title: HPC5-HPC5 replicate 2_R14BR20B

description: Biological replicate 2 of 3. Control HPC5 to HPC5 itself


title: CD8_MP_Zeb2-KO_lumi.1

status: Public on Sep 15 2015

type: RNA

city: New Haven

first: Susan

middle: M

last: Kaech

state: CT

address: 300 Cedar St, TAC S640

department: Immunobiology

country: USA

institute: Yale University

description:
Illumina Microarray of MP (KLRG1lo IL7Rhi) Zeb2-KO P14 CTLs isolated 8 d.p.i. with LCMV replicate 1
6096357002_A

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Utilized R::beadarray package with the readIdatFiles and normaliseIllumina functions to extract raw and normalised (neqc, log2 transformed) values.

label: biotin

molecule: polyA RNA

organism: Mus musculus

label_protocol: standard Illumina protocol

extract_protocol: Rneasy with on column digestion

tag: strain background

tag: genotype/variation

value: Zeb2-KO; GzmB-Cre Zeb2-fl/fl

tag: age

tag: time point

value: 8 d.p.i. with LCMV

tag: cell type

value: cytotoxic T lymphocyte (CTL)

tag: cell subtype

value: MP (KLRG1lo IL7Rhi)


title: HPC5-R20A replicate 1_R14AR20A

city: Leicestershire

first: Amy

last: John

address: Loughborough

country: United Kingdom

institute: University of Nottingham

description: Biological replicate 1 of 3. Control HPC5 to R20A

hyb_protocol: The slides used for the genome analysis were γ APS coated, A+ bar-coded Schott nexterion slides. The slides were printed according to campy dense array gal by Microgrid II 600 robot using TAS software version V2.4.03. They had 12 pins with a 26 x 26 pin grid configuration. The spacing between the spots was 0.165mm and the slides were prepared at 60% humidity. Each slide was printed with duplicate sets of oligos for NCTC 11168, RM1221 and RM2228. A sample of each labelled probe (one cy3, one cy5) for each slide was taken to be hybridized which contained 500ng of labelled DNA and placed them together in a 0.5 ml tube.  The volume was adjusted to 4.5µl total volume by adding nuclease free water. To each tube 0.5 µl of Fragmentation Buffer was added before being incubated at 70OC (in Thermo Cycler) for 2 min followed by 0.5 µl of Stop Solution (Ambion Kit 8740).  This was followed by the addition of 2µl Lithium Heperin (to reduce non specific hybridization). Add 100 µl of Schott 1x Hybridization Buffer which was pre-warmed to 50OC and added to the probe carefully to avoid introducing any air bubbles.  The total volume was 107.5 µl.  The DNA microarray slides were blocked before hybridisation by using blocking solution (5xSSC, 0.2%SDS, 1%BSA). After blocking, the slides were washed in ultra pure water and then in 100% ethanol. The prepared slides were kept in the slide holder and were inserted into the TECAN HS 4800 chamber. Approximately 5 min before the probes were inserted they were heated to 95o C for 2 min and then spun at 15.000rpm for 5 minutes in a microcentrifuge to pellet up any impurities. The probe was injected into the hybridisation chamber. The hybridisation was done at 45º C for 16h with gentle agitation. After hybridisation the slides were washed in 1 X SSC buffer with 0.6% SDS for 2 min, followed by two washes in 0.06 X SSC buffer, each for 2 min. The slides are then dried at 23º C with nitrogen.

scan_protocol: Slides were scanned using Axon Genepix 4200AL scanner (Molecular Devices Corporation, Sunnyvale, CA ) at 532 (Cy3) and 635 (Cy5) excitation wavelengths with 5 µm resolution. The slides were scanned using the Auto PMT function with the threshold for saturation set at 0.05%.  Fluorescent spot intensities were quantified using Genepix Pro 6.0 software. Spots were excluded from further analysis if they contain anomalous spot morphology or were within regions of non-specific fluorescence.

data_processing: The data was analysed by Genespring GX 7.3  and the oligos which have more than 2 fold change and p<0.05 were selected for further studies.

molecule: total RNA

organism: Campylobacter jejuni

source_name: Campylobacter cells isolated from Chicken

label_protocol: 1. Add 5 μl of nuclease free water and heat it to 42°C for 5 min.  2. Add 3 μl labelling buffer to it (25 mg/ ml sodium bicarbonate).  3. Dissolve 1 vial of AF555/645 (Fisher, UK) in 2 μl DMSO and vortex it for 10 sec and add it to 8 μl cDNA labelling buffer mix.  4. Incubate at room temperature for 1 hr in the dark.  5. Add 80 μl of water and 10 μl of sodium acetate (3M) and purify using QIA PCR purification kit but wash three times with 70% ethanol.  7. Precipitate DNA using 3M sodium acetate and 100% ethanol and resuspend it in nuclease free water.   8. Quantify and check label.

growth_protocol: C. jejuni HPC5 and its daughter strains, R14A and R20A were grown in Nutrient broth (NB No. 2, Oxoid, UK) until it reaches 107 – 108 cfu /ml (~ 9 hrs except for R20 which is grown for 12 h).

extract_protocol: The cells were collected by spinning it in pre chilled tubes @ 6000x g for 15 min in beckman centrifuge. Maximum Enhancement Reagent of 200 µl was preheated to 95ºC and was added to the tube. The cell mix was heated at 95 ºC for 4 min. To it 1ml of trizol was added and was mixed well. It was incubated at room temperature for 5 min. After incubation it was spun for 15 min at 12000 x g at 4 ºC. Approximately 400 µl of the top phase was transferred to a fresh eppendorf. To it 700 µl of 100% ethanol was added and mixed thoroughly. This was used in RNA clean up kit (Qiagen, UK) according to the manufacturer’s instructions. For the synthesis of cDNA, SuperscriptTM direct cDNA labelling system (Invitrogen, UK) was used according to manufacturer’s instructions.    QIA quick PCR Purification kit was used for purifying the product (Qiagen, UK).  The cDNA produced was ethanol precipitated by adding 0.1 v of sodium acetate (3M) and 2.5 v 100% ethanol.

treatment_protocol: Not applicable

tag: strain

tag: sample type

value: control (representing 7 independent preps of C. jejuni HPC5)

value: test


title: Developing seed at 72HAF drought, biological rep2

city: Gainesville

first: Kevin

last: Begcy

state: Florida

address: 1535 Fifield Hall

institute: University of Florida

description:
Gene expression of developing seeds
Endosperm - Whole seed
Wheat_72HAF_s2

hyb_protocol: Hybridization was done on a GeneChip Wheat Genome Array.

scan_protocol: GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: Affymetrix GeneChip Operating Software generated the images and probe set signal values as CEL files, and the CEL files were processed with the affy package using the robust multiarray analysis (RMA) to generate normalized signal values. The RMA signal values were log2 transformed. To detect differentially expressed genes, the transformed RMA expression values were analyzed with an empirical Bayes linear model. A probeset was considered differentially expressed when it satisfied two conditions, up-regulation or down-regulation more than 2-fold after drought treatment; and a false discovery rate-adjusted P-value was less than <0.05.

label: Biotin

organism: Triticum aestivum

source_name: Wheat seeds 72 hours after fertilization - drought

label_protocol: 15 µg of total RNA was used to synthesize cDNA using Affymetrix One-Cycle cDNA Synthesis Kit according to the manufacturer’s instructions (Affymetrix, Santa Clara, CA).

growth_protocol: Winter wheat cultivar Redland, PI 502907 (Triticum aestivum L.) seedlings were vernalized at 4°C for 6 weeks and then transplanted to a one gallon pot of soil-sand mixture (3:1, v/v) and grown in a growth chamber under the following conditions: relative humidity, 50–70%; 16-h light/8-h dark photoperiod; 21°C daytime temperature and 18°C nights. Plants were watered regularly twice daily at the rate of 100ml/ per pot. Because, wheat has an asynchronous fertilization pattern for ovlues in the inflorescence, each floret needs to be specifically marked for timing the fertilization and stress induction. After spikes developed, unfertilized ovules were monitored and observed for the fertilization process. Closed wheat spikes with anthers outside were marked as fertilized. Drought stress was imposed 24h after the fertilization (HAF).

extract_protocol: Total RNA were isolated from seeds of drought-stressed and control plants at 24, 48 and 72 HAF from. Total RNA was isolated using a Trizol (Invitrogen, Carlsbad, CA) protocol and puriﬁed using an RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany). Total RNA quality and concentration were determined on a 2100 Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: Drought stress treatment was initiated by discontinuing watering on the drought treatment plants while control plants were regularly watered twice daily. Stress treatment was applied at 48 HAF and relieved at 96 HAF (Fig. S1).

tag: stress

value: drought

tag: time

tag: tissue

value: developing seed


title: HPC5-R20A replicate 3_R14AR20A

description: Biological replicate 3 of 3. Control HPC5 to R20A


title: Developing seed at 72HAF control, biological rep1

description:
Gene expression of developing seeds
Endosperm - Whole seed
Wheat_72HAF_c1

source_name: Wheat seeds 72 hours after fertilization - control

value: control


title: HPC5-R14A replicate 3_R14AR20A

description: Biological replicate 3 of 3. Control HPC5 to R14A


title: CD8_MP_Zeb2-KO_lumi.2

description:
Illumina Microarray of MP (KLRG1lo IL7Rhi) Zeb2-KO P14 CTLs isolated 8 d.p.i. with LCMV replicate 2
6096357002_B


title: Developing seed at 72HAF drought, biological rep1

description:
Gene expression of developing seeds
Endosperm - Whole seed
Wheat_72HAF_s1


title: Developing seed at 48HAF drought, biological rep2

description:
Gene expression of developing seeds
Endosperm - Whole seed
Wheat_48HAF_s2

source_name: Wheat seeds 48 hours after fertilization - drought


title: HPC5-R20A replicate 2_R14AR20A

description: Biological replicate 2 of 3. Control HPC5 to R20A


title: Developing seed at 48HAF drought, biological rep1

description:
Gene expression of developing seeds
Endosperm - Whole seed
Wheat_48HAF_s1


title: CD8_TE_Zeb2-KO_lumi.3

description:
Illumina Microarray of TE (KLRGhi IL7Rlo) Zeb2-KO P14 CTLs isolated 8 d.p.i. with LCMV replicate 3
6096357004_C

value: TE (KLRGhi IL7Rlo)


title: CD8_TE_Zeb2-KO_lumi.2

description:
Illumina Microarray of TE (KLRGhi IL7Rlo)Zeb2-KO P14 CTLs isolated 8 d.p.i. with LCMV replicate 2
6096357004_B


title: CD8_MP_WT_lumi.3

description:
Illumina Microarray of MP (KLRG1lo IL7Rhi) P14 CTLs isolated 8 d.p.i. with LCMV replicate 3
6096357002_F

value: wild type; GzmB-Cre Zeb2+/+


title: HPC5-R20 replicate 3_R14R20

description: Biological replicate 3 of 3. Control HPC5 to R20

growth_protocol: C. jejuni HPC5 and its daughter strains were grown in Nutrient broth (NB No. 2, Oxoid, UK) until it reaches 107 – 108 cfu /ml (~ 9 hrs except for R20 which is grown for 12 h).


title: HPC5-R14A replicate 2_R14AR20A

description: Biological replicate 2 of 3. Control HPC5 to R14A


title: HPC5-HPC5 replicate 1_R14AR20A

description: Biological replicate 1 of 3. Control HPC5 to HPC5 itself


title: Developing seed at 48HAF control, biological rep2

description:
Gene expression of developing seeds
Endosperm - Whole seed
Wheat_48HAF_c2

source_name: Wheat seeds 48 hours after fertilization - control


title: CD8_TE_Zeb2-KO_lumi.1

description:
Illumina Microarray of TE (KLRGhi IL7Rlo) Zeb2-KO P14 CTLs isolated 8 d.p.i. with LCMV replicate 1
6096357004_A


title: HPC5-R20 replicate 2_R14R20

description: Biological replicate 2 of 3. Control HPC5 to R20


title: HPC5-HPC5 replicate 2_R14AR20A

description: Biological replicate 2 of 3. Control HPC5 to HPC5 itself


title: HPC5-HPC5 replicate 3_R14AR20A

description: Biological replicate 3 of 3. Control HPC5 to HPC5 itself


title: HPC5-R14A replicate 1_R14AR20A

description: Biological replicate 1 of 3. Control HPC5 to R14A


title: Developing seed at 48HAF control, biological rep1

description:
Gene expression of developing seeds
Endosperm - Whole seed
Wheat_48HAF_c1


title: CD8_MP_WT_lumi.1

description:
Illumina Microarray of MP (KLRG1lo IL7Rhi) P14 CTLs isolated 8 d.p.i. with LCMV replicate 1
6096357002_D


title: Ly49- CD8 cells, rep2

city: Boston

first: Hye-Jung

last: Kim

state: MA

address: 450 Brookline

department: Cancer Immunology and Virology

institute: Dana Farber Cancer Institute

description:
HC2010110805_Ly49-2
Gene expression data from Ly49- CD8 T cells.

hyb_protocol: Hybridization was done according to the Affymetrix 3' IVT Express protocol.

scan_protocol: The arrays were scanned on the GeneChip Scanner 3000 7G.

data_processing: Data were analyzed using the GenePattern software package obtained from the Broad Institute. The raw microarray data were normalized using Expression FileCreater and analyzed using the MultiPlot module in GenePattern.

source_name: Ly49- CD8 T cells

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

extract_protocol: Total RNA was extracted from sorted CD8 T cells using RNeasy kit (Qiagen) according to the manufacturer's instructions.

tag: strain/background

value: wild-type

tag: tissue derivation

value: spleen

value: conventional memory type of CD8+ T cells (CD44+CD122+Ly49-)


title: Developing seed at 24HAF, biological rep2

description:
Gene expression of developing seeds
Endosperm - Whole seed
Wheat_24HAF_c2

source_name: Wheat seeds 24 hours after fertilization


title: HPC5-R20 replicate 1_R14R20

description: Biological replicate 1 of 3. Control HPC5 to R20


title: CD8_TE_WT_lumi.3

description:
Illumina Microarray of TE (KLRGhi IL7Rlo) P14 CTLs isolated 8 d.p.i. with LCMV replicate 3
6096357004_F


title: HPC5-R14 replicate 2_R14R20

description: Biological replicate 2 of 3. Control HPC5 to R14


title: HPC5-R14 replicate 1_R14R20

description: Biological replicate 1 of 3. Control HPC5 to R14


title: Ly49- CD8 cells, rep1

description:
HC2010110802_Ly49-1
Gene expression data from Ly49- CD8 T cells.


title: CD8_MP_WT_lumi.2

description:
Illumina Microarray of MP (KLRG1lo IL7Rhi) P14 CTLs isolated 8 d.p.i. with LCMV replicate 2
6096357002_E


title: HPC5-HPC5 replicate 3_R14R20


title: Ly49+ CD8 cells, rep2

description:
HC2010110804_Ly49+2
Gene expression data from Ly49+ CD8 T cells.

source_name: Ly49+ CD8 T cells


title: CD8_TE_WT_lumi.2

description:
Illumina Microarray of TE (KLRGhi IL7Rlo) P14 CTLs isolated 8 d.p.i. with LCMV replicate 2
6096357004_E


title: HPC5-R14 replicate 3_R14R20

description: Biological replicate 3 of 3. Control HPC5 to R14


title: HPC5-HPC5 replicate 2_R14R20


title: CD8_TE_WT_lumi.1

description:
Illumina Microarray of TE (KLRGhi IL7Rlo) P14 CTLs isolated 8 d.p.i. with LCMV replicate 1
6096357004_D


title: HPC5-HPC5 replicate 1_R14R20

description: Biological replicate 1 of 3. Control HPC5 to HPC5 itself


title: Diffuse large B-cell lymphoma JC24

city: Stanford

first: Andrew

last: Gentles

state: CA

address: 1201 Welch Road

institute: Stanford University

hyb_protocol: Performed according to manufacturer's instructions

data_processing: MAS5 using Custom CDF chip definition files

organism: Homo sapiens

source_name: Diffuse large B-cell lymphoma

extract_protocol: Briefly, tissue sections were deparaffinized by 2 repeated incubations in 1.5 mL xylene at 37°C for 20 minutes, followed by 2 repeated incubations with 100% ethanol at 37°C for 30 minutes. Ethanol was aspirated and the pellet was allowed to air dry for 5 minutes at room temperature. The pellet was resuspended in 540 L RNA lysis buffer containing 10 mM Tris/HCL (pH 8.0), 0.1 mM EDTA (ethylenediaminetetraacetic acid; pH 8.0), 2% sodium dodecyl sulfate (SDS; pH 7.3) supplemented with 60L of 60 mg/mL proteinase K (Sigma-Aldrich, St Louis, MO) and incubated at 60°C for 20 hours until the tissue was completely solubilized. RNA was purified with an equal volume of 70% phenol (pH 4.3): 30% chloroform at room temperature and precipitated with an equal volume of isopropanol in the presence of 0.1 volume of 3 M sodium acetate (pH 5.2 (Hitachi Genetic Systems, Alameda, CA)), and 1L of 10 mg/mL of carrier glycogen at  -20°C for 1 hour. The RNA pellet was washed once in 75% ethanol, dried, and resuspended in 20- 100 L of RNase-free water. All solutions, including lysis buffer and ethanol/water solutions, were prepared using diethyl pyrocarbonate (DEPC)–treated water.

treatment_protocol: FFPE paraffin embedded

tag: morphology

value: DLBCL

value: Diffuse large B-cell lymphoma


title: Developing seed at 24HAF, biological rep1

description:
Gene expression of developing seeds
Endosperm - Whole seed
Wheat_24HAF_c1


title: Diffuse large B-cell lymphoma JC25

scan_protocol: Performed according to manufacturer's instructions


title: 1221-C101 replicate 3

type: genomic

description: Biological replicate 3 of 3. Control 1221 to C101

molecule: genomic DNA

organism: Campylobacter jejuni RM1221

source_name: Lab Stock

label_protocol: 1. Set up a labelling reaction by mixing.   9 µg Random primers (Promega, UK).  3 µg Template genome.  Make the volume to 41.5 µl by adding nuclease free water.  2. Heat at 95° C for 5 min and snap cool.  3. Add final reaction elements.  41.5 µl heated template.  1.5 µl dye-dCTP  1 µl dNTP mix (5mM dA, dT, dG, 2mM dC)  5 µl Klenow Reaction mix. (Fermentas, UK)  1 µl Klenow @ 10 U/ µl (Fermentas, UK)   4. Heat at 37° C for 1.5 hrs.   5. Min elute reaction clean up kit was used to clean up the reaction mix according to the manufacturers instructions (Qiagen, UK).

growth_protocol: The control and the sample strains (sample strains first isolated from pig) were grown in blood agar plates {Blood Agar Base no: 2 (CM271, Oxoid, UK) supplemented with 5% defibrinated horse blood (TCS, UK)} overnight at 42ºC in an anaerobic jar (Oxoid, UK) vacuumed to - 22 psi and  atmospheric pressure was restored with a gas mixture consisting of 85 % v / v nitrogen, 10 % v / v carbon dioxide and 5 % v / v hydrogen (Air Products, Crewe, UK).

extract_protocol: Genomic DNA was isolated using Qiagen genomic extraction kit (using genomic DNA buffer set Cat no: 19060 and Genomic tip20/G Cat No: 10223) according to the manufacturer’s instructions.

value: control (representing 5 independent DNA preps of C. jejuni RM1221)

organism: Campylobacter coli

source_name: Campylobacter cells isolated from pig intestinal cells


title: 1221-U101 replicate 3

description: Biological replicate 3 of 3. Control 1221 to U101


title: 1221-L101 replicate 2

description: Biological replicate 2 of 3. Control 1221 to L101


title: 1221-L101 replicate 3

description: Biological replicate 3 of 3. Control 1221 to L101


title: 1221-C101 replicate 2

description: Biological replicate 2 of 3. Control 1221 to C101


title: 1221-U101 replicate 2

description: Biological replicate 2 of 3. Control 1221 to U101


title: Diffuse large B-cell lymphoma JC23

label_protocol: Performed according to manufacturer's instructions


title: 1221-U101 replicate 1

description: Biological replicate 1 of 3. Control 1221 to U101


title: Diffuse large B-cell lymphoma JC21


title: Diffuse large B-cell lymphoma JC22


title: 1221-L101 replicate 1

description: Biological replicate 1 of 3. Control 1221 to L101


title: Diffuse large B-cell lymphoma JC19


title: Ly49+ CD8 cells, rep1

description:
HC2010110801_Ly49+1
Gene expression data from Ly49+ CD8 T cells.


title: 1221-C101 replicate 1

description: Biological replicate 1 of 3. Control 1221 to C101


title: Diffuse large B-cell lymphoma JC20


title: Lame133 Area3

city: Quebec

first: Annie

last: Gagnon

state: Quebec

address: 2440 boul. Hochelaga

country: Canada

institute: Laval University

description: Array 5

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: According to Tecan scanning protocol.

data_processing: LOESS normalized within array, background subtracted and quantile normalized between array data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Bos taurus

label_protocol:
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.
This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: Approximately 66 ± 2 hours after the second injection of PGF2 alpha, granulosa cells populations were collected by transvaginal ovarian pick-up (OPU) of the preovulatory follicle. Only follicles with a diameter equal to or greater than 12 mm were collected. In the absence of preovulatory follicle on day 57 ± 3, a second OPU was performed on day 71 ± 3. OPU was performed under the effect of an epidural injection of lidocaine, with a 19 gauge needle 1 - ½ inch and a vacuum pump. Granulosa cells were sorted under a stereomicroscope. To isolate the cells from the follicular fluid, a centrifugation at 800 × g was performed for 2 minutes at room temperature before storage. The follicular fluid was then decanted, measured and quickly immersed in liquid nitrogen. The pellet was suspended in 500 μl of PBS at 4 °C. After centrifugation for 2 minutes at 800 × g, the supernatant was removed and granulosa cells frozen in liquid nitrogen. Samples were stored at -80 °C until used.

extract_protocol: This document applies to the total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.

treatment_protocol: Cows were given folic acid and vitamin B12 (treatment group) or physiological saline (control group) three weeks before calving till 57±2 days post-calving.

tag: compound added

value: Folic Acid (320mg) and vitamin B12 (10mg)

source_name: CTR

value: Physiological saline 0.9%


title: Lame133 Area4

description: Array 6


title: Lame132 Area4

description: Array 2


title: Diffuse large B-cell lymphoma JC17


title: Lame133 Area1

description: Array 3


title: USP7_1

city: Philadelphia

first: Wayne

middle: W

last: Hancock

state: PA

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

hyb_protocol: 10 microgram of labeled aRNA was fragmented, and 6.5 microgram of the fragmented aRNA was hybridized to the Affymetrix Mouse 430A_2 chips.  Hybridization conditions were 16hrs at 45C.

scan_protocol: The chips were washed using Fluidics protocol midiEuk2v3_450 on an Affymetrix GeneChip Fluidics Station 450 and scanned on an Affymetrix Genechip Scanner.

data_processing: Microarray experiments were performed using whole-mouse-genome oligoarrays (Mouse430a, Affymetrix). Array data were analyzed using MAYDAY version 2.14

source_name: Regulatory T-cells CD4+YFP+

label_protocol: 100ng of totalRNA was labeled using Ambion's MessageAmp Premier RNA Amplification Kit (PN:4383452)

extract_protocol: Total RNA was isolated using Rneasy (Quiagen). RNA integrity and quantity was analyzed using a DU640 (Beckman-Coulter).

tag: background strain

tag: genotype

value: Regulatory T-cells (Treg)

tag: cell population


title: Diffuse large B-cell lymphoma JC18


title: B6_WT_2


title: USP7_3


title: Plasmablastic lymphoma JC15

source_name: Plasmablastic lymphoma

value: Plasmacytic

value: Plasmablastic lymphoma


title: USP7_2


title: Plasmablastic lymphoma JC13


title: Plasmablastic lymphoma JC14


title: Plasmablastic lymphoma JC12


title: Lame132 Area3

description: Array 1


title: Lame133 Area2

description: Array 4


title: B6_WT_1


title: Plasmablastic lymphoma JC11

value: Plasmablastic


title: Plasmablastic lymphoma JC9


title: Plasmablastic lymphoma JC10


title: B6_WT_3


title: Plasmablastic lymphoma JC8


title: Plasmablastic lymphoma JC6


title: Plasmablastic lymphoma JC7


title: Plasmablastic lymphoma JC5


title: Plasmablastic lymphoma JC4


title: Diffuse large B-cell lymphoma JC16


title: Plasmablastic lymphoma JC3


title: MM_Z2NHh

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

country: France

institute: ICO (Integrated Center of Oncology Nantes)

description: SUBMITTER_COMMENT: Relevant clinical data are included in the original paper, please read the article.

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

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

data_processing: Affymetrix Genotyping Console 4.0 for processing SNPs, detecting copy number abnormalities with default parameters.

source_name: Bone marrow

label_protocol: According to manufacturer protocol

extract_protocol: DNA was extracted using the DNA AllPrep DNA/RNA MiniKit (Qiagen, Valencia, CA). DNA quality and quantity were assessed using the Nanodrop Spectrophotometer (NanoDrop Technologies, Inc. Wilmington, DE).

tag: tumor

value: multiple myeloma

value: bone marrow

value: purified CD138+ plasma cells


title: MM_ip4Gc


title: MM_snHgD


title: MM_tnefp


title: MM_URlgT


title: MM_y8Kq3


title: Plasmablastic lymphoma JC2


title: MM_mdibp


title: MM_fODGQ


title: MM_xlYdQ


title: MM_JcAnb


title: Plasmablastic lymphoma JC1


title: MM_bzaI4


title: MM_qeNxi


title: MM_Ueagf


title: MM_SRFEi


title: MM_DkM0x


title: MM_OpWMR_mrc7


title: MM_SBsPK


title: MM_MgSrY


title: MM_LYN6H


title: CS_standard_biol.rep1 [re-analysis]

city: Turku

first: Taina

last: Tyystjarvi

address: Pharmacity/Itäinen Pitkäkatu 4 C, 6th floor

department: Biochemistry

country: Finland

institute: University of Turku

description:
wt1_10038_1_1_001
GSM1213398

hyb_protocol: 500 ng Cy3-labelled sample was hybridized overnight at 65 °C following instruction of Agilent's Gene Expression Hybridization kit. Washes was performed using wash buffers from Gene Expression Wash Pack (Agilent) and following the manufacturers instructions.

scan_protocol: Slides were scanned on the Agilent Technologies Scanner (G2565CA) using scan profile AgilentHD_GX_1Color (Agilent HD 1- color gene expression microarrays).

data_processing:
The scanned images were analyzed with Agilent's Feature Extraction program version 10.7.3. using  protocol GE1_107_Sep09 and Grid 016989_D_F_20070606. gProcessedSignal value and SystematicName were used to get normalized signal intensities. Data were normalized using the quantile-method.
Normalized signal intensity calculated with Chipster v3.1 analysis software

organism: Synechocystis sp. PCC 6803

source_name: cells from control strain_standard growth conditions

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 7 μg of total RNA using One-Color Microarray-Based Prokaryote Analysis (FairPlay III Labeling) Protocol Version 1.3 (August 2010) (Agilent). Agilent’s RNA Spike-In Kit was added to the samples allowing to monitor microarray workflow. Dye incorporation and cDNA concentration were measured with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Cell were grown in BG-11 medium in standard growth conditions (continuous illumination at the PPFD of 40 µmol m-2s-1, 32°C, ambient CO2)

extract_protocol: RNA isolation was done as described previously (Eisenhut, M., von Wobeser, E.A., Jonas, L., Schubert, H., Ibelings, B.W., Bauwe, H. et al. (2007) Plant Physiol. 144: 1946-1959). RNA was purified and DNase treated using RNeasy mini kit (Qiagen).

tag: genotype/variation

value: control strain

tag: phenotype

value: glucose tolerant


title: CS_standard_biol.rep3 [re-analysis]

description:
wt3_10039_1_3_003
GSM1213400


title: MM_Gw8Iv

tag: cell type


title: MM_E3Hb5


title: CS_standard_biol.rep2 [re-analysis]

description:
wt2_10038_2_3_002
GSM1213399


title: MM_Bbn6c


title: MM_5ne4V


title: MM_QC8j6


title: MM_sIk67


title: CS_standard_biol.rep4 [re-analysis]

description:
wt4_10043_2_4_004
GSM1213401


title: MM_OpWMR_w6jU


title: MM_Bbn6c_Zofy


title: 400 Resistant 5.3S line

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description: Sample name: 400 5.3S

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization in R

source_name: Resistant 5.3S line

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with murine IL-3 (10 ng/mL), 20% fetal calf serum, penicillin (100 units/mL), streptomycin (100 ug/mL), amphotericin B (250ng/mL) and gentamycin (50 ug/mL)

extract_protocol: RNA was prepared using the Qiagnen RNeasy kit

treatment_protocol: Cell lines were grown in 0.1% DMSO or 400, 600, 800nM of I-BET151

value: haematopoietic progenitor

tag: cell line

value: 5.3S line

tag: condition

value: Resistant


title: 600 Resistant 5.3 line

description: Sample name: 600 5.3

source_name: Resistant 5.3 line

tag: strain

value: 5.3 line


title: 800 Resistant 5.1 line

description: Sample name: 800 5.1

source_name: Resistant 5.1 line

value: 5.1 line


title: 400 Resistant 5.1 line

description: Sample name: 400 5.1


title: MM_8oSFD


title: 600 Resistant 5.3S line

description: Sample name: 600 5.3S


title: 600 Resistant 5.2 line

description: Sample name: 600 5.2

source_name: Resistant 5.2 line

value: 5.2 line


title: Sensitive 9.2 line

description: Sample name: DMSO 9.2

source_name: Sensitive 9.2 line

value: 9.2 line

value: Sensitive


title: 800 Resistant 5.3S line

description: Sample name: 800 5.3S


title: 600 Resistant 4.1 line

description: Sample name: 600 4.1

source_name: Resistant 4.1 line

value: 4.1 line


title: Sensitive 9.1 line

description: Sample name: DMSO 9.1

source_name: Sensitive 9.1 line

value: 9.1 line


title: ZG of ADR061

city: Cambridge

first: Junhua

last: Zhou

state: Cambridgeshire

address: CPU, Level 6, ACCI, Addenbrooke’s Hospital

institute: University of Cambridge

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-9

hyb_protocol: Hybridization cocktails containing the fragmented and labeled cDNA and additional Affymetrix hybridization controls, were incubated on the Affymetrix arrays for 17hrs +/- 1hr at 45°C.

scan_protocol: GeneChips were scanned using the GeneChip® (GCS3000) Scanner.

data_processing:
Data processing and analysis was performed using AffymetrixGeneChip Command Console Software and PartekGenomicSuite 6.5 (Partek Inc., St. Louis, MO).
Gene expressions were portrayed as the summarized log-signal of the Robust Multichip Average (RMA) with quantile normalisation and median polish for probe set summarisation.

source_name: Conn's Syndrome_ZG

label_protocol: Total RNA obtained through LCM were sent to Genomics Corelab, Cambridge Biomedical Research Centre for microarray measurement. Each RNA sample (total RNA, 1 µg) was converted to cDNA by reverse transcription. NuGEN Technologies’ Ovation Pico WTA System V2 kit was used to generate the first strand cDNA from total RNA. A DNA/RNA hetero-duplex-tagged double strand cDNA was then generated and amplified using a DNA/RNA chimeric primer (SPIA® primer), DNA polymerase and RNase H. This cDNA was fragmented by a chemical and enzymatic process using the NuGEN Technologies Encore Biotin Module to fragments between 50 and 100 base pairs in length. These fragmented products were then labeled via enzymatic attachment of a biotin-labeled nucleotide to the 3-hydroxyl ends of the fragments.

extract_protocol:
Adrenal collection protocol: The aldosterone-producing adenoma (APA) and their paired adjacent adrenal gland (for ZG and ZF) or adrenal gland cortex adjacent to pheochromocytomas were sanp-frozen by liquid nitrogen and collected from the Human Research Tissue Bank in Addenbrooke's hospital. Local ethical approval and informed consent were obtained for each patient.
Laser capture microdissection was used to acquire samples. For differentiation of ZG from ZF, sections were stained with cresyl violet using the LCM Staining Kit (AM1935, Ambion, USA). The acquired cell samples were stored in RNAlater (Ambion, USA) and TRIzol® reagent (Life Technologies, USA) at -70°C till extracted for RNA. Total DNA-free RNA was isolated using the PureLink® RNA Mini Kit and DNase Set (Life Technologies, USA) according to manufacturer’s instruction. Reverse transcription was performed using the Reverse Transcription System (Promega, USA) with a 1:1 mixture of random hexamer and oligo-dT primers according to manufacturer’s instruction. One RNA sample from the ZG of ADR121 was not analyzed as it did not pass quality control.

tag: disease

value: Conn's Syndrome

tag: patient/tissue id

value: Human adrenal tissue

tag: tissue subtype

value: Zona Glomerulosa


title: Sensitive 7.3 line

description: Sample name: DMSO 7.3

source_name: Sensitive 7.3 line

tag: tissue

value: 7.3 line


title: 600 Resistant 5.1 line

description: Sample name: 600 5.1


title: Parental MLL-AF9 line

description: Sample name: MLL-AF9

source_name: Parental MLL-AF9 line

value: MLL-AF9 line

value: Parental


title: PMSC-iPSCs

city: Beijing

first: Yang

last: Li

address: Xueyuan Road

department: cell biology department

country: China

institute: Peking University

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at Capital Bio Corporation .

scan_protocol: Arrays were scanned using an Affymetrix GCS3000 device and images were analyzed by the GCOS software (Affymetrix)

data_processing: The raw gene expression data were extracted using the GeneChip Operating Software, and the signal intensities from the mRNA channel in all arrays were normalized using the Robust Multiple-chip Analysis (RMA) algorithm and the DNA-Chip Analyzer (dChip) software (www.dchip.org)

source_name: iPS generated from PMSCs

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

growth_protocol: PMSCs were cultured in  medium consisting of DMEM/F12 (1:1), 2 mM glutamine, penicillin (100 U/mL), streptomycin (100 U/mL) and fibroblast growth factors (FGF, 5ng/mL). PMSC-iPSCs were cultured in PSCeasy medium.

extract_protocol: Total RNA was isolated using an RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions.

tag: gender

value: male

value: parotid gland


title: MM_5MGzE

value: multiple myeloma

value: bone marrow

value: purified CD138+ plasma cells


title: PMSCs

source_name: mesenchymal stem cells isolated from parotid gland


title: ZF of ADR044

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-7

source_name: Conn's Syndrome_ZF

value: Zona Fasciculata


title: MM_0DQjo


title: APA of ADR061

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-8

source_name: Conn's Syndrome_APA

value: Aldosterone-Producing Adenoma


title: ZF of ADR119

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-55


title: ZG of ADR119

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-53


title: ZF of ADR116

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-57

value: Pheochromocytoma


title: APA of ADR044

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-5


title: APA of ADR119

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-54


title: MM_3dGKy


title: APA of ADR131

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-48


title: ZG of ADR131

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-47


title: ZF of ADR121

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-42


title: ZF of ADR113

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-40


title: ZF of ADR131

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-46


title: ZG of ADR118

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-51


title: ZG of ADR044

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-6


title: MM_3wi8s

description: SUBMITTER_COMMENT: Relevant clinical data are included in the original paper, please read the article.


title: MM_14KBq


title: ZF of ADR085

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-4


title: ZG of ADR032

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-36


title: APA of ADR118

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-52


title: ZG of ADR113

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-41


title: ZF of ADR118

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-50


title: APA of ADR032

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-37


title: Sensitive 5.3 line

description: Sample name: DMSO 5.3

source_name: Sensitive 5.3 line

value: haematopoietic progenitor

value: 5.3 line

value: Sensitive


title: APA of ADR113

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-49

value: Conn's Syndrome


title: ZG of ADR086

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-31

value: Human adrenal tissue


title: KMS 28PE

source_name: Bone marrow


title: ZF of ADR032

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-35


title: ZF of ADR074

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-32


title: ZG of ADR074

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-33

value: Zona Glomerulosa


title: ZG of ADR112

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-39


title: ZF of ADR086

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-30


title: ZG of ADR115

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-28


title: APA of ADR115

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-29


title: ZF of ADR017

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-23


title: ZG of ADR116

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-56


title: APA of ADR121

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-45


title: APA of ADR106

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-24


title: ZG of ADR120

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-26


title: ZF of ADR120

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-25


title: ZF of ADR115

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-27


title: APA of ADR111

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-19


title: TU_Root_24 h_2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Treatment duration was kept 24 h

hyb_protocol: The labeled cRNA samples were hybridized on to a Whole Genome Rice 8x60k (AMADID No: 064772). 600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Slides were scanned using the Agilent Microarray Scanner G2505C at 3 micron resolution.

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

organism: Oryza sativa

source_name: Root

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

growth_protocol: Seedlings were grown hydroponically for 15 d and then treated with either control, arsenic, arsenic+thiourea and thiourea alone treatments. At 24 h after treatment, samples were harvested for RNA isolation and microarray.

extract_protocol: Using the mirVANA kit from Ambion (AM 1560).

treatment_protocol: Treatment was given through hydroponics medium.

tag: age

value: 15 d old Seedling

value: Root

tag: treatment

value: Tu


title: ZF of ADR110

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-18


title: ZF of ADR111

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-21


title: ZG of ADR085

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-3


title: ZF of ADR106

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-2


title: TU_Root_24 h_1

description: Treatment duration was kept 24 h


title: ZF of ADR112

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-38


title: As+TU_Root_24 h_2

description: Treatment duration was kept 24 h

value: As+Tu


title: ZG of ADR110

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-17


title: ZF of ADR026

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-15


title: ZG of ADR017

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-22


title: As+TU_Root_24 h_1

description: Treatment duration was kept 24 h


title: ZG of ADR111

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-20


title: APA of ADR110

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-16


title: ZF of ADR031

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-13


title: Control_Root_24 h_2

description: Treatment duration was kept 24 h

value: Control


title: As_Root_24 h_2

description: Treatment duration was kept 24 h

value: As


title: APA of ADR031

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-11


title: ZG of ADR026

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-14


title: Control_Root_24 h_1

description: Treatment duration was kept 24 h


title: ZF of ADR061

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-10


title: genomic DNA from tumor tissue_MD 118

city: Kyotofu Kyotoshi

first: Kohichiroh

last: Yasui

address: Kamigyoku Kajicho 465

department: Molecular Gastroenterology and Hepatology

country: Japan

institute: Kyoto Prefectural University of Medicine Graduate School of Medical Science

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, raw data is available in the file Unmethylated_and_methylated_signal.txt availabe on the series record.

label: Cy3 and Cy5

source_name: tumor tissue_MD 118

label_protocol: Standard Illumina Protocol

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

value: hepatocellular carcinoma

tag: hbs ag

value: negative

tag: hcv ab

tag: liverdamage

value: A

tag: child-pugh class

tag: clinical stage

value: IVa

tag: background of the liver tissue

value: Chronic hepatitis

tag: reccurence

value: reccurence


title: genomic DNA from non-tumor tissue_MD 113

source_name: non-tumor tissue_MD 113

value: non-tumorous liver

value: positive

value: no reccurence


title: TU_Shoot_24 h_1

description: Treatment duration was kept 24 h

source_name: Shoot

value: Shoot


title: genomic DNA from tumor tissue_MD 110

source_name: tumor tissue_MD 110

value: II


title: genomic DNA from tumor tissue_MD 113

source_name: tumor tissue_MD 113


title: genomic DNA from non-tumor tissue_MD 112

source_name: non-tumor tissue_MD 112

value: Iva

value: Normal liver


title: genomic DNA from tumor tissue_MD 117

source_name: tumor tissue_MD 117


title: genomic DNA from non-tumor tissue_MD 118

source_name: non-tumor tissue_MD 118


title: genomic DNA from non-tumor tissue_MD 117

source_name: non-tumor tissue_MD 117


title: genomic DNA from non-tumor tissue_MD 111

source_name: non-tumor tissue_MD 111

value: B


title: As_Shoot_24 h_2

description: Treatment duration was kept 24 h

value: 15 d old Seedling


title: As+TU_Shoot_24 h_2

description: Treatment duration was kept 24 h

value: As+Tu


title: As+TU_Shoot_24 h_1

description: Treatment duration was kept 24 h


title: genomic DNA from non-tumor tissue_MD 109

source_name: non-tumor tissue_MD 109

value: Liver cirrhosis


title: genomic DNA from tumor tissue_MD 111

source_name: tumor tissue_MD 111

value: hepatocellular carcinoma


title: Control_Shoot_24 h_1

description: Treatment duration was kept 24 h

value: Control


title: genomic DNA from non-tumor tissue_MD 108

source_name: non-tumor tissue_MD 108

value: negative

value: A

value: III


title: genomic DNA from non-tumor tissue_MD 106

source_name: non-tumor tissue_MD 106

value: reccurence


title: genomic DNA from tumor tissue_MD 112

source_name: tumor tissue_MD 112

value: IVa


title: genomic DNA from tumor tissue_MD 109

source_name: tumor tissue_MD 109

value: positive


title: genomic DNA from tumor tissue_MD 108

source_name: tumor tissue_MD 108


title: Control_Shoot_24 h_2

description: Treatment duration was kept 24 h


title: genomic DNA from non-tumor tissue_MD 110

source_name: non-tumor tissue_MD 110

value: non-tumorous liver

value: Chronic hepatitis

value: no reccurence


title: As_Shoot_24 h_1

description: Treatment duration was kept 24 h

value: Shoot

value: As


title: ZG of ADR031

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-12

source_name: Conn's Syndrome_ZG

value: Conn's Syndrome

value: Human adrenal tissue

value: Zona Glomerulosa


title: genomic DNA from non-tumor tissue_MD 103

source_name: non-tumor tissue_MD 103


title: genomic DNA from non-tumor tissue_MD 104

source_name: non-tumor tissue_MD 104

value: B

value: Liver cirrhosis


title: genomic DNA from non-tumor tissue_MD 60

source_name: non-tumor tissue_MD 60


title: genomic DNA from non-tumor tissue_MD 101

source_name: non-tumor tissue_MD 101

value: II


title: genomic DNA from tumor tissue_MD 106

source_name: tumor tissue_MD 106

value: hepatocellular carcinoma

value: negative


title: genomic DNA from tumor tissue_MD 104

source_name: tumor tissue_MD 104

value: A

value: III


title: genomic DNA from non-tumor tissue_MD 51

source_name: non-tumor tissue_MD 51


title: genomic DNA from tumor tissue_MD 60

source_name: tumor tissue_MD 60

value: reccurence


title: genomic DNA from non-tumor tissue_MD 50

source_name: non-tumor tissue_MD 50

value: positive


title: genomic DNA from non-tumor tissue_MD 59

source_name: non-tumor tissue_MD 59

value: non-tumorous liver


title: genomic DNA from tumor tissue_MD 103

source_name: tumor tissue_MD 103

value: Chronic hepatitis


title: genomic DNA from tumor tissue_MD 50

source_name: tumor tissue_MD 50


title: As_Root_24 h_1

description: Treatment duration was kept 24 h

source_name: Root

value: 15 d old Seedling

value: Root


title: genomic DNA from tumor tissue_MD 55

source_name: tumor tissue_MD 55


title: APA of ADR074

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-34

source_name: Conn's Syndrome_APA

value: Aldosterone-Producing Adenoma


title: genomic DNA from tumor tissue_MD 51

source_name: tumor tissue_MD 51

value: no reccurence


title: WT2 vs. CDPK4KO1

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: Hybridizations were done to Agilent-024169 custom whole genome Plasmodium berghei 44K arrays according to the supplier’s protocol (Agilent Technologies) using the SSC wash protocol.

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies).

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent). The data were normalized by the Agilent Feature Extraction Version A.10.5.1 using the GE2_1100_Jul11 protocol, which applies the Normalization Correction Method 'Linear And Lowess'. The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware).

organism: Plasmodium berghei

source_name: gametocytes, CDPK4(-)

label_protocol: RNA labeling was performed with the Quick Amp Fluorescent Linear Amplification Kit (Agilent Technologies) according to supplier's instructions.

growth_protocol: Wild type parasites were P. berghei strain ANKA 2.34 and WT-GFP. The act2(-) and CDPK4(-) mutant parasites have been previously described.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer's protocol.

treatment_protocol: P. berghei parasites were maintained in Theiler’s Original mice. Gametocytes were isolated from sulfadiazine-treated mice. The samples were monitored using Giemsa-stained blood smears and immunolabelling using the NAP antibody (previously called SET).

tag: strain/background

value: ANKA 2.34

tag: genotype/variation

value: CDPK4 knock out

tag: cell type

value: gametocytes

tag: biological replicate

source_name: gametocytes, WT

value: wild type


title: genomic DNA from tumor tissue_MD 48

source_name: tumor tissue_MD 48

value: B

value: II

value: Liver cirrhosis


title: genomic DNA from tumor tissue_MD 59

source_name: tumor tissue_MD 59

value: hepatocellular carcinoma

value: negative

value: A


title: genomic DNA from non-tumor tissue_MD 48

source_name: non-tumor tissue_MD 48

value: positive


title: genomic DNA from tumor tissue_MD 101

source_name: tumor tissue_MD 101


title: genomic DNA from non-tumor tissue_MD 45

source_name: non-tumor tissue_MD 45

value: non-tumorous liver


title: genomic DNA from tumor tissue_MD 45

source_name: tumor tissue_MD 45


title: genomic DNA from non-tumor tissue_MD 55

source_name: non-tumor tissue_MD 55

value: reccurence


title: CDPK4KO2 vs. WT1


title: ex5_6x Replicate 2

city: Chicago

first: Emanuele

last: Canestrari

address: 900 S. Ashland Ave.(M/C 669)

institute: University of Illinois at Chicago

hyb_protocol: The hybridization was performed according to the miRCURY LNA miRNA Array Instruction manual using a Tecan HS4800 hybridization station.

scan_protocol: The miRCURY LNA micro RNA Array slides were scanned using the Agilent G2565 BA Microarray Scanner System.

data_processing: The quantified signals were background corrected (Normexp with offset value 10) and normalized using the global Lowess regression algorithm. The normalized expression levels are expressed in a log2 scale.

source_name: RKO dicer hypomorph (ex5) cells

label_protocol: 750 ng total RNA from both sample and reference was labeled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA miRNA Hi-Power Labeling kit, Hy3/Hy5 (Exiqon,Denmark) following the procedure described by the manufaturer.

growth_protocol: Cells were cultured in serum-free PC-1 media (Lonza).

extract_protocol: Total RNA extracted using Trizol followed by two additional round of phenol-chloroform extraction.

value: dicer ex5 RKO

tag: transgene

value: cells expressing mutant RNase1


title: dicerwt_6x Replicate 1

source_name: RKO dicer wild-type cells

value: dicer wt


title: ex5_R1 Replicate 1

value: cells expressing wild-type RNase1


title: WT1 vs. A2KO2

value: ANKA 2.34

source_name: gametocytes, act2(-)

value: act2 knock out


title: genomic DNA from non-tumor tissue_MD 41

source_name: non-tumor tissue_MD 41

value: III

value: no reccurence


title: ex5_R1 Replicate 2


title: ex5_6x Replicate 1


title: dicerwt_6x Replicate 2


title: dicerwt_R1 Replicate 1


title: dicerwt_R1 Replicate 2


title: genomic DNA from tumor tissue_MD 41

source_name: tumor tissue_MD 41


title: A2KO1 vs. WT2

value: gametocytes

value: wild type


title: TU_Shoot_24 h_2

description: Treatment duration was kept 24 h

source_name: Shoot

value: 15 d old Seedling

value: Shoot

value: Tu


title: cell line control4

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: human cholangiocellular carcinoma

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Cells were grown in RPM I 1640(sample1～4) or DMEM (sample5～8) supplemented with 10% fetal bovine serum in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: CCC cells were treated with 0.1μg/ml gemcitabine or without gemcitabine for 48 h.

tag: cell line

value: CCC


title: ZG of ADR106

description:
Gene expression data from snap-frozen human adrenals using liquid nitrogen and the cells for RNA extraction were collected by laser capture microdissection
Affy0257-1

source_name: Conn's Syndrome_ZG

tag: disease

value: Conn's Syndrome

tag: patient/tissue id

tag: tissue

value: Human adrenal tissue

tag: tissue subtype

value: Zona Glomerulosa


title: cell line gemcitabine4

tag: treatment

value: 0.1ug/ml gemcitabine for 48hrs


title: cell line control3


title: cell line gemcitabine3


title: X8942326097_PO1.1

city: Huddinge

first: Ingrid

last: Dahlman

address: Hälsovägen 7

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

description:
4876b
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

data_processing: data was normalized and analyzed using Genom Studio software, R packages and Qlucore software.

label_protocol: Standard Illumina protocol for Human Methylation 450K DNA Analysis bead chip

extract_protocol: Genomic DNA was prepared from fat cells using the  QiAamp DNA Mini kit (cat no. 51304, Qiagen, Hilden, Germany).

tag: gender

value: Female

value: Fat cell

tag: disease state

value: obese

tag: age

tag: bmi


title: cell line control2


title: cell line gemcitabine2


title: X8942326097_PO1.3

description:
4982b
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: cell line gemcitabine1


title: X8942326097_PO1.2

description:
4957b
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: cell line control1


title: X8942300210_PO1.2

description:
4958b
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: X8942300210_PO1

description:
4985b
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: X8942326097_PO1

description:
4991b
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: TB08.0589_benign

status: Public on Sep 14 2015

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

description:
tumour robotic radical prostatectomy tissue from patient TB08.0589
processed data file: A1942_8_processed_matrix.txt, column TB08.0589_1_T

hyb_protocol: Standard Illumina hyb protocol; samples run by AROS (Denmark)

scan_protocol: Standard Illumina scan protocol; samples run by AROS (Denmark)

data_processing:
Data were pre-processed and quality checked using ‘Call Rate QC’ (AROS), gender calls from PennCNV (Wang et al., 2007); sample pairings were confirmed using BADGER (Lynch et al., 2012).
Processed data files include Genotype: AA,AB,BB,or NC (no call), GC_Score,  Theta, R, B_Allele_Freq and Log_R_Ratio.

source_name: tissue core

label_protocol: Standard Illumina label protocol; samples run by AROS (Denmark)

extract_protocol: Qiagen AllPrep, according to manufacturer's instructions.

treatment_protocol: When available (i.e not CRPC samples), matched tumour and benign tissues were identified and prepared from RP surgical tissue as described in Warren et al. (2013).  The Prostate.  73:  194-202.  Matched whole blood samples were obtained from selected samples at treatment clinics.

value: prostate

tag: sample type

value: benign

tag: tumour %


title: X8942300210_PO1.1

description:
4938b
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: TB08.0327_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0327
processed data file: A1942_5_processed_matrix.txt, column TB08.0327_1_T

value: tumour

tag: tumour gleason

tag: (derived data) iclusterplus group

tag: extra-capsular extension (ece)

value: N

tag: positive surgical margins (psm)

tag: biochemical relapse (bcr)

tag: time to bcr (months)

value: ERG gene fusion status:EDEL


title: X8942326001_PO1.3

description:
4971b
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

tag: cell type


title: TB09.0448_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.0448
processed data file: A1942_3_processed_matrix.txt, column TB09.0448_8_T

value: ERG gene fusion status:N


title: X8942326001_PO1

description:
4979b
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: TB09.0592_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.0592
processed data file: A1942_8_processed_matrix.txt, column TB09.0592_17_T

value: Y

value: ERG gene fusion status:2ESPLIT


title: TB09.0421_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.0421
processed data file: A1942_8_processed_matrix.txt, column TB09.0421_15_T

value: ERG gene fusion status:2EDEL


title: TB08.1053_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.1053
processed data file: A1942_8_processed_matrix.txt, column TB08.1053_5_T

value: ERG gene fusion status:ESPLIT


title: X8942326001_PO1.2

description:
4946b
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: X8221932080_PO1

description:
4975b
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: TB08.0588_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0588
processed data file: A1942_8_processed_matrix.txt, column TB08.0588_1_T


title: TB08.0533_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0533
processed data file: A1942_8_processed_matrix.txt, column TB08.0533_6_T


title: TB08.0691_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0691
processed data file: A1942_8_processed_matrix.txt, column TB08.0691_13_T


title: TB08.0816_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0816
processed data file: A1942_8_processed_matrix.txt, column TB08.0816_2_T


title: TB08.0877_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0877
processed data file: A1942_8_processed_matrix.txt, column TB08.0877_19_T


title: TB08.0997_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0997
processed data file: A1942_8_processed_matrix.txt, column TB08.0997_2_T


title: TB09.0550_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.0550
processed data file: A1942_8_processed_matrix.txt, column TB09.0550_15_T


title: X8942326001_PO1.1

description:
4666b
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: TB09.0720_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.0720
processed data file: A1942_8_processed_matrix.txt, column TB09.0720_19_T


title: TB09.0706_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.0706
processed data file: A1942_8_processed_matrix.txt, column TB09.0706_5_T


title: X8221932080_PO1.3

description:
4966b
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: TB09.0443_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.0443
processed data file: A1942_8_processed_matrix.txt, column TB09.0443_3_T


title: TB09.0295_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.0295
processed data file: A1942_8_processed_matrix.txt, column TB09.0295_2_T


title: TB09.0272_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.0272
processed data file: A1942_8_processed_matrix.txt, column TB09.0272_6_T


title: TB09.0238_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.0238
processed data file: A1942_8_processed_matrix.txt, column TB09.0238_5_T


title: TB09.0219_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.0219
processed data file: A1942_8_processed_matrix.txt, column TB09.0219_2_T


title: TB08.0927_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0927
processed data file: A1942_8_processed_matrix.txt, column TB08.0927_5_T


title: TB09.0217_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.0217
processed data file: A1942_8_processed_matrix.txt, column TB09.0217_7_T


title: X8221932080_PO1.2

description:
4649b
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: TB08.1063_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.1063
processed data file: A1942_8_processed_matrix.txt, column TB08.1063_8_T


title: X8221932080_PO1.1

description:
4595b
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: TB08.1026_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.1026
processed data file: A1942_8_processed_matrix.txt, column TB08.1026_17_T


title: TB08.1083_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.1083
processed data file: A1942_8_processed_matrix.txt, column TB08.1083_3_T


title: TB08.1019_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.1019
processed data file: A1942_8_processed_matrix.txt, column TB08.1019_2_T


title: 455-750K

city: Shanghai

first: Feng

last: Xu

state: Shanghai

address: 600 Yishan Road

department: Hematology

institute: Shanghai Jiaotong University Affiliated Sixth People's Hospital

description: Hybridized to 750K

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner7G.

data_processing:
The data were analyzed using the Nexus Copy Number (version 7.5, Biodiscovery Inc., El Segundo, CA,USA) software program.Data was normalized using the SNP-FASST2 segmentation algorithm.
Normalized probe intensity and allele ratio data were visualized in Nexus v7.5.

source_name: myelodysplastic syndromes

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix

growth_protocol: primary MDS mononuclear cells, no growth protocol

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of primary MDS mononuclear cells at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Spectrophotometer and agarose gel electrophoresis.

value: myelodysplastic syndromes

value: primary MDS mononuclear cells


title: TB08.1015_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.1015
processed data file: A1942_8_processed_matrix.txt, column TB08.1015_9_T


title: 2000-750K

description: Hybridized to 750K


title: TB09.0413_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.0413
processed data file: A1942_8_processed_matrix.txt, column TB09.0413_8_T


title: TB08.0872_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0872
processed data file: A1942_8_processed_matrix.txt, column TB08.0872_2_T


title: 1694-750K

description: Hybridized to 750K


title: 574-750K

description: Hybridized to 750K


title: TB08.0986_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0986
processed data file: A1942_8_processed_matrix.txt, column TB08.0986_2_T


title: 2131-750K

description: Hybridized to 750K


title: TB08.0987_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0987
processed data file: A1942_8_processed_matrix.txt, column TB08.0987_6_T


title: TB08.0848_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0848
processed data file: A1942_8_processed_matrix.txt, column TB08.0848_10_T


title: TB08.0817_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0817
processed data file: A1942_8_processed_matrix.txt, column TB08.0817_14_T


title: TB08.0763_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0763
processed data file: A1942_8_processed_matrix.txt, column TB08.0763_12_T


title: TB08.0719_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0719
processed data file: A1942_8_processed_matrix.txt, column TB08.0719_11_T


title: TB08.0973_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0973
processed data file: A1942_8_processed_matrix.txt, column TB08.0973_9_T


title: 2023-750K

description: Hybridized to 750K


title: TB08.0667_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0667
processed data file: A1942_8_processed_matrix.txt, column TB08.0667_9_T


title: TB08.0598_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0598
processed data file: A1942_8_processed_matrix.txt, column TB08.0598_12_T


title: TB08.0519_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0519
processed data file: A1942_8_processed_matrix.txt, column TB08.0519_14_T


title: TB08.0341_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0341
processed data file: A1942_7_processed_matrix.txt, column TB08.0341_5_T


title: TB08.0501_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0501
processed data file: A1942_7_processed_matrix.txt, column TB08.0501_8_T


title: TB08.0311_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0311
processed data file: A1942_7_processed_matrix.txt, column TB08.0311_2_T


title: TB08.0262_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0262
processed data file: A1942_7_processed_matrix.txt, column TB08.0262_3_T


title: TB11.1693_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.1693
processed data file: A1942_7_processed_matrix.txt, column TB11.1693_12_B

value: see matched tumour sample

value: ERG gene fusion status:see matched tumour sample


title: 1000-750K

description: Hybridized to 750K


title: TB12.0392_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.0392
processed data file: A1942_7_processed_matrix.txt, column TB12.0392_3_B


title: TB11.1833_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.1833
processed data file: A1942_7_processed_matrix.txt, column TB11.1833_14_B


title: TB11.1035_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.1035
processed data file: A1942_7_processed_matrix.txt, column TB11.1035_1_B


title: TB12.1505_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.1505
processed data file: A1942_7_processed_matrix.txt, column TB12.1505_11_B


title: TB12.1447_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.1447
processed data file: A1942_7_processed_matrix.txt, column TB12.1447_6_B


title: 1450-750K

description: Hybridized to 750K


title: 1974-750K

description: Hybridized to 750K


title: TB12.0942_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.0942
processed data file: A1942_7_processed_matrix.txt, column TB12.0942_4_B


title: TB11.0461_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.0461
processed data file: A1942_7_processed_matrix.txt, column TB11.0461_3_B


title: TB11.0387_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.0387
processed data file: A1942_7_processed_matrix.txt, column TB11.0387_2_B


title: TB12.0654_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.0654
processed data file: A1942_7_processed_matrix.txt, column TB12.0654_15_B


title: TB12.0560_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.0560
processed data file: A1942_7_processed_matrix.txt, column TB12.0560_16_B


title: 1931-750K

description: Hybridized to 750K


title: TB11.0205_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.0205
processed data file: A1942_7_processed_matrix.txt, column TB11.0205_5_B


title: 865-750K

description: Hybridized to 750K


title: TB12.1498_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.1498
processed data file: A1942_7_processed_matrix.txt, column TB12.1498_2_B


title: 915-750K

description: Hybridized to 750K


title: TB11.1943_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.1943
processed data file: A1942_7_processed_matrix.txt, column TB11.1943_1_B


title: 1667-750K

description: Hybridized to 750K


title: TB11.1861_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.1861
processed data file: A1942_7_processed_matrix.txt, column TB11.1861_1_B


title: TB11.0308_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.0308
processed data file: A1942_7_processed_matrix.txt, column TB11.0308_2_B


title: TB11.0637_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.0637
processed data file: A1942_7_processed_matrix.txt, column TB11.0637_2_B


title: TB11.0753_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.0753
processed data file: A1942_7_processed_matrix.txt, column TB11.0753_11_B


title: TB10.1146_benign

description:
benign robotic radical prostatectomy tissue from patient TB10.1146
processed data file: A1942_7_processed_matrix.txt, column TB10.1146_8_B


title: TB10.1284_benign

description:
benign robotic radical prostatectomy tissue from patient TB10.1284
processed data file: A1942_7_processed_matrix.txt, column TB10.1284_13_B


title: TB09.1008_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.1008
processed data file: A1942_7_processed_matrix.txt, column TB09.1008_2_B


title: TB09.1408_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.1408
processed data file: A1942_7_processed_matrix.txt, column TB09.1408_26_B


title: TB09.1365_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.1365
processed data file: A1942_7_processed_matrix.txt, column TB09.1365_11_B


title: TB12.1408_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.1408
processed data file: A1942_7_processed_matrix.txt, column TB12.1408_2_B


title: TB09.0504_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB09.0504
processed data file: A1942_8_processed_matrix.txt, column TB09.0504_4_T


title: TB10.1416_benign

description:
benign robotic radical prostatectomy tissue from patient TB10.1416
processed data file: A1942_7_processed_matrix.txt, column TB10.1416_3_B


title: TB09.1424_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.1424
processed data file: A1942_7_processed_matrix.txt, column TB09.1424_15_B


title: TB10.1062_benign

description:
benign robotic radical prostatectomy tissue from patient TB10.1062
processed data file: A1942_7_processed_matrix.txt, column TB10.1062_2_B


title: TB09.1083_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.1083
processed data file: A1942_7_processed_matrix.txt, column TB09.1083_16_B


title: TB09.0817_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.0817
processed data file: A1942_7_processed_matrix.txt, column TB09.0817_16_B


title: TB08.1128_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.1128
processed data file: A1942_8_processed_matrix.txt, column TB08.1128_16_T


title: TB11.0461_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.0461
processed data file: A1942_6_processed_matrix.txt, column TB11.0461_1_T


title: TB08.1115_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.1115
processed data file: A1942_7_processed_matrix.txt, column TB08.1115_23_B


title: 1471-750K

description: Hybridized to 750K


title: TB10.0244_benign

description:
benign robotic radical prostatectomy tissue from patient TB10.0244
processed data file: A1942_7_processed_matrix.txt, column TB10.0244_17_B


title: TB10.0747_benign

description:
benign robotic radical prostatectomy tissue from patient TB10.0747
processed data file: A1942_7_processed_matrix.txt, column TB10.0747_4_B


title: TB12.1408_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.1408
processed data file: A1942_6_processed_matrix.txt, column TB12.1408_17_T


title: TB11.1693_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.1693
processed data file: A1942_6_processed_matrix.txt, column TB11.1693_6_T


title: TB09.1254_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.1254
processed data file: A1942_7_processed_matrix.txt, column TB09.1254_22_B


title: TB12.1447_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.1447
processed data file: A1942_6_processed_matrix.txt, column TB12.1447_1_T


title: TB12.1498_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.1498
processed data file: A1942_6_processed_matrix.txt, column TB12.1498_16_T


title: TB12.0677_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.0677
processed data file: A1942_6_processed_matrix.txt, column TB12.0677_7_T


title: TB12.1505_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.1505
processed data file: A1942_6_processed_matrix.txt, column TB12.1505_2_T


title: TB12.0942_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.0942
processed data file: A1942_6_processed_matrix.txt, column TB12.0942_3_T


title: TB11.2230_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.2230
processed data file: A1942_7_processed_matrix.txt, column TB11.2230_16_B


title: TB10.1416_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB10.1416
processed data file: A1942_6_processed_matrix.txt, column TB10.1416_15_T


title: TB12.0135_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.0135
processed data file: A1942_6_processed_matrix.txt, column TB12.0135_20_T


title: TB10.1062_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB10.1062
processed data file: A1942_6_processed_matrix.txt, column TB10.1062_6_T


title: TB12.0560_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.0560
processed data file: A1942_6_processed_matrix.txt, column TB12.0560_9_T


title: TB12.0654_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.0654
processed data file: A1942_6_processed_matrix.txt, column TB12.0654_5_T


title: TB12.0322_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.0322
processed data file: A1942_6_processed_matrix.txt, column TB12.0322_12_T


title: TB08.0949_benign

description:
benign robotic radical prostatectomy tissue from patient TB08.0949
processed data file: A1942_7_processed_matrix.txt, column TB08.0949_15_B


title: TB12.0170_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.0170
processed data file: A1942_6_processed_matrix.txt, column TB12.0170_2_T


title: TB12.0392_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.0392
processed data file: A1942_6_processed_matrix.txt, column TB12.0392_2_T


title: TB11.1447_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.1447
processed data file: A1942_6_processed_matrix.txt, column TB11.1447_10_T


title: TB11.1889_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.1889
processed data file: A1942_6_processed_matrix.txt, column TB11.1889_3_T


title: TB12.1231_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.1231
processed data file: A1942_6_processed_matrix.txt, column TB12.1231_11_T


title: TB11.1035_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.1035
processed data file: A1942_6_processed_matrix.txt, column TB11.1035_12_T


title: TB11.1912_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.1912
processed data file: A1942_6_processed_matrix.txt, column TB11.1912_2_T


title: TB11.1437_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.1437
processed data file: A1942_6_processed_matrix.txt, column TB11.1437_8_T


title: TB11.1861_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.1861
processed data file: A1942_6_processed_matrix.txt, column TB11.1861_11_T


title: TB11.1833_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.1833
processed data file: A1942_6_processed_matrix.txt, column TB11.1833_17_T


title: TB11.1766_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.1766
processed data file: A1942_6_processed_matrix.txt, column TB11.1766_28_T


title: TB11.1943_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.1943
processed data file: A1942_6_processed_matrix.txt, column TB11.1943_12_T


title: TB11.0675_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.0675
processed data file: A1942_6_processed_matrix.txt, column TB11.0675_12_T


title: TB11.0205_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.0205
processed data file: A1942_6_processed_matrix.txt, column TB11.0205_1_T


title: TB11.0308_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.0308
processed data file: A1942_6_processed_matrix.txt, column TB11.0308_11_T


title: TB11.0387_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.0387
processed data file: A1942_6_processed_matrix.txt, column TB11.0387_14_T


title: TB11.0340_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.0340
processed data file: A1942_6_processed_matrix.txt, column TB11.0340_1_T


title: TB11.0753_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.0753
processed data file: A1942_6_processed_matrix.txt, column TB11.0753_10_T

value: ERG gene fusion status:UNKNOWN


title: TB11.1083_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.1083
processed data file: A1942_6_processed_matrix.txt, column TB11.1083_6_T


title: TB11.2230_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.2230
processed data file: A1942_6_processed_matrix.txt, column TB11.2230_2_T


title: TB10.1284_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB10.1284
processed data file: A1942_6_processed_matrix.txt, column TB10.1284_12_T


title: TB11.2442_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.2442
processed data file: A1942_6_processed_matrix.txt, column TB11.2442_19_T


title: TB12.0518_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB12.0518
processed data file: A1942_6_processed_matrix.txt, column TB12.0518_4_T


title: TB10.0709_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB10.0709
processed data file: A1942_5_processed_matrix.txt, column TB10.0709_5_T


title: TB10.0323_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB10.0323
processed data file: A1942_5_processed_matrix.txt, column TB10.0323_2_T


title: TB10.0747_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB10.0747
processed data file: A1942_6_processed_matrix.txt, column TB10.0747_8_T


title: TB10.0529_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB10.0529
processed data file: A1942_5_processed_matrix.txt, column TB10.0529_2_T


title: TB10.0230_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB10.0230
processed data file: A1942_5_processed_matrix.txt, column TB10.0230_10_T


title: TB10.0830_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB10.0830
processed data file: A1942_6_processed_matrix.txt, column TB10.0830_12_T


title: TB08.0618_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0618
processed data file: A1942_5_processed_matrix.txt, column TB08.0618_5_T


title: TB11.1447_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.1447
processed data file: A1942_5_processed_matrix.txt, column TB11.1447_2_B


title: TB11.2182_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.2182
processed data file: A1942_5_processed_matrix.txt, column TB11.2182_9_B


title: TB10.0244_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB10.0244
processed data file: A1942_5_processed_matrix.txt, column TB10.0244_2_T


title: TB12.0518_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.0518
processed data file: A1942_5_processed_matrix.txt, column TB12.0518_12_B


title: TB12.0322_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.0322
processed data file: A1942_5_processed_matrix.txt, column TB12.0322_2_B


title: TB12.1231_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.1231
processed data file: A1942_5_processed_matrix.txt, column TB12.1231_4_B


title: TB08.0949_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.0949
processed data file: A1942_5_processed_matrix.txt, column TB08.0949_4_T


title: TB12.0135_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.0135
processed data file: A1942_5_processed_matrix.txt, column TB12.0135_21_B


title: TB12.0144_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.0144
processed data file: A1942_5_processed_matrix.txt, column TB12.0144_17_B


title: TB11.0598_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB11.0598
processed data file: A1942_6_processed_matrix.txt, column TB11.0598_2_T


title: TB12.0677_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.0677
processed data file: A1942_5_processed_matrix.txt, column TB12.0677_14_B


title: TB11.1912_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.1912
processed data file: A1942_5_processed_matrix.txt, column TB11.1912_20_B


title: TB11.1889_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.1889
processed data file: A1942_5_processed_matrix.txt, column TB11.1889_15_B


title: TB11.0695_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.0695
processed data file: A1942_5_processed_matrix.txt, column TB11.0695_12_B


title: TB11.1766_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.1766
processed data file: A1942_5_processed_matrix.txt, column TB11.1766_15_B


title: TB11.0135_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.0135
processed data file: A1942_5_processed_matrix.txt, column TB11.0135_10_B


title: TB11.1083_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.1083
processed data file: A1942_5_processed_matrix.txt, column TB11.1083_17_B


title: TB11.0340_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.0340
processed data file: A1942_5_processed_matrix.txt, column TB11.0340_2_B


title: TB11.0081_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.0081
processed data file: A1942_5_processed_matrix.txt, column TB11.0081_3_B


title: TB08.1115_tumour

description:
tumour robotic radical prostatectomy tissue from patient TB08.1115
processed data file: A1942_5_processed_matrix.txt, column TB08.1115_13_T


title: TB12.2336_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.2336
processed data file: A1942_5_processed_matrix.txt, column TB12.2336_6_B


title: TB11.0598_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.0598
processed data file: A1942_5_processed_matrix.txt, column TB11.0598_17_B


title: TB10.1104_benign

description:
benign robotic radical prostatectomy tissue from patient TB10.1104
processed data file: A1942_5_processed_matrix.txt, column TB10.1104_2_B


title: TB12.2315_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.2315
processed data file: A1942_5_processed_matrix.txt, column TB12.2315_23_B


title: TB12.1852_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.1852
processed data file: A1942_5_processed_matrix.txt, column TB12.1852_5_B


title: TB10.0323_germline

description:
whole blood sample from patient TB10.0323
processed data file: A1942_4_processed_matrix.txt, column TB10.0323_G

source_name: blood

value: blood


title: TB12.0170_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.0170
processed data file: A1942_5_processed_matrix.txt, column TB12.0170_5_B


title: TB12.1843_benign

description:
benign robotic radical prostatectomy tissue from patient TB12.1843
processed data file: A1942_5_processed_matrix.txt, column TB12.1843_1_B


title: TB08.1083_germline

description:
whole blood sample from patient TB08.1083
processed data file: A1942_4_processed_matrix.txt, column TB08.1083_G


title: TB09.1402_benign

description:
benign robotic radical prostatectomy tissue from patient TB09.1402
processed data file: A1942_5_processed_matrix.txt, column TB09.1402_18_B


title: TB11.2279_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.2279
processed data file: A1942_5_processed_matrix.txt, column TB11.2279_1_B


title: TB09.0725_germline

description:
whole blood sample from patient TB09.0725
processed data file: A1942_4_processed_matrix.txt, column TB09.0725_G


title: TB09.0413_germline

description:
whole blood sample from patient TB09.0413
processed data file: A1942_4_processed_matrix.txt, column TB09.0413_G


title: TB08.0327_germline

description:
whole blood sample from patient TB08.0327
processed data file: A1942_4_processed_matrix.txt, column TB08.0327_G


title: TB11.2442_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.2442
processed data file: A1942_5_processed_matrix.txt, column TB11.2442_1_B


title: TB10.0244_germline

description:
whole blood sample from patient TB10.0244
processed data file: A1942_4_processed_matrix.txt, column TB10.0244_G


title: TB10.1284_germline

description:
whole blood sample from patient TB10.1284
processed data file: A1942_4_processed_matrix.txt, column TB10.1284_G


title: TB11.0675_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.0675
processed data file: A1942_5_processed_matrix.txt, column TB11.0675_1_B


title: TB10.1062_germline

description:
whole blood sample from patient TB10.1062
processed data file: A1942_4_processed_matrix.txt, column TB10.1062_G


title: TB08.0949_germline 1

description:
whole blood sample from patient TB08.0949, first sample
processed data file: A1942_4_processed_matrix.txt, first column of TB08.0949_G


title: TB11.1437_benign

description:
benign robotic radical prostatectomy tissue from patient TB11.1437
processed data file: A1942_5_processed_matrix.txt, column TB11.1437_2_B


title: TB08.0262_germline

description:
whole blood sample from patient TB08.0262
processed data file: A1942_4_processed_matrix.txt, column TB08.0262_G


title: TB08.0973_germline

description:
whole blood sample from patient TB08.0973
processed data file: A1942_4_processed_matrix.txt, column TB08.0973_G


title: TB08.0311_germline

description:
whole blood sample from patient TB08.0311
processed data file: A1942_4_processed_matrix.txt, column TB08.0311_G


title: TB09.0219_germline

description:
whole blood sample from patient TB09.0219
processed data file: A1942_4_processed_matrix.txt, column TB09.0219_G


title: TB09.0448_germline

description:
whole blood sample from patient TB09.0448
processed data file: A1942_4_processed_matrix.txt, column TB09.0448_G


title: TB08.0986_germline

description:
whole blood sample from patient TB08.0986
processed data file: A1942_4_processed_matrix.txt, column TB08.0986_G