title: SAMPLE 11 PBMC

description:
SAMPLE 11 PBMC
Normal Control biological replicate 11


title: prostate_2444

status: Public on Mar 05 2010

type: RNA

city: New York

first: Andrea

last: Sboner

state: NY

address: 1305 York Ave, Box 104

department: Pathology; Computational Biomedicine

country: USA

institute: Weill Cornell Medical College

description: Training set

hyb_protocol: Refer to the Illumina DASL Assay System Manual. Hybridization was performed for 4 DASL assay oligo pool (DAP)s, DAP1~4, including 1536 probes each on 4 separate microarrays

data_processing: For each probe, Red and Green intensities are computed as average of single bead values. The final signal is the sum of the Red and Green intensities. Data were median-centered by subtraction of median (log2 scale) within sample and within DAP, and median set to a target value computed as the overall within DAP median. Data were then normalized using the qspline algorithm (on the log2 intensity scale) with reference distribution computed as the marginal (always within DAP) mean of every gene

label: Cy3, Cy5

molecule: total RNA

organism: Homo sapiens

source_name: primary prostate cancer

extract_protocol: Using 3 biopsy cores (0.6µm each) taken from formalin-fixed paraffin-embeded tissue blocks, total RNA was extracted using Trizol LS reagent (Invitrogen).

tag: gleason

tag: batch

tag: extreme

value: Lethal

tag: age

value: Dead

tag: fusion


title: prostate_21808

description: Training set

scan_protocol: Refer to the Illumina DASL Assay System Manual.

value: Indolent

value: Alive


title: prostate_21881

description: Training set

label_protocol: Refer to the Illumina DASL Assay System Manual.


title: prostate_21758

description: Training set


title: prostate_21667

description: Training set


title: SAMPLE 12 PBMC

city: Baltimore

first: Alan

middle: E.

last: Berger

state: MD

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

description:
SAMPLE 12 PBMC
Normal Control biological replicate 12

hyb_protocol: cRNA was hybridized to Illumina HumanRef-8 v2 Expression BeadChips, and signal was detected with streptavidin-Cy3, using the standard Illumina hybridization protocol.

scan_protocol: All signal intensity quantification was performed using an Illumina BeadStation 500GX Genetic Analysis Systems scanner, using the standard Illumina scanning protocol.

data_processing: A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina BeadStudio software with standard settings and no background correction.  The expression values for all the probes for each sample were scaled to have median 256 (28) and then log (base 2) transformed.

label: biotin

source_name: PBMC_Normal Control

label_protocol: Biotin-labeled, complementary RNA (cRNA) was prepared from total RNA according to the chip manufacturer’s protocol (Illumina, San Diego, CA).

extract_protocol: Venous blood was collected by simple venipuncture under aseptic conditions.  All samples were processed within one hour of collection to minimize gene expression variations associated with longer sample incubation times.  PBMCs were separated by Ficoll density gradient, and PMNs isolated following 1-3 rounds of hypotonic RBC lysis.  Cells were assessed for viability by trypan blue dye exclusion, were immediately lysed in Trizol reagent (Invitrogen, Carlsbad, California) and stored at -80°C.  Total RNA was extracted from either the PBMC or PMN fractions using the Trizol reagent method (Invitrogen, Carlsbad, California).  Additional purification was performed on RNAeasy columns (Qiagen, Valencia, CA), and the quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: cell type

value: PBMC

tag: wg signature status

value: normal control


title: SAMPLE 7 PBMC

description:
SAMPLE 7 PBMC
Normal Control biological replicate 7


title: SAMPLE 9 PBMC

description:
SAMPLE 9 PBMC
Normal Control biological replicate 9


title: SAMPLE 8 PBMC

description:
SAMPLE 8 PBMC
Normal Control biological replicate 8


title: SAMPLE 25 PBMC

description:
SAMPLE 25 PBMC
Wegener's granulomatosis biological replicate 2

source_name: PBMC_Wegener's granulomatosis

value: WG Sig -


title: SAMPLE 6 PBMC

description:
SAMPLE 6 PBMC
Normal Control biological replicate 6


title: SAMPLE 3 PBMC

description:
SAMPLE 3 PBMC
Normal Control biological replicate 3


title: PARN-1 OvEx (6) 3-6-09

city: Newark

first: Christopher

last: Utter

state: NJ

address: 225 Warren St.

department: Microbiology and Molecular Genetics

institute: University of Medicine and Dentistry of New Jersey-New Jersey Medical School

description: None.

hyb_protocol: Labeled cDNAs were purified using the QiaQuick PCR purification kit, combined, and dried to ~1 µl by speedvac. Samples were resuspended in hybridization buffer containing 40% formamide, 5x SSC, 0.1% SDS, and 0.6 µg/µl salmon sperm DNA and heated (2x, 5 min, 95°C). T. brucei DNA microarrays version 1 or 3, obtained from the Pathogen Functional Genomic Research Center (PFGRC) were prehybridized at (2 hr, 42°C) in 5x SSC, 0.1% SDS, and 1% BSA. Slides were washed in water then dried using centrifugation. Samples were applied to the microarray slides, covered with a 24 x 60 cm glass cover slip (Fisher) and placed in a HybChamber (GeneMachines). The chamber was placed in a 42°C water bath, covered in aluminum foil, and incubated for 16 h. Slides were washed (2x SSC and 0.1% SDS; 0.1x SSC and 0.1% SDS; 0.1x SSC; water) and dried by centrifugation.

scan_protocol: Slides were scanned using GenePix 4000A microarray scanner (Axon Instruments) and data was analyzed using GenePixPro 6.0 (Axon Instruments) and MultiExperiment Viewer v4.1 software (PFGRC).

data_processing: Data was normalized with the WinPrintTip application.

organism: Trypanosoma brucei

source_name: PARN-1 OvEx cells

label_protocol: Four µg of poly A+ RNA were reverse-transcribed for 16 h at 42°C in a reaction containing 12 µg of random hexamers (Invitrogen), 50 mM Tris-HCl pH 8.3, 75 mM KCl, 3 mM MgCl2, 10 mM DTT, 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.17 mM dTTP, 1 mM 5-(3-aminoallyl)-dUTP, 0.33 mM KPO4, 80 U RNaseOUT (Invitrogen), and 800 U SuperScript III reverse transcriptase (Invitrogen). RNA in the cDNA/RNA mixture was hydrolyzed in 100 mM EDTA and 200 mM NaOH. The reaction was incubated (15 min, 65°C), then the pH was adjusted to ~7.0 with 333 mM Tris (pH 7.0). cDNA was purified using the QiaQuick PCR purification kit (Qiagen) and dried to ~1 µL by speedvac. cDNA was resuspended in 100 mM sodium carbonate buffer (pH 9.3) and labeled with Cy5 mono-reactive dye (GE Healthcare). Reactions was incubated for 2 hr at room temperature and stopped with 80 mM NaOAc (pH 5.2).

extract_protocol: Total RNA was extracted from procyclic cells grown to 8 x 106 cells/mL using Qiagen’s RNeasy mini kit. Poly A+ RNA was isolated from the total RNA using Qiagen’s Oligotex mRNA midi kit.

tag: cell line

value: PARN-1 overexpressed procyclic cells

source_name: Control cells

label_protocol: Four µg of poly A+ RNA were reverse-transcribed for 16 h at 42°C in a reaction containing 12 µg of random hexamers (Invitrogen), 50 mM Tris-HCl pH 8.3, 75 mM KCl, 3 mM MgCl2, 10 mM DTT, 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.17 mM dTTP, 1 mM 5-(3-aminoallyl)-dUTP, 0.33 mM KPO4, 80 U RNaseOUT (Invitrogen), and 800 U SuperScript III reverse transcriptase (Invitrogen). RNA in the cDNA/RNA mixture was hydrolyzed in 100 mM EDTA and 200 mM NaOH. The reaction was incubated (15 min, 65°C), then the pH was adjusted to ~7.0 with 333 mM Tris (pH 7.0). cDNA was purified using the QiaQuick PCR purification kit (Qiagen) and dried to ~1 µL by speedvac. cDNA was resuspended in 100 mM sodium carbonate buffer (pH 9.3) and labeled with Cy3 mono-reactive dye (GE Healthcare). Reactions was incubated for 2 hr at room temperature and stopped with 80 mM NaOAc (pH 5.2).

value: TAP tag overexpressed procyclic cells


title: SAMPLE 5 PBMC

description:
SAMPLE 5 PBMC
Normal Control biological replicate 5


title: SAMPLE 4 PBMC

description:
SAMPLE 4 PBMC
Normal Control biological replicate 4


title: SAMPLE 1 PBMC

description:
SAMPLE 1 PBMC
Normal Control biological replicate 1


title: PARN-1 OvEx (2) 1-30-09

description: None.

source_name: Control Cells


title: PARN-1 OvEx (3) 2-12-09

description: None.


title: SAMPLE 2 PBMC

description:
SAMPLE 2 PBMC
Normal Control biological replicate 2


title: PARN-1 OvEx (1) 1-30-09

description: None.


title: Pooled Control vs. R5020 + MAA + U0126 (A)

status: Public on Mar 04 2010

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression analysis was conducted using Agilent Human Oligo Microarrays (Agilent Technologies, Palo Alto, CA).  Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer’s protocol.  For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.  Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner.  Two arrays were utilized for each comparison allowing for dye reversals.  Data was obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).

scan_protocol: Slides were washed as indicated in the Agilent 60-mer oligo microarray processing protocol and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters.

source_name: Pooled Control

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Total RNA from frozen cell lines were isolated with standard protocol.

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy5 labeled cRNA was produced according to manufacturer’s protocol.


title: Pooled Control vs. U0126 (A)

hyb_protocol: For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.

data_processing: Data was obtained using the Agilent Feature Extraction software (v7.5), using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).


title: Pooled Control vs. R5020 + U0126 (A)


title: R5020 + U0126 (A) vs. Pooled Control


title: U0126 (A) vs. Pooled Control


title: PARN-1 OvEx (5) 3-6-09

description: None.

source_name: PARN-1 OvEx Cells


title: Pooled Control vs. R5020 + MAA (A)


title: R5020 + U0126 (B) vs. Pooled Control


title: Pooled Control vs. R5020 + MAA (B)


title: PARN-1 OvEx (4) 2-12-09

description: None.


title: R5020 + MAA + U0126 (A) vs. Pooled Control


title: Pooled Control vs. MAA (B)

source_name: MAA (B)


title: MAA (B) vs. Pooled Control


title: MAA (A) vs. Pooled Control

source_name: MAA (A)


title: Pooled Control vs. R5020 (A)


title: R5020 (A) vs. Pooled Control


title: U0126 (B) vs. Pooled Control


title: Pooled Control vs. U0126 (B)


title: Pooled Control vs. R5020 (B)


title: Pooled Control vs. MAA (A)


title: SN/VTA_MM_Rep2

first: Jean

middle: Lud

last: Cadet

address: 251 Bayview Blvd.

department: Molecular Neuropsychiatry Research Branch

institute: DHHS/NIH/NIDA  Intramural Research Program

description: The four groups of animals were: saline/saline (SS), saline/METH (SM), METH/saline (MS), and METH/METH (MM).

hyb_protocol: 750 ng of each cRNA sample were hybridized to Illumina arrays at 55 oC overnight according to the Illumina Whole-Genome Gene Expression Protocol for BeadStation (Illumina Inc., San Diego, CA, cat. # 11201828). Hybridized biotinylated cRNA was detected with Cyanine3-streptavidin (Amersham Biosciences, Piscataway, NJ, cat. #146065).

scan_protocol: Signals quantified using Illumina's BeadStation 500GX Genetic Analysis Systems scanner.

data_processing: The Illumina Inc. BeadStudio background corrected data is processed by the standard one-color GeneSpring normalized protocol. Briefly, in the data transformation process, values less than 0.01 become 0.01, per-chip procedure normalized the data to the median of the array, and per-gene procedure normalized the gene probes to their median across all arrays.

organism: Rattus norvegicus

label_protocol: 600 ng aliquot of total RNA from each striatal sample was amplified using Ambion’s Illumina RNA Amplification kit (cat. no. IL1791; Ambion, Austin, TX). Single-stranded RNA (cRNA) was generated and labeled by incorporating biotin-16-UTP (Roche Diagnostics GmbH, Mannheim, Germany, cat. no. 11388908910)

growth_protocol: Animals were housed in a humidity- and temperature-controlled room and were given free access to food and water.

extract_protocol: Total RNA was isolated using Qiagen RNeasy Midi kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) and showed no degradation.

treatment_protocol:
Following habituation, rats were injected intraperitoneally with either (+-)-METH-hydrochloride (NIDA, Baltimore, MD) or an equivalent volume of 0.9% saline for a period of three weeks as described in Table S1 in supplemental data. The saline- or METH-pretreated animals received either saline or METH (5 mg/kg x 8 at 1 h intervals) challenges 72 hours after the preconditioning period (See Below). Similar doses of METH are known to cause significant decreases in the levels of monoamines in the rat striatum (Graham et al., J. Neurochem. 2008; 105:1873-1885, Cadet et al, Neurotox. Res. 2009; 15:252-259) which received dopaminergic terminals from midbrain dopaminergic cell bodies located in the substantia nigra (SN) and ventral tegmental area (VTA) (Lindvall and Björklund, Biochem Psychopharmacol 1978; 19:1-23, Domesick, Ann N Y Acad Sci. 1988; 537:10-26). Thus, the four groups of animals were: saline/saline (SS), saline/METH (SM), METH/saline (MS), and METH/METH (MM). The animals were euthanized 24 h later by decapitation. Their brains were quickly removed, striatal and SN/VTA tissues were dissected on ice, snap frozen on dry ice, and stored at -80°C until used.
Table S1. Schedule of METH pretreatment and challenges
	Monday	Tuesday	Wednesday	Thursday	Friday
Week 1
9:00	0.5 mg/kg	1 mg/kg	1 mg/kg	1.5 mg/kg
10:00
11:00			1 mg/kg	1.5 mg/kg
12:00
13:00			1 mg/kg	1.5 mg/kg
14:00
15:00	0.5 mg/kg	1 mg/kg	1 mg/kg	1.5 mg/kg
16:00

Week 2
9:00	1 mg/kg	1.5 mg/kg	2 mg/kg	2.5 mg/kg
10:00			2 mg/kg	2.5 mg/kg
11:00	1 mg/kg	1.5 mg/kg	2 mg/kg	2.5 mg/kg
12:00			2 mg/kg	2.5 mg/kg
13:00	1 mg/kg	1.5 mg/kg	2 mg/kg	2.5 mg/kg
14:00			2 mg/kg	2.5 mg/kg
15:00	1 mg/kg	1.5 mg/kg
16:00

Week 3
9:00	2 mg/kg		5 mg/kg
10:00	2 mg/kg		5 mg/kg
11:00	2 mg/kg		5 mg/kg
12:00	2 mg/kg		5 mg/kg
13:00	2 mg/kg		5 mg/kg
14:00	2 mg/kg		5 mg/kg
15:00			5 mg/kg
16:00			5 mg/kg

Initially the rats were divided into two groups, with one group receiving saline and the other group getting METH pretreatment according to the schedule described below during first and second weeks as well as Monday of the third week. The saline pretreatment was followed by with either saline (SAL/SAL) or METH challenges (SAL/METH), the METH pretreatment was followed by METH challenges (METH/METH) or METH followed by Saline (METH/SAL) on Wednesday of the third week and killed 24 h later.

tag: animal

value: Rat

tag: strain

value: Sprague-Dawley

tag: gender

value: Male

value: 8 weeks

tag: weight

tag: tissue

tag: treatment

value: injected with increasing doses of methamphetamine, challenged 72 hours later with a toxic dose of methamphetamine


title: SN/VTA_MM_Rep1

value: substantia nigra (SN) and ventral tegmental area (VTA)


title: SN/VTA_MS_Rep4

value: injected with increasing doses of methamphetamine, challenged 72 hours later with saline


title: SN/VTA_MS_Rep1

treatment_protocol:
Following habituation, rats were injected intraperitoneally with either (+-)-METH-hydrochloride (NIDA, Baltimore, MD) or an equivalent volume of 0.9% saline for a period of three weeks as described in Table S1 in supplemental data. The saline- or METH-pretreated animals received either saline or METH (5 mg/kg x 8 at 1 h intervals) challenges 72 hours after the preconditioning period (See Below). Similar doses of METH are known to cause significant decreases in the levels of monoamines in the rat striatum (Graham et al., J. Neurochem. 2008; 105:1873-1885, Cadet et al, Neurotox. Res. 2009; 15:252-259) which received dopaminergic terminals from midbrain dopaminergic cell bodies located in the substantia nigra (SN) and ventral tegmental area (VTA) (Lindvall and Björklund, Biochem Psychopharmacol 1978; 19:1-23, Domesick, Ann N Y Acad Sci. 1988; 537:10-26). Thus, the four groups of animals were: saline/saline (SS), saline/METH (SM), METH/saline (MS), and METH/METH (MM). The animals were euthanized 24 h later by decapitation. Their brains were quickly removed, striatal and SN/VTA tissues were dissected on ice, snap frozen on dry ice, and stored at -80°C until used.
Table S1. Schedule of METH pretreatment and challenges
	Monday	Tuesday	Wednesday	Thursday	Friday
Week 1
9:00	0.5 mg/kg	1 mg/kg	1 mg/kg	1.5 mg/kg
10:00
11:00			1 mg/kg	1.5 mg/kg
12:00
13:00			1 mg/kg	1.5 mg/kg
14:00
15:00	0.5 mg/kg	1 mg/kg	1 mg/kg	1.5 mg/kg
16:00

Week 2
9:00	1 mg/kg	1.5 mg/kg	2 mg/kg	2.5 mg/kg
10:00			2 mg/kg	2.5 mg/kg
11:00	1 mg/kg	1.5 mg/kg	2 mg/kg	2.5 mg/kg
12:00			2 mg/kg	2.5 mg/kg
13:00	1 mg/kg	1.5 mg/kg	2 mg/kg	2.5 mg/kg
14:00			2 mg/kg	2.5 mg/kg
15:00	1 mg/kg	1.5 mg/kg
16:00

Week 3
9:00	2 mg/kg		5 mg/kg
10:00	2 mg/kg		5 mg/kg
11:00	2 mg/kg		5 mg/kg
12:00	2 mg/kg		5 mg/kg
13:00	2 mg/kg		5 mg/kg
14:00	2 mg/kg		5 mg/kg
15:00			5 mg/kg
16:00			5 mg/kg
Initially the rats were divided into two groups, with one group receiving saline and the other group getting METH pretreatment according to the schedule described below during first and second weeks as well as Monday of the third week. The saline pretreatment was followed by with either saline (SAL/SAL) or METH challenges (SAL/METH), the METH pretreatment was followed by METH challenges (METH/METH) or METH followed by Saline (METH/SAL) on Wednesday of the third week and killed 24 h later.


title: SN/VTA_MS_Rep3


title: R5020 (B) vs. Pooled Control


title: SN/VTA_SM_Rep3

value: injected with saline, challenged 72 hours later with a toxic dose of methamphetamine


title: R5020 + MAA + U0126 (B) vs. Pooled Control


title: SN/VTA_MS_Rep2


title: Pooled Control vs. R5020 + MAA + U0126 (B)


title: SN/VTA_MM_Rep3


title: R5020 + MAA (B) vs. Pooled Control


title: Pooled Control vs. R5020 + U0126 (B)


title: R5020 + MAA (A) vs. Pooled Control


title: SN/VTA_SM_Rep4


title: SN/VTA_SM_Rep1


title: SN/VTA_SS_Rep3

value: injected with saline, challenged 72 hours later with saline


title: Dm_sn_kv_40

city: Jyvaskyla

first: Maaria

last: Kankare

address: Survontie 9

country: Finland

institute: University of Jyvaskyla

description: In addition to the 101 candidate genes we placed on our chip, we used seven genes, Ef1α48D, eIF-4a Gapdh1, Gapdh2, RpL11, RpL19 and RpL27A, which have been used as control genes in Drosophila whole genome microarrays (GeneChip Drosophila genome 2.0 Array, Affymetrix, 2006). These genes were added on the chip to select the best control genes for microarray validation with qRT-PCR analysis.

hyb_protocol: 600 ng of each cRNA sample was hybridized to Agilent’s 8x15K D. montana custom arrays with Gasket slide at 65˚C overnight (17 h) using Agilent’s Gene Expression Hybridization Kit and washed with Agilent’s Gene Expression Wash Pack and Stabilization and Drying solution

scan_protocol: Arrays were scanned with Agilent Technologies Scanner (model G2505B) and numerical results were extracted with Feature Extraction version 9.5.3.1 using 018413_D_F_20071204 grid, GE1-v5_95_Feb07 protocol and GE1_QCM_Feb07 QC metric set.

data_processing: The microarray data were normalized within the groups and across all samples using the VSN method. The statistical analyses were carried out using Bioconductor related Limma package [10] and the differentially expressed genes in each comparison were selected requiring a strict selection criteria of fold-change > 2.0 and false discovery rate (fdr) < 0.05.

organism: Drosophila montana

source_name: Whole body

label_protocol: 350 ng total RNA of each sample was amplified and Cy3-labeled with Agilent’s Low RNA Input Linear Amplification Kit PLUS (One Color) and processed together with Agilent’s One-Colour RNA Spike-in Kit.

growth_protocol: Female flies for the present study were collected under a light CO2 anaesthesia within one day after their emergence. Samples of young flies (three replicates, each including 13 flies) were transferred straight from the culturing conditions into liquid nitrogen for RNA extractions. The rest of the females were placed in vials (13-15 flies per vial) containing 7 ml of yeast-sucrose-agar medium with 1 mg of yeast sprinkled on top of the medium. The samples of reproducing females were obtained by maintaining the vials in a climate chamber in continuous light (24:0) for two weeks. Samples of diapausing females were maintained by keeping the vials in a climate chamber in a L:D cycle of 16:8 for the same time period.

extract_protocol: Total RNA was extracted from the whole body of 13 individuals per sample, three replicates per sample. Qiagen RNA extraction kit with RNase-Free DNase treatment was used according to the manufacturer's protocols (Qiagen). The RNA was purified using Qiagen RNAeasy purification kit and the concentration and the purity of each sample was measured with NanoDrop ND-1000 spectrofotometer (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: Flies were maintained in vials in the laboratory under diapause-preventing conditions (continuous light, 19°C) since summer 2003.

tag: isofemale line

value: O3F66 from Oulanka, Finland


title: Dm_nn_17


title: Dm_sn_d_43


title: Dm_nn_16


title: Dm_sn_d_42


title: Dm_sn_kv_22

hyb_protocol: 600 ng of each cRNA sample was hybridized to Agilent’s 8x15K D. montana custom arrays with Gasket slide at 65˚C overnight (17 h) using Agilent’s Gene Expression Hybridization Kit and washed with Agilent’s Gene Expression Wash Pack and Stabilization and Drying solution.


title: SN/VTA_SS_Rep2


title: Dm_nn_12


title: Dm_sn_kv_23


title: SN/VTA_SS_Rep4


title: Ruptured, Rep4

city: Krakow

first: Marcin

last: Piechota

address: Smetna 12

department: Molecular Neuropharmacology

country: Poland

institute: Institute of Pharmacology PAS

description: Ruptured, Replicate 4, Gender unknown

hyb_protocol: Labeled cDNA was hybridized to an Affymetrix GeneChip Human Gene ST 1.0 array (Affymetrix) at 45oC for 17 hours as recommended by the manufacturer. These arrays contain 764,885 probes representing 28,869 well-annotated genes. Arrays were washed and stained in Fluidic Station 450 (Affymetrix) according to manufacturer’s standard protocol.

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA).

data_processing: Data was normalized by dChip 2008 (quantile normalization, PM only)

source_name: Full-thickness vessel wall sample

label_protocol: A starting amount of 1μg of high-quality total RNA was used for rRNA reduction. mRNA (rRNA reduced) was converted to double-stranded cDNA and further to cRNA using GeneChip® WT Sense Target Labeling and Control Reagents (Affymetrix, Santa Clara, CA). The procedure consists of double-stranded cDNA synthesis, cRNA amplification, second cycle of cDNA synthesis and fragmentation of the single-stranded DNA. Each sample was synthesized from an independent biological sample. The fragmented single-stranded DNA was subsequently labeled using recombinant terminal deoxynucleotidyl transferase (TdT).

extract_protocol: Specimens were homogenized with a rotor-stator homogenizer in buffer RLT. Next, total RNA was isolated using RNeasy Fibrous Tissue Minikit (Qiagen) according to the manufacturer’s protocol and treated with DNase I (Qiagen). RNA concentration was determined by product absorbance at 260 nm measured by NanoDrop ND-1000 (NanoDrop Technologies, Montchanin, DE). The quality of RNA was additionally assessed using RNA 6000 Nano LabChip Kit and Agilent Bioanalyzer 2100 (Agilent, Palo Alto, CA).

value: Full-thickness vessel wall sample

tag: type

value: Ruptured


title: prostate_2469

description: Training set

value: Lethal

value: Dead


title: Control, Rep5

description: Control, Replicate 5, Female

value: Control


title: Ruptured, Rep7

description: Ruptured, Replicate 7, Male


title: Ruptured, Rep8

description: Ruptured, Replicate 8, Male


title: Unruptured, Rep6

description: Unruptured, Replicate 6, Gender unknown

value: Unruptured


title: Ruptured, Rep6

description: Ruptured, Replicate 6, Gender unknown


title: Ruptured, Rep5

description: Ruptured, Replicate 5, Female


title: Ruptured, Rep3

description: Ruptured, Replicate 3, Gender unknown


title: Unruptured, Rep3

description: Unruptured, Replicate 3, Female


title: Unruptured, Rep5

description: Unruptured, Replicate 5, Gender unknown


title: Unruptured, Rep2

description: Unruptured, Replicate 2, Gender unknown


title: Control, Rep3

description: Control, Replicate 3, Gender unknown


title: Control, Rep4

description: Control, Replicate 4, Gender unknown


title: Control, Rep1

description: Control, Replicate 1, Gender unknown


title: Unruptured, Rep4

description: Unruptured, Replicate 4, Female


title: female embryo H3K27me3

type: genomic

city: Seattle

first: Fan

last: Yang

state: WA

address: 1959 NE pacific street

institute: University of Washington

description: ChIP-chip female embryo H3K27me3

hyb_protocol: hybridization was done according to nimblegen stardand protocol (http://www.nimblegen.com/products/lit/index.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. The log2-ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. Nimblescan software (Roche) was used to search for peaks of enrichment using a 500bp-sliding window. A false discovery rate (FDR) score was assigned to each enriched region using a stringent cutoff of <0.05% FDR.  Log2 ratio data is contained in Sample tables, peak data is available in the '_peak.txt' supplementary file.

molecule: genomic DNA

organism: Mus musculus

source_name: H3K27me3 ChIP DNA female embryo

label_protocol: 1 ug of ChIP DNA and corresponding input DNA were amplified using a whole genome amplification kit (Sigma), and labeled with Cy5 and Cy3, respectively, according to Roche’s protocol (http://www.nimblegen.com/products/lit/index.html)

extract_protocol: ChIP was performed according to a fast chromatin immunoprecipitation method (Nelson et al. 2006). Briefly, after cross-linking with 1% formaldehyde chromatin was sonicated to ~500bp fragments and immunoprecipitated with a histone H3K27me3 antibody (Upstate) followed by pull-down using protein A sepharose beads (Amersham). Controls included ChIP carried out without antibody (no antibody fraction) and the input fraction. After incubation with the antibody overnight, protein A sepharose beads were added to pull down the chromatin. DNA was purified from the ChIP fractions using a PCR purification kit (Qiagen).

value: whole embryo

tag: developmental stage

tag: chip antibody

source_name: input DNA female embryo

value: none, input DNA


title: female liver H3K27me3

description: ChIP-chip female liver H3K27me3

source_name: H3K27me3 ChIP DNA female liver

value: liver tissue

value: adult

source_name: input DNA female liver


title: Ruptured, Rep1

description: Ruptured, Replicate 1, Gender unknown


title: male liver H3K27me3

description: ChIP-chip male liver H3K27me3

source_name: H3K27me3 ChIP DNA male liver

source_name: input DNA male liver


title: Ruptured, Rep2

description: Ruptured, Replicate 2, Gender unknown


title: gln3- rep2

city: Boston

first: Amnon

last: Koren

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
raw data column: Strains18 (block4)
S vs G1 Replication timing

hyb_protocol: Agilent

scan_protocol: Agilent, 5micron, 100%PMT

data_processing: Images were analyzed with SpotReader (Niles Scientific). Weak (<2std above control probe mean) and saturated probe reads were removed from further analysis. Data was LOWESS-normalized.

organism: Saccharomyces cerevisiae

source_name: G1-phase cells

label_protocol: DNA was digested with DpnII and amplified by four ronds of random-octamer-primed Exo-Klenow DNA synthesis (Invitrogen BioPrime ArrayCGH amplification kit) with amino-allyl modified nucleotides and subsequently labeled with Cy dyes

growth_protocol: Cells were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) at 30º to log phase and fixated.

extract_protocol: DNA was extracted using the MasterPure Yeast DNA purification kit (Epicentre)

treatment_protocol: G1- and S- phase cells were sorted by FACS

source_name: S-phase cells


title: arg2- rep4

description:
raw data column: Strains20 (block3)
S vs G1 Replication timing


title: arg2- rep1

description:
raw data column: Strains17 (block2)
S vs G1 Replication timing


title: gln3- rep3

description:
raw data column: Strains19 (block1)
S vs G1 Replication timing


title: met7- rep3

description:
raw data column: Strains20 (block1)
S vs G1 Replication timing


title: met7- rep2

description:
raw data column: Strains17 (block1)
S vs G1 Replication timing


title: gln3- rep1

description:
raw data column: Strains16 (block4)
S vs G1 Replication timing


title: arg2- rep3

description:
raw data column: Strains19 (block2)
S vs G1 Replication timing


title: Control, Rep2

description: Control, Replicate 2, Gender unknown


title: Unruptured, Rep1

description: Unruptured, Replicate 1, Gender unknown


title: met7- rep4

description:
raw data column: Strains20 (block2)
S vs G1 Replication timing


title: gln3- rep4

description:
raw data column: Strains20 (block4)
S vs G1 Replication timing


title: met7- rep1

description:
raw data column: Strains16 (block3)
S vs G1 Replication timing


title: yhr009c- rep4

description:
raw data column: Strains19 (block3)
S vs G1 Replication timing


title: yhr009c- rep1

description:
raw data column: Strains15 (block4)
S vs G1 Replication timing


title: yhr009c- rep2

description:
raw data column: Strains17 (block3)
S vs G1 Replication timing


title: yhr009c- rep3

description:
raw data column: Strains18 (block3)
S vs G1 Replication timing


title: rad27- rep4

description:
raw data column: Strains13 (block1)
S vs G1 Replication timing


title: rnr1- rep4

description:
raw data column: Strains16 (block2)
S vs G1 Replication timing


title: ura7- rep4

description:
raw data column: Strains19 (block4)
S vs G1 Replication timing


title: ura7- rep1

description:
raw data column: Strains15 (block1)
S vs G1 Replication timing


title: ura7- rep3

description:
raw data column: Strains17 (block4)
S vs G1 Replication timing


title: rnr1- rep1

description:
raw data column: Strains9 (block2)
S vs G1 Replication timing


title: rad27- rep1

description:
raw data column: Strains8 (block3)
S vs G1 Replication timing


title: ura7- rep2

description:
raw data column: Strains16 (block1)
S vs G1 Replication timing


title: rad27- rep3

description:
raw data column: Strains11 (block4)
S vs G1 Replication timing


title: dpb4- rep4

description:
raw data column: Strains11 (block2)
S vs G1 Replication timing


title: rnr1- rep3

description:
raw data column: Strains15 (block3)
S vs G1 Replication timing


title: rad27- rep2

description:
raw data column: Strains8 (block4)
S vs G1 Replication timing


title: rnr1- rep2

description:
raw data column: Strains13 (block2)
S vs G1 Replication timing


title: dpb4- rep3

description:
raw data column: Strains11 (block1)
S vs G1 Replication timing


title: dpb4- rep2

description:
raw data column: Strains8 (block2)
S vs G1 Replication timing


title: dpb4- rep1

description:
raw data column: Strains5 (block3)
S vs G1 Replication timing


title: dpb3- rep3

description:
raw data column: Strains9 (block4)
S vs G1 Replication timing


title: dpb3- rep2

description:
raw data column: Strains9 (block3)
S vs G1 Replication timing


title: dpb3- rep4

description:
raw data column: Strains14 (block2)
S vs G1 Replication timing


title: dpb3- rep1

description:
raw data column: Strains4 (block4)
S vs G1 Replication timing


title: rrm3- rep2

description:
raw data column: Strains10 (block2)
S vs G1 Replication timing


title: rrm3- rep1

description:
raw data column: Strains10 (block1)
S vs G1 Replication timing


title: mrc1- rep1

description:
raw data column: Strains6 (block1)
S vs G1 Replication timing


title: mrc1- rep3

description:
raw data column: Strains10 (block3)
S vs G1 Replication timing


title: clb5- rep3

description:
raw data column: Strains3 (block1)
S vs G1 Replication timing


title: mrc1- rep2

description:
raw data column: Strains6 (block2)
S vs G1 Replication timing


title: GPF_13285935_gacA_mutant_late_rep4

city: Sydney

first: Ian

last: Paulsen

state: NSW

address: Macquarie University

department: Department of Chemistry and Biomolecular Sciences

country: Australia

institute: Macquarie University

description: This slide measures gene expression of a gacA mutant as compared to wild type. The gacA mutant of Pf-5 was constructed by replacing 626 bp internal to gacA with aphI, which confers kanamycin resistance.

hyb_protocol: Combine Cy3 and Cy5 samples and 1 microliter cy-labeled arabidopsis 70-mer positional controls (This is a pool of 4 70-mers labeled with Cy3 and Cy5 for a  total of 8 70-mers at 2 ng/microliter each.  The sequences are:  At2g14610a_219_rev -  AAAAAAATATATCAACAATGGCAAAGCTACCGATACGAAACAATATTAGGAAAAATGTGTGTAAGGACAA; At2g14610b_265_rev -  AATTTAAACTGCGTATTAGTGTTTGGAAAAAAAAAACAAAGTGTATACAATGTCAATCGGTGATCTTTTT; At2g14610c_305_rev -  TTAATAACATATAATATTGAATAGGATATCATAGGATATTATTACGTAATAATATCCTATGGTGTCATTT; At2g14610d_298_rev -  CGACTTTTCTTGCTTAGAAGTCTTTGCATTGTTAATAGATTGTTGAAAAGGTTTATTCATTACTTTCATG). Dry using a speed vac. Make pre-hybridization buffer by combining: 0.5 g BSA; 37 mL DEPC water; 12.5 mL 20X SSC; 0.5 mL 10% SDS. Incubate pre-hybridization buffer for 20 minutes at 42 degrees C. Filter using a 0.45 micrometer cellulose acetate filter into a coplin jar. Incubate for 20 minutes at 42 degrees C. Make hybridization buffer by combining: 500 microliters fomamide; 250 microliters 20X SSC; 10 microliters 10% SDS; 240 microliters DEPC water. Filter hybridization buffer through a 0.45 micrometer cellulose acetate filter. Add 50 uL sheared salmon sperm DNA (Ambion) to hybridization buffer. Add 60 microliters hybridization buffer to speed vac-dried probes. Put slide into pre-hybridization buffer in coplin jar. Incubate for 45 minutes at 42 degrees C. Wash slide 4 times in water and 3 times in isopropanol for 2 minutes per wash with gentle shaking by hand. Dry slide by spinning. Clean 25 mm x 60 mm lifterslip (Erie Scientific Company) by dipping in MilliQ water for 5 minutes at room temperature. Dip in 100% EtOH and dry with a Chem Wipe. Heat probes for 15 minutes at 95 degrees C with occassional "flicking" to resuspend probes. Remove probes from heat block and centrifuge for 2 minutes at 15,000g. Place lifterslip onto slide and add probes by allowing capillary action to pull the probes under the lifterslip. Hybridize overnight at 42 degrees C. Wash slide 2 times in glass staining dish with 1X SSC, 0.2% SDS for 5 minutes at 42 degrees C. Wash slide in 0.1X SSC, 0.1% SDS for 5 minutes at room temperature. Wash slide 3 times in 0.1X SSC for 5 minutes at room temperature. Dry slide by spinning.

scan_protocol: Slides were scanned at 10 micrometer resolution using an Axon 4000B scanner with GenePix 4.0 software.

data_processing: Tiff images were processed using TIGR-Spotfinder (www.tigr.org/software) with Otsu thresholding, a minimum spot size of 10 and a maximum spot size of 15,  and applying the default quality control filter options.  The data were normalized ignoring controls with the LOWESS algorithm in block mode with a smooth  parameter of 0.33 by using TIGR-MIDAS (www.tigr.org/software).

organism: Pseudomonas protegens Pf-5

label_protocol:
Make spike-in control pools from RNA amplified from cloned Arabidopsis thaliana genes (cab, ltp4, rca, rbcL, ltp6, rcp1, nac, xcp2, prk, and tim) using the  MegaScript Kit (Ambion) by combining for Cy5 pool:
5.2 microliters 20.3 ng/microliter cab RNA;
12.5 microliters 16.839 ng/microliter ltp4 RNA;
18.6 microliters 22.634 ng/microliter rca RNA;
41.8 microliters 15.068 ng/microliter rbcL RNA;
4.7 microliters 13.279 ng/microliter ltp6 RNA;
11.8 microliters 21.313 ng/microliter rcp1 RNA;
40.7 microliters 23.23 ng/microliter nac RNA;
4.6 microliters 18.177 ng/microliter xcp2 RNA;
14.7 microliters 11.436 ng/microliter prk RNA;
18.9 microliters 11.084 ng/microliter tim RNA;
826.5 microliters water.
And for Cy3 pool:
5.2 microliters 20.3 ng/microliter cab RNA;
12.5 microliters 16.839 ng/microliter ltp4 RNA;
18.6 microliters 22.634 ng/microliter rca RNA;
41.8 microliters 15.068 ng/microliter rbcL RNA;
1.6 microliters 13.279 ng/microliter ltp6 RNA;
3.9 microliters 21.313 ng/microliter rcp1 RNA;
13.6 microliters 23.23 ng/microliter nac RNA;
13.9 microliters 18.177 ng/microliter xcp2 RNA;
44.1 microliters 11.436 ng/microliter prk RNA;
56.8 microliters 11.084 ng/microliter tim RNA;
788.1 microliters water.
To label RNA sample combine:
4 micrograms RNA;
2 microliters 3 mg/mL random hexamers (Invitrogen);
2 microliters arabidopsis spike-in control RNA;
DEPC water to a final volume to 17.5 microliters.
Mix and incubated at 70 degrees C for 10 minutes.
Snap-freeze in dry ice/ethanol for 30 seconds and centrifuged for 1 minute at approximately 16,000g.
Add:
6 microliters 5X Superscript II buffer (Invitrogen);
3 microliters 0.1 M dithiothreitol;
1.2 microliters aminoallyl-dNTP mix containing 12.5 mM dATP, 12.5 mM dCTP, 12.5 mM dGTP, 4.16 mM dTTP, and 8.33 mM aadUTP;
2 microliters SuperScript II (Invitrogen).
Mix and incubated overnight at 42 degrees C.
Add:
10 microliters 1 M NaOH;
10 microliters 0.5 M EDTA.
Incubate for 15 minutes at 65 degrees C.
Add:
25 microliters 1 M Tris pH 7.4;
400 microliters PB buffer (Qiagen).
Apply sample to QIAquick column (Qiagen).
Centrifuge for 1 minute at 15,000g.
Wash with 750 microliters phosphate wash buffer (84.25 mL 95% EtOH + 15.25 mL water + 0.5 mL 1 M KPO4 pH 8.5 solution made by combining 0.5 mL 1M KH2PO4  with 9.5 mL 1M K2HPO4).
Centrifuge for 1 minute at 15,000g.
Repeat wash.
Empty collection tube and centrifuge for 1 minute at 15,000g.
Transfer column to fresh tube.
Add 30 microliters phosphate elution buffer (4 mM KPO4 solution made by diluting 1 M KPO4 pH 8.5 solution).
Incubate for 1 minute.
Centrifuge for 1 minute at 15,000g.
Repeat elution for a final volume of 60 microliters.
Dry sample using a speed vac.
Resuspend cDNA in 4.5 microliters 0.1 M carbonate buffer (1 M Na2CO3 buffer pH 9.0 diluted 1:10 with water).
Allow the sample to resuspend for 15 minutes at room temperature.
Add 4.5 microliters NHS-Cy (Amersham) resuspended in 73 microliters DMSO.
Incubate for 1 hour at room temperature in the dark.
Add 4.5 microliters 4 M hydroxylamine.
Incubate for 15 minutes at room temperature in the dark.
Add:
35 microliters 100 mM NaOAc pH 5.2;
500 microliters PB buffer.
Apply to Qiaquick column.
Centrifuge for 1 minute at 15,000g.
Wash with 750 microliters PE buffer (Qiagen).
Centrifuge for 1 minute at 15,000g.
Repeat wash.
Empty collection tube and centrifuge for 1 minute at 15,000g.
Transfer column to fresh tube.
Add 30 microliters EB buffer (Qiagen).
Incubate for 1 minute.
Centrifuge for 1 minute at 15,000g.
Repeat elution for a final volume of 60 microliters.
Check quality of probes spectrophotometrically from 200nm to 700nm.
Store at -80 degrees C.
Use this protocol to label 12 ug RNA and combine products for one hyb.

growth_protocol:
Bacterial cultures were first inoculated from frozen stocks onto King’s Medium B agar (King, et al., 1954) for overnight incubation at 27ºC.  This plate was used to
inoculate a 5 ml broth culture of nutrient broth amended with 1% glycerol (NBgly) grown shaking at 200 rpm for 16-18 hours at 27ºC.  Inoculum was washed in
sterile NBgly broth prior to inoculation and resuspended in 20 ml of NBgly broth in a 125 ml erlenmeyer flask to an OD600 of ~0.05.  Three replicate cultures were
grown with shaking (200 rpm) at 20ºC until harvest at the specified optical density of 2.4.  For each replicate culture, RNA was pretreated with RNAProtect
(Qiagen, Valencia, CA) for 10 minutes, centrifuged and pellets were stored at -80°C until extracted.

extract_protocol: Extractions were done using the RNA/DNA Midi Kit (Qiagen, Valencia, CA) followed by an on-column DNAse treatment (RNeasy Mini Kit with DNAse I; Qiagen, Valencia, CA).  PCR was performed on the RNA to determine that detectable DNA had been removed and RNA samples were analyzed for quality using the BioAnalyzer 2100 (Agilent, Palo Alto, CA).

value: Wild-type strain of Pf-5

source_name: G3-gacA mutant

growth_protocol:
Bacterial cultures were first inoculated from frozen stocks onto King’s Medium B agar (King, et al., 1954) for overnight incubation at 27ºC.  This plate was used to
inoculate a 5 ml broth culture of nutrient broth amended with 1% glycerol (NBgly) grown shaking at 200 rpm for 16-18 hours at 27ºC.  Inoculum was washed in
sterile NBgly broth prior to inoculation and resuspended in 20 ml of NBgly broth in a 125 ml erlenmeyer flask to an OD600 of ~0.05.  Three replicate cultures were
grown with shaking (200 rpm) at 20ºC until harvest at the specified optical density of 2.3.  For each replicate culture, RNA was pretreated with RNAProtect
(Qiagen, Valencia, CA) for 10 minutes, centrifuged and pellets were stored at -80°C until extracted.

value: gacA mutant of Pf-5


title: mrc1- rep4

description:
raw data column: Strains10 (block4)
S vs G1 Replication timing


title: clb5- rep4

description:
raw data column: Strains3(block2)
S vs G1 Replication timing


title: clb5- rep2

description:
raw data column: Strains2 (block4)
S vs G1 Replication timing


title: GPF_13285933_gacA_mutant_late_rep3


title: GPF_13285928_gacA_mutant_late_rep1

source_name: G2-gacA mutant


title: GPF_13285932_gacA_mutant_late_rep6

source_name: G5-gacA mutant


title: GPF_13285929_gacA_mutant_late_rep2


title: GPF_13285930_gacA_mutant_late_rep5


title: dia2- rep2

description:
raw data column: Strains7 (block4)
S vs G1 Replication timing


title: clb5- rep1

description:
raw data column: Strains2 (block3)
S vs G1 Replication timing


title: GPF_13285920_gacA_mutant_early_rep1

growth_protocol:
Bacterial cultures were first inoculated from frozen stocks onto King’s Medium B agar (King, et al., 1954) for overnight incubation at 27ºC.  This plate was used to
inoculate a 5 ml broth culture of nutrient broth amended with 1% glycerol (NBgly) grown shaking at 200 rpm for 16-18 hours at 27ºC.  Inoculum was washed in
sterile NBgly broth prior to inoculation and resuspended in 20 ml of NBgly broth in a 125 ml erlenmeyer flask to an OD600 of ~0.05.  Three replicate cultures were
grown with shaking (200 rpm) at 20ºC until harvest at the specified optical density of 0.50.  For each replicate culture, RNA was pretreated with RNAProtect
(Qiagen, Valencia, CA) for 10 minutes, centrifuged and pellets were stored at -80°C until extracted.

growth_protocol:
Bacterial cultures were first inoculated from frozen stocks onto King’s Medium B agar (King, et al., 1954) for overnight incubation at 27ºC.  This plate was used to
inoculate a 5 ml broth culture of nutrient broth amended with 1% glycerol (NBgly) grown shaking at 200 rpm for 16-18 hours at 27ºC.  Inoculum was washed in
sterile NBgly broth prior to inoculation and resuspended in 20 ml of NBgly broth in a 125 ml erlenmeyer flask to an OD600 of ~0.05.  Three replicate cultures were
grown with shaking (200 rpm) at 20ºC until harvest at the specified optical density of 0.47.  For each replicate culture, RNA was pretreated with RNAProtect
(Qiagen, Valencia, CA) for 10 minutes, centrifuged and pellets were stored at -80°C until extracted.


title: dia2- rep4

description:
raw data column: Strains13 (block5)
S vs G1 Replication timing


title: dia2- rep1

description:
raw data column: Strains7 (block3)
S vs G1 Replication timing


title: GPF_13285926_gacA_mutant_early_rep6


title: GPF_13285922_gacA_mutant_early_rep2


title: dia2- rep3

description:
raw data column: Strains13 (block3)
S vs G1 Replication timing


title: GPF_13285919_gacA_mutant_early_rep5


title: sic1- rep4

description:
raw data column: Strains12 (block2)
S vs G1 Replication timing


title: GPF_13285918_gacA_mutant_early_rep4

source_name: G4-gacA mutant


title: sic1- rep1

description:
raw data column: Strains7 (block1)
S vs G1 Replication timing


title: sic1- rep2

description:
raw data column: Strains7 (block2)
S vs G1 Replication timing


title: GPF_13285917_gacA_mutant_early_rep3


title: sic1- rep3

description:
raw data column: Strains12 (block1)
S vs G1 Replication timing


title: Wild type- rep4

description:
raw data column: Strains2 (block2)
S vs G1 Replication timing


title: Wild type- rep2

description:
raw data column: Strains1 (block2)
S vs G1 Replication timing


title: Ls2r3

status: Public on Mar 03 2010

city: Philadelphia

first: Jay

last: Johnson

state: PA

address: 422 Curie Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

description: Replicate #3

hyb_protocol: Hybridization of the labeled aRNA to the U133-Plus 2.0 arrays was carried out in the presence of herring sperm DNA and probe array controls provided by the manufacturer. The probe array was stained and washed on station using the following fluidics protocol: Wash A1 Recovery Mixes=0 Wash A1 Temperature (C)=30 Number of Wash A1 Cycles=10 Mixes per Wash A1 Cycle=2 Wash B Recovery Mixes=0 Wash B Temperature (C)=50 Number of Wash B Cycles=6 Mixes per Wash B Cycle=15 Stain Temperature (C)=35 First Stain Time (seconds)=300 Wash A2 Recovery Mixes=0 Wash A2 Temperature (C)=30 Number of Wash A2 Cycles=10 Mixes per Wash A2 Cycle=4 Second Stain Time (seconds)=300 Third Stain Time (seconds)=300 Wash A3 Recovery Mixes=0 Wash A3 Temperature (C)=35 Number of Wash A3 Cycles=15 Mixes per Wash A3 Cycle=4< Holding Temperature (C)=25

scan_protocol: The probe array was scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: standard Affymetrix protocol

label: Biotin

source_name: Liposarcoma 5228, Tumor 27

label_protocol: The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix.  The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).

growth_protocol: LS2 is maintained in RPMI 1640 + Glutamax (Invitrogen) supplemented with 20% FBS (Invitrogen), MEM Vitamin Mixture (BioWhittaker), ITES (Lonza), Penicillin (4U/ml) Streptomycin (4 ug/ml) L-Glutamine (0.29 mg/m) mixture (Invitrogen), 1mM sodium pyruvate (CellGro) and MEM Eagle Non-essential amino acid solution (Lonza) with 5% CO2.

extract_protocol: Total RNA was isolated using Trizol reagent and purified using RNeasy spin columns (Qiagen). RNA purity was determined by analysis using a NanoDrop spectrophotometer. The quality of the RNA was determined using the Agilent 2100 Bioanalyzer.

tag: source

value: Liposarcoma

tag: subtype

value: pleomorphic

value: LS2 derived from sample 5228, Tumor 27


title: Wild type- rep1

description:
raw data column: Strains1 (block1)
S vs G1 Replication timing


title: 5228r3

description: Replicate #3

source_name: Liposarcoma

tag: tumor


title: Wild type- rep3

description:
raw data column: Strains2 (block1)
S vs G1 Replication timing


title: Simmental4

city: Beltsville

first: George

last: Liu

address: 10300 Baltimore Ave

institute: United States Department of Agriculture

description: Hybridization of test sample and reference sample

hyb_protocol: Performed by NimbleGen standard protocol

data_processing: NimbleScan2.3 was used to analyze the data with qspline normalization (Christopher Workman, et al., 2002). The high confidence calls are filtered and merged according to the following criteria: we merged overlapping CNV coordinates across hybridizations to form unique CNV regions using the 40% overlapping threshold as previously described (Redon et al., 2006; Graubert et al., 2007). For cattle CNV calling, we first migrated the probes from Btau_3.1 to Btau_4.0 and made calls on Btau_4.0 coordinates. We then tested a series of log2 ratio shift and affected neighboring probe counts and their impact on the false discovery rate (FDR) in the self-self control hybridizations. We selected a set of conservative calling criteria for the final set of high confidence CNVs, requiring that alternations of *0.5* log2 ratios over *5* neighboring probes (0.5_5), under no false positive was found for self-self control hybridizations. For chrX, the baselines were shifted to negative. Copy number variation regions are available in the "CNVR.txt" file on the Series record.

organism: Bos taurus

source_name: normal bull semen from Simmental4

label_protocol: Labeled by NimbleGen

extract_protocol: Qiagen QIAamp DNA Mini Kit

tag: breed

value: Simmental

value: Male

value: semen

source_name: Whole blood from Hereford L1 Dominette 01449

extract_protocol: Qiagen QIAamp DNA Blood Maxi Kit

value: Hereford L1 Dominette 01449

value: Female

value: whole blood


title: Simmental6

scan_protocol: Performed by NimbleGen standard protocol

source_name: normal bull semen from Simmental6


title: Simmental7

source_name: normal bull semen from Simmental7


title: Simmental5

source_name: normal bull semen from Simmental5


title: RedAngus6

source_name: normal bull semen from RedAngus6

value: Red Angus


title: Limousin10

source_name: normal bull semen from Limousin10

value: Limousin


title: RedAngus3

source_name: normal bull semen from RedAngus3


title: RedAngus8

source_name: normal bull semen from RedAngus8


title: Limousin8

source_name: normal bull semen from Limousin8


title: Simmental3

source_name: normal bull semen from Simmental3


title: Limousin7

source_name: normal bull semen from Limousin7


title: Simmental8

source_name: normal bull semen from Simmental8


title: male embryo H3K27me3

description: ChIP-chip male embryo H3K27me3

source_name: H3K27me3 ChIP DNA male embryo

value: whole embryo

source_name: input DNA male embryo


title: RedAngus4

source_name: normal bull semen from RedAngus4


title: RedAngus7

source_name: normal bull semen from RedAngus7


title: Limousin9

source_name: normal bull semen from Limousin9


title: RedAngus5

source_name: normal bull semen from RedAngus5

source_name: Whole blood from Hereford L1 Dominette 01449


title: Limousin6

source_name: normal bull semen from Limousin6


title: Hereford12

source_name: normal bull semen from Hereford12

value: Hereford


title: Hereford11

source_name: normal bull semen from Hereford11


title: 60049

city: East Melbourne

first: Dariush

last: Etemadmoghadam

address: St Andrew's Place

institute: Peter MacCallum Cancer Centre

hyb_protocol: DNA was Sty/Nsp restriction digested, adapter ligated, PCR amplified, fragmented, labelled and hybridized to a SNP 6.0 array according to the manufacturer's instructions.

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

data_processing:
Data files (CEL) were generated using the Affymetrix GeneChip® Command Console (AGCC) v1.0 and normalized using the R package Aroma.Affymetrix (Bengtsson et al., 2008).
primary_data: log2 tumor copy number ratio at each marker was then estimated by normalization to the mean signal obtained from normal reference samples profiled at the Peter MacCallum Cancer Centre

source_name: ovary

label_protocol: The mapping array assays were performed according to the manufacturer’s 'cytogenetics copy number assay' protocol (Affymetrix, Santa Clara, CA).

growth_protocol: NA (Fresh-frozen (LN2) tissue collected at surgery)

extract_protocol: Genomic DNA was extracted using a DNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol

treatment_protocol: DNA was extracted from whole tumor tissue for samples with ≥ 80% neoplastic cells. For samples with < 80% overall tumor cells, needle dissection of serial tumor sections was performed to enrich for the epithelial fraction prior to DNA extraction. Needle-dissected samples were stained with cresyl-violet to facilitate  morphological distinction between tumor and stromal elements.

tag: cell type

value: tumour

tag: disease state

value: Stage IIIC, Grade 3, Serous carcinoma


title: 23221

value: High-grade tumour of uncertain primary/histology


title: Hereford9

source_name: normal bull semen from Hereford9


title: 60258

value: Stage IIIC, Grade 3, Papillary serous adenocarcinoma


title: 60214

value: Stage IIIC, Grade 2, Serous carcinoma


title: Hereford8

source_name: normal bull semen from Hereford8


title: Hereford10

source_name: normal bull semen from Hereford10


title: 41358


title: 22029

value: Stage IV, Grade 3, Papillary serous adenocarcinoma


title: 533

value: Grade 2 with areas of Grade 1 and co-existing LMP


title: Hereford7

source_name: normal bull semen from Hereford7


title: Gelbvieh8

source_name: normal bull semen from Gelbvieh8

value: Gelbvieh


title: Gelbvieh5

source_name: normal bull semen from Gelbvieh5

value: Male


title: Gelbvieh6

source_name: normal bull semen from Gelbvieh6

value: semen


title: Gelbvieh7

source_name: normal bull semen from Gelbvieh7

value: Hereford L1 Dominette 01449


title: Gelbvieh3

source_name: normal bull semen from Gelbvieh3

value: Female


title: Charolais6

source_name: normal bull semen from Charolais6

value: Charolais

value: whole blood


title: Angus9

source_name: normal bull semen from Angus9

value: Angus


title: Charolais5

source_name: normal bull semen from Charolais5


title: Charolais7

source_name: normal bull semen from Charolais7

source_name: Whole blood from Hereford L1 Dominette 01449


title: Gelbvieh4

source_name: normal bull semen from Gelbvieh4


title: Angus8

source_name: normal bull semen from Angus8


title: Gelbvieh2

source_name: normal bull semen from Gelbvieh2


title: Limousin5

source_name: normal bull semen from Limousin5

value: Limousin


title: Angus6

source_name: normal bull semen from Angus6


title: Simmental2

source_name: normal bull semen from Simmental2

value: Simmental


title: miR - MM - RB deletion - p709

status: Public on Mar 18 2010

city: Salamanca

first: Norma

middle: Carmen

last: Gutierrez

department: Hematology

country: Spain

institute: University Hospital

description: miR - MM - RB deletion - p709

data_processing:
The SDS files are the raw files for real-time PCR data and are readable by Applied Biosystems SDS Software v2.3. SDS Software is available for download from the Applied Biosystems website.
Normalization was performed with the mean of RNU44 and RNU48.
CT = threshold cycle value
dCT = CT_(miRNA) - CT_(control miRNA) for comparisons between MM samples and normal PC.
ddCT = dCT_(MM) - dCT_(average normal PC) for comparisons between MM samples.
The dCT and ddCT data are presented as log10 of the relative quantity of each miRNA.

label: FAM

source_name: Bone marrow, MM

label_protocol: Standard Taqman Assay

extract_protocol: Total RNA was extracted from normal and tumor plasma cells using miRNEasy Mini Kit (Qiagen, Valencia, USA) following manufacturer's protocol. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

value: bone marrow

value: CD138-positive plasma cell

tag: disease

value: multiple myeloma


title: Charolais10

source_name: normal bull semen from Charolais10


title: Charolais11

source_name: normal bull semen from Charolais11


title: Charolais8

source_name: normal bull semen from Charolais8


title: Angus7

source_name: normal bull semen from Angus7


title: Charolais9

source_name: normal bull semen from Charolais9


title: Angus11

source_name: normal bull semen from Angus11


title: Simmental1

source_name: normal bull semen from Simmental1


title: Angus10

source_name: normal bull semen from Angus10


title: Romosinuano1

source_name: normal bull semen from Romosinuano1

value: Romosinuano


title: Angus5

source_name: normal bull semen from Angus5

source_name: Whole blood from Hereford L1 Dominette 01449


title: Ndama3

source_name: normal bull semen from Ndama3

value: Ndama


title: RedAngus2

source_name: normal bull semen from RedAngus2

value: Red Angus


title: Ndama1

source_name: normal bull semen from Ndama1


title: RedAngus1

source_name: normal bull semen from RedAngus1


title: Ndama2

source_name: normal bull semen from Ndama2


title: Romosinuano2

source_name: normal bull semen from Romosinuano2


title: Limousin4

source_name: normal bull semen from Limousin4


title: Limousin3

source_name: normal bull semen from Limousin3


title: Gir1

source_name: normal bull semen from Gir1

value: Gir


title: Guzerat3

source_name: normal bull semen from Guzerat3

value: Guzerat


title: Charolais2

source_name: normal bull semen from Charolais2

value: Male


title: Holstein1

source_name: normal bull semen from Holstein1

value: Holstein

value: semen


title: Hereford3

source_name: normal bull semen from Hereford3

value: Hereford

value: Hereford L1 Dominette 01449

value: Female


title: Hereford4

value: whole blood

source_name: normal bull semen from Hereford4


title: Charolais1

source_name: normal bull semen from Charolais1

value: Charolais


title: SantaGertrudis1

source_name: normal bull semen from SantaGertrudis1

value: Santa Gertrudis


title: Charolais4

source_name: normal bull semen from Charolais4

source_name: Whole blood from Hereford L1 Dominette 01449


title: Charolais3

source_name: normal bull semen from Charolais3


title: Guzerat2

source_name: normal bull semen from Guzerat2


title: Brangus2

source_name: normal bull semen from Brangus2

value: Brangus


title: Limousin2

source_name: normal bull semen from Limousin2

value: Limousin


title: Gir3

source_name: normal bull semen from Gir3


title: Gir2

source_name: normal bull semen from Gir2


title: Limousin1

source_name: normal bull semen from Limousin1


title: Hereford2

source_name: normal bull semen from Hereford2


title: Holstein2

source_name: normal bull semen from Holstein2


title: Hereford1

source_name: normal bull semen from Hereford1


title: Guzerat1

source_name: normal bull semen from Guzerat1


title: Hereford5

source_name: normal bull semen from Hereford5


title: Gelbvieh1

source_name: normal bull semen from Gelbvieh1

value: Gelbvieh


title: Brangus1

source_name: normal bull semen from Brangus1


title: Beefmaster1

source_name: normal bull semen from Beefmaster1

value: Beefmaster


title: Brahman2

source_name: normal bull semen from Brahman2

value: Brahman


title: Hereford6

source_name: normal bull semen from Hereford6

source_name: Whole blood from Hereford L1 Dominette 01449


title: HB01a_exp - HB01a_stat (C)

city: Amsterdam

first: Douwe

last: Molenaar

address: De Boelelaan 1085

department: Systems Bioinformatics

country: Netherlands

institute: Vrije Universiteit Amsterdam

description: HB01a_exp - HB01a_stat  (C)

hyb_protocol: Two individual differentially labeled cDNAs were incubated at 95° C for 3' cooled down to 68° C and mixed (final-volume 20 µl). To these mixed cDNAs 180 µl of pre-heated (68° C) Slidehyb#1 hybridization buffer (Ambion Austin USA) was added and the resulting solution was applied on a pre-heated slide (68° C). Slides were then hybridized at 44° C for 16 hours. Subsequently slides were washed at 42°C once in 1 x SSC/0.2% SDS and twice in 1 x SSC and dried by centrifugation (1 x SSC is 0.15 M NaCl and 0.15 M Sodium Citrate). This method was described by Santos et al. Appl Environ Microbiol. 2009 Jun;75(12):3930-6

scan_protocol: Using the Scan Array Express microarray scanner. 1.Turn on the scanner and the computer (in this order) 2.Login: scanner 3.Double click the 'ScanArray Express' icon 4.Switch on lasers 1 and 3 at least 15 minutes prior to scanning arrays 5.Click the 'File' button This is to prevent you from accidentally turning off the laser after the 15 minutes warming-up phase 6.Insert the slide with the array-side up and the label towards the outside. On Agilent slides the array side is the side with the label that has the word Agilent"" on it 7.Press 'Scan | Prescan' 8.Put resolution at 50 m select both labels used and set PMT values for both channels 9.Press 'Start' 10.Press 'Palette ' 'Green' as soon as projection of the image has started (first dye) select the red colour as soon as scanning of the second layer (second dye) has started 11.Adjust PMT values to balance signals obtained for both channels. If necessary do a few low-resolution scans to obtain a optimal balance 12.Click the 'Scan' button again 13.Select frame for high resolution scan adjust resolution (to 10 m) and scan the array for both dyes 14.Press 'File | Save' to save the files 'Save all' saves both dye layers ," Create a new folder for each array 'Save all' saves the signals from both layers in individual files 15.Switch off the lasers. This method was described by Santos et al. Appl Environ Microbiol. 2009 Jun;75(12):3930-6

data_processing: After blank spots had been removed, array measurements were normalized by local fitting of an M-A plot using the Loess algorithm and the Limma package in R (http://www.r-project.org). Normalized intensities were used for further analysis. The regulation ratios between the different samples were calculated per probe from the hybridizations using linear modeling functions from the Limma package. The statistical significance of regulation ratios was calculated from variation in biological duplicates, using the eBayes function in Limma (cross-probe variance estimation) and false discovery rate (FDR) adjustment of the p-values. Subsequently, the probe regulation ratios and the p-values were averaged per gene over all probes targeting the gene. Although clearly the averaged p-values do not represent an FDR-corrected p-value anymore, low average p-values for a gene are still indicative of highly significant regulation ratios, and in fact they are likely to underestimate the significance of the observed regulation. In case of the comparison between strain KF147, the mutants derived from it, and strain IL594 (an ancestor of the sequenced IL1403 strain), only probes from the array that exactly matched both the KF147 and IL1403 genome sequences (7725 distinct probes) were taken into consideration in the calculations of the regulation ratios. This way, the scoring of regulation differences caused by sequence differences was avoided.

organism: Lactococcus lactis subsp. lactis

label_protocol: Annealing Mix: x µl RNA preparation (=5µg); y µl nuclease-free water; 1 µl Random Nonamers; 11 µl TOTAL 1. mix Annealing Mix in a 200 µl PCR tube gently by pipetting up and down 2. incubate for 5’ 70°C 3. cool at room temperature for 10’ (annealing) 4. spin down the mixture to the bottom of the tube 5. place on ice Reverse transcription Reverse Transcription Mix 4 µl 5x buffer 2 µl 0.1 M DTT 1 µl dNTP-mix 1 µl AA-dUTP 1 µl TMIII (keep only briefly outside 20°C) 20 µl TOTAL 1. Mix by very gently by pipetting up and down (vigorous pipetting will denature the enzyme!) 2. Incubate for 3 hrs at 42°C (in PCR-machine) 3. Cool on ice for immediate purification or place at 20°C for storage Degradation of mRNA 1. Add 2 µl 2.5 M NaOH 2. Mix (vortex) and spin down 3. Incubate for 15 min. at 37°C 4. Add 10 µl 2 M HEPES free acid 5. Mix (vortex) and spin down 6. Ready for purification or store at 20°C Labelling and purification of cDNA with cyanine dyes Followed Ge Healthcare kit "Amersham CyDye (Cy3/Cy5)Reactive Dye Protocols for Post Labelling Aminoallyl-cDNA and Aminoallyl-aRNA" code RPN5661 Labelling of amino allyl-modified cDNA with CyDye 1. Add the amino allyl modified cDNA (in 0.1 M sodium bicarbonate) directly into one aliquot of CyDye NHS Ester. Resuspend the ester completely by pipetting several times and transfer the solution to an amber 1.5 ml tube 2. Incubate at room temperature, in the dark for 60 to 90 minutes 3. Add 15 µl 4 M Hydroxylamine to each coupling reaction 4. Mix by stirring and incubate at room temperature, in the dark, for 15 minutes 5. Proceed directly to purification of CyDye-labelled cDNA Purification of CyDye labelled cDNA Followed Ge Healthcare kit "Amersham CyDye (Cy3/Cy5)Reactive Dye Protocols for Post Labelling Aminoallyl-cDNA. This method was described by Santos et al. Appl Environ Microbiol. 2009 Jun;75(12):3930-6

growth_protocol: growth medium: reconstituted skimmed milk

extract_protocol: Cultured milk (25 ml) was cleared with 1 mL 25% (w/v) Na3Citrate (Merck) at -20 °C for 0,5 h and gently mixing every 5 min. Subsequently the pH was adjusted to 6,5 – 7,0 with 1 M NaOH (VWR) and the culture was centrifuged at -20 °C and 23000 G for 16 min. The obtained cell pellet was resuspended in 0.5 ml of a solution comprising 50% (w/v) guanidinethiocyanate (Sigma), 0.5% (w/v) N-laurylsarcosine (Sigma) and 2.5% (v/v) of a 1 M Na3Citrate solution, adjusted to pH 7.0 with 0,1 M NaOH. After centrifugation, the cells were resuspended in 500 µL 1xTE and applied to a RNA extraction tube containing 250 µL acidic phenol (Sigma), 250 µL chloroform (company), 30 µL NaAc (Merck) pH 5.2, 30 µL 10% SDS (Sigma) and 500 mg zirconium beads with 0.1 mm diameter (Biospec products Inc., OK, USA) which was immediately frozen in liquid nitrogen and kept at -80 °C until RNA extraction. For RNA extraction cells were disrupted 3 times 45 s in a Fastprep (Qbiogene Inc., France) at 5,5 m/s separated by placing the samples for 1 min on ice. After centrifugation for 1 min at 20800 G, 500 μL of the aqueous phase was purified with 400 μL chloroform and a second centrifugation step was performed. The aqueous phase was used for RNA isolation with a High Pure kit (Roche Diagnostics, Mannheim, Germany), which included 1 h of treatment with DNase I. RNA was stored at -80 °C. Quantity and quality were checked using a ND-1000 photospectometer (Nanodrop Technologies, Wilmington, DE, USA) and capillary electrophoresis on a RNA 6000 Nano LabChip® kit (Agilent Technologies, Santa Clara, CA, USA) in a 2100 Bioanalyzer (Agilent). This method was described by Sieuwerts et al. 2009, PhD-thesis, Wageningen University, The Netherlands.

tag: growth phase

value: exponential

value: stationary


title: KF147_exp - KF147_stat (I)

description: KF147_exp - KF147_stat  (I)

tag: strain


title: Bonsmara2

source_name: normal bull semen from Bonsmara2

value: Bonsmara

tag: gender


title: KF147_exp - IL594_exp (K)

description: KF147_exp - IL594_exp  (K)


title: KF147prt_exp - HB03a_exp (E)

description: KF147prt_exp - HB03a_exp  (E)


title: IL594_stat - KF147_stat (M)

description: IL594_stat - KF147_stat  (M)

value: stat


title: KF147_stat - HB05a_stat (N)

description: KF147_stat - HB05a_stat  (N)


title: HB05a_stat - HB05a_exp (O)

description: HB05a_stat - HB05a_exp  (O)


title: HB03a_stat - KF147prt_stat (G)

description: HB03a_stat - KF147prt_stat  (G)


title: Brahman1

source_name: normal bull semen from Brahman1

value: Male


title: KF147prt_stat - KF147prt_exp (A)

description: KF147prt_stat - KF147prt_exp  (A)


title: HB01a_stat - KF147prt_stat (D)

description: HB01a_stat - KF147prt_stat  (D)


title: HB03a_exp - HB03a_stat (F)

description: HB03a_exp - HB03a_stat  (F)


title: Bonsmara1

source_name: normal bull semen from Bonsmara1

value: semen


title: Holstein3

source_name: normal bull semen from Holstein3

value: Holstein


title: Angus3

source_name: normal bull semen from Angus3

value: Angus

value: Hereford L1 Dominette 01449


title: Angus4

source_name: normal bull semen from Angus4

value: Female

value: whole blood


title: Angus2

source_name: normal bull semen from Angus2


title: Angus1

source_name: normal bull semen from Angus1


title: KF147prt_exp - KF147_exp (H)

description: KF147prt_exp - KF147_exp  (H)


title: KF147prt_exp - HB01a_exp (B)

description: KF147prt_exp - HB01a_exp  (B)


title: Wild-type_adrenal_rep1

city: La Jolla

first: Ryan

last: Friese

state: CA

institute: University of California San Diego

description: Gene expression data from wild-type mouse adrenal gland.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MG-U74Av2 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 2500.

source_name: Wild-type mouse, adrenal gland

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

extract_protocol: Total RNA was extracted from isolated adrenal glands from wild-type (n=3) and Chga knockout (n=3) mice with the RNAzol (guanidinium thiocyanate) kit (TelTest, Friendswood, TX), followed by RNase-free DNase I (Qiagen, Valencia, CA) treatment to eliminate residual genomic DNA.

value: Wild-type mouse (Mahapatra et al., 2005)

tag: sex

tag: age

value: Adrenal gland


title: Wild-type_adrenal_rep2

tag: tissue


title: Wild-type_adrenal_rep3


title: ChgaKO_adrenal_rep3

description: Gene expression data from chromogranin A knockout mouse adrenal gland.

source_name: Chromogranin A knockout mouse, adrenal gland

value: Chromogranin A knockout mouse (Mahapatra et al., 2005)


title: KF147_stat - KF147prt_stat (J)

description: KF147_stat - KF147prt_stat  (J)


title: ChgaKO_adrenal_rep2


title: ChgaKO_adrenal_rep1


title: Wild-type_liver_rep2

description: Gene expression data from wild-type mouse liver.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse430A_2 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software (GCOS v1.2) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 2500.

source_name: Wild-type mouse, liver

extract_protocol: Total RNA was extracted from liver from wild-type (n=3) and Chga knockout (n=3) mice with the RNAzol (guanidinium thiocyanate) kit (TelTest, Friendswood, TX), followed by RNase-free DNase I (Qiagen, Valencia, CA) treatment to eliminate residual genomic DNA.

value: Liver


title: ChgaKO_liver_rep1

description: Gene expression data from chromogranin A knockout mouse liver.

source_name: Chromogranin A knockout mouse, liver


title: ChgaKO_liver_rep2


title: Wild-type_liver_rep3


title: HB05a_exp - KF147_exp (P)

description: HB05a_exp - KF147_exp (P)


title: Wild-type_liver_rep1


title: ChgaKO_liver_rep3


title: LS2P14

description: Passage 14.

hyb_protocol: The sample was hybridized to the array as specified by the manufacturer. The probe array was then stained and washed on station.

source_name: Liposarcoma 5228, Tumor 27

label_protocol: 250 ng of purified DNA was digested with XbaI and the resulting fragments were ligated to adaptor sequences using T4 DNA ligase.  PCR-amplified product was then fragmented by DNaseI, denatured to generate single stranded product and end-labeled by terminal deoxynucleotidyl transferase.

extract_protocol: Genomic DNA was prepared by SDS lysis and phenol extraction and checked for purity using a NanoDrop spectrophotometer.  DNA was also checked for excessive shearing by agarose gel electrophoresis.

value: Liposarcoma

value: pleomorphic

tag: cell line

value: LS2 Derived from 5228, Tumor 27.


title: 5228_Tumor_27_SNP

description: This tumor has been characterized previously to determine which telomere maintenance mechanism is active and interrogated for copy number changes using whole genome profiling (Johnson, J. E., Varkonyi, R. J., Schwalm, J., Cragle, R., Klein-Szanto, A., Patchefsky, A., Cukierman, E., von Mehren, M., and Broccoli, D. (2005) Multiple mechanisms of telomere maintenance exist in liposarcomas. Clin Cancer Res. 11: 5347-5355; Johnson, J. E., Gettings, E. J., Schwalm, J., Pei, J., Testa, J. R., Litwin, S., von Mehren, M., and Broccoli, D. (2007) Whole-genome profiling in liposarcomas reveals genetic alterations common to specific telomere maintenance mechanisms. Cancer Res. 67: 9221-9228.)

source_name: Liposarcoma


title: NULL20_2

status: Public on Mar 02 2010

city: Göteborg

first: Goutham

middle: N

last: Vemuri

address: Kemivagen 10

department: Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

description: Null strain, t = 20, replicate 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 18 hr at 45C on GeneChip Yeast 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with dChip using PM-only normalization.

source_name: Null strain 20 min after perturbation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The two strains of S. cerevisiae were grown in ethanol-limited chemostats. Two samples, one at steady-state and another 20 minutes after pulsing with glucose were collected. An aliquot of cells amounting to 250 mg (dry weight) were separated from the broth by centrifugation and stored at -80C.

extract_protocol: Total RNA from the cells was extracted using Qiagen RNeasy mini kit. DNA contamination was removed by digesting the extract with DNase while on column.

treatment_protocol: The cells from the fermenter were collected in ice and centrifuged to separate the broth and ice. The cell pellet was flash frozen in liquid nitrogen and stored at -80C until subsequent use.


title: NULL20_3

description: Null strain, t = 20, replicate 3


title: NULL20_1

description: Null strain, t = 20, replicate 1


title: NULL0_3

description: Null strain, t = 0, replicate 3

source_name: Null strain before perturbation


title: NULL0_2

description: Null strain, t = 0, replicate 2


title: NULL0_1

description: Null strain, t = 0, replicate 1


title: LS2P2

description: Passage 2.


title: REF20_3

description: Reference strain, t = 20, replicate 3

source_name: Reference strain 20 min after perturbation


title: REF0_3

description: Reference strain, t = 0, replicate 3

source_name: Reference strain before perturbation


title: REF20_1

description: Reference strain, t = 20, replicate 1


title: REF0_2

description: Reference strain, t = 0, replicate 2


title: REF20_2

description: Reference strain, t = 20, replicate 2


title: REF0_1

description: Reference strain, t = 0, replicate 1


title: CA 9- transfected C33-A

city: Goyang-si

first: Hye-Jin

last: Shin

state: Gyeonggi-do

address: 323 Ilsan-ro, Ilsandong-gu

department: Research Institute and Hospital

country: South Korea

institute: National Cancer Center

description: Gene expression data from C33-A expressing CA9 protein fiercely

hyb_protocol: Following fragmentation, 10~15ug of labeled cRNA were hybridized on the Human Genome U133 Plus 2.0 arrays at 45°C for 16hr, according to the Affymetrix standard protocol. After hybridization, the arrays were washed in a GeneChip Fluidics Station 450 with a non-stringent wash buffer at 25°C followed by a stringent wash buffer at 50°C. After washing, the arrays were stained with a streptavidin-phycoerythrin complex.

scan_protocol: After staining, intensities were determined with a GeneChip scanner 3000 (Affymetrix)

data_processing: Scanned data were processed using APT(Affymetrix Power Tool) program, RMA(Robust Multiarray Average) as quantification method, Quantile as normalization method and PM-only as PM intensity adjustment.

source_name: C33-A cell line transfected with full-length human CA 9 cDNA / pcDNA3.0 DNA construct

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocols from 5ug total RNA

growth_protocol: Cells were maintained at 5% CO2 in RPMI medium with 10% fetal bovine serum supplemented with 1% Streptomycin and Penicillin.

extract_protocol:
RNA was extracted at fourth day after seeding with 5x105 cells/ml on 100mmx20 dish.
Total RNA was prepared using a TRIzol® (Invitrogen, Carlsbad, CA, USA) method, followed by the clean-up with the RNeasy® Mini kit isolation method (Qiagen GmbH, Hilden, Germany). The purity and integrity of the total RNA were checked using the NanoDrop (NanoDrop Technologies) and the Experion (Biorad), respectively.

tag: morphology

value: epithelial

tag: growth properties

value: adherent

tag: organ

value: Cervix

value: carcinoma


title: PTIP+ 2

city: Ann Arbor

first: Adam

middle: B.

last: Stein

state: MI

address: 108 Zina Pitcher Dr

department: Medicine

institute: University of Michigan

description: Dressler 10730

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Affymetrix Scanner 3000.

data_processing:
We fit a weighted linear model designed specifically for microarray analysis to the data (Smyth (2004)) and then computed the contrasts of interest. This technique is almost identical to fitting individual t-statistics to each probeset, but we increase our power to detect differences by improving the accuracy of our variance estimate by pooling information from all the probesets to adjust the variance estimate. Also, by using weights we can downweight chips that are considered less reproducible by an efficiency estimate of their array variances (Ritchie et al. (2006)). This technique will not hurt the results if all the chips are of good quality because the weights for each chip can be equal. We filtered out those probesets that had a variance over all samples less than 0.1. This removes probesets that don't change expression in any sample, which by definition are not interesting to us. We then selected probesets based on an adjusted p-value of 0.05 (adjusted for multiple comparisons using false discovery rate (FDR) Benjamini and Hochberg (1995)). This adjustment is different from say, a Bonferroni, which aims to keep the overall p-value at 0.05 (e.g., a Bonferroni correction attempts to limit the probability of any false positives at 5%). Instead, with FDR we choose the number of probesets we think are significantly different, and estimate how many are false positives. So a FDR of 0.05 indicates that we think there are at most 5% false positives.
We calculated expression values for each gene using a robust multi-array average (RMA) Irizarry et al. (2003). This is a modeling strategy that converts the PM probe values into an expression value for each gene. Note that the expression values are log2 transformed data. These data can be converted to the natural scale by exponentiating (e.g., convert by using 2x, where x is the expression value).

source_name: Female mouse heart 5 days after tamoxifen injection

label_protocol: RNA was prepared using the NuGen Ovation Biotin labeling system.

growth_protocol: Mice were maintained in microisolator cages according to the standard protocols outlined by the University of Michigan ULAM.

extract_protocol: Hearts were removed after euthanasia and left ventricle (LV) apices were used to prepare RNA. Total RNA was extracted using the Qiagen RNA extraction kit.

treatment_protocol: 8-week-old female mice that were a cross between C57BL6 and B6129 were treated with tamoxifen (20mg/kg intraperitoneal) for 5 days.

tag: background

value: mixed C57B6 and B6129

tag: ptip status

value: :PTIP+

value: heart

value: female


title: PTIP+ 1

description: Dressler 10721


title: PTIP+ 3

description: Dressler 10731


title: Mock-transfected C33-A

description: Gene expression data from C33-A Control

source_name: C33-A cell line transfected with empty vector DNA


title: PTIP KO3

description: Dressler 10728

source_name: Female mouse heart 5 days after PTIP deletion (tamoxifen injection)

value: :PTIP KO


title: MDCC30_Tumor_51

description: This tumor is ALT-positive.

data_processing: Standard Affymetrix protocol

label_protocol: The Message II Biotin Enhanced Single Round aRNA Amplification Kit (Ambion) was used to synthesize cDNAs using 1 ug of total RNA and protocols provided by the manufacturer. Synthesis of biotin-labeled RNA was carried out using the Ambion kit as above with T7 RNA polymerase in the presence of a biotinylated nucleotide analog/ribonucleotide mix. The aRNA yield was determined by spectrophotometric analysis at 260 nm and size distribution of aRNA was determined with the Agilent 2100 Bioanalyzer. A fragmentation reaction resulted in a distribution of 35-200 nt aRNA fragments (reaction mix provided by Ambion).

tag: tumor

tag: subtype

value: dedifferentiated


title: MDCC19_Tumor_50

description: This tumor is ALT-positive.


title: 44978_Tumor_54

description: This tumor is telomerase-positive.


title: IL594_exp - IL594_stat (L)

description: IL594_exp - IL594_stat  (L)

value: exponential

value: stationary


title: TL11 (S2629)

status: Public on Mar 01 2010

city: Chiba

first: Takashi

last: Takabatake

state: Chiba

address: Anagawa 4-9-1, Inage-ku

country: Japan

institute: National Institute of Radiological Sciences

description: US45103097_252041010004_S01_CGH-v4_95_Feb07_1_1.txt

hyb_protocol: Cy3 and Cy5 labeled probes were mixed with Mouse Cot I DNA (Invitrogen, Carlsbad, CA), 10x Blocking Agent and 2x Hybridization Buffer included in Agilent Oligo aCGH/ChIP-on-chip Hybridization Kit (Agilent). After denaturation at 95°C for 3 min and succeeding preincubation at 37 °C  for 30 min, hybridization was done for 24 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: A slide was scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using two color scan setting for 8x15k array slides (Scan Area 61x21.6mm, Scan resolution 5um).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters (protocol CGH-v4_95_Feb07 and Grid: 017823_D_F_20071007) to obtain background subtracted Processed Signal intensities. Data were analyzed with CGH analytics software v3-5-14.

source_name: reference normal tissue of S2629

label_protocol: Fluorescence labeling of DNA was carried out according to the manufacturer’s protocol (version 5) for oligonucleotide array-CGH for genomic DNA analysis (Agilent, Santa Clara, CA, USA). Briefly, 0.4 µg of genomic DNA were dizested by AluI and RsaI, then fluorescenly labeled by Cy3 or Cy5 using Genomic DNA labeling Kit Plus (Agilent). Clean-up of labeled DNA was carried out with Microcon YM-30 filters (Millopore, Billerica, MA, USA).

extract_protocol: Genomic DNA was isolated using a Maxwell 16 DNA Purification Kit (Promega Co., Madison, WI, USA).

treatment_protocol: Female B6C3F1 mice were exposed weekly to 2.0 Gy whole-body X-rays for 4 consecutive weeks starting at 4 weeks of age. X-ray irradiation was performed with a Pantak HF-320 X-ray generator (Pantak Ltd., East Haven, CT, USA) at a dose rate of 0.7 Gy/min. Mice were observed daily until moribund and then were killed under ether anesthesia.

value: ear

value: normal

source_name: thymic lymphoma of S2629

value: thymus

value: lymphoma


title: MDCC39_Tumor_56

description: This tumor is ALT-positive.

value: Liposarcoma


title: PTIP KO2

description: Dressler 10666


title: PTIP KO1

description: Dressler 10663


title: TL8 (S2511)

description: US45103097_252041010004_S01_CGH-v4_95_Feb07_1_2.txt

source_name: reference normal tissue of S2511

source_name: thymic lymphoma of S2511


title: 21158_Tumor_49

description: This tumor is ALT-positive.


title: LBC Cytol_22

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

country: United Kingdom

institute: University College London

description: normal and preinvasive (high-grade squamous intraepithelial lesion) cervical samples, matched for age, were drawn from routine cytopathology workload of the Cytology Department.

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

source_name: genomic DNA from cervical smear Cytol_22

label_protocol: Standard Illumina Protocol for Infinium 27k Chip

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

tag: source

value: bi-sulphite converted genomic DNA from control-HPVneg

tag: diseasestatus

value: control-HPVneg

tag: ageatdraw

tag: bs conversion c1

tag: bs conversion c2

tag: sentrix id


title: LBC Cytol_94

source_name: genomic DNA from cervical smear Cytol_94


title: LBC Cytol_28

source_name: genomic DNA from cervical smear Cytol_28


title: TL20 (S2498)

description: US45103097_252041010004_S01_CGH-v4_95_Feb07_1_3.txt

source_name: reference normal tissue of S2498

tag: strain

tag: gender

tag: disease state

source_name: thymic lymphoma of S2498


title: LBC Cytol_39

source_name: genomic DNA from cervical smear Cytol_39

value: bi-sulphite converted genomic DNA from case-HPVpos

value: case-HPVpos


title: LBC Cytol_47

source_name: genomic DNA from cervical smear Cytol_47


title: LBC Cytol_66

source_name: genomic DNA from cervical smear Cytol_66


title: LBC Cytol_26

source_name: genomic DNA from cervical smear Cytol_26


title: LBC Cytol_45

source_name: genomic DNA from cervical smear Cytol_45

value: bi-sulphite converted genomic DNA from control-HPVpos

value: control-HPVpos


title: LBC Cytol_56

source_name: genomic DNA from cervical smear Cytol_56


title: LBC Cytol_49

source_name: genomic DNA from cervical smear Cytol_49


title: LBC Cytol_89

source_name: genomic DNA from cervical smear Cytol_89


title: LBC Cytol_80

source_name: genomic DNA from cervical smear Cytol_80


title: LBC Cytol_11

source_name: genomic DNA from cervical smear Cytol_11


title: LBC Cytol_99

source_name: genomic DNA from cervical smear Cytol_99


title: LBC Cytol_43

source_name: genomic DNA from cervical smear Cytol_43


title: LBC Cytol_93

source_name: genomic DNA from cervical smear Cytol_93


title: LBC Cytol_86

source_name: genomic DNA from cervical smear Cytol_86


title: LBC Cytol_58

source_name: genomic DNA from cervical smear Cytol_58


title: LBC Cytol_33

source_name: genomic DNA from cervical smear Cytol_33


title: LBC Cytol_51

source_name: genomic DNA from cervical smear Cytol_51


title: LBC Cytol_16

source_name: genomic DNA from cervical smear Cytol_16


title: LBC Cytol_01

source_name: genomic DNA from cervical smear Cytol_01


title: LBC Cytol_64

source_name: genomic DNA from cervical smear Cytol_64


title: LBC Cytol_09

source_name: genomic DNA from cervical smear Cytol_09


title: LBC Cytol_36

source_name: genomic DNA from cervical smear Cytol_36


title: LBC Cytol_100

source_name: genomic DNA from cervical smear Cytol_100


title: LBC Cytol_79

source_name: genomic DNA from cervical smear Cytol_79


title: LBC Cytol_75

source_name: genomic DNA from cervical smear Cytol_75


title: LBC Cytol_41

source_name: genomic DNA from cervical smear Cytol_41


title: LBC Cytol_73

source_name: genomic DNA from cervical smear Cytol_73


title: LBC Cytol_61

source_name: genomic DNA from cervical smear Cytol_61


title: LBC Cytol_53

source_name: genomic DNA from cervical smear Cytol_53


title: LBC Cytol_63

source_name: genomic DNA from cervical smear Cytol_63


title: LBC Cytol_57

source_name: genomic DNA from cervical smear Cytol_57


title: LBC Cytol_13

source_name: genomic DNA from cervical smear Cytol_13


title: LBC Cytol_23

source_name: genomic DNA from cervical smear Cytol_23


title: LBC Cytol_74

source_name: genomic DNA from cervical smear Cytol_74


title: LBC Cytol_78

source_name: genomic DNA from cervical smear Cytol_78


title: LBC Cytol_02

source_name: genomic DNA from cervical smear Cytol_02


title: LBC Cytol_19

source_name: genomic DNA from cervical smear Cytol_19


title: LBC Cytol_95

source_name: genomic DNA from cervical smear Cytol_95


title: LBC Cytol_52

source_name: genomic DNA from cervical smear Cytol_52


title: LBC Cytol_91

source_name: genomic DNA from cervical smear Cytol_91


title: LBC Cytol_50

source_name: genomic DNA from cervical smear Cytol_50


title: LBC Cytol_25

source_name: genomic DNA from cervical smear Cytol_25


title: LBC Cytol_32

source_name: genomic DNA from cervical smear Cytol_32


title: LBC Cytol_54

source_name: genomic DNA from cervical smear Cytol_54


title: LBC Cytol_21

source_name: genomic DNA from cervical smear Cytol_21


title: Whole Blood DN192r

description: whole blood from cases and controls, matched for age and sex, were drawn from two irish cohorts. Three replicates labeled with an r are included.

source_name: genomic DNA from whole blood DN192r

extract_protocol: DNA was extracted from whole blood of T1D patients using a salting out method

value: bi-sulphite converted genomic whole blood DNA from Case

tag: case/control

value: Case

tag: ageatdiagnosis

tag: sex

value: F

tag: cohort

value: Belfast

value: L


title: Whole Blood DDC57r

source_name: genomic DNA from whole blood DDC57r

value: bi-sulphite converted genomic whole blood DNA from Control

value: Control

value: M

value: Dublin

value: J


title: Whole Blood DDC22r

source_name: genomic DNA from whole blood DDC22r

value: H


title: Whole Blood DN330

source_name: genomic DNA from whole blood DN330

value: K


title: Whole Blood DC542

source_name: genomic DNA from whole blood DC542

value: D


title: Whole Blood DC472

source_name: genomic DNA from whole blood DC472

value: B


title: Whole Blood DDC128

source_name: genomic DNA from whole blood DDC128

value: A


title: Whole Blood DN117

source_name: genomic DNA from whole blood DN117


title: Whole Blood DC538

source_name: genomic DNA from whole blood DC538


title: Whole Blood DC471

source_name: genomic DNA from whole blood DC471


title: Whole Blood DN147

source_name: genomic DNA from whole blood DN147

value: C


title: Whole Blood DDC10

source_name: genomic DNA from whole blood DDC10

value: I


title: Whole Blood DN83

source_name: genomic DNA from whole blood DN83

value: bi-sulphite converted genomic whole blood DNA from Case


title: Whole Blood DN329

source_name: genomic DNA from whole blood DN329

value: Case


title: Whole Blood DN198

source_name: genomic DNA from whole blood DN198

value: G


title: Whole Blood DDN67

source_name: genomic DNA from whole blood DDN67

value: F


title: Whole Blood DDN50

source_name: genomic DNA from whole blood DDN50


title: Whole Blood DDC113

source_name: genomic DNA from whole blood DDC113


title: Whole Blood DC229

source_name: genomic DNA from whole blood DC229

value: Belfast


title: Whole Blood DDN23

source_name: genomic DNA from whole blood DDN23


title: Whole Blood DC103

source_name: genomic DNA from whole blood DC103

value: bi-sulphite converted genomic whole blood DNA from Control


title: Whole Blood DDC102

source_name: genomic DNA from whole blood DDC102

value: Control

value: E


title: Whole Blood DC172

source_name: genomic DNA from whole blood DC172


title: Whole Blood DDC82

source_name: genomic DNA from whole blood DDC82

value: Dublin


title: Whole Blood DDC37

source_name: genomic DNA from whole blood DDC37


title: Whole Blood DDC49

source_name: genomic DNA from whole blood DDC49

value: M

value: L


title: Whole Blood DDN81

source_name: genomic DNA from whole blood DDN81

value: K


title: Whole Blood DDN66

source_name: genomic DNA from whole blood DDN66


title: Whole Blood DDC100

source_name: genomic DNA from whole blood DDC100


title: Whole Blood DDN8

source_name: genomic DNA from whole blood DDN8


title: Whole Blood DDN6

source_name: genomic DNA from whole blood DDN6


title: Whole Blood DDN21

source_name: genomic DNA from whole blood DDN21


title: Whole Blood DDC112

source_name: genomic DNA from whole blood DDC112

value: D


title: Whole Blood DDN49

source_name: genomic DNA from whole blood DDN49


title: Whole Blood DC35

source_name: genomic DNA from whole blood DC35

value: J


title: Whole Blood DC95

source_name: genomic DNA from whole blood DC95


title: Whole Blood DDC22

source_name: genomic DNA from whole blood DDC22

value: H

value: Grn 787

value: Grn 576


title: Whole Blood DDC66

source_name: genomic DNA from whole blood DDC66

value: A


title: Whole Blood DDC111

source_name: genomic DNA from whole blood DDC111


title: Whole Blood DDC6

source_name: genomic DNA from whole blood DDC6


title: Whole Blood DDN20

source_name: genomic DNA from whole blood DDN20

value: bi-sulphite converted genomic whole blood DNA from Case

value: Case


title: Whole Blood DDC110

source_name: genomic DNA from whole blood DDC110

value: F

value: G


title: Whole Blood DN81

source_name: genomic DNA from whole blood DN81

value: Belfast


title: Whole Blood DDN63

source_name: genomic DNA from whole blood DDN63


title: Whole Blood DDN35

source_name: genomic DNA from whole blood DDN35


title: Whole Blood DDC93

source_name: genomic DNA from whole blood DDC93

value: bi-sulphite converted genomic whole blood DNA from Control

value: Control


title: Whole Blood DDN62

source_name: genomic DNA from whole blood DDN62

value: Dublin


title: Whole Blood DDN47

source_name: genomic DNA from whole blood DDN47

value: M


title: Whole Blood DN35

source_name: genomic DNA from whole blood DN35

value: B


title: Whole Blood DDC79

source_name: genomic DNA from whole blood DDC79

value: C


title: Whole Blood DDN46

source_name: genomic DNA from whole blood DDN46

value: L


title: Whole Blood DDC5

source_name: genomic DNA from whole blood DDC5


title: Whole Blood DDN19

source_name: genomic DNA from whole blood DDN19


title: Whole Blood DC5

source_name: genomic DNA from whole blood DC5


title: Whole Blood DDN18

source_name: genomic DNA from whole blood DDN18


title: Whole Blood DN78

source_name: genomic DNA from whole blood DN78


title: Whole Blood DDC57

source_name: genomic DNA from whole blood DDC57

value: I

value: Grn 830


title: Whole Blood DC234

source_name: genomic DNA from whole blood DC234


title: Whole Blood DDN44

source_name: genomic DNA from whole blood DDN44


title: Whole Blood DDC108

source_name: genomic DNA from whole blood DDC108

value: D


title: Whole Blood DDN32

source_name: genomic DNA from whole blood DDN32

value: E


title: Whole Blood DDN5

source_name: genomic DNA from whole blood DDN5


title: Whole Blood DC17

source_name: genomic DNA from whole blood DC17

value: K


title: Whole Blood DDN34

source_name: genomic DNA from whole blood DDN34

value: bi-sulphite converted genomic whole blood DNA from Case

value: J


title: Whole Blood DN108

source_name: genomic DNA from whole blood DN108

value: Case

value: F


title: Whole Blood DDN92

source_name: genomic DNA from whole blood DDN92


title: Whole Blood DDN55

source_name: genomic DNA from whole blood DDN55


title: Whole Blood DN106

source_name: genomic DNA from whole blood DN106

value: Belfast

value: G


title: Whole Blood DDN42

source_name: genomic DNA from whole blood DDN42


title: Whole Blood DDC91

source_name: genomic DNA from whole blood DDC91

value: bi-sulphite converted genomic whole blood DNA from Control

value: Control


title: Whole Blood DDC29

source_name: genomic DNA from whole blood DDC29

value: Dublin


title: Whole Blood DDN74

source_name: genomic DNA from whole blood DDN74

value: Grn 0


title: Whole Blood DDC87

source_name: genomic DNA from whole blood DDC87

value: M


title: Whole Blood DN54

source_name: genomic DNA from whole blood DN54


title: Whole Blood DDC41

source_name: genomic DNA from whole blood DDC41

value: L


title: Whole Blood DDN79

source_name: genomic DNA from whole blood DDN79


title: Whole Blood DDN76

source_name: genomic DNA from whole blood DDN76

value: C


title: Whole Blood DDN54

source_name: genomic DNA from whole blood DDN54

value: A


title: Whole Blood DDC3

source_name: genomic DNA from whole blood DDC3


title: Whole Blood DC28

source_name: genomic DNA from whole blood DC28

value: Grn 602

value: Grn 278


title: Whole Blood DDN3

source_name: genomic DNA from whole blood DDN3


title: Whole Blood DDN86

source_name: genomic DNA from whole blood DDN86


title: Whole Blood DDC14

source_name: genomic DNA from whole blood DDC14


title: Whole Blood DDN16

source_name: genomic DNA from whole blood DDN16

value: H


title: Whole Blood DDN41

source_name: genomic DNA from whole blood DDN41

value: bi-sulphite converted genomic whole blood DNA from Case


title: Whole Blood DDN29

source_name: genomic DNA from whole blood DDN29

value: J