room with the Agilent scanner GA2505C (Agilent Technologies).

scan_protocol: Slides were scanned at 3 μm resolution using a Agilent scanner GA2505C .

data_processing: Microarray data were extracted with Feature Extraction software version 10.7.1 (Agilent Technologies). To avoid technical variation introduced by these procedures, labeling and hybridization were performed for all samples at the same day.

source_name: Oocytes_single sample_RiboAmp

label_protocol: 5 µg of amplified RNA obtained with the Arcturus RiboAmp HS Plus protocol (Arcturus RAHSP) was dried in a speedvac, dissolved in 5 µl 50 mM carbonate buffer (pH 8.5) and placed at 37°C for 10 min. 10 µl of CyDye (1 µg/µl) (Cy3 for test samples and Cy5 for reference samples) diluted in DMSO was added to each reaction. The samples were subsequently incubated in the dark at room temperature for 60 min. The reactions were quenched by addition of 5 µl of 4 M hydroxylamine for 15 min. at room temperature in the dark. The RNA was purified according to the MicroElute RNA Cleanup protocol (Omega Bio-Tek). The labeled RNA was finally eluted in 15 µl RNase/DNase free water.  2 µg of amplified cDNA obtained with the NuGEN WT-Ovation One-Direct protocol (NuGEN WTOOD) was labeled and purified using the SureTag DNA labeling kit (Agilent Technologies) according to the sample labeling and clean-up protocols for 4x microarrays described in the Agilent Oligonucleotide Array-based CGH for Genomic DNA Analysis manual. In both cases, pooled RNA/cDNA from the amplified samples was used as reference. The yield and CyDye incorporation of labeled RNA/cDNA were measured with the NanoDrop ND-1000 (Thermo Scientific).

growth_protocol: Oocytes in the germinal vesicle stage (GVs) were used for the technical validation. Couples undergoing ICSI treatment at the Center for Reproductive Medicine of the Academic Medical Center of the University of Amsterdam (Amsterdam, the Netherlands) were asked to donate their immature oocytes for research and written informed consent was obtained in all cases. Since spare immature human oocytes were used, no ethical approval was deemed necessary by the Central Ethics Committee on Research involving human subjects. All patients did sign informed consent to donate their spare immature oocytes for research.

extract_protocol: RNA was isolated from 25 human oocytes. From twelve oocytes, RNA was individually isolated. To eliminate biological variation, thirteen human oocytes were pooled together right after the addition of extraction buffer of the isolation protocol. The pooled material was homogenized and split into twelve identical samples for further RNA isolation. Six individual and six pooled samples were subsequently amplified using the NuGEN WT-Ovation One-Direct (called NuGEN Single; NS 1-6 and NuGEN Pooled-and-Split; NPS 1-6) and the rest were amplified using the Arcturus RiboAmp HS Plus (called RiboAmp Single; RS 1-6 and RiboAmp Pooled-and-Split; RPS 1-6). All samples amplified with one protocol were processed in the same round.

treatment_protocol: Individual oocytes were transferred shortly to a drop containing 0.05% HCl/Tween-20 to remove the zona pellucida, subsequently they were washed using oocyte culture medium and transferred to PCR tubes. The oocytes were snap-frozen in liquid nitrogen and stored at -80°C till analysis.

value: Oocytes

source_name: Common Reference


title: Sir2 of wild-type cells-2

source_name: WT_Sir2 ChIP-DNA


title: c_D_1104 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_B06_609770


title: BA47 sample #39

data_processing: All samples were analyzed using the Affymetrix Human Gene 1.1 ST microarray platform. Gene expression values were corrected, quantile-normalized, and log2-transformed via Affymetrix Expression Console software (build 1.2.1.20) using RMA algorithm. A total of 33,297 probe sets were available on each array; only those probe sets with annotated gene symbols were selected (20,237 gene symbols). If a gene was represented by multiple probe sets, the one with the largest intensity interquartile region was selected to represent that gene. Microarray data for each brain region were analyzed separately.


title: Oocytes_single sample_RiboAmp_4


title: Oocytes_single sample_Nugen_4

source_name: Oocytes_single sample_Nugen


title: Oocytes_pooled sample_RiboAmp_3

source_name: Oocytes_pooled sample_RiboAmp


title: Sir3 of Ysa1 deleted cells-1

source_name: ysa1 deleted_Sir3 ChIP-DNA

value: Myc-antibody


title: Oocytes_pooled sample_RiboAmp_1


title: c_D_1045 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_B01_609828


title: c_TL_11 (CN)

description:
tumor
LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_H08_609616

data_processing:
Copy number values were inferred from raw CEL files with a GenePattern pipeline which runs the following modules: SNPFileCreator, CopyNumberInference, RemoveCopyNumberOutliers, DivideByNormals and Quality Control.
input_to_gistic.seg.txt:  Segmented copy number file containing all of the 41 samples and addtionally 180 primary DLBCLs previously deposited at GEO under the accesison number GSE34171 from Monti and Chapuy et al. Cancer Cell 2012.

label: Biotin

source_name: TL

label_protocol: PCR prodicts were labled with a single biotin according to the Affymetrix protocol.

growth_protocol: 10-20 x 20 um sections from snap-frozen tumor specimens from newly diasnosted previously untreated samples were directly transferred to G2-extraction buffer (provided in the Qiagen DNA extraction kit).

extract_protocol: DNA was extracted using the genomic buffer kit with 20/G genomic-tips (Qiagen) following the manufacturer's recommendations.

tag: disease state

value: primary TL


title: c_D_1044 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_A06_609810


title: c_TL_10 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_D05_566470


title: Sir2 of wild-type cells-1


title: Sir3 of wild-type cells-1

source_name: WT_Sir3 ChIP-DNA


title: c_TL_08 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_G07_566362


title: c_TL_07 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_A02_566494


title: c_D_1123 (CN)

description: ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_C12_609904


title: Sir2 of Ysa1 deleted cells-1


title: BA47 sample #38

label_protocol: According to standard affymetrix protocol: • 10ul  Purified cDNA10ul • DEPC H2O • 4ul  10x IVT Labeling Buffer • 12ul  IVT Labeling NTP mix • 4ul  IVT Labeling Enzyme mix - Incubate at 37C 16 hour in an incubating oven or thermal cycler with heated lid to avoid condensation. - Purify labeled cRNA generated from either IVT labeling reaction using RNeasy RNA Purification Mini kit (Qiagen) using the RNA Cleanup Protocol according to manufacturers instructions. - Quantitate Biotin labeled cRNA using 260nm/280nm spectrophotometric assay.

extract_protocol: Total RNA was extracted from frozen samples stored in TRIzol (Invitrogen, Carlsbad, Calif.) and processed for microarray analysis according to the microarray manufacturer’s protocol (Affymetrix, Santa Clara, Calif.)

value: brain


title: Oocytes_pooled sample_Nugen_3

source_name: Oocytes_pooled sample_Nugen

tag: cell type


title: c_TL_05 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_A01_566420


title: Sir3 of wild-type cells-2


title: Sir3 of Ysa1 deleted cells-2


title: BA47 sample #37