title: H9 ES-derived neural precursor cells 2

city: Daejeon

first: Mirang

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Personalized Genomic Medicine Research Center

institute: KRIBB(Korea Research Institute of Bioscience and Biotechnology

description: ES-derived neural precursor cells

hyb_protocol: Amplified DNA was hybridized on the Infinium HumanMethylation 450 BeadChip (Illumina), following the Illumina Infinium HD Methylation protocol.

scan_protocol: The arrays were imaged using the Illumina HiScan SQ scanner, and image processing and extraction of intensity data were performed according to Illumina’s instructions.

data_processing: Each methylation signal was used to compute the β value, which is a quantitative measure of DNA methylation ranging from 0 (for completely unmethylated cytosines) to 1 (for completely methylated cytosines) (Bibikova et al., 2006).

source_name: Neural precursor cells

label_protocol: standard Illumina protocol

growth_protocol: Differentiation of the hES cell line H9 (WiCell, Madison, WI, USA; passages 35-38) into NP cells and terminally into DA neurons was performed as described (Ko et al., 2007).

extract_protocol: Genomic DNA (1 µg) from each sample was bisulfite converted using the EZ DNA methylation kit (Zymo Research), and 200 ng of the converted DNA was used for amplification.

value: ES-derived neural precursor cells

tag: quantification

value: MethylFlash methylated DNA quantification kit (Epigentek, Catalog No. P-1035)

tag: parental cell line


title: genomic DNA from differentiated, untransduced H9 hESC, replicate C

status: Public on Nov 04 2013

type: genomic

city: Houston

first: Sangeetha

middle: Kaveri

last: Mahadevan

state: Texas

address: 1250 Moursund St, Room 1025

department: Obsterics and Gynecology

country: USA

institute: Baylor College of Medicine

description:
samples were hybridized on to 2 different arrays, this sample was done on array 2
H9-4C

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
non_normalized_array*.txt contains unmethylated and methylated signal intensities
Illumina Genome Studio Methylation data were imported into the Illumina Genome Studio software and converted to a Partek Project File (.ppj) with the Partek Methylation Module
GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.1.0

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: differentiated_untransduced H9 hESC

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cultured cells using Gentra Puregene DNA extraction Kit according to standard instructions

tag: cell line

tag: cell type

value: Cultured hESC

tag: genotype/variation

value: untransduced control


title: genomic DNA from undifferentiated, NLRP7 knockdown H9 hESC, replicate B

description:
samples were hybridized on to 2 different arrays, this sample was done on array 2
H9-3B

source_name: undifferentiated_NLRP7 knockdown H9 hESC

value: NLRP7 knockdown


title: 5B1 Replicate 2 Batch 3 ; Immunogen= 2007-08 ; Survive = Yes

type: protein

city: Tempe

first: Joseph

middle: Barten

last: Legutki

state: Arizona

address: 1001 S. McAllister Ave

department: Center for Innovations in Medicine

institute: The Biodesign Institute at Arizona State University

hyb_protocol: No hybridization was done, but antibodies were incubated with the peptide microarrays for 1 hour at room temperature according to Stafford et al. (Stafford, Halperin, Legutki, Magee, Galgiani, Johnston, Physical characterization of the Immunosignaturing Effect, MCP 11(4), 2012).

scan_protocol: Scanning was done on an Agilent C type scanner at 10um resolution, high laser power, 100% PMT, autofocus ON, 635nm.

data_processing:
Median normalization per array was done, and any negative values were adjusted to 0.01. ComBat normalization was used to remove batch effects with the Immunogen as the covariate.  Replicates were averaged.
GeneSpring 7.3.1 was used to load and median-normalize raw gpr files.  Matrix of values was copied directly from GeneSpring into Excel as double-precision values.

label: biotinylated anti-mouse IgG & streptavidin-Alexaflour647

molecule: protein

organism: Mus musculus

source_name: ASU

label_protocol: Alexafluor 647-labeled Streptavidin was used to detect biotinylated anti-mouse secondary antibody.

tag: source

value: serum

tag: immunogen

tag: survival

value: Yes


title: H9 ES-derived dopamine neuron cells 2

country: South Korea

description: ES-derived dopamine neuron cells

source_name: Dopamine neuron cells

value: ES-derived dopamine neuron cells


title: genomic DNA from differentiated, scrambled H9 hESC, replicate B

description:
samples were hybridized on to 2 different arrays, this sample was done on array 2
H9-5B

source_name: differentiated_scrambled H9 hESC

value: scrambled control


title: genomic DNA from undifferentiated, scrambled H9 hESC, replicate B

description:
samples were hybridized on to 2 different arrays, this sample was done on array 2
H9-2B

source_name: undifferentiated_scrambled H9 hESC


title: genomic DNA from undifferentiated, scrambled H9 hESC, replicate C

description:
samples were hybridized on to 2 different arrays, this sample was done on array 2
H9-2C


title: 5B2 Replicate 2 Batch 4 ; Immunogen= 2007-08 ; Survive = No

value: No


title: genomic DNA from differentiated, scrambled H9 hESC, replicate A

description:
samples were hybridized on to 2 different arrays, this sample was done on array 1
H9-5A


title: 5B1 Replicate 1 Batch 1 ; Immunogen= 2007-08 ; Survive = Yes


title: genomic DNA from undifferentiated, NLRP7 knockdown H9 hESC, replicate C

description:
samples were hybridized on to 2 different arrays, this sample was done on array 2
H9-3C


title: Shoot Tip Untreated 6 23

type: RNA

city: University Park

first: Timothy

last: McNellis

state: PA

address: 318 Buckhout Lab

department: Plant Pathology and Environmental Microbiology

institute: The Pennsylvania State University

hyb_protocol: After fragmentation, samples are dried down completely in a speed-vac and then resuspended in tracking controls and hybridization solution according to the microarray manufacturer’s instructions (Roche NimbleGen). Pairs of samples were hybridized overnight at 42°C with active mixing in a MAUI Hybridization System.

scan_protocol: Following hybridization, microarrays were washed and scanned according to the manufacturer’s protocol (Roche NimbleGen).  Images were burst and gridded.

data_processing:
Pair files were generated using NimbleScan software.
DNA microarray were normalized using R software.

molecule: total RNA

organism: Malus domestica

source_name: Actively growing shoot tips

label_protocol: Fifteen micrograms of aRNA was dye coupled with either Cy3 or Cy5 (GE Health Care #RPN5661), as appropriate. Following quenching and cleanup of dye coupling reactions, 1.5 μg of a Cy3 labeled sample is combined with 1.5 μg of a Cy5 labeled sample and fragmented using RNA Fragmentation Reagents (Ambion AM8740) according the manufacturer’s instructions.

growth_protocol: Stoolbed grown apple shoots

extract_protocol: The protocol is described in Gasic et al., (2004) Plant Molecular Biology Reporter 22:437-438.

treatment_protocol: There was no treatment of plants prior to sample collection, since we were looking at steady-state gene expression patterns within the population.

tag: sample type

value: segregating population

tag: phenotype

value: Powdery Mildew Intermediate

tag: tissue

value: shoot tip

tag: genetic background

value: segregating F1 population from a cross of 'Ottawa 3' x 'Robusta 5'


title: genomic DNA from differentiated, NLRP7 knockdown H9 hESC, replicate A

description:
samples were hybridized on to 2 different arrays, this sample was done on array 1
H9-6A

source_name: differentiated_NLRP7 knockdown H9 hESC


title: H9 ES-derived dopamine neuron cells 1

description: ES-derived dopamine neuron cells


title: Shoot Tip Untreated 5 9

value: Powdery Mildew Resistant


title: 5B0 Replicate 2 Batch 5 ; Immunogen= 2007-08 ; Survive = Yes


title: 5B0 Replicate 1 Batch 5 ; Immunogen= 2007-08 ; Survive = Yes


title: H9 ES-derived neural precursor cells 1

description: ES-derived neural precursor cells


title: Shoot Tip Untreated 5 34

value: Powdery Mildew Susceptible


title: genomic DNA from undifferentiated, untransduced H9 hESC, replicate B

description:
samples were hybridized on to 2 different arrays, this sample was done on array 2
H9-1B

source_name: undifferentiated_untransduced H9 hESC


title: Shoot Tip Untreated 5 3


title: genomic DNA from undifferentiated, scrambled H9 hESC, replicate A

description:
samples were hybridized on to 2 different arrays, this sample was done on array 1
H9-2A


title: 5A4 Replicate 2 Batch 3 ; Immunogen= 2007-08 ; Survive = Yes


title: genomic DNA from differentiated, untransduced H9 hESC, replicate B

description:
samples were hybridized on to 2 different arrays, this sample was done on array 2
H9-4B


title: H9 Embryonic stem (ES) cells 2

description: Embryonic stem(ES) cells H9

source_name: Embryonic stem cells

value: Embryonic stem (ES) cells H9

tag: passages


title: 5A4 Replicate 1 Batch 1 ; Immunogen= 2007-08 ; Survive = Yes


title: 5A3 Replicate 1 Batch 2 ; Immunogen= 2007-08 ; Survive = Yes


title: 5A2 Replicate 2 Batch 5 ; Immunogen= 2007-08 ; Survive = Yes


title: 5A3 Replicate 2 Batch 4 ; Immunogen= 2007-08 ; Survive = Yes


title: Shoot Tip Untreated 5 31


title: Shoot Tip Untreated 5 29


title: H9 Embryonic stem (ES) cells 1

description: Embryonic stem(ES) cells H9


title: 5A2 Replicate 1 Batch 4 ; Immunogen= 2007-08 ; Survive = Yes


title: 5A0 Replicate 2 Batch 4 ; Immunogen= 2007-08 ; Survive = Yes


title: Shoot Tip Untreated 4 7


title: Shoot Tip Untreated 5 25


title: 4B3 Replicate 2 Batch 3 ; Immunogen= 2006-07 ; Survive = No


title: 5A0 Replicate 1 Batch 2 ; Immunogen= 2007-08 ; Survive = Yes


title: 5A1 Replicate 1 Batch 3 ; Immunogen= 2007-08 ; Survive = Yes


title: Shoot Tip Untreated 5 22


title: 4B4 Replicate 2 Batch 4 ; Immunogen= 2006-07 ; Survive = Yes


title: 4B4 Replicate 1 Batch 2 ; Immunogen= 2006-07 ; Survive = Yes


title: Shoot Tip Untreated 4 21


title: 4B2 Replicate 2 Batch 3 ; Immunogen= 2006-07 ; Survive = No


title: 4B3 Replicate 1 Batch 2 ; Immunogen= 2006-07 ; Survive = No


title: Shoot Tip Untreated 4 29


title: 5A1 Replicate 2 Batch 5 ; Immunogen= 2007-08 ; Survive = Yes


title: Shoot Tip Untreated 4 30


title: Shoot Tip Untreated 5 1


title: 4B2 Replicate 1 Batch 2 ; Immunogen= 2006-07 ; Survive = No


title: Shoot Tip Untreated 5 32


title: Shoot Tip Untreated 4 17


title: 4B1 Replicate 2 Batch 4 ; Immunogen= 2006-07 ; Survive = Yes


title: Shoot Tip Untreated 4 20


title: Shoot Tip Untreated 3 3


title: Shoot Tip Untreated 4 27


title: 4A4 Replicate 2 Batch 3 ; Immunogen= 2006-07 ; Survive = Yes


title: Shoot Tip Untreated 3 7


title: Shoot Tip Untreated 3 4


title: Shoot Tip Untreated 3 33


title: Shoot Tip Untreated 3 36


title: 4B0 Replicate 1 Batch 1 ; Immunogen= 2006-07 ; Survive = No


title: 4A3 Replicate 2 Batch 4 ; Immunogen= 2006-07 ; Survive = Yes


title: 4A4 Replicate 1 Batch 1 ; Immunogen= 2006-07 ; Survive = Yes


title: Shoot Tip Untreated 3 30


title: 4B0 Replicate 2 Batch 3 ; Immunogen= 2006-07 ; Survive = No


title: Shoot Tip Untreated 3 22


title: 4A2 Replicate 2 Batch 3 ; Immunogen= 2006-07 ; Survive = Yes


title: 4A3 Replicate 1 Batch 2 ; Immunogen= 2006-07 ; Survive = Yes


title: Shoot Tip Untreated 3 23


title: Shoot Tip Untreated 3 21


title: 4B1 Replicate 1 Batch 1 ; Immunogen= 2006-07 ; Survive = Yes


title: 4A1 Replicate 2 Batch 4 ; Immunogen= 2006-07 ; Survive = No


title: 4A2 Replicate 1 Batch 1 ; Immunogen= 2006-07 ; Survive = Yes


title: Shoot Tip Untreated 4 33


title: 4A1 Replicate 1 Batch 2 ; Immunogen= 2006-07 ; Survive = No


title: Shoot Tip Untreated 3 18


title: Shoot Tip Untreated 3 19


title: Shoot Tip Untreated 3 20


title: 3B4 Replicate 1 Batch 2 ; Immunogen= Killed PR8 ; Survive = Yes

value: Killed PR8


title: 4A0 Replicate 1 Batch 1 ; Immunogen= 2006-07 ; Survive = Yes


title: Shoot Tip Untreated 3 16


title: Shoot Tip Untreated 3 13


title: 3B4 Replicate 2 Batch 3 ; Immunogen= Killed PR8 ; Survive = Yes


title: 3B2 Replicate 2 Batch 4 ; Immunogen= Killed PR8 ; Survive = Yes


title: Shoot Tip Untreated 2 6


title: 3B3 Replicate 2 Batch 4 ; Immunogen= Killed PR8 ; Survive = Yes


title: Shoot Tip Untreated 3 17


title: 3B3 Replicate 1 Batch 1 ; Immunogen= Killed PR8 ; Survive = Yes


title: 3B2 Replicate 1 Batch 2 ; Immunogen= Killed PR8 ; Survive = Yes


title: Shoot Tip Untreated 2 15


title: 3B0 Replicate 2 Batch 4 ; Immunogen= Killed PR8 ; Survive = Yes


title: 4A0 Replicate 2 Batch 4 ; Immunogen= 2006-07 ; Survive = Yes


title: Shoot Tip Untreated 2 35


title: Shoot Tip Untreated 2 27


title: Shoot Tip Untreated 2 31


title: 3B1 Replicate 1 Batch 2 ; Immunogen= Killed PR8 ; Survive = Yes


title: Shoot Tip Untreated 1 3


title: Shoot Tip Untreated 1 4


title: Shoot Tip Untreated 2 26


title: Shoot Tip Untreated 1 2


title: Shoot Tip Untreated 2 2


title: 3B1 Replicate 2 Batch 3 ; Immunogen= Killed PR8 ; Survive = Yes


title: 3A4 Replicate 1 Batch 1 ; Immunogen= Killed PR8 ; Survive = Yes


title: Shoot Tip Untreated 1 19


title: 3A2 Replicate 2 Batch 3 ; Immunogen= Killed PR8 ; Survive = Yes


title: Shoot Tip Untreated 2 12


title: Shoot Tip Untreated 1 18


title: 3A3 Replicate 2 Batch 3 ; Immunogen= Killed PR8 ; Survive = Yes


title: 3A1 Replicate 2 Batch 4 ; Immunogen= Killed PR8 ; Survive = Yes


title: 3A4 Replicate 2 Batch 4 ; Immunogen= Killed PR8 ; Survive = Yes


title: C2_VITRO38H-cy5_VITRO8H-cy3

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description:
in vitro 38h growth vs. in vitro 8h growth.
Biological replicate 2 of 2. Dye swap 2 of 2.

hyb_protocol: Samples were applied to microarrays enclosed in hybridization chambers in a water bath in the dark for 16-20h. After hybridization, slides were washed with washing buffers (http://bugs.sgul.ac.uk/bugsbase/tabs/protocol.php?protocol_id=30&action=view).

scan_protocol: Scanned on a GenePix Pro 5 dual-channel laser scanner (ScanArray 4000).

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicate : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

organism: Clostridioides difficile

source_name: strain 630E in TY 38H of growth

label_protocol: 10 µg of total RNA was used with a Genisphere 3DNA Array 900 MPX microarray kit for cDNA synthesis, labeling, and hybridization.

growth_protocol: C. difficile strain C630E was extracted after 8h, 14h and 38h in TY.

extract_protocol: Total RNA was extracted using the QIAgen RNeasy extraction kit.

tag: strain

value: C630E Mullany

tag: growth medium

value: TY

tag: time

value: 38h growth

source_name: strain 630E in TY 8H of growth (reference)

tag: culture medium

value: 8h growth


title: Shoot Tip Untreated 1 16


title: C2_VITRO14H-cy5_VITRO8H-cy3

description:
in vitro 14h growth vs. in vitro 8h growth.
Biological replicate 2 of 2. Dye swap 2 of 2.

source_name: strain 630E in TY 14H of growth

value: 14h growth


title: C2_VITRO38H-cy3_VITRO8H-cy5

description:
in vitro 38h growth vs. in vitro 8h growth.
Biological replicate 2 of 2. Dye swap 1 of 2.


title: C1_VITRO38H-cy5_VITRO8H-cy3

description:
in vitro 38h growth vs. in vitro 8h growth.
Biological replicate 1 of 2. Dye swap 2 of 2.


title: 3A2 Replicate 1 Batch 1 ; Immunogen= Killed PR8 ; Survive = Yes

value: serum

value: Yes


title: 2B3 Replicate 2 Batch 4 ; Immunogen= Live ; Survive = Yes

value: Live


title: 3A1 Replicate 1 Batch 1 ; Immunogen= Killed PR8 ; Survive = Yes


title: 2B4 Replicate 1 Batch 2 ; Immunogen= Live ; Survive = Yes


title: 3A0 Replicate 1 Batch 2 ; Immunogen= Killed PR8 ; Survive = Yes


title: 2B3 Replicate 1 Batch 1 ; Immunogen= Live ; Survive = Yes


title: 3A0 Replicate 2 Batch 3 ; Immunogen= Killed PR8 ; Survive = Yes


title: C1_VITRO38H-cy3_VITRO8H-cy5

description:
in vitro 38h growth vs. in vitro 8h growth.
Biological replicate 1 of 2. Dye swap 1 of 2.


title: 2B4 Replicate 2 Batch 4 ; Immunogen= Live ; Survive = Yes


title: C1_VITRO14H-cy5_VITRO8H-cy3

description:
in vitro 14h growth vs. in vitro 8h growth.
Biological replicate 1 of 2. Dye swap 2 of 2.


title: C2_VITRO14H-cy3_VITRO8H-cy5

description:
in vitro 14h growth vs. in vitro 8h growth.
Biological replicate 2 of 2. Dye swap 1 of 2.


title: 2B1 Replicate 1 Batch 1 ; Immunogen= Live ; Survive = Yes


title: 2B2 Replicate 2 Batch 3 ; Immunogen= Live ; Survive = Yes


title: 2B0 Replicate 2 Batch 5 ; Immunogen= Live ; Survive = Yes


title: Shoot Tip Untreated 1 13


title: 2B1 Replicate 2 Batch 3 ; Immunogen= Live ; Survive = Yes


title: 2B2 Replicate 1 Batch 2 ; Immunogen= Live ; Survive = Yes


title: VIVO14H4-cy5_VITRO8H-cy3

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 4 of 4. Dye swap 2 of 2.

source_name: Mouse8 14h after infection

growth_protocol: C. difficile strain C630E was extracted after 8h, 14h and 38h of an infection in mouse.

extract_protocol: RNA was extracted from the luminal content of mouse.

tag: host

value: mouse

value: 14h infection


title: C1_VITRO14H-cy3_VITRO8H-cy5

description:
in vitro 14h growth vs. in vitro 8h growth.
Biological replicate 1 of 2. Dye swap 1 of 2.


title: VIVO38H1-cy3_VITRO8H-cy5

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 1 of 4. Dye swap 1 of 2.

source_name: Mouse9 38h after infection

value: 38h infection


title: VIVO38H3-cy5_VITRO8H-cy3

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 3 of 4. Dye swap 2 of 2.

source_name: Mouse11 38h after infection


title: VIVO38H4-cy5_VITRO8H-cy3

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 4 of 4. Dye swap 2 of 2.

source_name: Mouse12 38h after infection


title: VIVO38H3-cy3_VITRO8H-cy5

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 3 of 4. Dye swap 1 of 2.


title: VIVO38H2-cy3_VITRO8H-cy5

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 2 of 4. Dye swap 1 of 2.

source_name: Mouse10 38h after infection


title: 2A3 Replicate 2 Batch 3 ; Immunogen= Live ; Survive = Yes


title: VIVO38H1-cy5_VITRO8H-cy3

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 1 of 4. Dye swap 2 of 2.


title: 2B0 Replicate 1 Batch 1 ; Immunogen= Live ; Survive = Yes


title: VIVO38H4-cy3_VITRO8H-cy5

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 4 of 4. Dye swap 1 of 2.


title: VIVO38H2-cy5_VITRO8H-cy3

description:
in vivo 38h after infection vs. in vitro 8h growth.
Biological replicate 2 of 4. Dye swap 2 of 2.


title: 2A4 Replicate 1 Batch 1 ; Immunogen= Live ; Survive = Yes


title: VIVO14H3-cy5_VITRO8H-cy3

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 3 of 4. Dye swap 2 of 2.

source_name: Mouse7 14h after infection


title: VIVO14H4-cy3_VITRO8H-cy5

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 4 of 4. Dye swap 1 of 2.


title: 2A3 Replicate 1 Batch 2 ; Immunogen= Live ; Survive = Yes

source_name: ASU


title: VIVO14H3-cy3_VITRO8H-cy5

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 3 of 4. Dye swap 1 of 2.


title: VIVO14H2-cy3_VITRO8H-cy5

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 2 of 4. Dye swap 1 of 2.

source_name: Mouse6 14h after infection


title: 2A1 Replicate 2 Batch 4 ; Immunogen= Live ; Survive = Yes


title: 2A1 Replicate 1 Batch 1 ; Immunogen= Live ; Survive = Yes


title: VIVO14H1-cy5_VITRO8H-cy3

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 1 of 4. Dye swap 2 of 2.

source_name: Mouse5 14h after infection


title: 2A0 Replicate 2 Batch 3 ; Immunogen= Live ; Survive = Yes


title: 2A2 Replicate 2 Batch 4 ; Immunogen= Live ; Survive = Yes


title: VIVO14H2-cy5_VITRO8H-cy3

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 2 of 4. Dye swap 2 of 2.


title: 1B4 Replicate 2 Batch 3 ; Immunogen= Mock ; Survive = No

value: Mock

value: No


title: VIVO8H4-cy3_VITRO8H-cy5

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 4 of 4. Dye swap 1 of 2.

source_name: Mouse4 8h after infection

value: 8h infection


title: VIVO14H1-cy3_VITRO8H-cy5

description:
in vivo 14h after infection vs. in vitro 8h growth.
Biological replicate 1 of 4. Dye swap 1 of 2.


title: VIVO8H3-cy3_VITRO8H-cy5

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 3 of 4. Dye swap 1 of 2.

source_name: Mouse3 8h after infection


title: 3B0 Replicate 1 Batch 1 ; Immunogen= Killed PR8 ; Survive = Yes


title: VIVO8H4-cy5_VITRO8H-cy3

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 4 of 4. Dye swap 2 of 2.


title: 1B4 Replicate 1 Batch 1 ; Immunogen= Mock ; Survive = No


title: VIVO8H3-cy5_VITRO8H-cy3

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 3 of 4. Dye swap 2 of 2.


title: 2A4 Replicate 2 Batch 4 ; Immunogen= Live ; Survive = Yes


title: 2A2 Replicate 1 Batch 2 ; Immunogen= Live ; Survive = Yes


title: 1B2 Replicate 2 Batch 4 ; Immunogen= Mock ; Survive = No


title: 1B3 Replicate 2 Batch 3 ; Immunogen= Mock ; Survive = No


title: VIVO8H2-cy3_VITRO8H-cy5

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 2 of 4. Dye swap 1 of 2.

source_name: Mouse2 8h after infection


title: VIVO8H1-cy3_VITRO8H-cy5

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 1 of 4. Dye swap 1 of 2.

source_name: Mouse1 8h after infection


title: 1B2 Replicate 1 Batch 2 ; Immunogen= Mock ; Survive = No


title: 1B1 Replicate 2 Batch 4 ; Immunogen= Mock ; Survive = No


title: 2A0 Replicate 1 Batch 2 ; Immunogen= Live ; Survive = Yes


title: 1B3 Replicate 1 Batch 1 ; Immunogen= Mock ; Survive = No


title: VIVO8H1-cy5_VITRO8H-cy3

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 1 of 4. Dye swap 2 of 2.


title: VIVO8H2-cy5_VITRO8H-cy3

description:
in vivo 8h after infection vs. in vitro 8h growth.
Biological replicate 2 of 4. Dye swap 2 of 2.


title: Internal organs_SVCV-resistant fish_biological replicate2

city: Madrid

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

hyb_protocol: The slides were pre-treated with 1% BSA fraction V, 5 X SSC, 0.1% SDS for 30 min. at 50 ºC, washed with 2 X SSC (3 min) and 0.2 X SSC (3 min) and hybridized overnight in cocktail containing 1.3 X Denhardt's, 3 X SSC, 0.3% SDS, 2.1 ug/ul polyadenylate and 1 ug/ul yeast tRNA.

scan_protocol: Signal was captured and processed using an Agilent scanner (G2565B, Agilent Technologies). The scanner images were segmented by the Agilent Feature Extraction Software (v9.5) with the protocol GE1-v5_95.

data_processing: The gProcessedSignal was chosen for statistical analysis. Normalization within each microarray was carried out by using the sum of all the signals. Data was first filtered by non-uniform pixel distributed outliers and other replicate outliers (glsFeatNonUnifOL, glsBGNonUnifOL, glsFeatPopnOL and glsBGPopnOL) according to the default Agilent feature Extraction criteria; ratio between processed signal and its error <2; differentiation from background signal; linear relationship between concentration and intensity below limits according to Spike-In information.

organism: Danio rerio

source_name: Head kidney+spleen of six SVCV-resistant fish 30 days post-inoculation

label_protocol: RNA were labeled with Cy3 (Amersham Pharmacia) by using SuperScript III reverse transcriptase (InVitroGen) and oligo(dT) primer, and the resulting cDNA was purified with Microcon YM30 (Millipore).

growth_protocol: Adult zebrafish of 2-3 g (~4 cm in length) were obtained from a local fish pet shop to study a situation that more closely resembles the variability of natural populations. Zebrafish were maintained at 24-26 ºC in 30 l aquaria with tap-dechlorinated carbon-filtered water with 1 g of CaCl2, 1 g of NaHCO3 and 0.5 g of Instant Ocean sea salts added to water resulting in a conductivity of 200-300 µS pH of 7.8-8.2. The aquaria were provided with biological filters and fish were fed with a commercial feed diet. For each experiment, groups of adult zebrafish were moved to 2 l aquaria provided with biological filters.

extract_protocol: RNA was extracted using the RNeasy Plus kit (Qiagen, Hilden, Germany).

treatment_protocol: To infect zebrafish with SVCV, cell culture medium containing 7.1±2 x10^7 pfu/ml was added to 2 l water tanks and fish were exposed to the virus for 90 minutes. Mock-infected zebrafish were incubated with cell culture medium in parallel experiments.

value: head kidney and spleen

tag: developmental stage

value: adult

tag: treatment

value: Spring Viremia Carp Virus (SVCV) infection

tag: time post-infection

value: 30 days

tag: number of fish in group


title: RSD CD11bNegPBMC 3

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

hyb_protocol: Standard Illumina hybridization protocol for gene expression profiling (carried out in UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out in UCLA Neuroscience Genomics Core).

data_processing: Raw probe data and quantile-normalized gene data were produced by Illumina GenomeStudio software.

label: biotin

source_name: Repeated Social Defeat (RSD) CD11bNegPBMC

label_protocol: Standard Illumina cRNA target synthesis for gene expression profiling (carried out in UCLA Neuroscience Genomics Core).

extract_protocol: Total PBMC and CD11b-depleted PBMC cell populations were isolated and total RNA was extracted by Qiagen RNeasy.

tag: cell type

value: CD11bNeg PBMC


title: 1B1 Replicate 1 Batch 1 ; Immunogen= Mock ; Survive = No

tag: source

tag: immunogen


title: HCC CD11bNegPBMC 3

source_name: Home Cage Control (HCC) CD11bNegPBMC


title: 1B0 Replicate 1 Batch 1 ; Immunogen= Mock ; Survive = No

tag: survival


title: RSD TotalPBMC 3

source_name: Repeated Social Defeat (RSD) TotalPBMC

value: Total PBMC


title: 1A4 Replicate 2 Batch 5 ; Immunogen= Mock ; Survive = No


title: 3A3 Replicate 1 Batch 2 ; Immunogen= Killed PR8 ; Survive = Yes

value: Killed PR8


title: 1B0 Replicate 2 Batch 3 ; Immunogen= Mock ; Survive = No


title: 1A0 Replicate 2 Batch 4 ; Immunogen= Mock ; Survive = No


title: 1A1 Replicate 1 Batch 1 ; Immunogen= Mock ; Survive = No


title: 1A0 Replicate 1 Batch 2 ; Immunogen= Mock ; Survive = No


title: 1A4 Replicate 1 Batch 2 ; Immunogen= Mock ; Survive = No


title: Internal organs_control_non-infected_fish_biological replicate1

source_name: Head kidney+spleen of six SVCV non-infected fish


title: Internal organs_SVCV-infected fish_biological replicate2

source_name: Head kidney+spleen of six SVCV-infected fish 2 days post-infection

value: 2 days


title: Internal organs_SVCV-resistant fish_biological replicate1


title: Internal organs_control_non-infected_fish_biological replicate3


title: HCC TotalPBMC 3

source_name: Home Cage Control (HCC) TotalPBMC


title: 1A2 Replicate 2 Batch 4 ; Immunogen= Mock ; Survive = No

value: serum


title: 1A3 Replicate 2 Batch 3 ; Immunogen= Mock ; Survive = No


title: Internal organs_SVCV-infected fish_biological replicate1


title: 1A3 Replicate 1 Batch 2 ; Immunogen= Mock ; Survive = No


title: RSD CD11bNegPBMC 2


title: Internal organs_control_non-infected_fish_biological replicate2


title: RSD Propranolol  2

source_name: Repeated Social Defeat (RSD) Propranolol

extract_protocol: CD11b+ PBMC (monocyte) cell populations were isolated and total RNA was extracted by Qiagen RNeasy.

value: CD11b+ PBMC


title: HCC CD11bNegPBMC 1


title: RSD TotalPBMC 2


title: RSD Propranolol  3


title: HCC TotalPBMC 2


title: HCC TotalPBMC 1


title: HCC CD11bNegPBMC 2


title: 1A1 Replicate 2 Batch 5 ; Immunogen= Mock ; Survive = No


title: RSD TotalPBMC 1


title: RSD CD11bNegPBMC 1


title: 1A2 Replicate 1 Batch 2 ; Immunogen= Mock ; Survive = No


title: RSD Vehicle  1

source_name: Repeated Social Defeat (RSD) Vehicle


title: HCC Propranolol  3

source_name: Home Cage Control (HCC) Propranolol


title: RSD Vehicle  3


title: HCC Propranolol  1


title: HCC Propranolol  2


title: RSD Vehicle  2


title: WT CLN CD64+ mig nonDC, DNFB, replicate 1

city: Marseille

first: Marc

last: DALOD

address: Parc scientifique de Luminy, Case 906

department: Dendritic cells and antiviral defense

institute: Center of Immunology of Marseille Luminy (CIML)

description: WT migratory CD11b+ Dermal DC from DNFB B6 mice, FACS sorted as: live, CD11c+ MHCIIhi CD11b+ CD24- Ly6C+ CD64+

hyb_protocol: Following fragmentation, 2 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse Gene 1.0 ST . GeneChips were washed and stained in the Affymetrix Fluidics Station 450 .

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

data_processing: The data were RMA normalized in R and Bioconductor, using the affy package.

label_protocol: Biotinylated double strand cDNA targets were prepared, from 5 ng to 20 ng of total RNA depending on the amount available per individual samples, using the NuGEN Ovation Pico WTA System V2 kit (Cat # 3302) and the NuGEN Encore Biotin Module kit (Cat # 4200) according to NuGEN recommendations.

extract_protocol: Total RNA was extracted from between 5x10E3 and 1x10E4 cells for each leukocyte subset with the Qiagen micro RNAeasy kit, according to the manufacturer protocol.

treatment_protocol: Inflammation was induced by application of 10µl of a 0.5% of DNFB diluted in acetone/olive oil (4:1). Ears and skin draining lymph nodes were harvested from untreated animals or 3 days post inflammation. Ear skin tissue was digested by dispase and collagenase 4 treatment, cells were enriched by percoll gradient and resuspended in PBS 2%FCS, EDTA 5mM before sorting by flow cytometry. Cutaneous lymph nodes were digested by collagenase 2 treatment, cells were enriched by optiprep gradient and resuspended in PBS 2%FCS, EDTA 5mM before sorting by flow cytometry.

tag: genotype/variation

value: WT

tag: tissue origin

value: CLN

value: Migratory Dermal Monocyte

tag: cell phenotype

value: CD11c+ MHCIIhi CD11b+ CD24- CD64+

tag: inflammation

value: DNFB

tag: gender

value: female

tag: age

value: 6 weeks-old


title: HCC Vehicle  3

source_name: Home Cage Control (HCC) Vehicle


title: HCC Vehicle  2


title: RSD Propranolol  1


title: Internal organs_SVCV-infected fish_biological replicate3

tag: tissue

value: head kidney and spleen


title: HCC Vehicle  1


title: E. coli MDS42, starvation, SHX 150 ng/ml, rep 3

city: Tsukuba

first: Bei-Wen

last: Ying

state: Ibaraki

address: 1-1-1 Tennoudai

country: Japan

institute: University of Tsukuba

description: growth rate ~ 0.28 (/h)

hyb_protocol: Following fragmentation, 3 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Microarray data were processed using custom scripts written in R based on the finite hybridisation (FH) model (Ono et al, 2008) and the thermodynamic model of non-specific binding (NSB) on short nucleotide microarrays (Furusawa et al, 2009).

organism: Escherichia coli

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were grown in the minimal media, M63. The final cell concentrations were controlled ~ 10^8 cells/mL within the exponential growth phase.

extract_protocol: Total RNAs were extracted using an RNeasy mini kit (Qiagen) in accordance with the manufacturer’s instructions.

treatment_protocol: The cell culture was put into cold phenol-ethanol solution (1 g of phenol in 10 mL of ethanol) prepared in advance. The cells were collected by centrifugation at 16,000 × g for 5 min at 4°C, and the pelleted cells were stored at –80°C prior to use.

tag: strain

tag: condition

value: starvation


title: WT CLN CD11b+ migDC, DNFB, replicate 3

description: WT migratory CD11b+ Dermal DC from DNFB B6 mice, FACS sorted as: live, CD11c+ MHCIIhi CD11b+ CD24- Ly6C- CD64-

value: Migratory Dermal DC

value: CD11c+ MHCIIhi CD11b+ CD24- CD64-


title: Tg2

city: shanghai

first: jinfeng

last: huang

address: No.800 xiangyin road

country: China

institute: second military medical university

description: LncRNA expression of HBx-transgenic mice liver

hyb_protocol: A total of 1μg of labeled cRNA was prepared for fragmentation adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, heated at 60 °C for 30 min, and finally diluted by addition with 55μl 2×GE Hybridization buffer. A volume of 100μl of hybridization solution was then dispensed in the gasket slide and assembled to the lcnRNA expression microarray slide. The slides were incubated for 17 h at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned.

scan_protocol: The hybridized arrays were scanned using the Agilent DNA microarray scanner (part number G2505B) following Agilent Technologies’ guidelines.

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing was performed using the GeneSpringGX v11.0 software package (Agilent Technologies).Following Quantile normalization of the raw data, low intensity are filtered, lncRNAs and mRNAs that at least 1 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: liver, Tg2

label_protocol: Sample labeling and hybridization reactions were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, for each sample 1 μg of total RNA was linearly amplified and labeled with Cy3-dCTP. Labelled cRNAs purified with Qiagen RNAeasy Mini Kit, and sample concentration and specific activity (pmol cy3/μg cRNA) were measured in a NanoDrop® ND-1000 spectrophotometer.

growth_protocol: All mice were bred and maintained in a specific pathogen-free facility and were used in accordance with the institutional guidelines for animal care.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. RNA quality was assessed by Nanodrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

tag: background strain

value: Male

value: Fresh liver

value: 20 months old

value: HBx-transgenic


title: E. coli MDS42, starvation, SHX 150 ng/ml, rep 2

description: growth rate ~ 0.28 (/h)


title: WT Dermis CD11b+ DC, DNFB, replicate 2

description: WT CD11b+ Dermal DC from DNFB B6 mice, FACS sorted as: live, CD11b+ CD24- Ly6C- CD64- MHCII+

value: Dermis

value: Dermal DC

value: CD11b+ CD24- CD64- MHCII+


title: E. coli MDS42, starvation, SHX 100 ng/ml, rep 3

description: growth rate ~ 0.44 (/h)


title: E. coli MDS42, starvation, SHX 100 ng/ml, rep 2

description: growth rate ~ 0.44 (/h)


title: E. coli MDS42, starvation, SHX 150 ng/ml, rep 1

description: growth rate ~ 0.28 (/h)


title: Tg1

source_name: liver, Tg1


title: WT Dermis CD11b+ DC, DNFB, replicate 1

value: WT


title: WT Dermis P2, DNFB, replicate 1

description: WT Dermal P2 from DNFB B6 mice, FACS sorted as: live, CD11b+ CD24- CD64+ Ly6Chigh CCR2+ MHCII+

value: Monocyte

value: CD11b+ CD64+ Ly6Chigh CCR2+ MHCII+


title: E. coli MDS42, starvation, SHX 100 ng/ml, rep 1

description: growth rate ~ 0.44 (/h)


title: E. coli MDS42, starvation, SHX 50 ng/ml, rep 3

description: growth rate ~ 0.59 (/h)

source_name: E. coli MDS42, starvation, SHX 50 ng/ml


title: ERF115OE_roottip5days_rep2

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of purified and fragmented biotinylated aRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix Arabidopsis ATH1 Genome arrays followed by staining and washing in a GeneChip® fluidics station 450  (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: RMA-normalized expression values as obtained with the affy package version 1.36 of BioConductor. The reported values are on log2-scale.

organism: Arabidopsis thaliana

source_name: root tips, 3 mm, 5 days old, overexpressing ERF115

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT express kit (Affymetrix). All steps were carried out according to the manufacturer's protocol (Affymetrix).

growth_protocol: Seeds were vernalized for one week in -70 degrees and plated after bleach sterilization on vertical plates containing full strength MS medium. The medium was covered by sterilized nylon meshes (Prosep) prior to seed plating, plants were grown for five days in a long day/short night regime (16h light, 8h dark) at 21 degrees prior to harvesting.

extract_protocol:
Root tips were excised using scalpels (facilitated by growth on the nylon meshes), immediately harvested into eppendorfs and flash frozen in liquid nitrogen. Root tips were grinded using a retch grinder by adding metal balls until the samples were pulverized.
Total RNA was extracted as described by the Rneasy Mini Kit from Qiagen.

treatment_protocol: Samples were not subjected to any specific kind of treament

tag: ecotype

value: Col-0 expressing the ERF115 ORF under control of the p35S constitutive promoter

value: overexpressing ERF115

value: root tips

value: 5 days


title: WT CLN CD11b+ migDC, DNFB, replicate 1

value: CLN

value: DNFB

value: female

value: 6 weeks-old


title: Col-0_roottip5days_rep3

source_name: root tips, 3 mm, 5 days old, wild-type

value: wild-type


title: WT CLN CD64+ mig nonDC, DNFB, replicate 2

value: Migratory Dermal Monocyte

value: CD11c+ MHCIIhi CD11b+ CD24- CD64+


title: ERF115OE_roottip5days_rep1


title: E. coli MDS42, starvation, SHX 50 ng/ml, rep 1

description: growth rate ~ 0.59 (/h)

value: starvation


title: WT Dermis P1, DNFB, replicate 2

description: WT Dermal P1 from DNFB B6 mice, FACS sorted as: live, CD11b+ CD24-CD64low Ly6Chigh CCR2+ MHCII-

value: Dermis

value: CD11b+ CD64low Ly6Chigh CCR2+ MHCII-


title: E. coli MDS42, starvation, SHX 50 ng/ml, rep 2

description: growth rate ~ 0.59 (/h)


title: Haemophilus ducreyi 35000HPfis relative to 35000HP rep5

city: Dallas

first: Eric

middle: J

last: Hansen

state: TX

address: 5323 Harry Hines Blvd

department: Microbiology

institute: University of Texas Southwestern Medical Center

hyb_protocol: Equal amounts of labeled cDNA from 35000HP or 35000HPfis were thoroughly mixed and used to hybridize microarray slides in Amersham microarray hybridization buffer.  Hybridization was carried out at 50C for 16 hr in the dark.

scan_protocol: After hybridization, the slides were washed in saline-sodium phosphate EDTA buffer and scanned with GenePix  4100A scanner and analyzed with GenePix Pro 5.0 software (Axon instruments)

data_processing: Data was subjected to two types of normalization, a ratio-based normalization so that the mean or median intensities are the same across the array, and a non-linear locally weighed scatterplot smoothing (LOWESS) normalization, which corrects intensity dependent variation in dye basis, before being combined into a single data set for further analysis.  Differential expression was defined as a minimum of two fold over or under expression of 35000HPfis relative to 35000HP.  The data were further scrutinized so as to only include expression profiles that were observed in at least 4 of the 6 experiments and had a p<0.05 after one t-test analysis

organism: [Haemophilus] ducreyi

source_name: Haemophilus ducreyi 35000HP grown in Columbia broth supplemented with 2.5% FCS for 8 hr

label_protocol: Ten micrograms of total RNA for cells grown in Columbia broth for 8 hr were used to generate cDNA using the Amino Allyl cDNA Labeling kit ragents (Ambion).  After reverse transcription, residual RNA was removed by alkaline treatment, followed by neutralization.  The cDNAs were purified using the Qiaquick gel extraction columns (Qiagen).  After purification, Cy3 dye (GE Healthcare) was added following manufacturer's instructions.  The labeled cDNAs were cleaned by using YM-30 Microcon centrifugal devices (Millipore) and labeling efficiency was determined using a Nanodrop spectrophotometer

growth_protocol: Haemophilus ducreyi strain was resucitated from frozen stock on Chocolate agar plates, and incubated ON at 33C in a humidified atmosphere containing 95% air and 5% CO2.  Columbia broth supplemented with 2.5% FCS is inoculated from the plate and cultures are grown in a 33C gyratory water bath at 100 rpm for 8 hrs

extract_protocol: Total RNA from 2-4 ml of culture was extracted using the Ribopure Bacteria kit (Ambion) following manufacturer's instructions.  After isolation, RNA was treated twice with DNaseI (NEB) for 1 hr at 37C, and purified using RNeasy system (Qiagen).  Samples were checked for residual DNA by PCR and re-treated if necessary. Quality assessment was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies)

treatment_protocol: After the fis mutant was generated, both strains were grown in Columbia Broth.  After 8 hr of growth RNA was isolated and processed for DNA microarray analysis.  This study includes three biological replicates (paired samples), and all three were subjected to dye swap.

source_name: Haemophilus ducreyi 35000HPfis grown in Columbia broth supplemented with 2.5% FCS for 8 hr


title: Col-0_roottip5days_rep2


title: WT Dermis CD11b+ DC, DNFB, replicate 3

value: WT

value: Dermal DC

value: CD11b+ CD24- CD64- MHCII+


title: Haemophilus ducreyi 35000HPfis relative to 35000HP rep6


title: Haemophilus ducreyi 35000HPfis relative to 35000HP rep4


title: E. coli MDS42, temperature change, 41.8 deg C, rep 3

description: growth rate ~ 0.23 (/h)

value: temperature change


title: E. coli MDS42, temperature change, 41.5 deg C, rep 3

description: growth rate ~ 0.36 (/h)


title: E. coli MDS42, temperature change, 41.8 deg C, rep 2

description: growth rate ~ 0.23 (/h)


title: WT1

description: LncRNA expression of wild-type mice liver

source_name: liver, WT1

value: Male

value: Fresh liver

value: 20 months old

value: Wild-type


title: E. coli MDS42, temperature change, 41.5 deg C, rep 2

description: growth rate ~ 0.36 (/h)


title: E. coli MDS42, temperature change, 41.8 deg C, rep 1

description: growth rate ~ 0.23 (/h)


title: Haemophilus ducreyi 35000HPfis relative to 35000HP rep2


title: Haemophilus ducreyi 35000HPfis relative to 35000HP rep1


title: WT Dermis P2, DNFB, replicate 2

value: Monocyte

value: CD11b+ CD64+ Ly6Chigh CCR2+ MHCII+

value: DNFB


title: E. coli MDS42, temperature change, 41.5 deg C, rep 1

description: growth rate ~ 0.36 (/h)


title: E. coli MDS42, temperature change, 40.0 deg C, rep 1

description: growth rate ~ 0.56 (/h)


title: E. coli MDS42, osmotic pressure, NaCl 0.55 M, rep 3

description: growth rate ~ 0.22 (/h)

value: osmotic pressure


title: E. coli MDS42, temperature change, 40.0 deg C, rep 3

description: growth rate ~ 0.56 (/h)


title: E. coli MDS42, temperature change, 40.0 deg C, rep 2

description: growth rate ~ 0.56 (/h)


title: E. coli MDS42, osmotic pressure, NaCl 0.55 M, rep 2

description: growth rate ~ 0.22 (/h)


title: E. coli MDS42, osmotic pressure, NaCl 0.55 M, rep 1

description: growth rate ~ 0.22 (/h)


title: Haemophilus ducreyi 35000HPfis relative to 35000HP rep3


title: Col-0_roottip5days_rep1

value: wild-type

value: root tips

value: 5 days


title: erf115ko_roottip5days_rep3

source_name: root tips, 3 mm, 5 days old, erf115 mutant

value: erf115 mutant


title: WT CLN CD64+ mig nonDC, DNFB, replicate 3

value: CLN

value: Migratory Dermal Monocyte

value: CD11c+ MHCIIhi CD11b+ CD24- CD64+

value: female

value: 6 weeks-old


title: WT CLN CD11b+ migDC, DNFB, replicate 2

value: WT

value: Migratory Dermal DC

value: CD11c+ MHCIIhi CD11b+ CD24- CD64-


title: E. coli MDS42, osmotic pressure, NaCl 0.45 M, rep 3

description: growth rate ~ 0.33 (/h)


title: E. coli MDS42, osmotic pressure, NaCl 0.45 M, rep 2

description: growth rate ~ 0.33 (/h)


title: E. coli MDS42, osmotic pressure, NaCl 0.45 M, rep 1

description: growth rate ~ 0.33 (/h)


title: ELSC Participant 12

city: Phoenix

first: Gabriel

last: Shaibi

state: AZ

address: 411 N. Central Avenue

institute: Arizona State University

description: ELSC 12

hyb_protocol: Labeled cRNA samples were fragmented using Agilent Gene Expression Hybridization Kit (Agilent Technologies, Palo Alto, CA), as per the instructions. The fragmented cRNA was hybridized onto whole human genome 4×44K 60-mer oligionucleotide arrays (G4112F, Agilent Technologies, Santa Clara, CA, USA) using a SureHyb DNA Microarray Hybridization chamber for 17 hours at 65°C in a rotating incubator, followed by washing with wash Buffers (Agilent Technologies, Palo Alto, CA). After the washing step, the slides were scanned using an Agilent Microarray Scanner (Agilent Technologies, Palo Alto, CA) and the hybridization signals were extracted using the Agilent Feature Extraction software, version 10.5.1.1 (Agilent Technologies, Palo Alto, CA).

scan_protocol: Hybridization signals were extracted using the Agilent Feature Extraction software, version 10.5.1.1 (Agilent Technologies, Palo Alto, CA).

data_processing: Expression values were analyzed using GeneSpring GX 11.5 (Agilent Technologies, Palo Alto, CA) to identify differentially expressed genes. Data were first normalized by Lowess to account for the 2-color labeling, quantile normalization, and baseline to median of all samples. The probes below 20% expression were filtered and the control probes were excluded from the analysis. The remaining 16,264 probes were subjected to a paired student-t test applying Benjamini-Hochberg multiple testing correction and only those that achieved a fold change ≥1.2 were included, P<0.05.

source_name: PRE intervention_whole blood

label_protocol: Total RNA (500 ng) and RNA spike-in kit, was amplified and labeled using the Agilent Quick Amp, two-color labeling kit (Agilent Technologies), as per manufacturer’s directions. RNA integrity was assessed using Agilent RNA 6000 Nano Kit (Agilent Technologies, Palo Alto, CA) and quantified using the NanoVue Spectrophotometer (GE Healthcare). The RNA integrity numbers (RIN) and RNA absorbance ratio (A260/A280) was 8.3 ± 0.066, and 2.1 ± 0.004, respectively. Complementary RNA (cRNA) was purified using RNeasy Mini Kit (Qiagen). After labeling, cRNA was quantified using NanoVue Spectrophotometer (GE Healthcare) for cyanine 3 (Cy3) and cyanine 5 (Cy5) dye labeled cRNA concentration, RNA absorbance ratio (260 nm/280 nm), A260 values, ADye values, and dye/probes values. Labeled cRNA samples were fragmented using Agilent Gene Expression Hybridization Kit (Agilent Technologies, Palo Alto, CA), as per the instructions.

extract_protocol: Fasting blood samples were collected in PAXgene blood RNA tubes containing a proprietary reagent that stabilizes RNA (BD Diagnostics, Franklin Lakes,NJ). Total RNA was isolated using the PAXgene Blood RNA Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: 15 overweight / obese Latino youth (7 male/8 female, age 15.0±0.9, BMI percentile = 96.3±1.1) who completed a comprehensive lifestyle intervention which consisted of 12-week intervention included weekly nutrition education classes along with three, 60-minute moderate to vigorous physical activity sessions per week.

tag: time point

value: PRE Intervention

tag: age (yrs)

tag: whole body insulin sensitivity index

tag: weight (kg)

tag: height (cm)

tag: bmi

tag: triglycerides (mg/dl)

source_name: POST intervention_whole blood

value: POST Intervention


title: WT Dermis P1, DNFB, replicate 1

tag: genotype/variation

tag: tissue origin

value: Dermis

tag: cell type

value: Monocyte

value: CD11b+ CD64low Ly6Chigh CCR2+ MHCII-


title: ELSC Participant 14

description: ELSC 14

tag: gender

value: male


title: ELSC Participant 17

description: ELSC 17


title: ELSC Participant 31

description: ELSC 31


title: ELSC Participant 23

description: ELSC 23


title: ERF115OE_roottip5days_rep3

value: Col-0 expressing the ERF115 ORF under control of the p35S constitutive promoter

value: overexpressing ERF115

value: root tips

tag: age


title: erf115ko_roottip5days_rep2

value: erf115 mutant

tag: tissue

value: 5 days


title: E. coli MDS42, osmotic pressure, NaCl 0.20 M, rep 2

description: growth rate ~ 0.52 (/h)

tag: strain

value: osmotic pressure


title: ELSC Participant 29

description: ELSC 29


title: erf115ko_roottip5days_rep1


title: WT Dermis P2, DNFB, replicate 3

tag: cell phenotype

value: CD11b+ CD64+ Ly6Chigh CCR2+ MHCII+

tag: inflammation

value: DNFB

value: female


title: WT2

source_name: liver, WT2

tag: background strain

value: Male

value: Fresh liver

value: 20 months old

value: Wild-type


title: E. coli MDS42, osmotic pressure, NaCl 0.20 M, rep 3

description: growth rate ~ 0.52 (/h)

tag: condition


title: E. coli MDS42, osmotic pressure NaCl 0.20 M, rep 1

description: growth rate ~ 0.52 (/h)


title: E. coli MDS42, regular, rep 3

description: growth rate ~ 0.76 (/h)

source_name: E. coli MDS42, regular

value: regular


title: E. coli MDS42, regular, rep 2

description: growth rate ~ 0.76 (/h)


title: ELSC Participant 21

description: ELSC 21

tag: time point

value: PRE Intervention

tag: age (yrs)

value: POST Intervention


title: E. coli MDS42, regular, rep 1

description: growth rate ~ 0.76 (/h)


title: ELSC Participant 08

description: ELSC 08

tag: whole body insulin sensitivity index

tag: weight (kg)


title: ELSC Participant 16

description: ELSC 16

tag: height (cm)

tag: bmi


title: ELSC Participant 33

description: ELSC 33

value: male

tag: triglycerides (mg/dl)


title: ELSC Participant 25

description: ELSC 25


title: ELSC Participant 19

description: ELSC 19


title: ELSC Participant 06

description: ELSC 06


title: ELSC Participant 03

description: ELSC 03


title: human_37_rep3

first: Mónica

last: Aguado-Urda

address: Avda. Puerta de Hierro s/n

department: Animal Health

institute: Complutense University of Madrid

description: Biological replicate 3 of 3. L. Garvieae str.21881 grown at 37 degrees celsius

hyb_protocol: Hybridization protocol followed was that suggested by Agilent´s according to the Two-color microarray-based prokaryote analysis protocol

scan_protocol: Image acquisition and scanning was done following Agilent's instruction and protocols (GE2_107_Sep09) on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS Normalization was done using BRB Array Express software

organism: Lactococcus garvieae

source_name: L. Garvieae 21881, 37C

label_protocol: A total of 5 ug of total RNA of each sample replicate was reverse transcripted and labeled by using the FairPlay III labeling kit (Agilent ) and according to the two color microarray-based prokaryote analysis protocol provided by the manufacturer except for the following: purification of the dye-coupled cDNA was performed by using QIAquick PCR purification kit (Qiagen). The yield and the specific activity of each labelling reaction were determined in a NanoDrop 1000 spectrophotometer.

growth_protocol: L. garvieae strains were grown aerobically in MRS broth at different temperatures (20ºC, 29ºC and 37ºC) and harvested at the mid-log phase (OD600 ~ 0.9) for RNA extraction.

extract_protocol: Total RNA from L. garvieae strains was isolated from three independent biological replicates of each temperature condition by using RNeasy protect bacteria mini kit (Qiagen) according to the manufacturer’s protocol. The quality and concentration of RNA was determined by using the RNA 6000 NanoKit on the Bioanalyzer 2100 (Agilent). Only high- quality RNA samples (RIN > 9) were used for labeling and hybridization.

tag: temperature

value: 37 degrees celsius

source_name: Reference control

tag: reference

value: Equimolar mixture of 21881 & 8831 strains at 29C


title: human_18_rep2

description: Biological replicate 2 of 3. L. Garvieae str.21881 grown at 18 degrees celsius

source_name: L. Garvieae 21881, 18C

growth_protocol: L. garvieae strains were grown aerobically in MRS broth at different temperatures (18ºC, 29ºC and 37ºC) and harvested at the mid-log phase (OD600 ~ 0.9) for RNA extraction.

value: 18 degrees celsius


title: ELSC Participant 01

description: ELSC 01

tag: gender


title: human_18_rep3

description: Biological replicate 3 of 3. L. Garvieae str.21881 grown at 18 degrees celsius


title: human_37_rep2

description: Biological replicate 2 of 3. L. Garvieae str.21881 grown at 37 degrees celsius


title: human_37_rep1

description: Biological replicate 1 of 3. L. Garvieae str.21881 grown at 37 degrees celsius


title: trout_37_rep3

description: Biological replicate 3 of 3. L. Garvieae str.8831 grown at 37 degrees celsius

source_name: L. Garvieae 8831, 37C


title: MB3 TREG

city: Kingswood

first: Grant

last: Parnell

state: NSW

address: Nepean Hospital

department: Nepean Clinical School

country: Australia

institute: University of Sydney

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was normalised using quantile normalisation algorithm in BRB arrayTools

source_name: MB3 TREG

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

extract_protocol: RNA was extracted using Qiagen Rneasy mini kit

treatment_protocol:
cells sorted by flow cytometry and added to cells to signal lysis buffer and stored at minus 80 degrees celcius until RNA extraction
Whole blood samples collected using PAXgene RNA tubes and stored at -20 degrees Celcius until processing

tag: cell type

value: Tregs (CD4+ CD25+ CD127lo)

tag: non pregnant, cord blood, or maternal blood

value: maternal blood


title: NP2 TREG

source_name: NP2 TREG

value: non pregnant


title: CB3 TREG

source_name: CB3 TREG

value: cord blood


title: MB1 non

source_name: MB1 non


title: trout_37_rep2

description: Biological replicate 2 of 3. L. Garvieae str.8831 grown at 37 degrees celsius

tag: strain


title: MB2 TREG

source_name: MB2 TREG


title: CB2 TREG

source_name: CB2 TREG


title: CB1 TREG

source_name: CB1 TREG


title: BA/F3_mifepriston_16h_TA_ChIP_rep1

city: Düsseldorf

first: Pablo

last: Landgraf

address: Moorenstraße 5

department: Clinic of Pediatric Oncology, Hematology and Clinical Immunology

country: Germany

institute: Heinrich-Heine University Düsseldorf

hyb_protocol: Hybridization was performed according to standard procedures by Roche Nimblegen

scan_protocol: Scanning was performed according to standard procedures by Roche Nimblegen.

data_processing: Log2 ratios, scaled using the Tukey biweight.

source_name: Ba/F3 cell line, mifepriston, 16h

label_protocol: 1 µg DNA was directly labeled by Klenow random priming with Cy5 nonamers (DNA precipitated with ETV6-RUNX1 antibody) or with Cy3 nonamers (DNA isolated from input material) per manufacturer's protocol (http://www.nimblegen.com/support/dna-microarray-support.html).

extract_protocol: ChIPs were performed as described by Lee, T. I., et al. (Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1, 729-748, doi:101284307 (2006)). 5 µg TEL-AML1 antibody for inducible cell lines or rat isotype control IgG fro controls (Abcam) were incubated with protein G magnetic beads (Dynal) pre-blocked with pre-immunization serum for 6 hours at 4°C. Beads were washed and incubated with DNA of 10 million cells sheared to ~ 500 bp length at 4°C over night. Chromatin-immunoprecipitated DNA was amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma-Aldrich Chemie GmbH)

treatment_protocol: 32.5 pM mifepristone, 16h, TEL-AML1 ChIP

tag: genotype

value: hsa ETV6-RUNX1 -

tag: sample type

value: immuoprecipitated DNA

tag: cell line

tag: chip antibody

value: IgG

treatment_protocol: 32.5 pM mifepristone, 16h

value: input


title: NP3 TREG

source_name: NP3 TREG


title: BA/F3_AML_ChIP_rep1

source_name: Ba/F3 cell line

label_protocol: 1 µg DNA was directly labeled by Klenow random priming with Cy5 nonamers ( DNA precipitated with AML1 antibody) or with Cy3 nonamers (DNA isolated from input material) per manufacturer's protocol (http://www.nimblegen.com/support/dna-microarray-support.html).

extract_protocol: ChIPs were performed as described by Lee, T. I., et al. (Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1, 729-748, doi:101284307 (2006)). The mouse endogenous  AML1 protein was immunoprecipitated with antibody anti-AML1 (Ab-1; Calbiochem/Merck) following the supplier's instructions.  Chromatin-immunoprecipitated DNA was amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma-Aldrich Chemie GmbH).

value: wt

value: anti-AML1 (Ab-1; Calbiochem/Merck)


title: human_18_rep1

description: Biological replicate 1 of 3. L. Garvieae str.21881 grown at 18 degrees celsius


title: BA/F3_TEL_ChIP_rep3

label_protocol: 1 µg DNA was directly labeled by Klenow random priming with Cy5 nonamers ( DNA precipitated with TEL antibody) or with Cy3 nonamers (DNA isolated from input material) per manufacturer's protocol (http://www.nimblegen.com/support/dna-microarray-support.html).

extract_protocol: ChIPs were performed as described by Lee, T. I., et al. (Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc 1, 729-748, doi:101284307 (2006)). The mouse endogenous TEL protein was immunoprecipitated with antibody anti-TEL (N-19; Santa Cruz Biotechnology) following the suppliers instructions.  Chromatin-immunoprecipitated DNA was amplified using the GenomePlex® Complete Whole Genome Amplification Kit (Sigma-Aldrich Chemie GmbH)


title: trout_37_rep1

description: Biological replicate 1 of 3. L. Garvieae str.8831 grown at 37 degrees celsius


title: CB4 TREG

source_name: CB4 TREG


title: MB4 TREG

source_name: MB4 TREG


title: BA/F3_AML_ChIP_rep2


title: BA/F3_TEL_ChIP_rep1

value: anti-TEL (N-19; Santa Cruz Biotechnology)


title: MB3 non

source_name: MB3 non

value: non‐Treg cells (CD4+ CD25‐ CD127hi)


title: TA+BA/F3_mifepriston_16h_TA_ChIP_rep2

source_name: TEL-AML1 Inducible BA/F3 cell line, mifepriston, 16h

value: hsa ETV6-RUNX1 +


title: BA/F3_mifepriston_16h_TA_ChIP_rep2


title: TA+BA/F3_mifepriston_16h_TA_ChIP_rep1


title: BA/F3_AML_ChIP_rep3


title: BA/F3_TEL_ChIP_rep2


title: MB4 non

source_name: MB4 non


title: NP1 TREG

source_name: NP1 TREG


title: NP4 TREG

source_name: NP4 TREG


title: NP4 non

source_name: NP4 non


title: NP3 non

source_name: NP3 non


title: CB4 non

source_name: CB4 non


title: PB_CD19+_ctrl3

description: control

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver® gene expression data analysis system (Rosetta Biosoftware).

source_name: TEL-AML1 negative control

label_protocol: 10 ng of each total RNA sample was used for linear T7-based amplification. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: Bone marrow samples of TEL-AML1 positive patients were collected at time of diagnosis. After isolation of mononuclear cells, samples were frozen and stored in the gas-phase of liquid nitrogen until RNA isolation. Peripheral blood samples were taken from TEL-AML1 negative healthy donors. The isolated mononuclear cells were sorted for CD19+ cells and stored until RNA isolation.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) according to manufacturer's protocol. Quality of the RNA was checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies).

tag: disease state

value: TEL-AML1 negative control

tag: tissue

value: peripheral blood

tag: timepoint of sample collection

value: any


title: CB3 non

source_name: CB3 non


title: PB_CD19+_ctrl4

description: control


title: bone_marrow_TA+_B-ALL_pat2

description: TEL-AML1 expression

source_name: TEL-AML1 positive B-ALL

value: TEL-AML1 positive B-ALL

value: bone marrow

value: diagnosis


title: MB2 non

source_name: MB2 non

value: maternal blood


title: bone_marrow_TA+_B-ALL_pat4

description: TEL-AML1 expression


title: CB2 non

source_name: CB2 non

value: cord blood


title: bone_marrow_TA+_B-ALL_pat3

description: TEL-AML1 expression


title: NP1 non

source_name: NP1 non

value: non pregnant


title: fasted, 24h, skeletal muscle, biological replicate 5

city: Graz

first: Andreas

last: Prokesch

state: Styria

address: Harrachgasse 21/7

department: Institute of Cell Biology, Histology, and Embryology

country: Austria

institute: Medical University Graz

description: gene expression of skeletal muscle of fasted (24h) male C57Bl/6 mice

hyb_protocol: Genechip hybridization, wash, stain and scan were performed using the GeneTitan hyb-wash-stain kit (Affymetrix) and GeneTitan Instrument.

scan_protocol: GeneTitan instrument was used for scanning.

data_processing: Raw array data were automatically collected by GeneTitan.  Data were normalized using default RMA method within Partek Genomics Suite software. A two-way ANOVA model with an interaction term between diet (fed or fasted) and tissue (liver, skeletal muscle and white adipose tissue) was set up. Pairwise comparisons were made between fed and fasted diet for each tissue. The resulting p-values of significance were corrected for multiple testing using Benjamini-Hochberg's false discovery rate (FDR) method. Genes within 5% FDR and changed at least by 1.3-fold in either direction were called differentially expressed.

source_name: skeletal muscle from C57BL/6 mice, fasted, 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150ng total RNA.

growth_protocol: mice were kept under standard conditions according to the institutional guidelines of the University of Pennsylvania. Mice were kept with normal chow diet in a 12h day/ 12h night cycle.

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

treatment_protocol: Food was withdrawn from the fasting group (n=5) for 24 hours.

value: male

tag: age

value: 10-12 weeks

value: skeletal muscle


title: Pashtun10_17Af

city: Tartu

first: Mait

last: Metspalu

address: Riia 23

country: Estonia

institute: Estonian Biocentre

description: Genomic DNA extracted from blood was genotyped using Human660W-Quad v1.0 Genotyping BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using Genomestudio v2011.1 with GT module 1.9.4 (Illumina).

label: Cy3, Cy5

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

value: Male

tag: population

value: Pashtun

tag: region

value: Central Asia

value: blood


title: bone_marrow_TA+_B-ALL_pat1

description: TEL-AML1 expression


title: MB1 TREG

source_name: MB1 TREG

value: Tregs (CD4+ CD25+ CD127lo)


title: Pashtun2_22Af


title: Hazara6_2Af

value: Hazara


title: NALM6_rep3

source_name: NALM6 cell line

value: WT

value: immuoprecipitated DNA

tag: tag

value: input


title: Pashtun2_6Af


title: NP2 non

source_name: NP2 non

value: non‐Treg cells (CD4+ CD25‐ CD127hi)


title: s36_SIV_ARM_sc_wk2

city: Baltimore

first: Maria

last: Salvato

state: MD

address: 725 W Lombard Street

department: Institute of Human Virology

description: Gene expression data from Monkey PBMC

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning was carried out by using the GeneArray scanner (Hewlett-Packard).

data_processing: The data were analyzed using the R Bioconductor package using the gcRMA algorithm

organism: Macaca mulatta

source_name: Monkey PBMC

label_protocol: Staining with R-phycoerythrin-streptavidin (Molecular Probes) was followed by antibody amplification with a biotinylated streptavidin antibody (Vector Laboratories).

growth_protocol: Rhesus macaques were purchased from the Caribbean Primate Colony.  Experimental protocols were approved by the Institutional Animal Care and Use Committee at the University of Maryland School of Medicine.

extract_protocol: PBMC were isolated from blood using density centrifugation. RNA was extracted using Trizol (Gibco-BRL) followed by a Qiagen Rneasy kit to clean the RNA.

treatment_protocol: Of the 8 ML29-vaccinees, 5 were inoculated subcutaneously (sc) with 0.5 ml, 1000 PFU ML29 and 3 were inoculated intragastrically (ig) with 2 ml, 1000000 PFU ML29. In addition, 5 healthy control animals were vaccinated sc with 0.5 ml of ML29 at 1000 PFU. Blood was collected every week. Six weeks after their first vaccination, 6 macaques (ML-1, SIV/ML-1, SIV/ML-2, SIV/ML-6, SIV/ML-7, SIV/Arm-1) were boosted sc with 1000 pfu ML29.

value: PBMC

tag: infection status


title: Pashtun2_8Af


title: Hazara6_27Af


title: fasted, 24h, skeletal muscle, biological replicate 4


title: fasted, 24h, skeletal muscle, biological replicate 3


title: s38_ML29_iv_wk2

institute: University of Maryland School of Medicine

description: Gene expression data from Monkey PBMC


title: s35_SIV_ARM_sc_wk2

description: Gene expression data from Monkey PBMC


title: fasted, 24h, skeletal muscle, biological replicate 2


title: Pashtun2_20Af


title: Hazara6_66Af


title: Hazara6_68Af


title: s33_SIV_ML29_ig_wk2

description: Gene expression data from Monkey PBMC


title: fasted, 24h, liver, biological replicate 5

description: gene expression of liver of fasted (24h) male C57Bl/6 mice

source_name: liver from C57BL/6 mice, fasted, 24h

value: liver


title: fasted, 24h, liver, biological replicate 4


title: NALM6_rep2


title: s29_SIV_ML29_sc_wk2

description: Gene expression data from Monkey PBMC


title: Uzbek8_10Af

value: Uzbeks


title: s31_SIV_ML29_sc_wk2

description: Gene expression data from Monkey PBMC


title: fasted, 24h, liver, biological replicate 3


title: fasted, 24h, skeletal muscle, biological replicate 1


title: Uzbek8_86Af


title: Tadjik1_39Af

value: Tajiks


title: s27_SIV_ML29_sc_wk2

description: Gene expression data from Monkey PBMC


title: Uzbek8_68Af


title: fasted, 24h, liver, biological replicate 2

value: male


title: NALM6_rep1


title: fasted, 24h, liver, biological replicate 1

value: 10-12 weeks


title: Hazara6_6Af


title: fasted, 24h, white adipose tissue, biological replicate 5

description: gene expression of white adipose tissue of fasted (24h) male C57Bl/6 mice

source_name: epididymal white adipose tissue from C57BL/6 mice, fasted, 24h

value: epididymal white adipose tissue


title: s25_ML29_iv_wk1

description: Gene expression data from Monkey PBMC


title: Tadjik10_16Af

value: Male


title: s23_SIV_ARM_sc_wk1

description: Gene expression data from Monkey PBMC


title: s30_SIV_ML29_sc_wk2

description: Gene expression data from Monkey PBMC


title: Tadjik1_44Af


title: Uzbek8_18Af


title: fasted, 24h, white adipose tissue, biological replicate 4


title: Uzbek8_20Af


title: fasted, 24h, white adipose tissue, biological replicate 3


title: s22_SIV_ARM_sc_wk1

description: Gene expression data from Monkey PBMC


title: TA+BA/F3_mifepriston_16h_TA_ChIP_rep2

description: TEL-AML1 expression

hyb_protocol: Samples were hybridized using the GeneChip Hybridization, Wash and Stain Kit (Affymetrix), the GeneChip Fluidics Station 450 (Affymetrix) and the GeneChip Hybridization Oven 645 (Affymetrix) according to manufacturer's instruction. This service was provided by the BMFZ (University Duesseldorf).

scan_protocol: This service was provided by the BMFZ (University Duesseldorf) using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: We used GCRMA bioconductor package (version 2.28.0) to normalize the data, only default parameters were used.

label: Biotin

source_name: TEL-AML1 Inducible BA/F3 cell line, mifepriston, 16h

label_protocol: GeneChip 3' IVT Express Kit (Affymetrix) according to manufacturer's instructions.

extract_protocol: Total RNA of 5 Mio cells was isolated with standard triZOL procedure (Invitrogen) according to manufacturer's instructions.

treatment_protocol: Cells carrying the inducible ETV6-RUNX1 (TA+) and control cells were treated with 32.5 pM mifepristone for 16 hours

value: hsa ETV6-RUNX1 +


title: fasted, 24h, white adipose tissue, biological replicate 2


title: fasted, 24h, white adipose tissue, biological replicate 1


title: s20_SIV_ML29_ig_wk1

description: Gene expression data from Monkey PBMC


title: s17_SIV_ML29_sc_wk1

description: Gene expression data from Monkey PBMC


title: ad libitum chow, 24h, skeletal muscle, biological replicate 5

description: gene expression of skeletal muscle of ad libitum fed male C57Bl/6 mice

source_name: skeletal muscle from C57BL/6 mice, ad libitum, 24h

value: skeletal muscle


title: s18_SIV_ML29_sc_wk1

description: Gene expression data from Monkey PBMC


title: BA/F3_mifepriston_16h_TA_ChIP_rep2

description: control

source_name: Ba/F3 cell line, mifepriston, 16h

value: hsa ETV6-RUNX1 -


title: Tadjik1_6Af

value: Central Asia

value: blood


title: Turkmen9_46Af

value: Turkmens


title: BA/F3_mifepriston_16h_TA_ChIP_rep1

description: TEL-AML1 expression


title: s28_SIV_ML29_sc_wk2

description: Gene expression data from Monkey PBMC


title: ad libitum chow, 24h, skeletal muscle, biological replicate 4


title: s16_SIV_ML29_sc_wk1

description: Gene expression data from Monkey PBMC


title: ad libitum chow, 24h, skeletal muscle, biological replicate 3


title: Turkmen9_5Af


title: s14_SIV_ML29_sc_wk1

description: Gene expression data from Monkey PBMC


title: Tadjik1_18Af


title: TA+BA/F3_mifepriston_16h_TA_ChIP_rep1

description: control


title: Turkmen9_36Af


title: ad libitum chow, 24h, skeletal muscle, biological replicate 2


title: s12_uninfect

description: Gene expression data from Monkey PBMC

value: uninfect


title: Turkmen9_10Af


title: ad libitum chow, 24h, skeletal muscle, biological replicate 1


title: s10_SIV

description: Gene expression data from Monkey PBMC

value: SIV


title: ad libitum chow, 24h, liver, biological replicate 4

description: gene expression of liver of ad libitum fed male C57Bl/6 mice

source_name: liver from C57BL/6 mice, ad libitum, 24h


title: ad libitum chow, 24h, liver, biological replicate 5


title: ad libitum chow, 24h, liver, biological replicate 3


title: s15_SIV_ML29_sc_wk1

description: Gene expression data from Monkey PBMC


title: Mantle cell lymphoma  M031 Normal

city: Barcelona

first: Sílvia

last: Beà

state: Barcelona

address: Rossello, 153

department: HematoPathology

institute: Hospital Clinic

description: Hybridized to SNP 6.0

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

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

data_processing: Image data were analysed with Genotyping Console 4.0 to obtain the CEL data files, which were also exported to the Nexus Biodiscovery Edition for data analysis and visualization. Quality controls assessed by Genotyping Console included Contrast Quality Control (CQC>0.4) produced by Birdseed and Median of the Absolute values of all Pairwise Differences (MAPD<0.35). Tumour and normal DNA samples were analysed individually with the Nexus Biodiscovery Edition using the SNP-FASST2 segmentation algorithm and using segment reporting tool filters: minimum of 100 Kb minimum genomic size of a segment, as well as by visual inspection.

source_name: Normal

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic B cells obtained from peripheral blood and other tissues using the Qiagen Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, and agarose gel electrophoresis.

value: Normal genomic DNA

tag: subject

value: Mantle cell lymphoma


title: s5_SIV

description: Gene expression data from Monkey PBMC

value: PBMC


title: s9_SIV

description: Gene expression data from Monkey PBMC


title: ad libitum chow, 24h, liver, biological replicate 2

tag: gender

value: liver


title: ad libitum chow, 24h, liver, biological replicate 1


title: Mantle cell lymphoma M030 Peripheral Blood

description: Hybridized to SNP 6.0

source_name: Peripheral Blood

value: Female

value: Peripheral Blood

tag: cell type

value: mononuclear cell preparations of leukemic B cells


title: s7_SIV

description: Gene expression data from Monkey PBMC


title: ad libitum chow, 24h, white adipose tissue, biological replicate 5

description: gene expression of white adipose tissue of ad libitum fed male C57Bl/6 mice

source_name: epididymal white adipose tissue from C57BL/6 mice, ad libitum, 24h

value: male

value: 10-12 weeks

value: epididymal white adipose tissue


title: s4_SIV

description: Gene expression data from Monkey PBMC


title: Mantle cell lymphoma  M030 Normal

description: Hybridized to SNP 6.0


title: ad libitum chow, 24h, white adipose tissue, biological replicate 4


title: Mantle cell lymphoma  M028 Normal

description: Hybridized to SNP 6.0

value: Male


title: Mantle cell lymphoma  M029 Normal

description: Hybridized to SNP 6.0


title: s2_salvato_PBMC.CEL

description: Gene expression data from Monkey PBMC


title: ad libitum chow, 24h, white adipose tissue, biological replicate 3


title: Mantle cell lymphoma M029 Peripheral Blood

description: Hybridized to SNP 6.0


title: Control 96h vs. siNTE 96h 2

city: ELCHE

first: MIGUEL

middle: A

last: SOGORB

state: ALICANTE

address: AVENIDA DE LA UNIVERSIDAD S/N

department: INSTITUTO DE BIOINGENIERÍA

institute: UNIVERSIDAD MIGUEL HERNÁNDEZ DE ELCHE

hyb_protocol: Labeled samples were hybridisez using Hi-RPM Gene Expression Hybridization Kit (Agilent) according to manufacturer protocol

scan_protocol: Scanned on an Agilent G2565CA scanner

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and LOWESS normalization. Final analysis was made with Limma package from Bioconductor.

source_name: siNTE stem cells 96h

label_protocol: 200 ng of total RNA were labeled using Low Input Quick Amp Labeling Kit (Agilent) according to manufacturer protocol

growth_protocol: D3 cells were grown in differentiation (in absence of LIF) in DMEM medium supplemented with 15% heat-inactivated fetal bovine serum, 1% nonessential amino acids, antibiotics and 0.1 mM β-mercaptoethanol. Incubation conditions were 37°C, 5% CO2 and 95% humidity.

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

treatment_protocol: siRNA was transfected into D3 cells using RNAiMAX lipofectamine. Ten µl of lipofectamine were added to 250 µl of Opti-MEM medium to be incubated after mixing at room temperature for 15 min. In parallel, 1.25 pmoles of each siRNA were added to 250 µl of Opti-MEM medium, and were also incubated after mixing at room temperature for 15 min. These two solutions were mixed and incubated again at room temperature for 15 min. One million D3 cells were subsequently added. After an additional 15-minute period, the transfection solution was diluted by adding 4 ml of fresh medium. Transfected cells were seeded as embryonic bodies and cultured in the absence of LIF as described above.

value: D3 Embryonic stem

tag: developmental stage

value: 96 hours

source_name: Control stem cells 96h


title: ad libitum chow, 24h, white adipose tissue, biological replicate 2

tag: strain


title: GSM135292_blood

description: Gene expression data from Monkey PBMC


title: s1_SIV

description: Gene expression data from Monkey PBMC


title: s3_SIV

description: Gene expression data from Monkey PBMC


title: GSM135290_blood

description: Gene expression data from Monkey PBMC


title: ad libitum chow, 24h, white adipose tissue, biological replicate 1


title: Mantle cell lymphoma  M027 Normal

description: Hybridized to SNP 6.0


title: Control 24h vs. siNTE 24h 2

source_name: siNTE stem cells 24h

value: 24 hours

source_name: Control stem cells 24h


title: Control 96h vs. siNTE 96h 1


title: Control 24h vs. siNTE 24h 1


title: Mantle cell lymphoma M026 Peripheral Blood

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M025 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M028 Peripheral Blood

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M027 Peripheral Blood

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M026 Normal

description: Hybridized to SNP 6.0


title: GSM135291_blood

description: Gene expression data from Monkey PBMC


title: Mantle cell lymphoma M025 Lymph Node

description: Hybridized to SNP 6.0

source_name: Lymph Node

value: Lymph Node


title: Mantle cell lymphoma  M024 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M023 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M026 Lymph Node

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M024 Lymph Node

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M021 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M022 Lymph Node

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M023 Peripheral Blood

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M023 Lymph Node

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M031 Lymph Node

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M021 Peripheral Blood

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M031 Peripheral Blood

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M020 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M020 Peripheral Blood

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M016 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M019 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M015 Peripheral Blood

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M019 Peripheral Blood

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M014 Lymph Node

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M012 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M018 Peripheral Blood

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M015 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M014 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M018 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M011 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M013 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M010 Peripheral Blood

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M011 Lymph Node

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M012 Lymph Node

description: Hybridized to SNP 6.0


title: Chromosomal distribution of Pht1 in cd60

status: Public on Nov 03 2013

city: Kami

first: Kojiro

last: Ishii

state: Kochi

address: 185 Miyanokuchi, Tosayamada

institute: Kochi University of Technology

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Pht1-GFP (Cy5) from Schizosaccharomyces pombe cd60.

hyb_protocol: Hybridisation was carried out at 65 °C for 40 h against the KU-LSI Schizosaccharomyces pombe genome tiling array 4x44K_v1.0 (Agilent Technologies) according to the manufacturer's instructions. The slide was then washed with Wash Buffer 1 for 5 min at room temperature and with Wash Buffer 2 for 5 min at 31 ºC, according to the manufacturer's instructions (Agilent Technologies), in ozone-depleted surroundings.

scan_protocol: Microarray slides were scanned using the Agilent Microarray Scanner G2505B and Scan Control Software G2565BA, followed by extraction of information from the probe features using Agilent Feature Extraction Software 9.5.1.1.

data_processing: For each data set, intra-array Lowess (intensity-dependent) normalization was performed using the Agilent ChIP Analytics Software 1.3.1, and the enrichment ratios were calculated by dividing the normalised ChIP (Cy5) signals over corresponding WCE (Cy3) signals.

organism: Schizosaccharomyces pombe

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Pht1-GFP

label_protocol: ChIP-purified DNA was treated with RNase A, flush-ended using T4 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy5-dUTP by using the Agilent Genomic DNA Labeling Kit PLUS.

growth_protocol: Cells were fixed with 3% formaldehyde at 18 °C for 35 min. The fixation reaction was terminated by adding 330 mM final concentration of glycine and incubating for 10 min. The cells were collected by centrifugation and washed 3 times with 1x PBS.

extract_protocol: Cell lysates were prepared by glass bead vortexing in FA-lysis buffer (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 1x Complete) containing 0.5% SDS. The cross-linked chromatin was then pelleted by centrifuging the lysate, and after a wash with ice-cold FA-lysis buffer containing 0.1% SDS, the chromatin pellet was sonicated to yield soluble fragments with an average size of 500 bp and a range between 300 and 1000 bp. The reaction was clarified by centrifugation, and the chromatin solution was supplemented with 1% Triton X-100. To elute DNA and revert cross-links, the beads were incubated with SDS-TE (1% SDS, 10 mM Tris-HCl (pH 8.0), 1 mM EDTA) for 15 h at 65 °C, followed by digestion with proteinase K at 42 °C. After extraction with phenol, DNA was precipitated with isopropanol and resuspended in TE.

treatment_protocol: Exponentially growing fission yeast cells were asynchronously cultured at 33 °C in YES, and transferred to 18 °C for 2 h prior to fixation.

value: neocentric

value: h- leu1 ura4 cen1D::kanR cd60

tag: genotype

value: GFP

tag: antibody vendor

value: Roche

tag: antibody catalog#

tag: antibody lot#

source_name: Chromatin-input DNA (WCE) for Pht1-GFP

label_protocol: WCE DNA was treated with RNase A, flush-ended using T4 DNA polymerase, and ligated with the double-stranded DNA linker using T4 DNA ligase. Linker-ligated DNA was PCR-amplified using AmpliTaq DNA polymerase, and then labelled with Cy3-dUTP by using the Agilent Genomic DNA Labeling Kit PLUS.


title: Chromosomal distribution of Pht1 in cd389

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Pht1-GFP (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389.

value: h- leu1 ura4 cen3D::kanR cd389

tag: chip antibody


title: Mantle cell lymphoma M008 Peripheral Blood

description: Hybridized to SNP 6.0

tag: tissue

tag: sample type

tag: disease state

value: Mantle cell lymphoma


title: Mantle cell lymphoma M016 Spleen

description: Hybridized to SNP 6.0

source_name: Spleen

value: Female

value: Spleen


title: Mantle cell lymphoma  M008 Normal

description: Hybridized to SNP 6.0

value: Normal genomic DNA


title: Chromosomal distribution of Pht1 in cd385

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Pht1-GFP (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd385.

value: h- leu1 ura4 cen3D::kanR cd385


title: Mantle cell lymphoma M007 Colonic biopsy

description: Hybridized to SNP 6.0

source_name: Colonic biopsy

value: Colonic biopsy

value: mononuclear cell preparations of leukemic B cells


title: Chromosomal distribution of Pht1 in Dmsc1

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Pht1-GFP (Cy5) from Schizosaccharomyces pombe Dmsc1.

value: h- leu1 ura4 Dmsc1::hygR


title: Chromosomal distribution of Pht1 in cd389-r1

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Pht1-GFP (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389-r1.

value: h- leu1 ura4 cen3D::kanR cd389-r1


title: Mantle cell lymphoma  M006 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M004 Normal

description: Hybridized to SNP 6.0

value: Male

value: Normal


title: Mantle cell lymphoma M002 Peripheral Blood 3.2 years after diagnosis

description: Hybridized to SNP 6.0

value: Peripheral Blood


title: Mantle cell lymphoma M006 Peripheral Blood

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M007 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M002 Tonsil

description: Hybridized to SNP 6.0

source_name: Tonsil

value: Tonsil


title: Mantle cell lymphoma M001 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M004 Peripheral Blood

description: Hybridized to SNP 6.0


title: Chromosomal distribution of Pht1 in WT

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Pht1-GFP (Cy5) from Schizosaccharomyces pombe wild-type.

value: wild-type

value: h- leu1 ura4


title: Mantle cell lymphoma M002 Normal

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma M009 Peripheral Blood

description: Hybridized to SNP 6.0


title: Mantle cell lymphoma  M003 Normal

description: Hybridized to SNP 6.0


title: Chromosomal distribution of Scm3 in cd389

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Scm3-GFP (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Scm3-GFP

value: neocentric

source_name: Chromatin-input DNA (WCE) for Scm3-GFP


title: Chromosomal distribution of Swi6 in cd389-vector

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Swi6 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389-vecint.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Swi6

value: h- leu1 ura4 cen3D::kanR cd389-vector

source_name: Chromatin-input DNA (WCE) for Swi6


title: Mantle cell lymphoma M001 Peripheral Blood

description: Hybridized to SNP 6.0

value: Mantle cell lymphoma


title: Chromosomal distribution of Pht1 in cd39

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Pht1-GFP (Cy5) from Schizosaccharomyces pombe cd39.

value: h- leu1 ura4 cen1D::kanR cd39

value: GFP

value: Roche


title: Chromosomal distribution of Cnp1 in cd389-vector

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Cnp1 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389-vecint.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Cnp1

source_name: Chromatin-input DNA (WCE) for Cnp1


title: Chromosomal distribution of H3me2K9 in cd389-r1

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with H2me2K9 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389-r1.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for H3me2K9

value: abcam

source_name: Chromatin-input DNA (WCE) for H3me2K9


title: Cholangio non-malignant sample 3001N SNP6

city: Singapore

first: Ioana

last: Cutcutache

state: Singapore

address: 8 College Rd

department: Centre for Computational Biology

country: Singapore

institute: Duke-NUS

description: Hybridized to SNP6 array

data_processing:
The data in each tumor raw CEL file was normalized using CRMA-v2 and TumorBoost, and then analyzed with version 2 of the ASCAT algorithm which simultaneously models the aberrant cell fraction, regions of copy number changes and allele counts. The matched non-malignant CEL file is used as a reference in this processing. For each heterozygous position found in the normal tissue, the minor allele frequency (BAF) and the log of the ratio of the total signal intensity in the tumor and matched non-tumor sample (Log R) were calculated for the tumor tissue. ASCAT determined the aberrant cell fraction and mean genomic ploidy that best fits these points.
LRR' = normalized logR value; 'normalized_BAF' = normalized B-allele frequency (after TumorBoost); 'nA' = copy number of allele A; 'nB' = copy number of allele B
**For the non-malignant tissue only the raw BAF value is provided, as this is the only information necessary for processing the tumor using TumorBoost and ASCAT.

source_name: Cholangio non-malignant sample 3001N

extract_protocol: Genomic DNA was extracted from patient specimens using Qiagen Blood and Cell Culture DNA kit (Qiagen, CA). Genomic DNA yield and quality were determined by Nanodrop ND1000 spectrophotometer (Thermo Scientific, MA) and further visually inspected by agarose gel electrophoresis.

value: cholangio non-malignant tissue


title: Chromosomal distribution of Cnp1 in cd389-r1

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Cnp1 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389-r1.


title: Cholangio non-malignant sample 1202N SNP6

description: Hybridized to SNP6 array

source_name: Cholangio non-malignant sample 1202N


title: Mantle cell lymphoma M001 Lymph Node

description: Hybridized to SNP 6.0

value: Lymph Node

value: mononuclear cell preparations of leukemic B cells


title: Chromosomal distribution of H3me2K9 in cd389-vector

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with H2me2K9 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389-vecint.


title: Chromosomal distribution of H3me2K9 in cd389-dh2.1

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with H3me2K9 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389-dh2.1int.

value: h- leu1 ura4 cen3D::kanR cd389-dh2.1


title: Cholangio non-malignant sample 930N SNP6

description: Hybridized to SNP6 array

source_name: Cholangio non-malignant sample 930N


title: Chromosomal distribution of Cnp1 in cd389-dh2.1

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Cnp1 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389-dh2.1int.


title: Chromosomal distribution of Mis12 in cd389

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Mis12-GFP (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Mis12-GFP

value: h- leu1 ura4 cen3D::kanR cd389

source_name: Chromatin-input DNA (WCE) for Mis12-GFP


title: Chromosomal distribution of Swi6 in cd389-dh2.1

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Swi6 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389-dh2.1int.


title: Cholangio tumor sample 1202T SNP6

description: Hybridized to SNP6 array

source_name: Cholangio tumor sample 1202T

value: cholangio primary tumor tissue


title: Mantle cell lymphoma M003 Peripheral Blood 3.5 years after diagnosis

description: Hybridized to SNP 6.0

source_name: Peripheral Blood

value: Male

value: Peripheral Blood


title: Chromosomal distribution of H3me2K9 in cd389

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with H3me2K9 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389.


title: Cholangio tumor sample 3001T SNP6

description: Hybridized to SNP6 array

source_name: Cholangio tumor sample 3001T


title: Chromosomal distribution of Mis6 in cd389

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Mis6-GFP (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Mis6-GFP

source_name: Chromatin-input DNA (WCE) for Mis6-GFP


title: Chromosomal distribution of Cnp3 in cd389

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Cnp3-GFP (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Cnp3-GFP

source_name: Chromatin-input DNA (WCE) for Cnp3-GFP


title: Chromosomal distribution of Cnp20 in cd389

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Cnp20-GFP (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Cnp20-GFP

source_name: Chromatin-input DNA (WCE) for Cnp20-GFP


title: Chromosomal distribution of Cnp1 in cd389

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Cnp1 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Cnp1

source_name: Chromatin-input DNA (WCE) for Cnp1


title: Cholangio non-malignant sample 715N SNP6

description: Hybridized to SNP6 array

source_name: Cholangio non-malignant sample 715N


title: Chromosomal distribution of Scm3 in cd389-r1

description: Comparing between genome DNA (Cy3) and DNA co-immunopurified with Scm3-GFP (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd389-r1

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Scm3-GFP

value: h- leu1 ura4 cen3D::kanR cd389-r1

source_name: Chromatin-input DNA (WCE) for Scm3-GFP


title: Chromosomal distribution of Cnp1 in cd386-r2

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Cnp1 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd386-r2.

value: h- leu1 ura4 cen3D::kanR cd386-r2


title: Cholangio non-malignant sample 824N SNP6

description: Hybridized to SNP6 array

source_name: Cholangio non-malignant sample 824N


title: Chromosomal distribution of H3me2K9 in cd385-vector

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with H3me2K9 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd385-vecint.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for H3me2K9

value: neocentric

value: h- leu1 ura4 cen3D::kanR cd385-vector

source_name: Chromatin-input DNA (WCE) for H3me2K9


title: Chromosomal distribution of Cnp1 in cd385-vector

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Cnp1 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd385-vecint.


title: Chromosomal distribution of Cnp1 in cd385-r1

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Cnp1 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd385-r1.

value: h- leu1 ura4 cen3D::kanR cd385-r1


title: Chromosomal distribution of Swi6 in cd385-dh2.1

description: Comparison between genome DNA (Cy3) and DNA co-immunopurified with Swi6 (Cy5) from the Schizosaccharomyces pombe cen3 deletion survivor cd385-dh2.1int.

source_name: Chromatin-immunoprecipitated (ChIP) DNA for Swi6

value: h- leu1 ura4 cen3D::kanR cd385-dh2.1

source_name: Chromatin-input DNA (WCE) for Swi6


title: Cholangio tumor sample 930T SNP6

description: Hybridized to SNP6 array

source_name: Cholangio tumor sample 930T


title: Cholangio non-malignant sample 77071507N SNP6

description: Hybridized to SNP6 array


title: Cholangio non-malignant sample 23474504N SNP6

description: Hybridized to SNP6 array