title: E0771 tumor biological rep3


title: Met-1 tumor biological rep1

status: Public on May 19 2015

type: RNA

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

country: USA

institute: National Cancer Institute, NIH

hyb_protocol: Labeled fragmented DNA was hybridized to the Affymetrix Mouse Gene 1.0ST array for 16 h at 45oC, 60 rpm.  GeneChips were washed and stained using an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip scanner 3000

data_processing:
Data were collected using Affymetrix AGCC software
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Met-1 primary mammary tumor

label_protocol: 100ng of RNA was reverse transcribed and amplified using Ambion WT expression kit following manufacturer's instructions.  Sense strand cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit.

growth_protocol: Subconfluent cell suspensions were surgically implanted in the orthotopic site (#4 mammary fat pad) of fully immunocompetent syngeneic mice and primary tumors were allowed to grow to 0.5-1.0cm diameter before harvesting and snap-freezing for RNA preparation.

extract_protocol: 15-30mg of frozen tumor was homogenized in lysis buffer and total RNA was extracted using an RNeasy Mini Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Primary tumors were dissected free of surrounding non-malignant tissue and any necrotic tissue and snap frozen in liquid nitrogen for later RNA extraction

tag: strain

value: FVB/N

tag: cell line origin

value: Genetically engineered mouse tumor


title: D2A1 tumor biological rep4

source_name: D2A1 primary mammary tumor

value: Balb/c

value: Spontanteous tumor


title: F311 tumor biological rep3

source_name: F311 primary mammary tumor


title: D2A1 tumor biological rep2


title: 64_B_2_rep_3

city: Vancouver

first: Shawn

last: Mansfield

state: BC

address: 2424 Main Mall

department: Department of Wood Science

country: Canada

institute: University of British Columbia

description: This sample is of P. chrysosporium incubated on substrate B for 20 days.  It is the third of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by The Laboratory for Advanced Genome Analysis (LAGA) at the Vancouver Prostate Centre (VPC) following NimbleGen standard operating protocol.

scan_protocol: Scanningn was performed by The Laboratory for Advanced Genome Analysis (LAGA) at the Vancouver Prostate Centre (VPC) using Axon4000B Scanner( Molecular Dynamics)

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis), quantile normalization , and background correction as implemented in the NimbleScan software package, version 2.4 (Roche NimbleGen, Inc.).

organism: Phanerodontia chrysosporium

source_name: P. chrysosporium on subsatrate B after 20 days

label_protocol: Labelling was performed by The Laboratory for Advanced Genome Analysis (LAGA) at the Vancouver Prostate Centre (VPC) following NimbleGen standard operating protocol.

growth_protocol: P. chrysosporium was cultured on malt extract agar (MEA) (Oxoid, UK) for 10 days prior to inoculation with wood wafers.

extract_protocol: Frozen wood wafers with fungal mycelia were ground to a fine powder with liquid nitrogen in an acid washed, pre-chilled mortar and pestle. Total fungal RNA was purified as previously described by Vanden Wymelenberg et al 2010 (Appl Enviro Microbiol 76:3599-3610).

treatment_protocol: Poplar wood stems were cut into 0.5 mm wafers on a microtome, sterilized for 20 min at 121°C, dried at 50°C overnight, and cooled to room temperature. The specimens were then inoculated in Petri dishes with actively growing mycelia. Approximately 5 g of wood wafers were placed in each Petri dish (exact weights were recorded), sealed and incubated at 22°C and 70 ± 5% relative humidity for 10, 20 or 30 days (time points: 10, 20 and 30, respectively). Following incubation, the wafers were removed from the Petri dishes, immediately snap-frozen in liquid nitrogen and stored at -80°C for later use. For substrates “A” and “B”, three(1) replicates were used for each substrate/fungus and incubation period combination. For substrate “C” only 2 biological replicates were employed. (1)One of the tree replicates of substrate B after 10 days failes, therfore only 2 replicates were used .

tag: substrate

value: B:low lignin, high glucose

tag: incubation time(days)

tag: tissue

value: Mycelium


title: D2A1 tumor biological rep1


title: F311 tumor biological rep4


title: 62_B_2_rep_1

description: This sample is of P. chrysosporium incubated on substrate B for 20 days.  It is the first of three biological replicates used in this experiment, each from separate cultures.


title: 6DT1 tumor biological rep4

source_name: 6DT1 primary mammary tumor


title: Met-1 tumor biological rep4


title: 60_A_2_rep_2

description: This sample is of P. chrysosporium incubated on substrate A for 20 days.  It is the second of three biological replicates used in this experiment, each from separate cultures.

source_name: P. chrysosporium on subsatrate A after 20 days

value: A:high lignin, low glucose


title: 61_A_2_rep_3

description: This sample is of P. chrysosporium incubated on substrate A for 10 days.  It is the third of three biological replicates used in this experiment, each from separate cultures.


title: TS/A-E1 tumor biological rep3

source_name: TS/A-E1 primary mammary tumor


title: F311 tumor biological rep2


title: 58_C_1_rep_2

description: This sample is of P. chrysosporium incubated on substrate C for 10 days.  It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: P. chrysosporium on subsatrate C after 10 days

value: C:average lignin, average glucose


title: 59_A_2_rep_1

description: This sample is of P. chrysosporium incubated on substrate A for 20 days.  It is the first of three biological replicates used in this experiment, each from separate cultures.


title: F311 tumor biological rep1


title: GP_022

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: Triple-negative breast cancer tumours

hyb_protocol: Double-stranded complementary DNA (cDNA) and labeled complementary RNA (cRNA) were synthesized from the total RNA and hybridized to the Affymetrix Human U133 Plus 2 gene chips (Affymetrix, Santa Clara, CA).

scan_protocol: The chips were further processed and scanned according to the manufacturer’s protocol using the GeneChip Scanner 3000 7G.

data_processing: The arrays were normzalized using the MAS 5.0 Affymetrix software (Expression Console - Affymetrix).

label: Biotin

organism: Homo sapiens

source_name: Breast tumor biospsie

label_protocol: According to manufacturer protocol

extract_protocol: Total RNA was prepared using the RNeasy® Mini kit (Qiagen, Valencia, CA). The integrity of the RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: diagnosis

value: triple negative breast cancer

tag: age at diag

tag: meta

tag: mfs (days)

tag: death

tag: os (days)

tag: er-ihc

tag: pr-ihc


title: 57_C_1_rep_1

description: This sample is of P. chrysosporium incubated on substrate C for 10 days.  It is the first of two biological replicates used in this experiment, each from separate cultures.


title: 56_B_1_rep_3

description: This sample is of P. chrysosporium incubated on substrate B for 10 days.  It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: P. chrysosporium on subsatrate B after 10 days


title: migratory CD11b+ sLN cDCs, lymph node, steady state, rep1

city: St Louis

first: Gary

middle: E

last: Grajales-Reyes

state: Mo

address: Room 7766, CSRB

department: Immunology

institute: Washington University in St. Louis

description: migratory CD11b+ sLN cDCs

hyb_protocol: Hybridized onto Mouse Gene 1.0 ST Arrays (Affymetrix).

scan_protocol: GeneChip scanner 7G+ 3000 model, Affymetrix Command Console.

data_processing: Data was analyzed using DNASTAR ArrayStar software and normalized with RMA.

source_name: Klf4fl/fl cre negative, migratory CD11b+ sLN cDCs

label_protocol: Amplified using NuGen Ovation Pico WTA amplification system. Fragmentation was performed with the NuGen encore biotin module.

growth_protocol: All animals were bred and maintained in a specific pathogen-free animal facility according to institutional guidelines and with protocols approved by the Animal Studies Committee at Washington University in St. Louis.

extract_protocol:
Progenitor sort: CDPs sorted as Lin- CD117int CD135+ CD115+ CD11c- MHC II- BM cells; pre-cDCs as Lin- CD135+ CD11c+ MHC II-BM cells.
Skin draining LN cells: migratory CD11b- sorted as CD11c+MHCIIhigh B220 neg CD11b-CD24-; migratory CD11b+ sorted as CD11c+MHC IIhigh B220 neg CD11b+CD24-; migratory CD24+ sorted as CD11c+MHC IIhigh B220 neg Sirpa neg; Resident CD11b+ sorted as CD11c+MHC II int B220 neg CD11b+CD24- Sirpa+.
Total RNA was extracted from the cells.

treatment_protocol: Mice were analyzed at steady-state.

tag: strain/background

tag: genotype/variation

value: Klf4fl/fl cre negative

tag: gender

value: female

value: lymph node

tag: cell type

value: migratory CD11b+ sLN cDCs


title: migratory CD11b- sLN cDCs, lymph node, steady state, rep1

description: migratory CD11b- sLN cDCs

source_name: Klf4fl/fl cre negative, migratory CD11b- sLN cDCs

value: migratory CD11b- sLN cDCs


title: migratory CD24+ sLN cDCs, lymph node, steady state, rep1

description: migratory CD24+ sLN cDCs

source_name: Klf4fl/fl cre negative, migratory CD24+ sLN cDCs

value: migratory CD24+ sLN cDCs


title: 53_A_1_rep_3

description: This sample is of P. chrysosporium incubated on substrate A for 10 days.  It is the thrird of three biological replicates used in this experiment, each from separate cultures.

source_name: P. chrysosporium on subsatrate A after 10 days

tag: strain


title: 55a_B_1_rep_1

description: This sample is of P. chrysosporium incubated on substrate B for 10 days.  It is the first of three biological replicates used in this experiment, each from separate cultures.


title: 63_B_2_rep_2

description: This sample is of P. chrysosporium incubated on substrate B for 20 days.  It is the second of three biological replicates used in this experiment, each from separate cultures.


title: resident CD11b sLN cDCs, lymph node, steady state, rep1

description: resident CD11b sLN cDCs

source_name: Klf4fl/fl cre negative, resident CD11b sLN cDCs

value: resident CD11b sLN cDCs


title: pre cDC cre neg, bone marrow, steady state, rep1

description: pre cDC cre neg 1

source_name: Klf4fl/fl cre negative, pre cDC cre neg

value: bone marrow

value: pre cDC cre neg


title: 52_A_1_rep_2

description: This sample is of P. chrysosporium incubated on substrate A for 10 days.  It is the second of three biological replicates used in this experiment, each from separate cultures.


title: pre cDC cre neg, bone marrow, steady state, rep2

description: pre cDC cre neg 2


title: CDP cre-pos, bone marrow, steady state, rep2

description: CDP cre pos 2

source_name: Klf4fl/fl Vav1-icre, CDP cre-pos

value: Klf4fl/fl Vav1-icre

value: CDP cre-pos


title: 51_A_1_rep_1

description: This sample is of P. chrysosporium incubated on substrate A for 10 days.  It is the first of three biological replicates used in this experiment, each from separate cultures.


title: pre cDC cre pos, bone marrow, steady state, rep1

description: pre cDC cre pos 1

source_name: Klf4fl/fl Vav1-icre, pre cDC cre pos

value: pre cDC cre pos


title: CDP cre-pos, bone marrow, steady state, rep1

description: CDP cre pos 1


title: pre cDC cre pos, bone marrow, steady state, rep2

description: pre cDC cre pos 2


title: AOCS_093_ICGC_DBDE_20131003_001

type: genomic

city: Herston

first: Ann-Marie

last: Patch

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: Raw data for arrays used for copy number analysis using GAP (Popova, et al 2009)

hyb_protocol: As per manufacturer’s instructions (Illumina, San Diego CA)

scan_protocol: Arrays were scanned  on iScan

data_processing: Data was extracted using  Genotyping module (v1.9.4) in GenomeStudio v2011.1 (Illumina, San Diego CA) to calculate B-allele frequencies (BAF) and LogR ratios.

molecule: genomic DNA

source_name: Ascites

label_protocol: DNA was assayed using Illumina SNP BeadChips as per manufacturer’s instructions (Illumina, San Diego CA) (HumanOmni2.5-8 BeadChips).

extract_protocol: Nucleic acids were extracted from frozen tissue sections were incubated in Buffer AL and proteinase K at 56°C overnight, while ascites cells were only incubated in Buffer AL and proteinase K at 56°C for 10min. Ethanol was added to sample which was applied to a DNeasy Mini spin column. Captured DNA was washed and eluted in Buffer AE. DNA was quantitated using the NanoDrop1000 (Thermo Scientific) and the Qubit® dsDNA BR assay.

value: Female

value: Ascites

value: high grade serous ovarian cancer


title: 55b_B_1_rep_2

description: This sample is of P. chrysosporium incubated on substrate B for 10 days.  It is the second of three biological replicates used in this experiment, each from separate cultures.

value: B:low lignin, high glucose

value: Mycelium


title: CDP cre-neg, bone marrow, steady state, rep2

description: CDP cre neg 2

source_name: Klf4fl/fl cre negative, CDP cre-neg

value: Klf4fl/fl cre negative

value: CDP cre-neg


title: AOCS_171_ICGC_DBDE_20131003_012


title: TS/A-E1 tumor biological rep2

value: Balb/c

tag: cell line origin

value: Spontanteous tumor


title: AOCS_171_ICGC_DBDE_20131003_011

source_name: Primarytumour

value: Primary Tumour


title: WT  T-36h

city: Boston

first: Richard

middle: Leslie

last: Stevens

state: MA

address: 1 Jimmy Fund Way

department: Medicine

institute: Harvard Medical School

description: Gene expression data of CD117+ splenocytes from C57BL/6 WT mice with  LPS stimulation for 36h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C onAffymetrix Mouse Gene 2.0 ST Array GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Ten Affymetrix Mouse Gene 2.0 ST Array GeneChips were used in these experiments and were analyzed with Affymetrix® Expression Console™ Software (Affymetrix). In this first step of the comparative analyses, the raw probe set data in each RNA/cDNA sample were normalized (Norm/Norm) based on the differences in varied isoforms of the housekeeping GAPDH transcript in the 10 samples. The deduced correction factors are indicated. The resulting GAPDH-adjusted  RasGRP4 and Kit/CD117 mRNA data are highlighted which are  the respective negative and positive controls in the experiment to document that the microarray approach worked in principle. The data with the highlighting annotation can be found on the series record in the file GAPDH-normalized data.xlsx.  The Plier output is available in the supplementary files and on the series record in the file GSE69011_PLIER.data.txt.

source_name: CD117+cell from C57BL/6 mice spleens with LPS stimulation for 36h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (MoGene-2_0-st).

extract_protocol: CD117+cells were purified from 5  C57BL/6 male  mice and 5 RasGRP4 KO male mice aged 9-12 week old with CD117 positive selection kit( StemCELL CO.) respectively.  RneasyPlus Mini kit from Qiagen Co, were used for total RNA extraction according to the manufacturer's instruction

treatment_protocol: CD117+cells were aliquoted and planted into 6-well plate with or without 1ug/ml  LPS and stimulated for 12h,24h,36h and 48h respectively

tag: background strain

tag: genotype

value: wildtype

value: spleen

tag: cells

value: CD117+ splenocytes

value: male

tag: age

value: 9-12 weeks


title: R3T tumor biological rep4

source_name: R3T primary mammary tumor

value: Genetically engineered mouse tumor


title: WT  T-48h

description: Gene expression data of CD117+ splenocytes from C57BL/6 WT mice with  LPS stimulation for 48h

source_name: CD117+cell from C57BL/6 mice spleens with LPS stimulation for 48h

tag: tissue


title: TS/A-E1 tumor biological rep4

source_name: TS/A-E1 primary mammary tumor


title: CDP cre-neg, bone marrow, steady state, rep1

description: CDP cre neg 1

value: female

value: bone marrow


title: AOCS_170_ICGC_DBDE_20131003_009

value: Female

value: Ascites


title: WT  T-24h

description: Gene expression data of CD117+ splenocytes from C57BL/6 WT mice with  LPS stimulation for 24h

source_name: CD117+cell from C57BL/6 mice spleens with LPS stimulation for 24h


title: Diff_preadipocyte_FGF21_rep20

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from differentiated preadipocytes from subject S033, FGF21-treated.

hyb_protocol: According to the Affymetrix expression protocol.

scan_protocol: According to the Affymetrix expression protocol, Scanner 3000 7G.

data_processing: Expression Console (v.1.3.0.187, Affymetrix) was used to obtain normalized RMA gene-level data (standard settings including median polish and sketch-quantile normalisation).

source_name: Differentiated preadipocytes from MHO subject S033, FGF21-treated

label_protocol: Ovation Pico WTA System V2 in combination with the Encore Biotin Module (Nugen).

growth_protocol: No growth.

extract_protocol: miRNeasy Micro Kit (Qiagen) including DNase treatment.

treatment_protocol: As described in the paper. Briefly, preadipocytes were isolated from the 20 hasc adipose tissue explants (as described in Schling,P, et al.; Evidence for a local renin angiotensin system in primary cultured human preadipocytes. Int.J.Obes.Relat Metab Disord. 23:336‐341, 1999) and expanded in α‐MEM/Ham’s nutrient mixture F12 (1:1) containing 20% fetal calf serum, 1% chicken embryo extract (Sera Laboratories, Haywards Heath, UK), 100 IU/mL penicillin, 0.1 mg/mL streptomycin, 0.5 μg/mL fungizone, and 2 mmol/L glutamine. Second‐pass cells were used for experiments. At confluence, adipose conversion was induced by shifting the cells into DMEM/Ham’s nutrient mixture F12 (1:1), 5% fetal calf serum, 17 μmol/L pantothenate, 1 μmol/L biotin, 2 μg/mL apo‐transferrin, 1 μmol/L human insulin, 1 μmol/L dexamethasone, 100 IU/mL penicillin, 0.1 mg/mL streptomycin, 0.5 μg/mL fungizone, and 2 mmol/L glutamine (differentiation medium) supplemented with 0.5 mmol/L 3‐isobutyl‐1‐methyl‐xanthine, 2 nmol/L triiodo‐thyronine, and 50 μmol/L indomethacin for seven days. Thereafter, the cells were allowed to terminally differentiate for another 11 days in differentiation medium alone. Differentiating preadipocytes were left untreated or were chronically treated for the whole 18‐day period with 50 ng/mL recombinant human (rh)FGF21 (PeproTech, Rocky Hill, NJ, USA). Culture media and supplements were obtained from Lonza (Basel, Switzerland) and Biochrom (Berlin, Germany).

tag: phenotype

value: morbidly obese

tag: insulin sensitivity

value: sensitive

value: differentiated preadipocytes

tag: treatment

tag: subject id


title: WT  T-12h

description: Gene expression data of CD117+ splenocytes from C57BL/6 WT mice with  LPS stimulation for 12h

source_name: CD117+cell from C57BL/6 mice spleens with  LPS stimulation for 12h


title: Diff_preadipocyte_FGF21_rep19

description: Gene expression data from differentiated preadipocytes from subject S026, FGF21-treated.

source_name: Differentiated preadipocytes from MHO subject S026, FGF21-treated


title: WT  T-0h

description: Gene expression data of CD117+ splenocytes from C57BL/6 WT mice without  LPS stimulation

source_name: CD117+cell from C57BL/6 mice spleens without LPS stimulation


title: Diff_preadipocyte_FGF21_rep18

description: Gene expression data from differentiated preadipocytes from subject S025, FGF21-treated.

source_name: Differentiated preadipocytes from MHO subject S025, FGF21-treated


title: AOCS_169_ICGC_DBDE_20131003_006

value: high grade serous ovarian cancer


title: AOCS_170_ICGC_DBDE_20131003_008


title: Diff_preadipocyte_FGF21_rep17

description: Gene expression data from differentiated preadipocytes from subject S023, FGF21-treated.

source_name: Differentiated preadipocytes from MHO subject S023, FGF21-treated


title: Diff_preadipocyte_FGF21_rep16

description: Gene expression data from differentiated preadipocytes from subject S019, FGF21-treated.

source_name: Differentiated preadipocytes from MHO subject S019, FGF21-treated


title: Diff_preadipocyte_FGF21_rep15

description: Gene expression data from differentiated preadipocytes from subject S015, FGF21-treated.

source_name: Differentiated preadipocytes from MHO subject S015, FGF21-treated


title: RasGRP4 KO  T-48h

description: Gene expression data of CD117+ splenocytes from RasGRP4 KO mice with LPS stimulation for 48h

source_name: CD117+cell from RasGRP4KO mice spleens with LPS stimulation for 36h

value: RasGRP4 KO


title: AOCS_168_ICGC_DBDE_20131003_004


title: AOCS_150_ICGC_DBDE_20131003_003

source_name: Ascites


title: RasGRP4 KO  T-24h

description: Gene expression data of CD117+ splenocytes from RasGRP4 KO mice with LPS stimulation for 24h

source_name: CD117+cell from RasGRP4KO mice spleens with LPS stimulation for 12h


title: Diff_preadipocyte_FGF21_rep14

description: Gene expression data from differentiated preadipocytes from subject S012, FGF21-treated.

source_name: Differentiated preadipocytes from MHO subject S012, FGF21-treated


title: AOCS_141_ICGC_DBDE_20131003_002


title: RasGRP4 KO  T-12h

description: Gene expression data of CD117+ splenocytes from RasGRP4 KO mice with LPS stimulation for 12h


title: PBD PEX12 mutation fibroblast derived iPS3

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

state: CA

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

hyb_protocol: Followed Illumina protocol

scan_protocol: Followed Illumina protocol

data_processing: Followed Illumina BeadStudio protocol

label: Cy5 and Cy3

source_name: iPSC derived from PBD-ZSD patient dermal fibroblast

label_protocol: Followed Illumina protocol

growth_protocol: Fibroblasts and iPSCs are cultured in 1:1 ratio of DMEM:F12 medium supplemented with 20% KSR at 37°C, 5% CO2 until confluence

extract_protocol: Extracted with Qiagen AllPrep DNA/RNA mini kit

value: iPSC

tag: group

value: PBD-ZSD patient


title: Diff_preadipocyte_FGF21_rep12

description: Gene expression data from differentiated preadipocytes from subject S005, FGF21-treated.

source_name: Differentiated preadipocytes from MHO subject S005, FGF21-treated


title: PBD PEX12 mutation fibroblast derived iPS1


title: Diff_preadipocyte_FGF21_rep11

description: Gene expression data from differentiated preadipocytes from subject S003, FGF21-treated.

source_name: Differentiated preadipocytes from MHO subject S003, FGF21-treated


title: Diff_preadipocyte_FGF21_rep13

description: Gene expression data from differentiated preadipocytes from subject S008, FGF21-treated.

source_name: Differentiated preadipocytes from MHO subject S008, FGF21-treated


title: PBD PEX10 mutation fibroblast derived iPS2


title: PBD PEX26 mutation fibroblast derived iPS1


title: AOCS_167_ICGC_DBDE_20130904_028

description: Raw data for arrays used for copy number analysis using GAP (Popova, et al 2009)


title: lung-SARS-CoV-Delta5-REP3

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: lung, SARS-CoV-Delta5 infected-REP3

hyb_protocol: The samples were placed on ice and quickly loaded onto arrays, hybridized at 65ºC for 17 hours in a Hybridization oven rotator and then washed in GE wash buffer 1 at room temperature (1 minute) and in GE Wash Buffer 2 at 37ºC (1 minute). Arrays were dried by centrifugation at 2000 rpm for 2 minutes.

scan_protocol: Images were captured with an Agilent Microarray Scanner and spots quantified using Feature Extraction Software (Agilent Technologies).

data_processing: Background correction by normexp method (with an offset of 50) and normalization of expression data by adjustment of quantiles were performed using LIMMA package (Smyth, 2004).

source_name: lung, SARS-CoV-Delta5 infected

label_protocol: Preparation of probes and hybridization was performed as described in One-Color Microarray Based Gene Expression Analysis Manual Ver. 6.5, Agilent Technologies. Briefly, for each hybridization 600 ng of Cy3 probes were mixed and added to 5 ul of 10x Blocking Agent, 1 ul of 25x Fragmentation Buffer and Nuclease free water in a 25 μl reaction, incubated at 60ºC for 30 minutes to fragment RNA and stopped with  25 ul of 2x Hybridization Buffer.

growth_protocol: 8 week-old specific-pathogen-free BALB/c Ola Hsd mice females were purchased from Harlan Laboratories.

extract_protocol: At 2 days post infection, lungs from infected mice were collected and homogenized using the gentleMACS Dissociator (Miltenyibiotec). Then, total RNA was extracted using the RNeasy purification kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: BALB/c mice were infected at the age of 16 weeks with 100000 pfu and all protocols were approved by the Ethical Review Committee at The Center for Animal Health Research (CISA-INIA). Infected mice were housed in a ventilated rack (Allentown, NJ).

tag: infection

value: lung

value: BALB/c


title: PBD PEX12 mutation fibroblast derived iPS2


title: PBD PEX26 mutation fibroblast derived iPS2


title: PBD PEX10 mutation fibroblast derived iPS1


title: PBD PEX1 frameshift mutation fibroblst 1 derived iPS2


title: PBD PEX10 mutation fibroblast derived iPS3


title: AOCS_167_ICGC_DBDE_20130904_027

source_name: Tumourmetastasistodistantlocation

value: Tumour Metastasis To Distant Location


title: Diff_preadipocyte_FGF21_rep10

description: Gene expression data from differentiated preadipocytes from subject R037, FGF21-treated.

source_name: Differentiated preadipocytes from MUHO subject R037, FGF21-treated

value: resistant


title: AOCS_167_ICGC_DBDE_20130904_024


title: lung-SARS-CoV-Delta5-REP2

description: lung, SARS-CoV-Delta5 infected-REP2


title: AOCS_165_ICGC_DBDE_20130904_019

source_name: Primarytumour

value: Primary Tumour


title: PBD PEX1 frameshift mutation fibroblst 2 derived iPS1


title: AOCS_164_ICGC_DBDE_20130904_018


title: PBD PEX1 frameshift mutation fibroblst 2 derived iPS2


title: AOCS_166_ICGC_DBDE_20130904_020


title: Diff_preadipocyte_FGF21_rep7

description: Gene expression data from differentiated preadipocytes from subject R029, FGF21-treated.

source_name: Differentiated preadipocytes from MUHO subject R029, FGF21-treated


title: PBD PEX1 frameshift mutation fibroblst 1 derived iPS1


title: PBD PEX1 missense mutation fibroblast 2 derived iPS5


title: Diff_preadipocyte_FGF21_rep8

description: Gene expression data from differentiated preadipocytes from subject R035, FGF21-treated.

source_name: Differentiated preadipocytes from MUHO subject R035, FGF21-treated


title: Diff_preadipocyte_FGF21_rep9

description: Gene expression data from differentiated preadipocytes from subject R036, FGF21-treated.

source_name: Differentiated preadipocytes from MUHO subject R036, FGF21-treated


title: lung-SARS-CoV-DeltaE-REP3

description: lung, SARS-CoV-DeltaE infected-REP3

source_name: lung, SARS-CoV-DeltaE infected

value: SARS-CoV-DeltaE


title: lung-SARS-CoV-DeltaE-REP2

description: lung, SARS-CoV-DeltaE infected-REP2


title: PBD PEX1 frameshift mutation fibroblst 2 derived iPS3


title: lung-SARS-CoV-Delta5-REP1

description: lung, SARS-CoV-Delta5 infected-REP1


title: PBD PEX1 missense mutation fibroblast 2 derived iPS4


title: Diff_preadipocyte_FGF21_rep6

description: Gene expression data from differentiated preadipocytes from subject R028, FGF21-treated.

source_name: Differentiated preadipocytes from MUHO subject R028, FGF21-treated


title: RasGRP4 KO  T-36h

description: Gene expression data of CD117+ splenocytes from RasGRP4 KO mice with LPS stimulation for 36h

source_name: CD117+cell from RasGRP4KO mice spleens with LPS stimulation for 24h

value: spleen

value: CD117+ splenocytes

value: male

value: 9-12 weeks


title: AOCS_163_ICGC_DBDE_20130904_017

value: Female


title: AOCS_162_ICGC_DBDE_20130904_016


title: AOCS_161_ICGC_DBDE_20130904_015


title: AOCS_160_ICGC_DBDE_20130904_014


title: lung-SARS-CoV-Delta3-REP3

description: lung, SARS-CoV-Delta3 infected-REP3

source_name: lung, SARS-CoV-Delta3 infected


title: lung-SARS-CoV-DeltaE-REP1

description: lung, SARS-CoV-DeltaE infected-REP1


title: PBD PEX1 missense mutation fibroblast 1 derived iPS5


title: AOCS_159_ICGC_DBDE_20130904_013


title: Diff_preadipocyte_FGF21_rep5

description: Gene expression data from differentiated preadipocytes from subject R021, FGF21-treated.

source_name: Differentiated preadipocytes from MUHO subject R021, FGF21-treated

value: morbidly obese


title: lung-SARS-CoV-Delta3-REP2

description: lung, SARS-CoV-Delta3 infected-REP2


title: Diff_preadipocyte_FGF21_rep1

description: Gene expression data from differentiated preadipocytes from subject R001, FGF21-treated.

source_name: Differentiated preadipocytes from MUHO subject R001, FGF21-treated

value: differentiated preadipocytes


title: Diff_preadipocyte_FGF21_rep3

description: Gene expression data from differentiated preadipocytes from subject R017, FGF21-treated.

source_name: Differentiated preadipocytes from MUHO subject R017, FGF21-treated


title: Diff_preadipocyte_Ctrl_rep20

description: Gene expression data from differentiated preadipocytes from subject S033, control.

source_name: Differentiated preadipocytes from MHO subject S033, control

value: sensitive

value: control


title: Escherichia coli wild type vs luxS mutants without H2O2 Rep2

city: Singapore

first: Aram

last: Kang

state: Singapore

address: 62 Nanyang Drive

department: School of Chemical and Biomedical Engineering

country: Singapore

institute: Nanyang Technological University

description: Biological replicate 2 of 2

hyb_protocol: Standard Agilent procedures

scan_protocol: Scanned on Agilent Scanner G2505B US45103124, and images were quantified using Agilent Feature Extraction Software v. 9.5.3.1

data_processing: Agilent Feature Extraction Software v. 9.5.3.1  was used for background subtraction and LOWESS normalization.

organism: Escherichia coli

source_name: wild type, without H2O2

label_protocol: Approximately 10 µg of total RNA was processed to produce Cy5 or Cy3-labelled cDNA targets

growth_protocol: Overnight culture of E. coli in LB was diluted in LB supplemented with 0.8% glucose to OD600=0.02 and was continuously incubated at 30 degree celcius with shaking until its OD600 reached 1.0

extract_protocol: Total RNA was extracted from 5ml cell culture after 30min incubation with or without H2O2 treatment using RNeasy Mini kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s protocol

treatment_protocol: three different concentrations, without H2O2, 10% (v/v) or 30% H2O2 were added directly to the cell cultures of wild type or luxS mutants, OD of which is 1.0. Treated samples were continuously incubated at 30 degree Celcius for 30min

value: wild type

source_name: luxS mutants, without H2O2

value: luxS


title: lung-SARS-CoV-Delta3-REP1

description: lung, SARS-CoV-Delta3 infected-REP1

value: lung


title: PBD PEX1 missense mutation fibroblast 1 derived iPS4

source_name: iPSC derived from PBD-ZSD patient dermal fibroblast

value: iPSC

value: PBD-ZSD patient


title: Diff_preadipocyte_FGF21_rep2

description: Gene expression data from differentiated preadipocytes from subject R007, FGF21-treated.

source_name: Differentiated preadipocytes from MUHO subject R007, FGF21-treated

value: resistant


title: Escherichia coli wild type vs luxS mutants with 30% H2O2 Rep2

description: Biological replicate 2 of 2

source_name: wild type, 30% H2O2

source_name: luxS mutants, 30% H2O2


title: Escherichia coli wild type vs luxS mutants without H2O2 Rep1

description: Biological replicate 1 of 2


title: PBD PEX1 missense mutation fibroblast 2 derived iPS1


title: PBD PEX1 missense mutation fibroblast 2 derived iPS3


title: PBD PEX1 missense mutation fibroblast 1 derived iPS2


title: PBD PEX1 missense mutation fibroblast 1 derived iPS1


title: AOCS_157_ICGC_DBDE_20130904_011

source_name: Primarytumour

value: Primary Tumour

value: high grade serous ovarian cancer


title: AOCS_139_ICGC_DBDE_20130729_002

source_name: TumourMetastasisToDistantLocation

value: Tumour Metastasis To Distant Location


title: AOCS_139_ICGC_DBDE_20130729_001


title: PBD PEX1 missense mutation fibroblast 1 derived iPS3


title: Escherichia coli wild type vs luxS mutants with 10% H2O2 Rep2

description: Biological replicate 2 of 2

source_name: wild type, 10% H2O2

source_name: luxS mutants, 10% H2O2


title: AOCS_065_ICGC_DBPC_20130607_008

source_name: Ascites

value: Ascites


title: AOCS_095_ICGC_DBPC_20130607_007

source_name: PrimaryTumour


title: Diff_preadipocyte_Ctrl_rep16

description: Gene expression data from differentiated preadipocytes from subject S019, control.

source_name: Differentiated preadipocytes from MHO subject S019, control


title: Escherichia coli wild type vs luxS mutants with 10% H2O2 Rep1

description: Biological replicate 1 of 2


title: Healthy control fibroblast 1 derived iPS4

source_name: iPSC derived from healthy control dermal fibroblast

value: healthy control


title: RasGRP4 KO  T-0h

description: Gene expression data of CD117+ splenocytes from RasGRP4 KO mice without LPS stimulation

source_name: CD117+cell from RasGRP4KO mice spleens without LPS stimulation

value: RasGRP4 KO

value: spleen

value: CD117+ splenocytes

value: male

value: 9-12 weeks


title: Diff_preadipocyte_FGF21_rep4

description: Gene expression data from differentiated preadipocytes from subject R020, FGF21-treated.

source_name: Differentiated preadipocytes from MUHO subject R020, FGF21-treated

value: morbidly obese

value: differentiated preadipocytes


title: Diff_preadipocyte_Ctrl_rep17

description: Gene expression data from differentiated preadipocytes from subject S023, control.

source_name: Differentiated preadipocytes from MHO subject S023, control

value: sensitive

value: control


title: Diff_preadipocyte_Ctrl_rep15

description: Gene expression data from differentiated preadipocytes from subject S015, control.

source_name: Differentiated preadipocytes from MHO subject S015, control


title: AOCS_123_ICGC_DBPC_20130607_006

description: Raw data for arrays used for copy number analysis using GAP (Popova, et al 2009)

value: Female


title: Healthy control fibroblast 1 derived iPS1

value: iPSC


title: Escherichia coli wild type vs luxS mutants with 30% H2O2 Rep1

description: Biological replicate 1 of 2

value: wild type

value: luxS


title: PBD PEX1 missense mutation fibroblast 2 derived iPS2

value: PBD-ZSD patient


title: Healthy control fibroblast 3 derived iPS1


title: Diff_preadipocyte_Ctrl_rep19

description: Gene expression data from differentiated preadipocytes from subject S026, control.

source_name: Differentiated preadipocytes from MHO subject S026, control


title: Healthy control fibroblast 1 derived iPS3


title: Diff_preadipocyte_Ctrl_rep18

description: Gene expression data from differentiated preadipocytes from subject S025, control.

source_name: Differentiated preadipocytes from MHO subject S025, control


title: Diff_preadipocyte_Ctrl_rep14

description: Gene expression data from differentiated preadipocytes from subject S012, control.

source_name: Differentiated preadipocytes from MHO subject S012, control


title: Healthy control fibroblast 1 derived iPS2


title: Diff_preadipocyte_Ctrl_rep13

description: Gene expression data from differentiated preadipocytes from subject S008, control.

source_name: Differentiated preadipocytes from MHO subject S008, control


title: AOCS_108_ICGC_DBPC_20130607_005

value: Primary Tumour

value: high grade serous ovarian cancer


title: AOCS_107_ICGC_DBPC_20130607_004


title: AOCS_106_ICGC_DBPC_20130607_003


title: AOCS_133_ICGC_DBPC_20130607_002


title: Diff_preadipocyte_Ctrl_rep12

description: Gene expression data from differentiated preadipocytes from subject S005, control.

source_name: Differentiated preadipocytes from MHO subject S005, control


title: AOCS_088_ICGC_DBPC_20130701_004

source_name: Primarytumour


title: AOCS_088_ICGC_DBPC_20130701_005

value: Ascites


title: AOCS_117_ICGC_DBPC_20130714_001


title: AOCS_155_ICGC_DBPC_20130701_009


title: AOCS_139_ICGC_DBDE_20130729_003

source_name: TumourMetastasisToDistantLocation

value: Tumour Metastasis To Distant Location


title: AOCS_158_ICGC_DBDE_20130904_012


title: Healthy control fibroblast 2 derived iPS4

value: healthy control


title: Diff_preadipocyte_Ctrl_rep8

description: Gene expression data from differentiated preadipocytes from subject R035, control.

source_name: Differentiated preadipocytes from MUHO subject R035, control

value: resistant


title: Diff_preadipocyte_Ctrl_rep10

description: Gene expression data from differentiated preadipocytes from subject R037, control.

source_name: Differentiated preadipocytes from MUHO subject R037, control


title: Diff_preadipocyte_Ctrl_rep11

description: Gene expression data from differentiated preadipocytes from subject S003, control.

source_name: Differentiated preadipocytes from MHO subject S003, control


title: Diff_preadipocyte_Ctrl_rep9

description: Gene expression data from differentiated preadipocytes from subject R036, control.

source_name: Differentiated preadipocytes from MUHO subject R036, control


title: Diff_preadipocyte_Ctrl_rep7

description: Gene expression data from differentiated preadipocytes from subject R029, control.

source_name: Differentiated preadipocytes from MUHO subject R029, control


title: Healthy control fibroblast 2 derived iPS3

source_name: iPSC derived from healthy control dermal fibroblast


title: Diff_preadipocyte_Ctrl_rep5

description: Gene expression data from differentiated preadipocytes from subject R021, control.

source_name: Differentiated preadipocytes from MUHO subject R021, control


title: PBD PEX1 frameshift mutation fibroblst 1

source_name: dermal fibroblast from PBD-ZSD patient

value: dermal fibroblast


title: Diff_preadipocyte_Ctrl_rep4

description: Gene expression data from differentiated preadipocytes from subject R020, control.

source_name: Differentiated preadipocytes from MUHO subject R020, control


title: PBD PEX1 frameshift mutation fibroblst 2


title: Diff_preadipocyte_Ctrl_rep1

description: Gene expression data from differentiated preadipocytes from subject R001, control.

source_name: Differentiated preadipocytes from MUHO subject R001, control


title: AOCS_176

description: miRNA count data

hyb_protocol: NanoString nCounter PrepStation immobilizes targets to cartridge

scan_protocol: NanoString Digital Analyzer set to high resolution

data_processing: NanoString nSolver Analysis Software was utilised to check QC metrics and extract raw counts. Expression was normalised for input using a subset of the housekeeping genes.

source_name: Fallopian Tube Cells

label_protocol: NanoString nCounter miRNA Human v2.1 assay

extract_protocol: Total RNA was isolated using mirVana miRNA Isolation Kit

value: Fallopian Tube

value: normal


title: AOCS_177

description: miRNA count data


title: AOCS_174

description: miRNA count data


title: AOCS_175

description: miRNA count data


title: Healthy control fibroblast 2 derived iPS1


title: PBD PEX10 mutation fibroblast


title: AOCS_178

description: miRNA count data


title: AOCS_173

description: miRNA count data


title: AOCS_171_ICGC_DBDE_20131003_011

description: miRNA count data

value: Primarytumour


title: PBD PEX12 mutation fibroblast


title: AOCS_172

description: miRNA count data


title: AOCS_171_ICGC_DBDE_20131003_012

description: miRNA count data

source_name: Ascites


title: AOCS_169_ICGC_DBDE_20131003_006

description: miRNA count data


title: Healthy control fibroblast 3

source_name: dermal fibroblast from healthy control


title: AOCS_167_ICGC_DBDE_20130904_028

description: miRNA count data


title: AOCS_170_ICGC_DBDE_20131003_008

description: miRNA count data


title: AOCS_168_ICGC_DBDE_20131003_004

description: miRNA count data


title: Diff_preadipocyte_Ctrl_rep6

description: Gene expression data from differentiated preadipocytes from subject R028, control.

source_name: Differentiated preadipocytes from MUHO subject R028, control

value: morbidly obese

value: differentiated preadipocytes


title: AOCS_167_ICGC_DBDE_20130904_027

description: miRNA count data

source_name: Tumourmetastasistodistantlocation

value: Female

value: Tumourmetastasistodistantlocation


title: PBD PEX26 mutation fibroblast


title: AOCS_165_ICGC_DBDE_20130904_019

description: miRNA count data

source_name: Primarytumour


title: AOCS_164_ICGC_DBDE_20130904_018

description: miRNA count data


title: PBD PEX1 missense mutation fibroblast 2


title: AOCS_167_ICGC_DBDE_20130904_024

description: miRNA count data


title: Healthy control fibroblast 2


title: Healthy control fibroblast 1


title: PBD PEX1 missense mutation fibroblast 1


title: AOCS_166_ICGC_DBDE_20130904_020

description: miRNA count data


title: Diff_preadipocyte_Ctrl_rep3

description: Gene expression data from differentiated preadipocytes from subject R017, control.

source_name: Differentiated preadipocytes from MUHO subject R017, control

value: control


title: AOCS_163_ICGC_DBDE_20130904_017

description: miRNA count data


title: AOCS_170_ICGC_DBDE_20131003_009

description: miRNA count data


title: AOCS_160_ICGC_DBDE_20130904_014

description: miRNA count data


title: AOCS_162_ICGC_DBDE_20130904_016

description: miRNA count data


title: AOCS_171_ICGC_DBDE_20131003_012

description: Raw data for arrays used for methylation analysis

hyb_protocol: Samples were hybridized to Infinium Human Methylation 450K BeadChips (Illumina) according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned on Iscan (Illumina)

data_processing: Data was background corrected, normalized to internal controls and QC was performed at the probe and sample level. COMBAT was used to remove batch effects (Johnson et al., 2007)

label_protocol: Bisulfite converted genomic DNAwas whole genome amplified and labeled using Illumina protocol

extract_protocol: DNA was extracted from fresh frozen tissues using AllPrep DNA/RNA Mini Kit (Qiagen). Genomic DNA (500ng) was bisulfite converted using EZ DNA methylation Kit (Zimo Research) following the manufacturer’s protocol with modification for Illumina Infinium Methyaltion arrays


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N57)

city: Tsu

first: Kana

last: Miyazaki

state: Mie

address: 2-174 Edobashi

department: Department of Hematology and Oncology

country: Japan

institute: Mie University

description:
DLBCL-CD5N57
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

hyb_protocol: Scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.1.3.1).

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and LOWESS normalization.

source_name: Human Universal Reference Total RNA

label_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

extract_protocol: Cy3-labeled cRNA and Cy5-labeled cRNA were generated from 0.5 ug of total RNA according to the manufacturer's protocol (Agilent Technology), respectively.

treatment_protocol: Frozen lymphoma tissues were ground to powder and lysed in lysis buffer TRIzol reagent (Invitrogen).

tag: sample type

value: Human Universal Reference total RNA

tag: cat. #

source_name: Total RNA from frozen gastric tissue

tag: disease

value: Diffuse large B-cell lymphoma

value: negative

value: Stomach


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N56)

description:
DLBCL-CD5N56
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

source_name: Total RNA from frozen lymph node tissue

value: lymph node


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N54)

description:
DLBCL-CD5N54
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N55)

description:
DLBCL-CD5N55
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_170_ICGC_DBDE_20131003_009

tag: gender

value: Ascites

tag: cell type

value: high grade serous ovarian cancer


title: AOCS_157_ICGC_DBDE_20130904_011

description: miRNA count data


title: Diff_preadipocyte_Ctrl_rep2

description: Gene expression data from differentiated preadipocytes from subject R007, control.

source_name: Differentiated preadipocytes from MUHO subject R007, control

value: resistant


title: AOCS_161_ICGC_DBDE_20130904_015

description: miRNA count data


title: AOCS_158_ICGC_DBDE_20130904_012

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N53)

description:
DLBCL-CD5N53
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_162_ICGC_DBDE_20130904_016


title: AOCS_159_ICGC_DBDE_20130904_013

description: miRNA count data


title: AOCS_155_ICGC_DBPC_20130701_009

description: miRNA count data


title: AOCS_153_ICGC_DBPC_20130205_176

description: miRNA count data

source_name: PrimaryTumour

value: PrimaryTumour


title: AOCS_166_ICGC_DBDE_20130904_020


title: AOCS_152_ICGC_DBPC_20130205_174

description: miRNA count data


title: AOCS_150_ICGC_DBPC_20130205_171

description: miRNA count data


title: AOCS_150_ICGC_DBDE_20131003_003

description: miRNA count data


title: AOCS_149_ICGC_DBPC_20130205_170

description: miRNA count data


title: AOCS_148_ICGC_DBPC_20130205_168

description: miRNA count data


title: AOCS_147_ICGC_DBPC_20130205_166

description: miRNA count data


title: AOCS_146_ICGC_DBPC_20130205_164

description: miRNA count data


title: AOCS_145_ICGC_DBPC_20130205_162

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N52)

description:
DLBCL-CD5N52
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_143_ICGC_DBPC_20130205_158

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N51)

description:
DLBCL-CD5N51
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_155_ICGC_DBPC_20130701_009


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N50)

description:
DLBCL-CD5N50
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

source_name: Total RNA from frozen smal intestinal tissue

value: small intestine


title: AOCS_150_ICGC_DBDE_20131003_003


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N48)

description:
DLBCL-CD5N48
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_150_ICGC_DBPC_20130205_171


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N42)

description:
DLBCL-CD5N42
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N47)

description:
DLBCL-CD5N47
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N46)

description:
DLBCL-CD5N46
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_144_ICGC_DBPC_20130205_160

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N43)

description:
DLBCL-CD5N43
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_142_ICGC_DBPC_20130205_155

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N44)

description:
DLBCL-CD5N44
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

source_name: Total RNA from frozen ileocecal tissue

value: Ileocecum


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N49)

description:
DLBCL-CD5N49
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N41)

description:
DLBCL-CD5N41
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N39)

description:
DLBCL-CD5N39
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

source_name: Total RNA from frozen mammary tissue

value: Breast


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N45)

description:
DLBCL-CD5N45
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N40)

description:
DLBCL-CD5N40
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

source_name: Total RNA from frozen tonsillar tissue

value: Tonsil


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N37)

description:
DLBCL-CD5N37
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N38)

description:
DLBCL-CD5N38
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

source_name: Total RNA from frozen subcutaneus tissue

value: Subcutaneus tissue


title: AOCS_138_ICGC_DBPC_20130205_146

description: miRNA count data

value: Female


title: AOCS_141_ICGC_DBPC_20130205_153

description: miRNA count data


title: AOCS_139_ICGC_DBDE_20130729_001

description: miRNA count data

source_name: TumourMetastasisToDistantLocation

value: TumourMetastasisToDistantLocation


title: AOCS_139_ICGC_DBPC_20130205_150

description: miRNA count data


title: AOCS_139_ICGC_DBDE_20130729_003

description: miRNA count data


title: AOCS_139_ICGC_DBDE_20130729_002

description: miRNA count data


title: AOCS_137_ICGC_DBPC_20130205_145

description: miRNA count data

source_name: Ascites


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N32)

description:
DLBCL-CD5N32
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N36)

description:
DLBCL-CD5N36
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P33)

description:
DLBCL-CD5P33
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient

value: positive


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N34)

description:
DLBCL-CD5N34
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

value: Human Universal Reference total RNA


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N33)

description:
DLBCL-CD5N33
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

source_name: Total RNA from frozen pharyngeal tissue

value: Diffuse large B-cell lymphoma

value: Pharynx


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N35)

description:
DLBCL-CD5N35
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

source_name: Total RNA from frozen sinonasal tissue

value: negative

value: Paranasal sinus


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N30)

description:
DLBCL-CD5N30
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

value: lymph node


title: AOCS_138_ICGC_DBPC_20130205_146

description: Raw data for arrays used for methylation analysis

value: Ascites

value: high grade serous ovarian cancer


title: AOCS_135_ICGC_DBPC_20130205_137

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N31)

description:
DLBCL-CD5N31
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_137_ICGC_DBPC_20130205_143

description: miRNA count data


title: AOCS_135_ICGC_DBPC_20130205_136

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N29)

description:
DLBCL-CD5N29
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_133_ICGC_DBPC_20130607_002

description: miRNA count data

value: PrimaryTumour


title: AOCS_134_ICGC_DBPC_20130205_134

description: miRNA count data


title: AOCS_137_ICGC_DBPC_20130205_145


title: AOCS_137_ICGC_DBPC_20130205_143


title: AOCS_135_ICGC_DBPC_20130205_136


title: AOCS_131_ICGC_DBPC_20130205_118

description: miRNA count data


title: AOCS_142_ICGC_DBPC_20130205_155


title: AOCS_132_ICGC_DBPC_20130205_120

description: miRNA count data


title: AOCS_135_ICGC_DBPC_20130205_137


title: AOCS_141_ICGC_DBPC_20130205_153


title: AOCS_130_ICGC_DBPC_20130205_116

description: miRNA count data


title: AOCS_128_ICGC_DBPC_20130205_112

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N27)

description:
DLBCL-CD5N27
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N25)

description:
DLBCL-CD5N25
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N23)

description:
DLBCL-CD5N23
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_126_ICGC_DBPC_20130205_110

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N22)

description:
DLBCL-CD5N22
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

source_name: Total RNA from frozen bone tissue

value: Bone


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N26)

description:
DLBCL-CD5N26
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N28)

description:
DLBCL-CD5N28
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_125_ICGC_DBPC_20130205_108

description: miRNA count data


title: AOCS_134_ICGC_DBPC_20130205_134


title: AOCS_141_ICGC_DBDE_20131003_002


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N21)

description:
DLBCL-CD5N21
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_124_ICGC_DBPC_20130205_106

description: miRNA count data


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P32)

description:
DLBCL-CD5P32
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: AOCS_123_ICGC_DBPC_20130607_006

description: miRNA count data


title: AOCS_122_ICGC_DBPC_20130205_102

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N19)

description:
DLBCL-CD5N19
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N20)

description:
DLBCL-CD5N20
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

source_name: Total RNA from frozen small intestinal tissue

value: small intestine


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N18)

description:
DLBCL-CD5N18
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_120_ICGC_DBPC_20130205_099

description: miRNA count data


title: AOCS_117_ICGC_DBPC_20130714_001

description: miRNA count data


title: AOCS_115_ICGC_DBPC_20130205_092

description: miRNA count data


title: AOCS_114_ICGC_DBPC_20130205_090

description: miRNA count data


title: AOCS_116_ICGC_DBPC_20130205_094

description: miRNA count data


title: AOCS_119_ICGC_DBPC_20130205_097


title: AOCS_120_ICGC_DBPC_20130205_099


title: AOCS_113_ICGC_DBPC_20130205_088

description: miRNA count data


title: AOCS_117_ICGC_DBPC_20130714_001


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N24)

description:
DLBCL-CD5N24
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

value: Breast


title: AOCS_119_ICGC_DBPC_20130205_097

description: miRNA count data


title: AOCS_112_ICGC_DBPC_20130205_133

description: miRNA count data


title: AOCS_111_ICGC_DBPC_20130205_131

description: miRNA count data


title: AOCS_108_ICGC_DBPC_20130607_005

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N17)

description:
DLBCL-CD5N17
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N15)

description:
DLBCL-CD5N15
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N12)

description:
DLBCL-CD5N12
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

source_name: Total RNA from frozen rectal tissue

value: Rectum


title: AOCS_109_ICGC_DBPC_20130205_086

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N11)

description:
DLBCL-CD5N11
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

source_name: Human Universal Reference Total RNA


title: AOCS_107_ICGC_DBPC_20130607_004

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N14)

description:
DLBCL-CD5N14
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N16)

description:
DLBCL-CD5N16
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N13)

description:
DLBCL-CD5N13
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_105_ICGC_DBPC_20130205_078

description: miRNA count data


title: AOCS_106_ICGC_DBPC_20130607_003

description: miRNA count data


title: AOCS_097_ICGC_DBPC_20130205_074

description: miRNA count data


title: AOCS_104_ICGC_DBPC_20130205_076

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N10)

description:
DLBCL-CD5N10
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N9)

description:
DLBCL-CD5N9
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N7)

description:
DLBCL-CD5N7
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_095_ICGC_DBPC_20130205_068

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N6)

description:
DLBCL-CD5N6
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

source_name: Total RNA from frozen gastric tissue

value: Stomach


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N2)

description:
DLBCL-CD5N2
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

source_name: Total RNA from frozen lymph node tissue


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N8)

description:
DLBCL-CD5N8
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: AOCS_094_ICGC_DBPC_20130205_067

description: miRNA count data

value: Female


title: AOCS_141_ICGC_DBDE_20131003_002

description: miRNA count data


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N5)

description:
DLBCL-CD5N5
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P31)

description:
DLBCL-CD5P31
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N4)

description:
DLBCL-CD5N4
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient

value: Tonsil


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N1)

description:
DLBCL-CD5N1
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-negative diffuse large B-cell lymphoma patient (DLBCL-CD5N3)

description:
DLBCL-CD5N3
Gene expression data from lymphoma tissue of CD5-negative diffuse large B-cell lymphoma patient


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P30)

description:
DLBCL-CD5P30
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient

value: positive


title: AOCS_094_ICGC_DBPC_20130205_066

description: miRNA count data

source_name: TumourLocalRecurrence

value: TumourLocalRecurrence


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P29)

description:
DLBCL-CD5P29
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient

value: Human Universal Reference total RNA

value: Diffuse large B-cell lymphoma


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P28)

description:
DLBCL-CD5P28
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: AOCS_093_ICGC_DBPC_20130205_064

description: miRNA count data

source_name: PrimaryTumour


title: AOCS_093_ICGC_DBPC_20130205_062

description: miRNA count data


title: AOCS_095_ICGC_DBPC_20130205_068

description: Raw data for arrays used for methylation analysis


title: AOCS_092_ICGC_DBPC_20130205_061

description: miRNA count data


title: AOCS_091_ICGC_DBPC_20130205_058

description: miRNA count data


title: AOCS_091_ICGC_DBPC_20130205_056

description: miRNA count data


title: AOCS_090_ICGC_DBPC_20130205_055

description: miRNA count data


title: AOCS_094_ICGC_DBPC_20130205_066


title: AOCS_088_ICGC_DBPC_20130701_004

description: miRNA count data

source_name: Primarytumour

value: Primarytumour


title: AOCS_093_ICGC_DBDE_20131003_001

description: miRNA count data


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P21)

description:
DLBCL-CD5P21
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P19)

description:
DLBCL-CD5P19
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient

source_name: Total RNA from frozen testicular tissue

value: Testis


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P23)

description:
DLBCL-CD5P23
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient

value: lymph node


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P20)

description:
DLBCL-CD5P20
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P24)

description:
DLBCL-CD5P24
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient

value: Paranasal sinus


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P26)

description:
DLBCL-CD5P26
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: AOCS_093_ICGC_DBPC_20130205_062

value: Ascites

value: high grade serous ovarian cancer


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P25)

description:
DLBCL-CD5P25
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P22)

description:
DLBCL-CD5P22
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P27)

description:
DLBCL-CD5P27
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P17)

description:
DLBCL-CD5P17
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: AOCS_088_ICGC_DBPC_20130701_005


title: AOCS_093_ICGC_DBDE_20131003_001


title: AOCS_092_ICGC_DBPC_20130205_059


title: AOCS_088_ICGC_DBPC_20130701_005

description: miRNA count data


title: AOCS_086_ICGC_DBPC_20130205_052

description: miRNA count data

value: PrimaryTumour


title: AOCS_086_ICGC_DBPC_20130205_050

description: miRNA count data


title: AOCS_084_ICGC_DBPC_20130205_047

description: miRNA count data


title: AOCS_083_ICGC_DBPC_20130205_045

description: miRNA count data


title: AOCS_081_ICGC_DBPC_20130205_043

description: miRNA count data


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P18)

description:
DLBCL-CD5P18
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: AOCS_080_ICGC_DBPC_20130205_041

description: miRNA count data


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P15)

description:
DLBCL-CD5P15
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: AOCS_079_ICGC_DBPC_20130205_039

description: miRNA count data


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P16)

description:
DLBCL-CD5P16
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P13)

description:
DLBCL-CD5P13
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: AOCS_078_ICGC_DBPC_20130205_126

description: miRNA count data


title: AOCS_077_ICGC_DBPC_20130205_037

description: miRNA count data


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P11)

description:
DLBCL-CD5P11
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P14)

description:
DLBCL-CD5P14
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: AOCS_076_ICGC_DBPC_20130205_035

description: Raw data for arrays used for methylation analysis


title: AOCS_086_ICGC_DBPC_20130205_050


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P8)

description:
DLBCL-CD5P8
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: AOCS_076_ICGC_DBPC_20130205_035

description: miRNA count data


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P7)

description:
DLBCL-CD5P7
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient

source_name: Total RNA from frozen mammary tissue


title: AOCS_065_ICGC_DBPC_20130607_008

description: miRNA count data


title: AOCS_065_ICGC_DBPC_20130205_031

description: miRNA count data


title: AOCS_091_ICGC_DBPC_20130205_056


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P5)

description:
DLBCL-CD5P5
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P6)

description:
DLBCL-CD5P6
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P12)

description:
DLBCL-CD5P12
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: AOCS_092_ICGC_DBPC_20130205_059

description: miRNA count data


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P4)

description:
DLBCL-CD5P4
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: AOCS_075_ICGC_DBPC_20130205_033

description: miRNA count data


title: AOCS_064_ICGC_DBPC_20130205_028

description: miRNA count data


title: AOCS_064_ICGC_DBPC_20130205_026

description: miRNA count data


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P9)

description:
DLBCL-CD5P9
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient

value: Bone


title: AOCS_063_ICGC_DBPC_20130205_025

description: miRNA count data


title: AOCS_065_ICGC_DBPC_20130607_008


title: AOCS_096_ICGC_DBPC_20130205_072

description: miRNA count data


title: AOCS_095_ICGC_DBPC_20130607_007

description: miRNA count data


title: AOCS_061_ICGC_DBPC_20130205_023

description: miRNA count data


title: AOCS_060_ICGC_DBPC_20130205_021

description: miRNA count data


title: AOCS_058_ICGC_DBPC_20130205_017

description: miRNA count data


title: AOCS_057_ICGC_DBPC_20130205_015

description: miRNA count data


title: AOCS_064_ICGC_DBPC_20130205_026


title: Control HeLa Cells-polysomal-REP2

description: Control HeLa Cells-polysomal-REP2

hyb_protocol: The samples were placed on ice and quickly loaded onto arrays, hybridized at 65ºC for 17 hours in a Hybridization oven rotator and then washed in GE wash buffer 1 at room temperature (1 minute) and in GE Wash Buffer 2 at 37ºC (1 minute).

data_processing: Raw intensities were background-corrected by normexp method with an offset of 50. Background-corrected signals were log2 transformed and normalized by quantile adjustment as described in limma package of bioconductor.

source_name: Control HeLa Cells-polysomal

label_protocol: Total RNA (200 ng) was amplified using One Color Low Input Quick Amp Labeling Kit (Agilent Technologies) and purified with RNeasy Mini Kit (Qiagen). Preparation of probes and hybridization was performed as described One-Color Microarray Based Gene Expression Analysis Manual Ver. 6.5, Agilent Technologies.

growth_protocol: Adherent HeLa cells were cultured under standard conditions. The TIA1 and TIAR shRNA-pSUPER constructs were generated with the pSUPER RNA interference (RNAi) System (OligoEngine, USA). Briefly, to knock-down TIA1 and TIAR, we have followed previously described methods (OligoEngine, USA) to generate TIA1 and TIAR short hairpin RNA (shRNA) pSUPER or empty pSUPER constructs from pSUPER.retro vectors. Sequences coding for short hairpin RNAs were inserted as double-stranded oligos followed by a short spacer, the reverse complement of the sense strand and five thymidines as an RNA polymerase III transcriptional stop signal into pSUPER vectors using the BglII and XhoI sites. The target sequences for the TIA1 and TIAR genes were 5'-AAGCTCTAATTCTGCAACTCT-3' and 5'-AACCATGGAATC AACAAGGAT-3', respectively. The configuration of the constructs was verified by DNA sequencing. The TIA1 and TIAR shRNA pSUPER constructs and the empty pSUPER vector as control were transfected into the cell line HeLa (1 μg of DNA/1×106 cells). Stable cell lines expressing empty or TIA1 and/or TIAR shRNA-pSUPER constructs were selected by plating for 3 weeks according to the manufacturer’s instructions (OligoEngine, USA). Clonal lines were isolated with cloning cylinders and verified by Western blotting.

extract_protocol: RNA from above HeLa cell lines was isolated and purified by using RNeasy kit (Qiagen). The quality of the RNAs was tested using the Agilent 2100 Bioanalyzer RNA Nano Chip

tag: cell line

value: Adherent HeLa cells

value: Normal

tag: rna fraction

value: Polysomal


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P3)

description:
DLBCL-CD5P3
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient


title: Rescue intestinal epithelial cells_P0_rep2

city: Durham

first: Nancy

middle: C

last: Andrews

state: North Carolina

address: Duke University Medical Center Box 3813, 450 Research Drive, LSRC C-125

department: Pharmacology and Cancer Biology

institute: Duke University

description: Gene expression data from mouse intestinal epithelial cells extracted from the small intestine and proximal colon

hyb_protocol: Targets were hybridized to the Mouse430 2.0 GeneChip (Affymetrix, Santa Clara, CA).  Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0  Array in the Affymetrix Hybridization Oven.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Partek Genomics Suite 6.5 (Partek Inc., St. Louis, MO) was used to perform data analysis. Robust multi-chip analysis (RMA) normalization was performed. Multi-way ANOVA and fold change were performed to select target genes that were differentially expressed between Tfr1fl/fl ; Tfr1 IEC-KO, and Tfr1 IEC-KO;ROSA26 Tfr1R654A/+ mice. Differentially expressed genes were selected with a p-value cut-off of 0.05 based on the ANOVA test and a fold change cut-off of 2.   Gene Set Enrichment Analysis [(GSEA/MSigDB v4.5) was performed on genes with >2-fold change.

source_name: P0 rescue intestinal epithelial cells

label_protocol: Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE). Hybridization targets were prepared with MessageAmp™ Premier RNA

growth_protocol: Tfr1fl/fl (wildtype), Tfr1 IEC-KO (knockout), and Tfr1 IEC-KO;ROSA26 Tfr1R654A/+ (rescue) pups were sacrificed at P0

extract_protocol: Fresh intestinal epithelial cells were isolated from small intestine and proximal colon by incubating intestinal pieces in ice-cold 2mM EDTA in PBS for 30 mins followed by vigourous shaking.  Cells were filtured through a 70micron mesh and washed with ice-cold PBS x3.  Qiagen RNeasy kit was used to extract mRNA.

treatment_protocol: Wildtype, knockout, and rescue pups were not treated with anything.

value: intestinal epithelial cells

tag: genotype

value: Tfr1 IEC-KO;ROSA26 Tfr1R654A/+ (rescue)


title: shRNA-depleted HeLa Cells-polysomal-REP2

source_name: shRNA-depleted HeLa Cells-polysomal

value: TIA-depleted


title: Rescue intestinal epithelial cells_P0_rep3


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P2)

description:
DLBCL-CD5P2
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient

value: positive


title: shRNA-depleted HeLa Cells-polysomal-REP1


title: AOCS_085_ICGC_DBPC_20130205_049

description: miRNA count data

value: Female


title: AOCS_059_ICGC_DBPC_20130205_019

description: miRNA count data


title: HeLA_DMSO5_24h

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

hyb_protocol: Hybridization mixture was prepared according to Affymetrix protocol. Each sample was hybridized to a GeneChip PrimeView Human Gene Expression Array (Affymetrix).

scan_protocol: Arrays were washed and stained in a Fluidics Station 450 and scanned in a GeneChip Scanner 3000 (both Affymetrix) according to manufacturer’s recommendations.

data_processing: Arrays were processed in Bioconductor, using RMA background correction and summarization. Foldchanges between samples were computed after MA mean and variance normalization using the GAM method. An empirical Bayes partial density model was then used to identify significant differentially expressed genes with a False Discovery Rate (FDR) of 5% and a log2 foldchange threshold of 3 (8 times up or down regulated).

source_name: HeLa vehicle 24h

label_protocol: RNA expression profiling was performed following the Pico Profiling method (Gonzalez-Roca et al., PLoS One, 2010), from 25 ng total RNA.

growth_protocol: The HeLa cervical adenocarcinoma cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine and antibiotics, and maintained at 37 ºC in a humidified atmosphere containing 5% CO2.

extract_protocol: Cells were washed with PBS and then lysed using a buffer containing β-mercaptoethanol. Isolation steps are done following PureLink® RNA Mini Kit technical manual. The optional step of DNAse treatment was performed

treatment_protocol: 24 h after sub-culturing cells were completely attached to the plate's surface. A final concentration of 5 μM RZ2 was added to the medium and treated cells were incubated for another 24 h. The same DMSO volume used as RZ2 solvent vehicle was used as control.

value: HeLa

value: cervical adenocarcinoma


title: lung cancer tissue 3- NNK treatment-95th week

city: Guangzhou

first: Jianjun

last: Wu

address: Xinzao Town, Panyu District

department: School of Public Health

country: China

institute: Guangzhou Medical University

description: lncRNA expression in matched lung cancer tissue 3 at the 95th week after NNK treatment

hyb_protocol: The labeled cRNAs were hybridized onto the Rat lncRNA Array (4x44K, ArrayStar)

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505B.

data_processing: Agilent Feature Extraction software (version 10.5.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5 software package (Agilent Technologies). After Quantile normalization of the raw data, lncRNAs and mRNAs that at least 1 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering. Pathway analysis and GO Analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable lncRNAs and mRNAs expression pattern among samples.

organism: Rattus norvegicus

source_name: matched lung cancer tissue 3 of NNK treatment group at 95th week

label_protocol: 1 μg of total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies)

extract_protocol: total RNA was extracted using Trizol reagent. The integrity of RNA can be assessed by electrophoresis on a denaturing agarose gel. Intact total RNA run on a denaturing gel will have sharp 28S and 18S rRNA bands (eukaryotic samples). The 28S rRNA band should be approximately twice as intense as the 18S rRNA band. This 2:1 intensity ratio indicates that the RNA is intact.The NanoDrop 1000 was used for accurately measuring RNA concentrations (OD260), protein contamination (ratio of OD260/OD280) and organic compound contamination (ratio of OD260/OD230). We typically ask our customers to provide total RNA with OD260/OD280 ratio higher than 1.8.

treatment_protocol: Three lung tumor tissues and three matched normal lung tissues and two blood samples from the control and NNK treatment group in the 95th week were collected from a rat lung cancer model induced by NNK.

value: lung cancer tissue

value: male

tag: strain


title: Control HeLa Cells-polysomal-REP1

description: Control HeLa Cells-polysomal-REP1


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P1)

description:
DLBCL-CD5P1
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient

value: Human Universal Reference total RNA

value: Diffuse large B-cell lymphoma

value: small intestine


title: shRNA-depleted HeLa Cells-non-polysomal-REP2

source_name: shRNA-depleted HeLa Cells-non-polysomal

value: Non-polysomal


title: Knockout intestinal epithelial cells_P0_rep3

source_name: P0 knockout intestinal epithelial cells

tag: age

value: Tfr1 IEC-KO (knockout)


title: shRNA-depleted HeLa Cells-non-polysomal-REP1

value: Adherent HeLa cells


title: HeLa_C5_24h

source_name: HeLa RZ2-treated 24h


title: Rescue intestinal epithelial cells_P0_rep1


title: Knockout intestinal epithelial cells_P0_rep1


title: Knockout intestinal epithelial cells_P0_rep2


title: clot-NNK treatment-95th week

source_name: clot from blood sample in NNK treatment group

tag: tissue

value: clot from whole blood


title: Control HeLa Cells-non-polysomal-REP2

description: Control HeLa Cells-non-polysomal-REP2

source_name: Control HeLa Cells-non-polysomal

value: Normal


title: AOCS_034_ICGC_DBPC_20130205_007

source_name: Ascites

value: Ascites

value: high grade serous ovarian cancer


title: AOCS_056_ICGC_DBPC_20130205_013

description: miRNA count data

value: PrimaryTumour


title: AOCS_004_ICGC_DBPC_20130205_004

description: miRNA count data


title: AOCS_001_ICGC_DBPC_20130205_002

description: miRNA count data


title: AOCS_055_ICGC_DBPC_20130205_011

description: miRNA count data


title: AOCS_034_ICGC_DBPC_20130205_009

description: miRNA count data


title: AOCS_034_ICGC_DBPC_20130205_007

description: miRNA count data


title: Control intestinal epithelial cells_P0_rep1

source_name: P0 control intestinal epithelial cells

value: intestinal epithelial cells

value: Tfr1fl/fl (wildtype)


title: Control intestinal epithelial cells_P0_rep3


title: lung cancer tissue 1- NNK treatment-95th week

description: lncRNA expression in matched lung cancer tissue 1 at the 95th week after NNK treatment

source_name: matched lung cancer tissue 1 of NNK treatment group at 95th week


title: Control HeLa Cells-non-polysomal-REP1

description: Control HeLa Cells-non-polysomal-REP1


title: normal lung tissue 1- NNK treatment-95th week

description: lncRNA expression in normal lung tissue 1 at the 95th week after NNK treatment

source_name: normal lung tissue 1 of NNK treatment group at 95th week

value: lung tissue


title: Control intestinal epithelial cells_P0_rep2


title: lung cancer tissue 2- NNK treatment-95th week

description: lncRNA expression in matched lung cancer tissue 2 at the 95th week after NNK treatment

source_name: matched lung cancer tissue 2 of NNK treatment group at 95th week


title: Tumor-treated-A19

description: Total RNA extracted from mammary tumor (treated with Lov) A19.

hyb_protocol: Following fragmentation, 10 µg of biotinylated cRNA were hybridized to Affymetrix chips (GeneChip Mouse Genome 430 2.0 Array). Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino)ethanesulfonic acid, 1 M Na+, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC . Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics Station 450 (Affymetrix).

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

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by the RMA method, using the Affy package from Bioconductor.

source_name: mammary tumor, Lov treated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Tumors were frozen immediately in liquid nitrogen and stored at -80ºC. Total RNA was extracted from tumor samples with TRI Reagent (Sigma-Aldrich) and further cleaned using RNeasy (Qiagen). RNA was determined to be of sufficient quality by electropherogram analysis (Agilent Bioanalyzer).

treatment_protocol: Samples were mammary tumors from Tg-neu female mice (Jackson Laboratories). Spontaneous mammary tumors in Tg-neu mice were detected by weekly palpation. From the onset of the first tumor, mice were inoculated intraperitoneally (i.p.) with Lov (Sigma-Aldrich; 10 mg/Kg body weight, or Vhcl (ethanol), n = 5/group), three times a week for six consecutive weeks until mice were sacrificed and tumors excised.

tag: strain/background

value: FVB/N-Tg(MMTVneu)

value: female

value: mammary tumor

value: lovastatin


title: Tumor-treated-A48

description: Total RNA extracted from mammary tumor (treated with Lov) A48.


title: OHT-3

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

institute: Institute of Molecular and Cell Biology

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with limma and beadarray in R

source_name: Fetal liver

label_protocol: cRNA was prepared with Illumina® TotalPrep RNA kit according to the manufacturer's protocol  Illumina Total Prep RNA Amplification Kit

growth_protocol: Lineage negative cells were isolated from E14.5 mouse fetal livers and cultured ex vivo.

extract_protocol: RNA was isolated with Life Technologies' PureLink RNA mini kit according to the manufacturer's protocol.

treatment_protocol: The cells were treated with 100nM OHT or EtOH (control) for 24h.

value: liver


title: normal lung tissue 2- NNK treatment-95th week

description: lncRNA expression in normal lung tissue 2 at the 95th week after NNK treatment

source_name: normal lung tissue 2 of NNK treatment group at 95th week

value: male


title: ctrl-4

description: replicate 4


title: Tumor-treated-A55

description: Total RNA extracted from mammary tumor (treated with Lov) A55.


title: clot-control-95th week

description: lncRNA expression in clot from whole blood at the 95th week in control group

source_name: clot from blood sample in control group


title: Tumor-treated-AB10

description: Total RNA extracted from mammary tumor (treated with Lov) AB10.


title: AOCS_005_ICGC_DBPC_20130205_006

description: miRNA count data

source_name: PrimaryTumour

value: Female


title: L_monocytogenes_LO28_delta_lhrC1-5_stressed_rep2

city: Odense

first: Birgitte

middle: Haar

last: Kallipolitis

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

description: This sample is of stressed delta-lhrC1-5 mutant Listeria monocytogenes LO28. It is the second of three stressed delta-lhrC1-5 mutant biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed following NimbleGen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed using NimbleScan v2.6. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Listeria monocytogenes LO28

source_name: Listeria monocytogenes LO28 delta-lhrC1-5, stressed.

label_protocol: Labeling was performed following NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Cultures were grown in Brain Heart Infusion (BHI) medium at 37°C until an OD600 of 0.35.

extract_protocol: 10 mL of each sample were treated with 2 volumes of RNA protect reagent (Quagen) as recommended by the manufacturer. The samples were vortexed and incubated at room temperature for 5 min followed by centrifugation (10 min, 5000g). RNA was extracted by using TRIzol Reagent (Ambion) as described previously (Nielsen et al., 2010, Nucleic Acids Res. 38: 907-19). DNase treatment was performed using 20 units of DNase 1 recombinant RNase-free (Roche) in the presence of 200 units RNasin Plus (Promega). RNA was purified by one phenol-chloroform extraction and one chlorofrom extraction followed by RNA precipitation. RNA was re-suspended in RNase free water (Ambion). RNA was quantified using a NanoDrop 2000 and the quality was assessend by the Agilent 2100 Bioanalyzer utilizing the RNA 6000 LapChip kit.

treatment_protocol: Each culture was split and 4 µg/mL cefuroxime was added to one of the samples. The samples were then incubated for 30 min.

tag: agent

value: cefuroxime

tag: genotype/variation

value: Deletion mutant delta-lhrC1-5


title: L_monocytogenes_LO28_delta_lhrC1-5_unstressed_rep3

description: This sample is of unstressed delta-lhrC1-5 mutant Listeria monocytogenes LO28. It is the third of three unstressed delta-lhrC1-5 mutant biological replicates used in this experiment, each from separate cultures.

source_name: Listeria monocytogenes LO28 delta-lhrC1-5, unstressed.


title: Tumor-treated-A50

description: Total RNA extracted from mammary tumor (treated with Lov) A50.

tag: treatment


title: L_monocytogenes_LO28_delta_lhrC1-5_unstressed_rep1

description: This sample is of unstressed delta-lhrC1-5 mutant Listeria monocytogenes LO28. It is the first of three unstressed delta-lhrC1-5 mutant biological replicates used in this experiment, each from separate cultures.


title: ctrl-3

description: replicate 3


title: CD5-positive diffuse large B-cell lymphoma patient (DLBCL-CD5P10)

description:
DLBCL-CD5P10
Gene expression data from lymphoma tissue of CD5-positive diffuse large B-cell lymphoma patient

source_name: Human Universal Reference Total RNA

value: Human Universal Reference total RNA

source_name: Total RNA from frozen lymph node tissue

value: Diffuse large B-cell lymphoma

value: positive

value: lymph node


title: L_monocytogenes_LO28_delta_lhrC1-5_stressed_rep1

description: This sample is of stressed delta-lhrC1-5 mutant Listeria monocytogenes LO28. It is the first of three stressed delta-lhrC1-5 mutant biological replicates used in this experiment, each from separate cultures.


title: Tumor-control-A54

description: Total RNA extracted from mammary tumor (not treated) A54.

source_name: mammary tumor, control

value: vehicle control


title: OHT-4

description: replicate 4


title: Tumor-control-AB11

description: Total RNA extracted from mammary tumor (not treated) AB11.


title: Tumor-control-A59

description: Total RNA extracted from mammary tumor (not treated) A59.


title: L_monocytogenes_LO28_wild-type_stressed_rep2

description: This sample is of stressed wild-type Listeria monocytogenes LO28. It is the second of three stressed wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Listeria monocytogenes LO28 wild-type, stressed.

value: Wild-type


title: L_monocytogenes_LO28_wild-type_stressed_rep3

description: This sample is of stressed wild-type Listeria monocytogenes LO28. It is the third of three stressed wild-type biological replicates used in this experiment, each from separate cultures.


title: normal lung tissue 3- NNK treatment-95th week

description: lncRNA expression in normal lung tissue 3 at the 95th week after NNK treatment

source_name: normal lung tissue 3 of NNK treatment group at 95th week


title: L_monocytogenes_LO28_wild-type_unstressed_rep3

description: This sample is of unstressed wild-type Listeria monocytogenes LO28. It is the third of three unstressed wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Listeria monocytogenes LO28 wild-type, unstressed.


title: L_monocytogenes_LO28_wild-type_unstressed_rep2

description: This sample is of unstressed wild-type Listeria monocytogenes LO28. It is the second of three unstressed wild-type biological replicates used in this experiment, each from separate cultures.


title: L_monocytogenes_LO28_wild-type_stressed_rep1

description: This sample is of stressed wild-type Listeria monocytogenes LO28. It is the first of three stressed wild-type biological replicates used in this experiment, each from separate cultures.


title: Tumor-control-A49

description: Total RNA extracted from mammary tumor (not treated) A49.


title: Tumor-control-A45

description: Total RNA extracted from mammary tumor (not treated) A45.


title: HDAC3_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 2.12

source_name: HDAC11_Regulatory T-cells CD4+CD25+

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: strain background

value: Regulatory T-cells CD4+CD25+


title: HDAC3_2


title: HDAC3_3


title: ctrl-2

description: replicate 2


title: L_monocytogenes_LO28_delta_lhrC1-5_unstressed_rep2

description: This sample is of unstressed delta-lhrC1-5 mutant Listeria monocytogenes LO28. It is the second of three unstressed delta-lhrC1-5 mutant biological replicates used in this experiment, each from separate cultures.


title: L_monocytogenes_LO28_wild-type_unstressed_rep1

description: This sample is of unstressed wild-type Listeria monocytogenes LO28. It is the first of three unstressed wild-type biological replicates used in this experiment, each from separate cultures.


title: OHT-2

description: replicate 2


title: ctrl-1

description: replicate 1


title: Iron deplete vs iron replete, experiment 3, technical replicate 1

status: Public on May 18 2015

city: Richmond

first: Janina

middle: P

last: Lewis

state: VA

address: 521 North 11th Street

department: Philips Institute of OCMB

institute: Virginia Commonwealth University

description: Biological replicate 3 of 4. Technical replicate 1.

hyb_protocol: Labeled cDNA probes were combined and mixed with hybridization buffer and applied to prehybridized array.  Array was placed in hybridization chamber and incubated ON at 42C.

scan_protocol: Scanned on an Axon 4200A microarray scanner. Images were quantified using GenePix software (v 6.0).

data_processing: Normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. LIMMA was used. LIMMA ( Linear Models for Microarray Data) package for statistical inference. LIMMA includes pre-processing capabilities for two-colour spotted arrays such as normalization of cDNA data, and background subtraction. LOWESS was used to normalize the data.  Data were analyzed for significant differences using the Significance Analysis for Oral Pathogen Microarrays (SAOPMD).   SAOPMD combines all the repeats within and between arrays and generates statistics.  Data included were derived from seven microarrays (biological replicates) each containing 4 technical replicates.

organism: Porphyromonas gingivalis

source_name: RNA from whole bacteria

label_protocol: 10 µg of total RNA were primed with random DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of ArrayScript reverse transcriptase (Applied Biosystems/Ambion, Austin, TX).  Dyes were incorporated into the reverse transcribed cDNAs (Cy3 and Cy5, GE Healthcare).

growth_protocol: Bacterial cells grown in iron replete and iron deplete conditions

extract_protocol: Total RNA extracted using Qiagen kit following manufacturer's instructions

treatment_protocol: No additional treatment performed

value: iron deplete

value: iron replete


title: Iron deplete vs iron replete, experiment 2, technical replicate 1

description: Biological replicate 2 of 4. Technical replicate 1.


title: Iron deplete vs iron replete, experiment 4

description: Biological replicate 4 of 4. Technical replicate 1.


title: OHT-1

description: replicate 1


title: Iron deplete vs iron replete, experiment 1, technical replicate 2

description: Biological replicate 1 of 4. Technical replicate 2.