title: 118-4h-sample4-BLOCK3

description:
118_4h_4_3
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416654_A03_118_4_4_2011-05-13_532_gridded.pair
416654_A03_118_4_4_2011-05-13_532_gridded_norm_RMA.pair


title: 118-4h-sample4-BLOCK1

status: Public on Dec 13 2013

type: RNA

city: Nijmegen

first: Jeroen

middle: Daniel

last: Langereis

address: PO Box 9101

department: Department of Pediatrics

country: Netherlands

institute: Radboud University Medical Centre

description:
118_4h_4_1
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416654_A03_118_4_4_2011-05-13_532_gridded.pair
416654_A03_118_4_4_2011-05-13_532_gridded_norm_RMA.pair

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

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

molecule: total RNA

organism: Haemophilus influenzae R2866

source_name: R2866Δ112 mutant  4 hours

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: NTHi strain R2866 was grown in supplemented brain-heart infusion medium for 4 hours.

extract_protocol: Bacteria were washed with PBS and total RNA was extracted with the RNeasy minikit (Qiagen) and was DNase treated (Ambion).

treatment_protocol: Growth of the R2866 wild-type and R2866Δ0112 gene mutant was compared.

tag: genotype/variation

value: R2866_0112 gene deletion mutant

tag: time

value: 4 hours


title: 118-4h-sample3-BLOCK4

description:
118_4h_3_4
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416694_A03_118_4_3_2011-05-13_532_gridded.pair
416694_A03_118_4_3_2011-05-13_532_gridded_norm_RMA.pair


title: WT-7h-sample1-BLOCK1

description:
WT_7h_1_1
This sample is wild-type Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416693_A01_WT_7_1_2011-05-13_532_gridded.pair
416693_A01_WT_7_1_2011-05-13_532_gridded_norm_RMA.pair

source_name: Wild-type 7 hours

growth_protocol: NTHi strain R2866 was grown in supplemented brain-heart infusion medium for 7 hours.

value: Wild-type

value: 7 hours


title: 118-4h-sample3-BLOCK2

description:
118_4h_3_2
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416694_A03_118_4_3_2011-05-13_532_gridded.pair
416694_A03_118_4_3_2011-05-13_532_gridded_norm_RMA.pair


title: 118-4h-sample3-BLOCK3

description:
118_4h_3_3
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416694_A03_118_4_3_2011-05-13_532_gridded.pair
416694_A03_118_4_3_2011-05-13_532_gridded_norm_RMA.pair


title: 118-4h-sample3-BLOCK1

description:
118_4h_3_1
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416694_A03_118_4_3_2011-05-13_532_gridded.pair
416694_A03_118_4_3_2011-05-13_532_gridded_norm_RMA.pair


title: 118-4h-sample4-BLOCK4

description:
118_4h_4_4
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416654_A03_118_4_4_2011-05-13_532_gridded.pair
416654_A03_118_4_4_2011-05-13_532_gridded_norm_RMA.pair


title: WT-7h-sample1-BLOCK4

description:
WT_7h_1_4
This sample is wild-type Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416693_A01_WT_7_1_2011-05-13_532_gridded.pair
416693_A01_WT_7_1_2011-05-13_532_gridded_norm_RMA.pair


title: 118-4h-sample2-BLOCK4

description:
118_4h_2_4
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416566_A03_118_4_2_2011-05-13_532_gridded.pair
416566_A03_118_4_2_2011-05-13_532_gridded_norm_RMA.pair


title: WT-7h-sample2-BLOCK1

description:
WT_7h_2_1
This sample is wild-type Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 7 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416566_A01_WT_7_2_2011-05-13_532_gridded.pair
416566_A01_WT_7_2_2011-05-13_532_gridded_norm_RMA.pair


title: 118-4h-sample2-BLOCK3

description:
118_4h_2_3
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416566_A03_118_4_2_2011-05-13_532_gridded.pair
416566_A03_118_4_2_2011-05-13_532_gridded_norm_RMA.pair


title: 118-4h-sample2-BLOCK2

description:
118_4h_2_2
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416566_A03_118_4_2_2011-05-13_532_gridded.pair
416566_A03_118_4_2_2011-05-13_532_gridded_norm_RMA.pair


title: 118-4h-sample1-BLOCK4

description:
118_4h_1_4
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416693_A03_118_4_1_2011-05-13_532_gridded.pair
416693_A03_118_4_1_2011-05-13_532_gridded_norm_RMA.pair


title: WT-4h-sample4-BLOCK4

description:
WT_4h_4_4
This sample is wild-type Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416654_A01_WT_4_4_2011-05-13_532_gridded.pair
416654_A01_WT_4_4_2011-05-13_532_gridded_norm_RMA.pair

source_name: Wild-type 4 hours


title: 118-4h-sample1-BLOCK1

description:
118_4h_1_1
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416693_A03_118_4_1_2011-05-13_532_gridded.pair
416693_A03_118_4_1_2011-05-13_532_gridded_norm_RMA.pair


title: 118-4h-sample1-BLOCK2

description:
118_4h_1_2
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416693_A03_118_4_1_2011-05-13_532_gridded.pair
416693_A03_118_4_1_2011-05-13_532_gridded_norm_RMA.pair


title: 118-4h-sample2-BLOCK1

description:
118_4h_2_1
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416566_A03_118_4_2_2011-05-13_532_gridded.pair
416566_A03_118_4_2_2011-05-13_532_gridded_norm_RMA.pair


title: WT-4h-sample4-BLOCK2

description:
WT_4h_4_2
This sample is wild-type Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416654_A01_WT_4_4_2011-05-13_532_gridded.pair
416654_A01_WT_4_4_2011-05-13_532_gridded_norm_RMA.pair


title: WT-4h-sample3-BLOCK4

description:
WT_4h_3_4
This sample is wild-type Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416694_A01_WT_4_3_2011-05-13_532_gridded.pair
416694_A01_WT_4_3_2011-05-13_532_gridded_norm_RMA.pair


title: WT-4h-sample4-BLOCK1

description:
WT_4h_4_1
This sample is wild-type Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416654_A01_WT_4_4_2011-05-13_532_gridded.pair
416654_A01_WT_4_4_2011-05-13_532_gridded_norm_RMA.pair


title: berghei_GNPm9_SCHIZONT_rep1a

city: Glasgow

first: Katie

middle: Ruth

last: Hughes

address: 120 University Place

department: GBRC, III, Wellcome Centre for Molecular Parasitology

country: United Kingdom

institute: University of Glasgow

hyb_protocol: Hybridization buffer (Agilent) was added to mixed Cy3/Cy5 labled samples and applied to microarrays enclosed in Agilent hybridization chambers. After overnight hybridization, slides were washed sequential washes and dried with aceton prior to scanning

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and normalised log2 ratio Cy5/Cy3 representing test/referencepool

organism: Plasmodium berghei

source_name: GNPm9 Schiz

label_protocol: 10 µg of total RNA were primed with a mixture of polyA and random decamer primers then reversed transcribed to incorporate amino allyl dUTP. Cy3/Cy5 coupling reaction carried out then purified samples hybridised overnight

growth_protocol: Plamodium berghei blood stage parasites were maintained in TO mice and synchronous schizont populations obtained by overnight cultures under standard procedures

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions after filtering of samples to remove leukocyte contamination and subsequent lysis of red blood cells

treatment_protocol: Synchronous schizont populations obtained by overnight cultures under standard procedures, after reinfection of synchronous cultures and 6h growth parasites were collected for 6h ring stages and returned to culture for troph stages.

tag: Stage

value: Schizont

tag: line

value: Pooled All stages

value: Wild Type (PBANKA)


title: berghei_GNPm9_SCHIZONT_rep1b


title: berghei_Mutant_G401_TROPHOZOITE_Filtered_Rep1

source_name: G401 Troph

value: Trophozoite

value: PBANKA_143750 Genetic Knockout (G401)

tag: additional processing

value: Magnetically depleted of mature parasites stages using variomacsD column at 6h


title: berghei_Mutant_G401_SCHIZONT_rep1

source_name: G401 Schiz


title: berghei_Mutant_G401_SCHIZONT_rep2


title: WT-4h-sample3-BLOCK3

description:
WT_4h_3_3
This sample is wild-type Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416694_A01_WT_4_3_2011-05-13_532_gridded.pair
416694_A01_WT_4_3_2011-05-13_532_gridded_norm_RMA.pair


title: 118-4h-sample1-BLOCK3

description:
118_4h_1_3
This sample is R2866_0112 gene deletion mutant of Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416693_A03_118_4_1_2011-05-13_532_gridded.pair
416693_A03_118_4_1_2011-05-13_532_gridded_norm_RMA.pair


title: WT-4h-sample3-BLOCK2

description:
WT_4h_3_2
This sample is wild-type Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416694_A01_WT_4_3_2011-05-13_532_gridded.pair
416694_A01_WT_4_3_2011-05-13_532_gridded_norm_RMA.pair


title: berghei_Mutant_G401_TROPHOZOITE_Filtered_Rep2


title: berghei_GNPm8_SCHIZONT_rep1a

source_name: GNPm8 Schiz


title: WT-4h-sample3-BLOCK1

description:
WT_4h_3_1
This sample is wild-type Haemophilus influenzae strain R2866. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416694_A01_WT_4_3_2011-05-13_532_gridded.pair
416694_A01_WT_4_3_2011-05-13_532_gridded_norm_RMA.pair


title: WT-4h-sample4-BLOCK3

description:
WT_4h_4_3
This sample is wild-type Haemophilus influenzae strain R2866. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416654_A01_WT_4_4_2011-05-13_532_gridded.pair
416654_A01_WT_4_4_2011-05-13_532_gridded_norm_RMA.pair


title: berghei_GNPm7_SCHIZONT_rep1b

source_name: GNPm7 Schiz


title: berghei_Mutant_G401_RING_rep3

source_name: G401 Ring

value: Ring


title: WT-4h-sample2-BLOCK4

description:
WT_4h_2_4
This sample is wild-type Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416566_A01_WT_4_2_2011-05-13_532_gridded.pair
416566_A01_WT_4_2_2011-05-13_532_gridded_norm_RMA.pair


title: berghei_GNPm7_SCHIZONT_rep1a


title: berghei_Mutant_G401_TROPHOZOITE_Filtered_Rep3


title: berghei_Mutant_G401_RING_rep2


title: WT-4h-sample2-BLOCK3

description:
WT_4h_2_3
This sample is wild-type Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416566_A01_WT_4_2_2011-05-13_532_gridded.pair
416566_A01_WT_4_2_2011-05-13_532_gridded_norm_RMA.pair


title: berghei_WT_820_SCHIZONT_rep3

source_name: 820 Schiz

value: PBANKA Parental (wild type 820)


title: berghei_WT_820_TROPHOZOITE_Filtered_rep1

source_name: 820 Troph


title: berghei_Mutant_G401_RING_Filtered_rep1a


title: berghei_WT_820_TROPHOZOITE_Filtered_rep2


title: berghei_WT_820_SCHIZONT_rep2


title: berghei_WT_820_SCHIZONT_rep1b


title: berghei_WT_820_TROPHOZOITE_Filtered_rep3


title: WT-4h-sample1-BLOCK4

description:
WT_4h_1_4
This sample is wild-type Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the fourth out of four replicate propbes on the microarray.
416693_A01_WT_4_1_2011-05-13_532_gridded.pair
416693_A01_WT_4_1_2011-05-13_532_gridded_norm_RMA.pair


title: WT-4h-sample1-BLOCK3

description:
WT_4h_1_3
This sample is wild-type Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the third out of four replicate propbes on the microarray.
416693_A01_WT_4_1_2011-05-13_532_gridded.pair
416693_A01_WT_4_1_2011-05-13_532_gridded_norm_RMA.pair


title: WT-4h-sample2-BLOCK1

description:
WT_4h_2_1
This sample is wild-type Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416566_A01_WT_4_2_2011-05-13_532_gridded.pair
416566_A01_WT_4_2_2011-05-13_532_gridded_norm_RMA.pair


title: berghei_Mutant_G401_RING_Filtered_rep1b


title: WT-4h-sample2-BLOCK2

description:
WT_4h_2_2
This sample is wild-type Haemophilus influenzae strain R2866. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416566_A01_WT_4_2_2011-05-13_532_gridded.pair
416566_A01_WT_4_2_2011-05-13_532_gridded_norm_RMA.pair


title: berghei_WT_820_SCHIZONT_rep1a


title: berghei_WT_820_RING_rep3

source_name: 820 Ring


title: WT-4h-sample1-BLOCK2

description:
WT_4h_1_2
This sample is wild-type Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the second out of four replicate propbes on the microarray.
416693_A01_WT_4_1_2011-05-13_532_gridded.pair
416693_A01_WT_4_1_2011-05-13_532_gridded_norm_RMA.pair


title: WG2415 [gene expression]

type: genomic

city: Montreal

first: Stephan

last: Busche

state: Quebec

address: 740 Dr. Penfield Avenue

department: Human Genetics

country: Canada

institute: McGill University

hyb_protocol: standard Illumina protocol

scan_protocol: arrays were imaged using iScan Reader using standard recommended Illumina scanner setting

data_processing: Data were log2 transformed and quantile normalized with the lumi package in R

organism: Homo sapiens

label_protocol: standard Illumina protocol

growth_protocol: Cells were grown in alpha MEM Medium (SigmaAldrich, Oakville, ON, Canada) supplemented with 2 mmol/l L-glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin, and 10% fetal bovine serum (SigmaAldrich) at 37°C with 5% CO2 to 70-80% confluence, then harvested and stored at -80°C until RNA and DNA was extracted.

extract_protocol: RNA was isolated using a standard protocol involving TRIzol and phenol-chloroform extraction.

tag: cell line

tag: gender

value: female

tag: cell type

value: primary skin fibroblast sample


title: WG3465 [gene expression]

value: male


title: WG3466 [gene expression]


title: WG2844 [gene expression]


title: berghei_WT_820_RING_Filtered_rep1b


title: WG2843 [gene expression]


title: EH004-LMX1A-mb-E12.5-b vs. EH004-LMX1A-control-mb-E12.5

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA

data_processing: Features were extracted using Imagene software from Biodiscovery. Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve.

organism: Mus musculus

label_protocol: robot amplification and labeling v1.0

extract_protocol: RNA isolation using Trizol v1.0 (tissue sections)

value: dissected midbrain, E12.5

tag: sample type


title: WT-4h-sample1-BLOCK1

description:
WT_4h_1_1
This sample is wild-type Haemophilus influenzae strain R2866. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures. RNA was isolated after 4 hours of growth in supplemented brain-heart infusion medium. This is the first out of four replicate propbes on the microarray.
416693_A01_WT_4_1_2011-05-13_532_gridded.pair
416693_A01_WT_4_1_2011-05-13_532_gridded_norm_RMA.pair


title: WG2276 [gene expression]


title: EH004-LMX1A-control-mb-E12.5 vs. EH004-LMX1A-mb-E12.5-c


title: berghei_WT_820_RING_rep2


title: WG2193 [gene expression]


title: EH004-LMX1A-mb-E12.5-d vs. EH004-LMX1A-control-mb-E12.5


title: WG2275 [gene expression]


title: WG2414 [gene expression]


title: berghei_WT_820_RING_Filtered_rep1a


title: WG2120 [gene expression]


title: EH004-LMX1A-control-mb-E12.5 vs. EH004-LMX1A-mb-E12.5-a


title: WG2194 [gene expression]


title: berghei_WT_820_GAM_rep1

source_name: 820 GAM

value: Gametocyte


title: WG2065 [gene expression]


title: WG2121 [gene expression]


title: 10-6M ATRA trMCF clone 11_rep2

city: Philadelphia

first: Sandra

middle: Viviana

last: Fernandez

state: PA

address: 233 South 10th Street

department: Medical Oncology

country: USA

institute: Thomas Jefferson University

hyb_protocol: Affymetrix U133 Plus 2.0 human oligonucleotide microarrays (Affymetrix, Santa Clara, CA), were hybridized with fragmented and biotin-labeled target (5 ug) in 220 ul of hybridization cocktail. Target denaturation was performed at 99°C for 2 min. and then 45°C for 5 min, followed by hybridization for 18 h.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: Background correction and normalization were done using Iterative Plier 16 with GeneSpring V12.0 software (Agilent, Palo Alto, CA, USA). 2-fold (p-value<0.05) differentially expressed gene list was generated. The differentially expressed gene list was loaded into Ingenuity Pathway Analysis (IPA) 8.0 software (http://www.ingenuity.com) to perform biological network and functional analyses.

label: biotin

source_name: Human breast epithelial cells

label_protocol: 5 ug cDNAs were fragmented and chemically labeled with biotin to generate biotinylated cDNA using FL-Ovation biotin module (NuGen Technologies, Inc.).

growth_protocol: The human breast epithelial cells were grown in vitro as described elsewhere (Fernandez et al, 2010, Mutat Res 688:28-35)

extract_protocol: RNA was isolated from the breast epithelial cells using RNAeasy Mini Kit (Qiagen) manufacturer’s protocol.

treatment_protocol: To study the effect of ATRA, trMCF clone 11 cells were treated continuously for 26 days with 10-5M to 10-8M ATRA and the media was replaced daily. As control, the cells were treated with 0.1% DMSO (vehicle).

tag: treatment

value: 10-6M ATRA

tag: disease state

value: premalignant


title: WG1983 [gene expression]


title: berghei_WT_820_GAM_rep2


title: 10-6M ATRA trMCF clone 11_rep1


title: 10-5M ATRA trMCF clone 11_rep2

value: 10-5M ATRA


title: WG1984 [gene expression]


title: WG2066 [gene expression]


title: WG1514 [gene expression]


title: WG1978 [gene expression]


title: WG1722 [gene expression]


title: berghei_WT_507_GAM_rep3

source_name: 507 GAM

value: PBANKA 507 Parental (wild type)


title: WG1977 [gene expression]


title: trMCFclone 11_rep2


title: 10-5M ATRA trMCF clone 11_rep1


title: WG1657 [gene expression]


title: MCF-10F_rep2

value: normal


title: WG1721 [gene expression]


title: trMCFclone 11_rep1


title: WG1658 [gene expression]


title: Treatment day 24 rep 3

city: Bremerhaven

first: Carla

last: Flöthe

address: Am Handelshafen 12

country: Germany

institute: Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung

description:
T0-grazed vs T24-grazed_3
Biological replicate 3 of 5. Treated F. vesiculosus, grazed by I. baltica, 21 days after start of experiment.

hyb_protocol: Hybridization was performed onto 4 x 44k microarray slides, containing oligonucleotide 60mers designed with the Agilent eArray online platform, using the Agilent Gene Expression Kit according to the manufacturer's protocol.

scan_protocol: Scanned on an Agilent G2565AA microarray scanner at 5 µm resolution.

data_processing: Raw data was extracted using the Agilent Feature Extraction Software (Version 10.7.3.1). Array quality was monitored using the Agilent QC tool with the metric set GE2_QCMT_Feb07.

organism: Fucus vesiculosus

source_name: Treatment day 24

label_protocol: 200 ng of total RNA were amplified, reverse transcribed and labelled using the Agilent Two-color Low Input Quick Amp Labeling Kit according to the manufacturer's protocol. As a minor modification, random hexamers with attached T7 promotor were added.

growth_protocol: Fucus vesiculosus pieces were kept in 25L aquaria at a mean (± SD) seawater flow rate of 464 (± 87) ml min-1. Mean (± SD) water temperature was 18.1 (± 0.5) °C. Light was provided in a light/dark cycle of 12/12 h at a mean (± SD) photon flow rate of 223 (± 5) µmol m-2 s-1 (PAR) during light periods.

extract_protocol: Total RNA was isolated with using 1 ml of a CTAB extraction buffer (2% CTAB, 1 M NaCl, 100 mM Tris pH 8, 50 mM EDTA pH 8) and 25 µl DTT 2 M. After incubation at 45°C for 15 min, an equal volume of chloroform:isoamylalcohol (24:1) was added, vortexed vigorously for 5 min and afterwards centrifugated for 20 min at RT and 12,000 g. Subsequently, the aqueous phase was transferred and 0.3 volumes of EtOH 96% were added. After mixing gently, a second chloroform extraction was performed. Subsequently, total RNA was extracted using the Qiagen Plant Mini Kit accoding to the manufacturer's protocol.

treatment_protocol: F. vesiculosus pieces were or were not grazed by Littorina obtusata for 3, 12, 15, 21, and 24 days.

tag: treatment group

value: grazed by Littorina obtusata for 24 days (T24)

tag: tissue

value: apical tips

tag: sample group

value: collected before onset of grazing (day 0; T0)


title: WG1309 [gene expression]


title: Treatment day 24 rep 2

description:
T0-grazed vs T24-grazed_2
Biological replicate 2 of 5. Treated F. vesiculosus, grazed by I. baltica, 21 days after start of experiment.


title: Treatment day 24 rep 4

description:
T0-grazed vs T24-grazed_4
Biological replicate 4 of 5. Treated F. vesiculosus, grazed by I. baltica, 21 days after start of experiment.


title: GM03075 [gene expression]


title: WG1282 [gene expression]


title: Treatment day 24 rep 1

description:
T0-grazed vs T24-grazed_1
Biological replicate 1 of 5. Treated F. vesiculosus, grazed by I. baltica, 21 days after start of experiment.


title: WG1513 [gene expression]


title: MCF-10F_rep1


title: Control day 24 rep 5

description:
T0-control vs T24-control_5
Biological replicate 5 of 5. Control F. vesiculosus, ungrazed, 21 days after start of experiment.

source_name: Control day 24

value: control (not grazed) day24 (C24)

value: day 0; T0


title: WG1283 [gene expression]


title: WG1310 [gene expression]


title: overexpression_oxyR_rich medium_rep2

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description: oxyR overexpression in rich medium

hyb_protocol: RNA was hybridized to GeneChip Pseudomonas aeruginosa Genome arrays (Affymetrix) according to instructions of Affymetrix GeneChip. Washing and staining of the arrays were performed according to the manufacturer’s instructions using a fluidics station 450 (Affymetrix).

scan_protocol: Microarray slides were scanned using the 2500 GeneArray Scanner (Agilent Technologies)

data_processing: Raw Affymetrix data were pre-processed in R environment using BioConductor packages including “affy”, “affyPLM”, “simpleaffy” and “limma”. The primary processing includes: (i) background correction based on the robust multichip average (RMA) convolution model; (ii) quantile normalization to make expression values from different arrays more comparable and (iii) summarization of multiple probe intensities for each probe set to one expression value per gene using RMA.

organism: Pseudomonas aeruginosa PAO1

source_name: oxyR overexpression in rich medium

label_protocol: cDNA synthesis, fragmentation, and labeling were performed according to the protocol for GeneChipR Pseudomonas aeruginosa Genome Array (Affymetrix). Ten micrograms of total RNA from each biological condition were used for cDNA synthesis and a Poly-A RNA control added to the RNA sample using the GeneChip eukaryotic poly-A control kit (Affymetrix). The cDNA synthesis was performed using denatured RNA with standard reaction as follows (50μl): 13 ng·μl-1 random hexamer primers (Roche), 0.5 U·μl-1 SUPERase In (Ambion), 25 U·μl -1 SuperScript II Reverse Transcriptase (Invitrogen), 0.5 nmol·μl -1 dNTPs in a buffer containing 10 nmol·μl -1 dithiothreitol (DTT). Synthesized cDNA was pooled and purified with QIAquick PCR Purification Kit (Qiagen) and quantified spectrophotometrically (Thermal Scientific). Eight micrograms of cDNA was partially digested to a fragment size range from 50~200 bp with DNase I (Promega) and fragmentation was verified by performing a 2% agarose gel electrophoresis. Fragmented cDNA was end-labeled with biotin-dUTP using the GeneChip DNA labeling reagent (Affymetrix) and terminal deoxynucleotidyl transferase (Promega)

growth_protocol: The P. aeruginosa wild-type PAO1 strain, its isogenic mutant oxyR as well as the oxyR-overexpression strain were used in this study and triplicate cultures were grown in Luria-Bertani (LB, BD) and Pseudomonas Medium (denoted PM in this study, also known as King’s A medium, BD) at 37°C. Overnight cultures of P. aeruginosa in LB were used to inoculate fresh LB and PM medium in a 1:1000 dilution. After 12 h of incubation, one millilitre of culture was immediately fixed with two milliliters of RNA Protect Reagent (Qiagen), following the manufacturer’s instructions, and the fixed cell pellets were frozen at -20°C until further use.

extract_protocol: Total RNAs from different strains were isolated according to the manuals provided with the RNeasy Mini Kit (Qiagen), followed by immediate DNase I treatment using DNA-free DNase kit (Ambion). RNA quality and quantity were assessed using the Agilent Bioanalyzer 2100 electrophoresis system (Agilent Technologies) and the Nanodrop ND-1000 spectrophotometer (Thermal Scientific), respectively.

treatment_protocol: No treatment, only differences in DNA content (wildtype – knock-out oxyR – overexpression oxyR)

value: oxyR overexpression

tag: medium

value: Luria Bertani medium


title: overexpression_oxyR_rich medium_rep3

description: oxyR overexpression in rich medium


title: GM02706 [gene expression]

value: female


title: GM03073 [gene expression]

value: primary skin fibroblast sample


title: Control day 24 rep 4

description:
T0-control vs T24-control_4
Biological replicate 4 of 5. Control F. vesiculosus, ungrazed, 21 days after start of experiment.


title: Control day 24 rep 3

description:
T0-control vs T24-control_3
Biological replicate 3 of 5. Control F. vesiculosus, ungrazed, 21 days after start of experiment.


title: GM02704 [gene expression]

value: male


title: overexpression_oxyR_rich medium_rep1

description: oxyR overexpression in rich medium


title: Wildtype_poor medium_rep2

description: wildtype mutant grown in poor medium

source_name: wildtype mutant grown in poor medium

value: wildtype

value: King’s A medium


title: GM02640 [gene expression]


title: GM02641 [gene expression]


title: GM02555 [gene expression]


title: Wildtype_poor medium_rep1

description: wildtype mutant grown in poor medium


title: Wildtype_poor medium_rep3

description: wildtype mutant grown in poor medium


title: Control day 24 rep 1

description:
T0-control vs T24-control_1
Biological replicate 1 of 5. Control F. vesiculosus, ungrazed, 21 days after start of experiment.


title: Wildtype_rich medium_rep3

description: wildtype mutant grown in rich medium

source_name: wildtype mutant grown in rich medium


title: GM02316 [gene expression]


title: Treatment day 21 rep 4

description:
T0-grazed vs T21-grazed_4
Biological replicate 4 of 5. Treated F. vesiculosus, grazed by I. baltica, 18 days after start of experiment.

source_name: Treatment day 21

value: grazed by Littorina obtusata for 21 days (T21)


title: GM02317 [gene expression]


title: Treatment day 21 rep 3

description:
T0-grazed vs T21-grazed_3
Biological replicate 3 of 5. Treated F. vesiculosus, grazed by I. baltica, 18 days after start of experiment.


title: Control day 24 rep 2

description:
T0-control vs T24-control_2
Biological replicate 2 of 5. Control F. vesiculosus, ungrazed, 21 days after start of experiment.


title: Treatment day 21 rep 5

description:
T0-grazed vs T21-grazed_5
Biological replicate 5 of 5. Treated F. vesiculosus, grazed by I. baltica, 18 days after start of experiment.


title: oxyRmutant_poor medium_rep3

description: oxyR mutant grown in poor medium

source_name: oxyR mutant grown in poor medium

value: oxyR knock-out


title: Treatment day 21 rep 2

description:
T0-grazed vs T21-grazed_2
Biological replicate 2 of 5. Treated F. vesiculosus, grazed by I. baltica, 18 days after start of experiment.


title: GM02456 [gene expression]


title: Control day 21 rep 5

description:
T0-control vs T21-control_5
Biological replicate 5 of 5. Control F. vesiculosus, ungrazed, 18 days after start of experiment.

source_name: Control day 21

value: control (not grazed) day21 (C21)


title: Wildtype_rich medium_rep2

description: wildtype mutant grown in rich medium


title: Wildtype_rich medium_rep1

description: wildtype mutant grown in rich medium


title: oxyRmutant_poor medium_rep1

description: oxyR mutant grown in poor medium


title: oxyRmutant_poor medium_rep2

description: oxyR mutant grown in poor medium


title: Treatment day 21 rep 1

description:
T0-grazed vs T21-grazed_1
Biological replicate 1 of 5. Treated F. vesiculosus, grazed by I. baltica, 18 days after start of experiment.


title: Control day 21 rep 4

description:
T0-control vs T21-control_4
Biological replicate 4 of 5. Control F. vesiculosus, ungrazed, 18 days after start of experiment.


title: GM02149 [gene expression]


title: GM02147 [gene expression]


title: GM02205 [gene expression]


title: Control day 21 rep 3

description:
T0-control vs T21-control_3
Biological replicate 3 of 5. Control F. vesiculosus, ungrazed, 18 days after start of experiment.


title: oxyRmutant_rich medium_rep3

description: oxyR mutant grown in rich medium

source_name: oxyR mutant grown in rich medium


title: oxyRmutant_rich medium_rep2

description: oxyR mutant grown in rich medium


title: oxyRmutant_rich medium_rep1

description: oxyR mutant grown in rich medium


title: GM01653 [gene expression]


title: GM01877 [gene expression]


title: GM01878 [gene expression]


title: Control day 21 rep 2

description:
T0-control vs T21-control_2
Biological replicate 2 of 5. Control F. vesiculosus, ungrazed, 18 days after start of experiment.


title: GM01650 [gene expression]


title: Treatment day 24 rep 5

description:
T0-grazed vs T24-grazed_5
Biological replicate 5 of 5. Treated F. vesiculosus, grazed by I. baltica, 21 days after start of experiment.


title: GM01516 [gene expression]


title: GM01393 [gene expression]


title: Control day 21 rep 1

description:
T0-control vs T21-control_1
Biological replicate 1 of 5. Control F. vesiculosus, ungrazed, 18 days after start of experiment.


title: t-AML patient_390369-A03

first: Matt

last: Walter

address: 4940 parkview

department: oncology

institute: washington university in st.louis school of medicine

description:
390369_A03
482711

hyb_protocol: Hybridization and washing according to manufacturer's recommendations (NG_CGH_guide_v5p1) using Nimblegen's Hybridization Kit (p/n 05223474001) and Washing Buffer kit (p/n 05223504001)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per Nimblegen's protocol (NG_CGH_guide_v5p1)

data_processing: Arrays were processed using NimbleScan v2.5

molecule: genomic DNA

source_name: chip DNA from skin

label_protocol: DNAs labeled according to manufacturer's recommendations (NG_CGH_guide_v5p1) using Nimblegen's Dual-Color DNA Labeling Kit (p/n 05223547001)

extract_protocol: Isolation of Genomic DNA from Cryopreserved Cells using the QIAamp DNA Blood Mini Kit

tag: subject status

value: therapy-related Acute Myeloid Leukemia (t-AML) patient

value: normal (skin)

source_name: chip DNA from bone marrow

value: therapy-related AML (t-AML) patient

value: tumor (bone marrow)


title: GM01392 [gene expression]


title: GM01376 [gene expression]


title: Treatment day 15 rep 4

description:
T0-grazed vs T15-grazed_4
Biological replicate 4 of 5. Treated F. vesiculosus, grazed by I. baltica, 15 days after start of experiment.

source_name: Treatment day 15

value: grazed by Littorina obtusata for 15 days (T15)

value: apical tips

value: collected before onset of grazing (day 0; T0)


title: Treatment day 15 rep 5

description:
T0-grazed vs T15-grazed_5
Biological replicate 5 of 5. Treated F. vesiculosus, grazed by I. baltica, 15 days after start of experiment.


title: t-AML patient_390501-A01

description:
390501_A01
266608


title: t-AML patient_390501-A02

description:
390501_A02
205133


title: GM01375 [gene expression]


title: GM01096 [gene expression]


title: GM01095 [gene expression]


title: t-AML patient_390369-A02

description:
390369_A02
557772


title: Treatment day 15 rep 2

description:
T0-grazed vs T15-grazed_2
Biological replicate 2 of 5. Treated F. vesiculosus, grazed by I. baltica, 15 days after start of experiment.


title: Treatment day 15 rep 1

description:
T0-grazed vs T15-grazed_1
Biological replicate 1 of 5. Treated F. vesiculosus, grazed by I. baltica, 15 days after start of experiment.


title: Control day 15 rep 4

description:
T0-control vs T15-control_4
Biological replicate 4 of 5. Control F. vesiculosus, ungrazed, 15 days after start of experiment.

source_name: Control day 15

value: control (not grazed) day15 (C15)

value: day 0; T0


title: Control day 15 rep 5

description:
T0-control vs T15-control_5
Biological replicate 5 of 5. Control F. vesiculosus, ungrazed, 15 days after start of experiment.


title: t-AML patient_390369-A01

description:
390369_A01
317821


title: GM00941 [gene expression]


title: t-AML patient_390365-A02

description:
390365_A02
983545


title: GM00940 [gene expression]

value: female


title: GM00935 [gene expression]

value: primary skin fibroblast sample


title: Treatment day 15 rep 3

description:
T0-grazed vs T15-grazed_3
Biological replicate 3 of 5. Treated F. vesiculosus, grazed by I. baltica, 15 days after start of experiment.


title: GM00520 [gene expression]

value: male


title: Control day 15 rep 3

description:
T0-control vs T15-control_3
Biological replicate 3 of 5. Control F. vesiculosus, ungrazed, 15 days after start of experiment.


title: Control day 15 rep 1

description:
T0-control vs T15-control_1
Biological replicate 1 of 5. Control F. vesiculosus, ungrazed, 15 days after start of experiment.


title: Control day 15 rep 2

description:
T0-control vs T15-control_2
Biological replicate 2 of 5. Control F. vesiculosus, ungrazed, 15 days after start of experiment.


title: GM00439 [gene expression]


title: GM00438 [gene expression]


title: t-AML patient_390365-A01

description:
390365_A01
706395


title: Treatment day 12 rep 3

description:
T0-grazed vs T12-grazed_3
Biological replicate 3 of 5. Treated F. vesiculosus, grazed by Littorina obtusata, 12 days after start of experiment.

source_name: Treatment day 12

value: grazed by Littorina obtusata for 12 days (T12)


title: t-AML patient_390333-A03

description:
390333_A03
658208


title: t-AML patient_390359-A03

description:
390359_A03
811184


title: GM00290 [gene expression]


title: Treatment day 12 rep 4

description:
T0-grazed vs T12-grazed_4
Biological replicate 4 of 5. Treated F. vesiculosus, grazed by Littorina obtusata, 12 days after start of experiment.


title: t-AML patient_390359-A01

description:
390359_A01
860923


title: GM00289 [gene expression]


title: Treatment day 12 rep 2

description:
T0-grazed vs T12-grazed_2
Biological replicate 2 of 5. Treated F. vesiculosus, grazed by Littorina obtusata, 12 days after start of experiment.


title: t-AML patient_390359-A02

description:
390359_A02
458613


title: GM00042 [gene expression]


title: GM00031 [gene expression]


title: t-AML patient_390316-A01

description:
390316_A01
942008


title: t-AML patient_390365-A03

description:
390365_A03
180866


title: t-AML patient_390316-A02

description:
390316_A02
644242


title: Treatment day 12 rep 1

description:
T0-grazed vs T12-grazed_1
Biological replicate 1 of 5. Treated F. vesiculosus, grazed by Littorina obtusata, 12 days after start of experiment.


title: Control day 12 rep 5

description:
T0-control vs T12-control_5
Biological replicate 5 of 5. Control F. vesiculosus, ungrazed, 12 days after start of experiment.

source_name: Control day 12

value: control (not grazed) day12 (C12)


title: t-AML patient_390333-A01

description:
390333_A01
530447


title: Control day 12 rep 4

description:
T0-control vs T12-control_4
Biological replicate 4 of 5. Control F. vesiculosus, ungrazed, 12 days after start of experiment.


title: t-AML patient_390316-A03

description:
390316_A03
751407


title: t-AML patient_389707-A03

description:
389707_A03
779828


title: GM00022 [gene expression]


title: Control day 12 rep 3

description:
T0-control vs T12-control_3
Biological replicate 3 of 5. Control F. vesiculosus, ungrazed, 12 days after start of experiment.


title: GM00016 [gene expression]


title: Calli

type: SRA

city: Brisbane

first: Peter

middle: Richard

last: Sternes

state: Queensland

address: John Hines Building, University of Queensland, St Lucia

department: School of Agriculture and Food Science

country: Australia

institute: University of Queensland

description: small RNA

library_source: transcriptomic

data_processing:
Sequencing adapter primers (proprietary) were trimmed using UNIX shell scripting
Sense and antisense matches to known tRNA, rRNA and chloroplast sequences from Rfam, Genomic tRNA, EMBL release 95 and SILVA rRNA databases were removed using UNIX shell scripting
Sequences were counted and displayed as tab delimited files containing a count and the unique sequence per line, using UNIX shell scripting
Supplementary_files_format_and_content: Tab delimited text files containing counts of trimmed and filtered small RNA sequences

organism: Saccharum sp.

source_name: Embryogenic callus tissue grown on plated media

extract_protocol:
Total RNA was isolated using TRIsure reagent (Bioline) as per the manufacturer's intstructions
Libraries were constructed using the TruSeq Small RNA kit (Illumina)

tag: cultivar

value: embryogenic calli

tag: tissue type

value: cultured


title: Treatment day 12 rep 5

description:
T0-grazed vs T12-grazed_5
Biological replicate 5 of 5. Treated F. vesiculosus, grazed by Littorina obtusata, 12 days after start of experiment.


title: Control day 12 rep 2

description:
T0-control vs T12-control_2
Biological replicate 2 of 5. Control F. vesiculosus, ungrazed, 12 days after start of experiment.


title: Treatment day 3 rep 4

description:
T0-grazed vs T3-grazed_4
Biological replicate 4 of 5. Treated F. vesiculosus, grazed by Littorina obtusata, 3 days after start of experiment.

source_name: Treatment day 3

value: grazed by Littorina obtusata for 3 days (T3)


title: t-AML patient_389707-A01

description:
389707_A01
572162

value: therapy-related Acute Myeloid Leukemia (t-AML) patient


title: Control day 12 rep 1

description:
T0-control vs T12-control_1
Biological replicate 1 of 5. Control F. vesiculosus, ungrazed, 12 days after start of experiment.


title: t-AML patient_390501-A03

description:
390501_A03
925964

value: normal (skin)


title: Treatment day 3 rep 5

description:
T0-grazed vs T3-grazed_5
Biological replicate 5 of 5. Treated F. vesiculosus, grazed by Littorina obtusata, 3 days after start of experiment.


title: Treatment day 3 rep 3

description:
T0-grazed vs T3-grazed_3
Biological replicate 3 of 5. Treated F. vesiculosus, grazed by Littorina obtusata, 3 days after start of experiment.


title: JeB1-L7 vs. JeB1-H7

hyb_protocol: 60 ul labeled sample was combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA. Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays were performed on a HS4800Pro Hybstation (Tecan). Priming: 5xSSC, 0.1%SDS. Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul. Hybridization: 45 min at 42C. Wash 2x: milliQ. Wash: 5xSSC, 0.1%SDS. Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul. Hybridization: 16 hours at 42C. Wash 2x: 1xSSC, 0.2%SDS at 23C. Wash 2x: 0.1xSSC, 0.2%SDS at 23C. Wash 2x: 0.1xSSC at 23C. Drying: blow with nitrogen for 3min at 30C.

scan_protocol: Slides were scanned using the Agilent G2565BA scanner. Features were extracted using ImaGene software from BioDiscovery.

data_processing:
Normalization was done using print-tip LOESS as described in (Yang et al. 2002) for all gene probes using no background subtraction and a span of 0.4. Probes flagged as absent or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.
Wu & Churchill's MAANOVA was run to obtain estimates for sample effect.

label_protocol:
All amplification and labeling procedures were performed in 96-well plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrophotometer (Molecular Devices), and a magnetic bead-locator (Beckman). mRNA was double-amplified, and the cRNA product was purified with RNAClean (Agencourt, Beckman) according to the manufacturer's protocol. The concentration of cRNA was measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot. The resulting cRNA plates were sampled for Bioanalyzer QC, snap-frozen and stored at -80C.
Labeling protocol: NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10). All subsequent steps are performed by the robot script: 8 ul of each cRNA (0.6 ug/ul) is put in a 96-well plate (Abgene), the accompanying reference sample is put in the next column (final step combines Cy3- and Cy5-labeled material ). 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells. 3 ul Cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour. 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes. Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to the manufacturer's protocol. RNA concentration and labeling incorporation are measured (SpectraMax 190). 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C. Samples are stored at -20C until hybridization.

growth_protocol: All the experimental procedures are in compliance with the animal ethics board of the Radboud University Nijmegen. Transgenic mice expressing eGFP under the parvalbumin (PV) promotor were kindly provided by Dr. Hannah Monyer (University of Heidelberg, Germany). Genotype was determined under UV light by checking fluorescent emission of muscular PV expression in the mouse legs. Littermates were housed in a temperature- and light-controlled room with the standard pellet chow (SSNIFF Spezialdiäten GmbH, Soest, Germany) and deionized drinking water available ad libitum until the start of the experiment. PV-eGFP-positive mice were selected for experiments at the age of 6-8 weeks at the time of tube isolations.

extract_protocol:
PV-eGFP-positive tubules were isolated as follows: mice were anesthetized and perfused transcardially with ice-cold KREBS buffer (in mM: 145 NaCl, 5 KCl, 1 NaH2PO4, 2.5 CaCl2, 1.8 MgSO4, 10 glucose, 10 HEPES/NaOH pH: 7.4). Kidneys were harvested and digested in KREBS buffer containing 1 mg/ml collagenase (Worthington, Lakewood, NJ, USA) and 2000 units/ml hyaluronidase (Sigma, Houten, the Netherlands) for 15 minutes at 37C. Subsequently, the kidney tubules sized between 100-um and 40-um were collected by filtration. Oversized material was digested again in two additional cycles of 10 minutes digestion and filtration. Tubules collected from the three digestions were ice-cooled and sorted by the Complex Object Parameric Analyzer and Sorter (COPAS, Union Biometrica, Holliston, MA, USA). Sorted tubules were directly collected in 1% (v/v) beta-mercaptoethanol containing RLT buffer that was supplied by the RNeasy RNA extraction kit (Qiagen, Venlo, the Netherlands).
4,000 tubules were pooled on a Qiagen RNeasy micro column for RNA extraction according to the manufacturer's protocol.

treatment_protocol: During the experiments, the mice were fed low=L-samples (0.02% wt/wt) or high=H-samples (0.48% wt/wt) Mg2+-containing diets for 15 days (SSNIFF Spezialdiäten GmbH, Soest, Germany). During the last 48 hrs of the experiment, the mice were housed in metabolic cages for urine and faeces collection (24 hr adaptation, 24 hr sampling). Blood samples were taken at the start of the experiment and just before sacrifice.

tag: background/strain

tag: genotype/variation

value: PV-eGFP transgenic

value: kidney

value: PV-eGFP-positive distal convoluted tubule cells

value: low-magnesium diet

value: high-magnesium diet


title: JeB1-H8 vs. JeB1-L8


title: t-AML patient_389325-A03

description:
389325_A03
476204

value: therapy-related AML (t-AML) patient

value: tumor (bone marrow)


title: JeB1-H3 vs. JeB1-L2


title: JeB1-L1 vs. JeB1-H1


title: t-AML patient_390333-A02

description:
390333_A02
377512


title: Treatment day 3 rep 2

description:
T0-grazed vs T3-grazed_2
Biological replicate 2 of 5. Treated F. vesiculosus, grazed by Littorina obtusata, 3 days after start of experiment.

value: apical tips

value: collected before onset of grazing (day 0; T0)


title: t-AML patient_389325-A02

description:
389325_A02
856024


title: t-AML patient_389707-A02

description:
389707_A02
189941


title: untreated, biological replicate 3

city: Graz

first: Birgit

last: Gallé

address: Stiftingtalstr. 24

country: Austria

institute: ZMF

hyb_protocol: AB1700 Chemiluminescence detection Kit, 12 Rxn, includes (Applied Biosystems, Cat No. 4342142);

scan_protocol: Instrument: 1700-Reader; Software Version  1.1.1, Firmware Version: AB 1700 Plate Reader 1.2.2

data_processing:
Software Version  1.1.1, Firmware Version: AB 1700 Plate Reader 1.2.2 using Applied default analysis settings for generation of txt.files. (Analysis Method: Primary Analysis)
Data Pre-Processing and Filtering (7.3v GeneSpring Software): values from txt-files: Assay_Normalized_Signal; Filter on Expression Level: “CEM” ;  Filter on Signal to Noise; Filter on Flag = 0  intra and inter-array normalization; pre-filtered based on signal to noise ratio; subtraction of non changing genes; remaining data were tested for d ifferentially expressed genes using ANOVA (7.3v GeneSpring Software)

label: DIG

label_protocol: Applied Biosystems Chemiluminescent RT-IVT Labeling Kit

growth_protocol: Cells were cultured in Dulbecco's modified Eagle's medium (Sigma Chemicals, Vienna, Austria) supplemented with 10% fetal calf serum, 1% penicillin/streptomycin, 1% L-glutamine and 0.25% fungizone (Gibco, Paisley, UK). The cells were maintained in a humidified 5% CO2 atmosphere at 37˚C.

extract_protocol: After the incubation period, cells were washed in PBS and scratched from the culture flasks with a plastic cell scraper, pelleted and washed again in PBS. RNA was extracted using the RNeasy Plus Mini kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. Integrity of the RNA samples was controlled by capillary electrophoresis on the Agilent 2100 Bioanalyzer using the RNA 6000 Nano kit (Agilent Technologies, Foster City, CA, USA). RNA samples with an integrity factor of ≥9 were used for expression profiling. 2 µg of total RNA was used for microarray analysis.

treatment_protocol: For the sorafenib treatment, experimental cells were passaged and seeded into 25-cm2 flasks. After 24 h, the medium was removed and replaced with culture medium containing 4 μM sorafenib (Bayer, Vienna, Austria), dissolved in distilled water. For the experiment, the cells were incubated for 72 h with the sorafenib solution. Control cells were incubated with culture medium alone. The experiment was performed three times.

value: ATCC CRL-1543™

value: human osteosarcoma cells (HOS)

tag: treated with

value: none (untreated control)


title: Control day 3 rep 5

description:
T0-control vs T3-control_5
Biological replicate 5 of 5. Control F. vesiculosus, ungrazed, 3 days after start of experiment.

source_name: Control day 3

value: control (not grazed) day3 (C3)

value: day 0; T0


title: untreated, biological replicate 2


title: treated, biological replicate 3

value: 4 µM Sorafenib


title: untreated, biological replicate 1


title: Treatment day 3 rep 1

description:
T0-grazed vs T3-grazed_1
Biological replicate 1 of 5. Treated F. vesiculosus, grazed by Littorina obtusata, 3 days after start of experiment.

value: grazed by Littorina obtusata for 3 days (T3)


title: t-AML patient_389325-A01

description:
389325_A01
864484

value: therapy-related Acute Myeloid Leukemia (t-AML) patient

value: normal (skin)


title: t-AML patient_389276-A01

description:
389276_A01
514901


title: Control day 3 rep 4

description:
T0-control vs T3-control_4
Biological replicate 4 of 5. Control F. vesiculosus, ungrazed, 3 days after start of experiment.


title: t-AML patient_389276-A03

description:
389276_A03
982895


title: Control day 3 rep 2

description:
T0-control vs T3-control_2
Biological replicate 2 of 5. Control F. vesiculosus, ungrazed, 3 days after start of experiment.


title: Vitiligo patient 4

status: Public on Dec 12 2013

city: Worcester

first: John

last: Harris

state: MA - Massachusetts

address: 364 Plantation St

department: Medicine - Dermatology

institute: UMass Medical School

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized with Matlab 2012b using quantile normalization and only genes significantly detected over background (p<0.05) in at least one sample were considered.

source_name: FFPE skin biopsy_vitiligo patient

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

extract_protocol: RNA was extracted using Roche high pure RNA paraffin kit according to the manufacturer’s instructions.

tag: patient group

value: vitiligo

value: lesional skin


title: t-AML patient_389276-A02

description:
389276_A02
548417


title: Control day 3 rep 1

description:
T0-control vs T3-control_1
Biological replicate 1 of 5. Control F. vesiculosus, ungrazed, 3 days after start of experiment.


title: Vitiligo patient 3


title: t-AML patient_388824-A02

description:
388824_A02
476081


title: Control patient 4

source_name: FFPE skin biopsy_control patient

value: control

value: control skin


title: treated, biological replicate 2

tag: cell line


title: Vitiligo patient 2


title: Vitiligo patient 5


title: Control patient 5


title: Vitiligo patient 1


title: t-AML patient_388824-A03

description:
388824_A03
501254

value: therapy-related AML (t-AML) patient


title: treated, biological replicate 1


title: Control patient 3


title: Control patient 2


title: Glioblastoma gbm-0409

city: Beijing

first: Tao

last: Jiang

address: Tiantan Xili No.6, Dongcheng District

department: Neurosurgery

country: China

institute: Beijing Tiantan Hospital, Capital Medical University

data_processing: The array results were analyzed with the BeadStudio software (Illumina).

source_name: Human glioblastoma

label_protocol: Standard Illumina labelling protocol

extract_protocol: Genomic DNA was isolated from frozen tumor tissues using the QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s protocol. DNA concentration and quality were measured using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Houston,TX).

treatment_protocol: No treatment was applied to the biological material before DNA extraction.

tag: ethnicity

value: Chinese population

value: brain tumor

tag: tumor grade

value: WHO grade 4

tag: patient gender

value: Glioblastoma


title: Control patient 1


title: Glioblastoma gbm-0214


title: t-AML patient_388824-A01

description:
388824_A01
180365

value: tumor (bone marrow)


title: Control day 3 rep 3

description:
T0-control vs T3-control_3
Biological replicate 3 of 5. Control F. vesiculosus, ungrazed, 3 days after start of experiment.

value: apical tips


title: Glioblastoma gbm-0139


title: Glioblastoma gbm-0161


title: Glioblastoma gbm-0182


title: Glioblastoma gbm-0305


title: Glioblastoma gbm-0130


title: Glioblastoma gbm-0013


title: Glioblastoma gbm-0088


title: Glioblastoma gbm-0525


title: Oligodendroglioma o-0672

description:
o-0672
glioma

label: Cy5 and Cy3

source_name: Human oligodendroglioma

value: WHO grade 2

tag: patient age

value: male

value: Oligodendroglioma


title: Glioblastoma gbm-0058

tag: disease state


title: Oligodendroglioma o-0579

description:
o-0579
glioma

value: female


title: Oligodendroglioma o-0485

description:
o-0485
glioma


title: Oligodendroglioma o-0639

description:
o-0639
glioma


title: ER+breast cancer pt #11

city: Goyangsi

first: In Hae

last: Park

address: 323 Ilsanro Madu 1 dong

country: South Korea

institute: National cancer center, Korea

description: miRNA

hyb_protocol: After purification, labeled samples were resuspended with Gene Expression blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s miRNA Microarray and hybridized for 20 hours at 55°C with 20 RPM rotating in Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: Whole Blood

label_protocol: For control and test RNAs, the synthesis of target miRNA probes and hybridization were performed using Agilent’s miRNA Labeling Reagent and Hybridization kit (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 100 ng of total RNA were dephosphorylated with ~15 Units of calf intestine alkaline phosphatase (CIP), followed by RNA denaturation with ~40% DMSO and 10 min incubation at 100 °C. Dephosphorylated RNA were ligated with pCp-Cy3 mononucleotide and purified with MicroBioSpin 6 columns (Bio-rad, USA).

extract_protocol: Total RNA was isolated from blood using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer s instructions.

value: Human whole blood

value: ER +/HER2- breast cancer


title: ER+breast cancer pt #10

description: miRNA


title: ER+breast cancer pt #9

description: miRNA


title: Glioblastoma gbm-0001


title: Oligodendroglioma o-0387

description:
o-0387
glioma


title: Glioblastoma gbm-0031


title: ER+breast cancer pt #7

description: miRNA


title: ER+breast cancer pt #8

description: miRNA


title: Oligodendroglioma o-0589

description:
o-0589
glioma


title: Oligodendroglioma o-0659

description:
o-0659
glioma


title: Oligodendroglioma o-0633

description:
o-0633
glioma


title: Oligodendroglioma o-0446

description:
o-0446
glioma


title: ER+breast cancer pt #5

description: miRNA


title: ER+breast cancer pt #4

description: miRNA


title: Oligodendroglioma o-0484

description:
o-0484
glioma


title: ER+breast cancer pt #3

description: miRNA


title: ER+breast cancer pt #6

description: miRNA


title: Oligodendroglioma o-0323

description:
o-0323
glioma


title: Oligodendroglioma o-0275

description:
o-0275
glioma


title: Glioblastoma gbm-0822

description:
gbm-0822
glioma


title: ER+breast cancer pt #2

description: miRNA


title: control #3

description: miRNA

value: healthy


title: Glioblastoma gbm-0557

description:
gbm-0557
glioma


title: ER+breast cancer pt #1

description: miRNA


title: Glioblastoma gbm-0593

description:
gbm-0593
glioma


title: Glioblastoma gbm-0444

description:
gbm-0444
glioma


title: control #2

description: miRNA


title: control #1

description: miRNA


title: control #4

description: miRNA


title: control #5

description: miRNA


title: Glioblastoma gbm-0419

description:
gbm-0419
glioma


title: Glioblastoma gbm-0401

description:
gbm-0401
glioma


title: Glioblastoma gbm-0547

description:
gbm-0547
glioma


title: Glioblastoma gbm-0518

description:
gbm-0518
glioma


title: Glioblastoma gbm-0439

description:
gbm-0439
glioma


title: Glioblastoma gbm-0462

description:
gbm-0462
glioma


title: Glioblastoma gbm-0366

description:
gbm-0366
glioma


title: Glioblastoma gbm-0346

description:
gbm-0346
glioma


title: Glioblastoma gbm-0308

description:
gbm-0308
glioma


title: Glioblastoma gbm-0203

description:
gbm-0203
glioma


title: Glioblastoma gbm-0380

description:
gbm-0380
glioma


title: Glioblastoma gbm-0168

description:
gbm-0168
glioma


title: Glioblastoma gbm-0255

description:
gbm-0255
glioma


title: Glioblastoma gbm-0225

description:
gbm-0225
glioma


title: Glioblastoma gbm-0156

description:
gbm-0156
glioma


title: Glioblastoma gbm-0178

description:
gbm-0178
glioma


title: Anaplastic oligodendrocytoma aoa-0596

description:
aoa-0596
glioma

source_name: Human anaplastic oligodendrocytoma

value: WHO grade 3

value: Anaplastic oligodendrocytoma


title: Glioblastoma gbm-0104

description:
gbm-0104
glioma


title: Anaplastic oligodendrocytoma aoa-0562

description:
aoa-0562
glioma


title: Anaplastic oligodendrocytoma aoa-0513

description:
aoa-0513
glioma


title: Glioblastoma gbm-0126

description:
gbm-0126
glioma


title: Anaplastic oligodendrocytoma aoa-0492

description:
aoa-0492
glioma


title: Anaplastic oligodendrocytoma aoa-0351

description:
aoa-0351
glioma


title: Anaplastic oligodendrocytoma aoa-0391

description:
aoa-0391
glioma


title: Anaplastic oligodendrocytoma aoa-0393

description:
aoa-0393
glioma


title: Glioblastoma gbm-0011

description:
gbm-0011
glioma


title: Anaplastic oligodendrocytoma aoa-0352

description:
aoa-0352
glioma


title: Anaplastic oligodendrocytoma aoa-0438

description:
aoa-0438
glioma


title: Anaplastic oligodendrocytoma aoa-0498

description:
aoa-0498
glioma


title: Anaplastic oligodendrocytoma aoa-0259

description:
aoa-0259
glioma


title: Anaplastic oligodendroglioma ao-0558

description:
ao-0558
glioma

source_name: Human anaplastic oligodendroglioma

value: Anaplastic oligodendroglioma


title: Anaplastic oligodendrocytoma aoa-0231

description:
aoa-0231
glioma


title: Glioblastoma gbm-0311

description:
gbm-0311
glioma


title: Anaplastic oligodendrocytoma aoa-0406

description:
aoa-0406
glioma


title: Anaplastic oligodendroglioma ao-0474

description:
ao-0474
glioma


title: Anaplastic oligodendroglioma ao-0403

description:
ao-0403
glioma


title: Anaplastic oligodendrocytoma aoa-0329

description:
aoa-0329
glioma


title: Anaplastic oligodendroglioma ao-0490

description:
ao-0490
glioma


title: Anaplastic oligodendroglioma ao-0508

description:
ao-0508
glioma


title: Anaplastic oligodendrocytoma aoa-0232

description:
aoa-0232
glioma


title: Anaplastic oligodendroglioma ao-0260

description:
ao-0260
glioma


title: Anaplastic astrocytoma aa-0334

description:
aa-0334
glioma

source_name: Human anaplastic astrocytoma

value: Anaplastic astrocytoma


title: Anaplastic oligodendroglioma ao-0364

description:
ao-0364
glioma

value: Chinese population


title: Anaplastic astrocytoma aa-0405

description:
aa-0405
glioma

value: brain tumor


title: Anaplastic astrocytoma aa-0476

description:
aa-0476
glioma


title: Astrocytoma a-0792

description:
a-0792
glioma

source_name: Human astrocytoma

value: Astrocytoma


title: Anaplastic astrocytoma aa-0249

description:
aa-0249
glioma


title: Astrocytoma a-0767

description:
a-0767
glioma


title: Anaplastic oligodendroglioma ao-0314

description:
ao-0314
glioma


title: Anaplastic astrocytoma aa-0353

description:
aa-0353
glioma


title: Anaplastic astrocytoma aa-0354

description:
aa-0354
glioma


title: Anaplastic astrocytoma aa-0412

description:
aa-0412
glioma


title: Astrocytoma a-0770

description:
a-0770
glioma


title: Anaplastic astrocytoma aa-0331

description:
aa-0331
glioma


title: Astrocytoma a-0746

description:
a-0746
glioma


title: Astrocytoma a-0718

description:
a-0718
glioma


title: Astrocytoma a-0743

description:
a-0743
glioma


title: Astrocytoma a-0736

description:
a-0736
glioma


title: Astrocytoma a-0712

description:
a-0712
glioma


title: Astrocytoma a-0711

description:
a-0711
glioma


title: Pyruvate-sulfate mono with sulfate in excess [C95_.027]

city: Berkeley

first: Jennifer

middle: V

last: Kuehl

state: California

address: 1 Cyclotron Road

department: Physical Biosciences

institute: Lawrence Berkeley National Laboratory

hyb_protocol: standard Nimblegen protocol

scan_protocol: standard Nimblegen protocol

data_processing: quantile normalized the probe intensities to match the G20 mono culture sample and averaged the log2 values for each gene and set the median log2 expression level in each sample to zero using custom R scripts.

label: Alexa fluor 555

organism: Oleidesulfovibrio alaskensis G20

label_protocol: prepared first-strand labeled cDNA with SuperScript Plus Indirect cDNA Labeling Module (Invitrogen)

growth_protocol: We collected expression data for 3 growth conditions: syntrophic, fermentative, and respiratory growth of Desulfovibrio alaskensis str. G20 on 30 mM pyruvate (for pyruvate-limited respiratory growth, 20 mM pyruvate was used). Desulfovibrio alaskensis str. G20 was grown in monoculture under sulfate-limited and pyruvate-limited conditions (5 mM or 10 mM sulfate, respectively) as well as fermentatively without the addition of the electron acceptor sulfate, and in in syntrophic coculture paired with the methanogen Methanococcus maripaludis or Methanospirillum hungatei. Cells were harvested from duplicate mono- and coculture chemostat runs after 5 volume turnovers at steady state in the chemostat at constant dilution rates of 0.027 h-1, 0.047h-1, and 0.036 h-1.

extract_protocol: Isolated total RNA with RNAeasy mini kit (Qiagen)

treatment_protocol: Varying growth conditions: syntrophic and fermentative growth versus sulfate respiration on substrate pyruvate

tag: culture type

value: monoculture grown in pyruvate-sulfate with sulfate in excess

tag: carbon source

value: pyruvate (20 mM)

tag: electron acceptor

value: sulfate (10 mM)

value: growth rate 0.047h-1 (chemostat growth)


title: Pyruvate-sulfate mono with sulfate in excess [C96_.047]

value: growth rate 0.027h-1 (chemostat growth)


title: Pyruvate-sulfate mono with sulfate in excess [C95_.047]


title: Pyruvate-sulfate mono with sulfate in excess [C96_.027]


title: Astrocytoma a-0692

description:
a-0692
glioma

tag: tissue

value: WHO grade 2

value: male


title: Astrocytoma a-0688

description:
a-0688
glioma


title: Astrocytoma a-0648

description:
a-0648
glioma

value: female


title: Astrocytoma a-0776

description:
a-0776
glioma


title: Astrocytoma a-0601

description:
a-0601
glioma


title: Astrocytoma a-0626

description:
a-0626
glioma


title: Pyruvate fermentation monoculture [C94_.036]

source_name: Pyruvate fermentation monoculture

value: monoculture grown in pyruvate fermention

value: pyruvate (30 mM)

value: growth rate 0.036h-1 (chemostat growth with standard gas flow rate 1 ml/min)


title: Pyruvate fermentation monoculture [C92_.036]

value: growth rate 0.036h-1 (chemostat growth with standard gas flow rate 1 ml/min)


title: Astrocytoma a-0595

description:
a-0595
glioma


title: Astrocytoma a-0673

description:
a-0673
glioma


title: Pyruvate fermentation monoculture [C93_.036]

value: growth rate 0.036h-1 (chemostat growth with high gas flow rate of 10 ml/min)


title: Astrocytoma a-0590

description:
a-0590
glioma


title: Vitiligo mouse 3

source_name: fresh ear skin_vitiligo mouse

extract_protocol: RNA was extracted using the Qiagen RNeasy kit according to the manufacturer’s instructions.

treatment_protocol: Vitiligo was induced in mice through adoptive transfer of PMEL CD8+ T cells as described previously (Harris et. al. JID 2012). Briefly, PMEL CD8+ T cells were isolated from the spleens of PMEL TCR transgenic mice through negative selection on microbeads (Miltenyi Biotech) according to the manufacturer’s instructions. Purified CD8+ T cells (1×106) were injected intravenously into sublethally irradiated (500 rads 1 day before transfer) Krt14-Kitl* hosts (16-18 weeks of age). Recipient mice also received i.p. injection of 1×106 pfu rVV-hPMEL (N Restifo, NCI, NIH) on the same day of transfer. Mice used as controls for vitiligo were irradiated but did not receive rVV-hPMEL or PMEL CD8+ T cell transfer.

tag: strain

value: vitiligo

tag: age

tag: gener

value: ear skin


title: Pyruvate coculture with Methanococcus maripaludis  [C76_.027]

value: syntrophic coculture with M. maripaludis grown on pyruvate (chemostat dilution rate 0.027h-1)


title: Pyruvate fermentation monoculture [C91_.036]


title: Vitiligo mouse 2


title: Astrocytoma a-0544

description:
a-0544
glioma

value: Chinese population

value: brain tumor

value: Astrocytoma


title: Astrocytoma a-0552

description:
a-0552
glioma


title: Anaplastic oligodendroglioma ao-0489

description:
ao-0489
glioma

value: WHO grade 3

value: Anaplastic oligodendroglioma


title: Vitiligo mouse 1


title: Astrocytoma a-0583

description:
a-0583
glioma


title: Astrocytoma a-0753

description:
a-0753
glioma


title: Control mouse 3

source_name: fresh ear skin_control mouse

value: control


title: Pyruvate coculture with Methanococcus maripaludis  [C76_.047]

value: syntrophic coculture with M. maripaludis grown on pyruvate (chemostat dilution rate 0.047h-1)

value: growth rate 0.047h-1 (chemostat growth)


title: Astrocytoma a-0542

description:
a-0542
glioma

value: WHO grade 2

value: male


title: cerebellum_650_control

city: Baltimore

first: Christine

last: Ladd-Acosta

state: MD

address: 615 N. Wolfe Street, E6518

department: Epidemiology

institute: Johns Hopkins University

description:
cerebellum_650_control
5730192008_R04C02

hyb_protocol: We utilized the standard Illumina protocol for the 450K BeadChip

scan_protocol: BeadChip arrays were imaged using the Illumina iScan using settings recommended by Illumina

data_processing: We used the minfi bioconductor package to process the raw data

extract_protocol: For the cerebellum samples genomic DNA was extracted using the MasterPure DNA purification kit (EpiCentre Biotechnologies) according to the manufacturers specifications. We utilized Trizol (Invitrogen) to isolate genomic DNA from the prefrontal and temporal cortex tissue samples according to the manufacturers recommendations. 500ng of genomic DNA was bisulfite treated using the EZ DNA methylation kit (Zymo Research), as specificed for downstrem Illumina BeadChip processing.

tag: Sex

value: female

value: brain

tag: brain region

value: cerebellum

tag: sampletype

value: postmortem brain tissue


title: cerebellum_4721l_autism

description:
cerebellum_4721l_autism
5730192041_R03C01

label_protocol: We utilized the standard Illumina protocol for the 450K BeadChip

value: autism


title: Pyruvate coculture with Methanospirillum hungatei [C75_.027]

value: syntrophic coculture with M. hungatei  grown on pyruvate (chemostat dilution rate 0.027h-1)

value: pyruvate (30 mM)

value: growth rate 0.027h-1 (chemostat growth)


title: cerebellum_7275_control

description:
cerebellum_7275_control
5730192041_R04C02


title: cerebellum_4278_control

description:
cerebellum_4278_control
5730192005_R05C02


title: cerebellum_4267_control

description:
cerebellum_4267_control
5730192008_R06C01


title: cerebellum_879_control

description:
cerebellum_879_control
5730192040_R06C02


title: cerebellum_4231_autism

description:
cerebellum_4231_autism
5730192055_R03C01


title: cerebellum_777_control

description:
cerebellum_777_control
5730192005_R03C02


title: cerebellum_4269_autism

description:
cerebellum_4269_autism
5730192055_R03C02


title: Control mouse 2

tag: genotype/variation

value: ear skin


title: Astrocytoma a-0522

description:
a-0522
glioma

value: Chinese population

value: brain tumor

value: Astrocytoma


title: cerebellum_1638_autism

description:
cerebellum_1638_autism
5730192040_R01C01


title: Pyruvate coculture with Methanospirillum hungatei [C75_.047]

value: syntrophic coculture with M. hungatei  grown on pyruvate (chemostat dilution rate 0.047h-1)


title: Astrocytoma a-0708

description:
a-0708
glioma


title: Pyruvate-sulfate mono with pyruvate in excess [C78_.047]

value: monoculture grown in pyruvate-sulfate with pyruvate in excess

value: sulfate (5 mM)


title: cerebellum_4899_autism

description:
cerebellum_4899_autism
5730192009_R05C02


title: cerebellum_4671_autism

description:
cerebellum_4671_autism
5730192055_R06C01


title: Anaplastic oligodendroglioma ao-0598

description:
ao-0598
glioma

value: WHO grade 3

value: Anaplastic oligodendroglioma


title: Astrocytoma a-0505

description:
a-0505
glioma

value: WHO grade 2

value: male


title: Astrocytoma a-0461

description:
a-0461
glioma


title: temporal_cortex_41_autism

description:
temporal_cortex_41_autism
6264496108_R05C01

value: brain

value: temporal cortex


title: Control mouse 1

value: control

value: female


title: Pyruvate-sulfate mono with pyruvate in excess [C78_.027]

value: pyruvate (30 mM)


title: T47D-Twist-JQ1 treatment

city: Lexington

first: Binhua

middle: P

last: Zhou

state: KY

address: 789 South Limestone

department: Markey Cancer Center/Biochemistry

hyb_protocol: Hyb protocol was performed at the core technician at the microarry core facility at the University of Kentucky School of Medicine

scan_protocol: Scan protocol was performed at the core technician at the microarry core facility at the University of Kentucky School of Medicine

data_processing: RMA

label_protocol: Label protocol was performed at the core technician at the microarry core facility at the University of Kentucky School of Medicine

growth_protocol: Cells were grown in DMEM/F12 plus 10%FBS in 5%CO2 at 37C

extract_protocol: Total RNA was extract from cells using Qiagene RNA purification kit following manfacturer's protocol

treatment_protocol: Cells were trypinized and harvested when in log-growth phase

tag: cell line

tag: treatment

tag: transfection

value: Twist

tag: cell type

value: Luminal breast cancer cells


title: Astrocytoma a-0459

description:
a-0459
glioma

tag: ethnicity

value: Chinese population

tag: tumor grade

tag: patient age

tag: patient gender


title: cerebellum_1349_autism

description:
cerebellum_1349_autism
5730192004_R03C01

value: cerebellum

tag: disease state

value: autism

value: postmortem brain tissue


title: Astrocytoma a-0469

description:
a-0469
glioma

tag: tissue

value: brain tumor

value: Astrocytoma


title: temporal_cortex_80_autism

description:
temporal_cortex_80_autism
6264496108_R04C02


title: T47D-Twist

institute: University of Kentucky School of Medicine


title: T47D-vector-JQ1 treatment

value: vector


title: Pyruvate-sulfate mono with pyruvate in excess [C77_.047]

tag: culture type

value: monoculture grown in pyruvate-sulfate with pyruvate in excess

tag: carbon source

tag: electron acceptor

value: sulfate (5 mM)

value: growth rate 0.047h-1 (chemostat growth)


title: Astrocytoma a-0434

description:
a-0434
glioma

value: WHO grade 2

value: male


title: Astrocytoma a-0447

description:
a-0447
glioma


title: HMLE-Twist-JQ1 treatment

source_name: HMLE

value: HMLE

value: Normal breast epithelial cells


title: T47D-vector

value: control


title: Astrocytoma a-0433

description:
a-0433
glioma


title: temporal_cortex_65_control

description:
temporal_cortex_65_control
6264496108_R02C02

tag: Sex

value: brain

value: temporal cortex

tag: age


title: Astrocytoma a-0396

description:
a-0396
glioma

value: Chinese population


title: HMLE-vector-JQ1 treatment


title: temporal_cortex_99_autism

description:
temporal_cortex_99_autism
6264496103_R01C02

tag: brain region

tag: sampletype


title: Astrocytoma a-0399

description:
a-0399
glioma


title: HMLE-Twist

tag: cell line

value: Twist


title: temporal_cortex_68_control

description:
temporal_cortex_68_control
6264496108_R02C01


title: temporal_cortex_89_control

description:
temporal_cortex_89_control
6264496108_R03C02


title: Osteocyte_ERaKO, biological rep3

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

country: Japan

institute: Ehime University

description: Gene expression data from osteocytes lacking ERa

hyb_protocol: For hybridization to the GeneChip Mouse Genome 430 2.0 Array (Affymetrix), 15 µg of fragmented cRNA probe was incubated with 50 pM control oligonucleotide B2, 1x eukaryotic hybridization control, 0.1 mg/ml herring sperm DNA, 0.5 mg/ml acetylated BSA, and 1x hybridization buffer in a 45°C rotisserie oven for 16 h. Washing and staining were performed by using a GeneChip Fluidic Station (Affymetrix) according to the manufacturer's protocol(Fluidics Protocol: EuKGE-WS2v4).

scan_protocol: Phycoerythrin-stained arrays were scanned as digital image files with GeneChip Scanner 3000 7G with AutoLoader.

data_processing:
Data transformation algorithm and normalization was done by Affymetrix GCOS.
Scaling:All Probe Sets, Target Signal=500
Normalization value:1
Parameters: defalut settings

source_name: Dmp1-GFP sorted calvarial osteocyte from osteocyte specific ERaKO

label_protocol: Total RNA was purified by using an RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturer's instructions. First-strand cDNA was synthesized from 5 µg of RNA by using 200 units of SuperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), 100 pmol T7-(dT)24 primer [5'-GGCCAGTGA AT TGTA ATACGACTCACTATAGGGAGGCGG-(dT)24-3'], 1x first-strand buffer, and 0.5 mM dNTPs at 42°C for 1 h. Second-strand synthesis was performed by incubating first-strand cDNA with 10 units of Escherichia coli ligase (Invitrogen), 40 units of DNA polymerase I (Invitrogen), 2 units of RNase H (Invitrogen), 1x reaction buffer, and 0.2 mM dNTPs at 16°C for 2 h, followed by 10 units of T4 DNA polymerase (Invitrogen) and incubation for another 5 min at 16°C. Double-stranded cDNA was purified by using GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions and labeled by in vitro transcription by using a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY). Briefly, dsDNA was mixed with 1x HY reaction buffer, 1x biotin-labeled ribonucleotides (NTPs with Bio-UTP and BioCTP), 1x DTT, 1x RNase inhibitor mix, and 1x T7 RNA polymerase and incubated at 37°C for 4 h. Labeled cRNA was then purified by using GeneChip Sample Cleanup Module and fragmented in 1x fragmentation buffer at 94°C for 35 min.

extract_protocol: Cells were isolated from 10-day-old fetal mice calvariae of ERαΔOcy/ΔOcy and ERαflox/flox harboring Dmp1-GFP. After removal of the sutures, pooled calvarial tissue was subjected to six sequential, 30-minute digestions in a mixture containing 0.05%/0.2 mM trypsin/EDTA and 1.5 U/ml collagenase-P (Roche) at 37°C. Cell fractions 4 to 6 were collected, pooled, and re-suspended in Dulbecco’s modified Eagle’s medium (DMEM, Life Technologies) containing 10% FBS (Hyclone) and centrifuged. Cells were rinsed with PBS and re-suspended in PBS/2% FBS and filtered through a 45-mm filter. Cell sorting was performed using BD FACS Aria. The gate for collecting GFP + cells was set as GFP + population to represent 10% to 15% of the total cells in GFP+ mice and 0.8% to 1.0% of total cells in GFP- mice (negative control). GFP+ cells were collected in a tube with 500 µl of PBS/3% FBS. Then, Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: strain

tag: gender

value: female

value: Calvarial osteocytes

tag: genotype/variation

value: Estrogen Receptor alpha knock-out


title: temporal_cortex_59_autism

description:
temporal_cortex_59_autism
6264496103_R03C02

value: autism

value: postmortem brain tissue


title: Osteocyte_ERaKO, biological rep2

tag: cell type


title: Osteocyte_ERaKO, biological rep1


title: temporal_cortex_113_autism

description:
temporal_cortex_113_autism
6264496048_R06C01


title: Astrocytoma a-0407

description:
a-0407
glioma

tag: ethnicity

value: brain tumor

tag: tumor grade

value: Astrocytoma


title: Astrocytoma a-0379

description:
a-0379
glioma

tag: patient age

tag: patient gender


title: HMLE-vector

tag: treatment

tag: transfection

value: vector


title: Non-inflamed_5-ASA_rep3

city: London

first: Charles

last: Mein

address: Charterhouse Square

department: Genome Centre

institute: Queen Mary University

description:
Sample name: NI 5ASA3
from patient with ulcerative colitis

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: The data were normalized using Illumina's quantile normalization method (GenomeStudio software).

source_name: rectal mucosa biopsy cultured ex vivo_Non-inflamed_5-ASA

label_protocol: Ambion Total Prep 96

extract_protocol: RNAlater (Qiagen) then stored at -20°C until RNA extraction by RNeasy mini kits (Qiagen) and Dnase step

treatment_protocol: Individual biopsies from areas of the rectum of patients with ulcerative colitis showing endoscopic signs of inflammation or not were placed luminal surface uppermost in a well of a 24-well tissue culture plate in 300µl of serum-free HL-1 chemically defined medium supplemented with 100 U/ml penicillin sodium, 100 mg/ml streptomycin sulphate, 50 µg/ml Gentamicin and cultured with or without 5-ASA (50mM) at 37°C, 95% air and 5% CO2 for 6h

tag: disease state

value: ulcerative colitis

tag: tissue

value: rectal mucosa biopsy cultured ex vivo

tag: inflammation

value: no

tag: agent


title: Osteocyte_WT, biological rep1

description: Gene expression data from control osteocytes

source_name: Dmp1-GFP sorted calvarial osteocyte from WT littermate

tag: age


title: temporal_cortex_8_control

description:
temporal_cortex_8_control
6264496048_R03C01

tag: Sex

value: male

tag: brain region

tag: sampletype


title: Astrocytoma a-0365

description:
a-0365
glioma

value: WHO grade 2


title: Non-inflamed_5-ASA_rep2

description:
Sample name: NI 5ASA2
from patient with ulcerative colitis


title: temporal_cortex_38_control

description:
temporal_cortex_38_control
6264496048_R04C02

value: brain

value: control


title: Osteocyte_WT, biological rep2

tag: strain

tag: gender


title: Non-inflamed_5-ASA_rep1

description:
Sample name: NI 5ASA1
from patient with ulcerative colitis


title: Non-inflamed_no drug_rep3

description:
Sample name: NI no drug3
from patient with ulcerative colitis

source_name: rectal mucosa biopsy cultured ex vivo_Non-inflamed_no drug

value: no drug


title: Astrocytoma a-0321

description:
a-0321
glioma

value: Chinese population


title: Phosphate-enriched roots at 10 min vs phosphate-enriched roots at 2 hrs

city: Irapuato

first: Enrique

middle: Ibarra

last: Laclette

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León, A.P. 629

country: Mexico

institute: Laboratorio Nacional de Genomíca (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV)

description: Slide11: Phosphate-enriched roots at 10 min vs hosphate-enriched roots at 2 hrs

hyb_protocol: Probes were mixed, concentrated by precipitation and resuspended in the hybridization solution (50% formamide, 5X SSC, 0.1% SDS, 0.4 μg/ l tRNA and 0.2 μg/ l Salmon Sperm DNA) for 14h. After hybridization, the slides were washed once in solutions 1–4 (wash solution 1: 2% SSC, 0.1% SDS at 45 ºC; wash solution 2: 0.1% SSC, 0.1% SDS; wash solution 3: 0.1% SSC; wash solution 4: 0.01% SSC) for 5 min with gentle stirring/agitation. Washed slides were dried by centrifugation.

scan_protocol: Slides were scanned with an Axon GenePix 4000 B scanner at a resolution of 10 µm adjusting the laser and gain parameters to obtain similar levels of fluorescence intensity in both channels. Spot intensities were quantified using Axon GenePix Pro 6.0 image analysis software. The mean of the signals and the median of backgrounds were used for further analysis.

data_processing: Raw data were imported into the R 2.2.1 software (http://www.R-project.org). Background correction was done using the method Robust Multi-array Average (RMA) whereas normalization of the signal intensities within slides was carried out using the printtiploess method and the Aquantile normalization (Yang et al., 2002) using the LIMMA package (Smyth et al., 2003, www.bioconductor.org).

organism: Arabidopsis thaliana

source_name: Phosphate-enriched medium, 10 min

label_protocol: For each treatment, four biological replicates were used for probe synthesis. For each sample, 1.5 µg total RNA were amplified in the presence of aminoallyl-dUTP (Ambion) using the Aminoallyl Message Amp II kit (Ambion). Resulting amplified RNA probes were further labeled with fluorescent Cy3 and Cy5 dyes (Amersham). The fluorescent dye-labeled probes were then purified using RNeasy columns (Qiagen).

growth_protocol: Arabidopsis thaliana (Col-0) seeds were surface sterilized with 95% (v/v) ethanol for 5 min and 20% (v/v) bleach for 7 min. Arabidopsis seedlings were germinated and grown in hydroponics with 125 mM Pi for 12 days, and then deprived of Pi by short-time (10 min, 30 min and 2 h)

extract_protocol: Total RNA was isolated from Arabidopsis root using the Trizol reagent (Invitrogen) and purified with the RNeasy kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: MS medium lacking phosphate or supplemented with 125 µM of this nutrient (Pi)

tag: cultivar

tag: time course period

value: 10 min

value: Arabidopsis roots

source_name: Phosphate-enriched medium, 2 hrs

value: 2 hrs


title: temporal_cortex_119_autism

description:
temporal_cortex_119_autism
6264496048_R02C01

value: temporal cortex

value: autism


title: Astrocytoma a-0285

description:
a-0285
glioma

tag: ethnicity

value: brain tumor

tag: tumor grade


title: Astrocytoma a-0317

description:
a-0317
glioma

tag: patient age

tag: patient gender

value: female

value: Astrocytoma


title: temporal_cortex_29_control

description:
temporal_cortex_29_control
6229076096_R04C02

value: postmortem brain tissue


title: Phosphate-deprived roots at 2 hrs vs phosphate-deprived roots at 10 min

description: Slide12: Phosphate-deprived roots at 2 hrs vs hosphate-deprived roots at 10 min

source_name: Phosphate-deprived medium, 2 hrs

source_name: Phosphate-deprived medium, 10 min


title: Non-inflamed_no drug_rep2

description:
Sample name: NI no drug2
from patient with ulcerative colitis

value: ulcerative colitis

value: rectal mucosa biopsy cultured ex vivo


title: Pyruvate-sulfate mono with pyruvate in excess [C77_.027]

tag: culture type

value: monoculture grown in pyruvate-sulfate with pyruvate in excess

tag: carbon source

value: pyruvate (30 mM)

tag: electron acceptor

value: sulfate (5 mM)

value: growth rate 0.027h-1 (chemostat growth)


title: temporal_cortex_2_control

description:
temporal_cortex_2_control
6229076096_R06C02

value: male

tag: tissue

value: brain

tag: disease state

value: control


title: Astrocytoma a-0281

description:
a-0281
glioma

value: Chinese population

value: WHO grade 2


title: Non-inflamed_no drug_rep1

description:
Sample name: NI no drug1
from patient with ulcerative colitis

tag: inflammation

value: no

tag: agent

value: no drug


title: Astrocytoma a-0258

description:
a-0258
glioma

value: brain tumor


title: Phosphate-enriched roots at 2 hrs vs phosphate-deprived roots at 2 hrs

description: Slide09: Phosphate-enriched roots at 2 hrs vs hosphate-deprived roots at 2 hrs

value: 2 hrs

value: Arabidopsis roots


title: Phosphate-deprived roots at 2 hrs vs phosphate-enriched roots at 2 hrs

description: Slide10: Phosphate-deprived roots at 2 hrs vs hosphate-enriched roots at 2 hrs


title: Astrocytoma a-0253

description:
a-0253
glioma

value: female

value: Astrocytoma


title: Phosphate-enriched roots at 2 hrs vs phosphate-enriched roots at 30 min

description: Slide08: Phosphate-enriched roots at 2 hrs vs hosphate-enriched roots at 30 min

source_name: Phosphate-enriched medium, 30 min

value: 30 min


title: inflamed_5-ASA_rep3

description:
Sample name: INF +5ASA3
from patient with ulcerative colitis

source_name: rectal mucosa biopsy cultured ex vivo_inflamed_5-ASA

value: ulcerative colitis

value: rectal mucosa biopsy cultured ex vivo

value: yes


title: temporal_cortex_23_control

description:
temporal_cortex_23_control
6264496048_R01C02

tag: Sex

tag: brain region

value: temporal cortex

tag: age

value: postmortem brain tissue


title: Phosphate-enriched roots at 30 min vs phosphate-enriched roots at 10 min

description: Slide04: Phosphate-enriched roots at 30 min vs hosphate-enriched roots at 10 min

value: 10 min


title: inflamed_5-ASA_rep2

description:
Sample name: INF +5ASA2
from patient with ulcerative colitis


title: Phosphate-deprived roots at 30 min vs phosphate-deprived roots at 2 hrs

description: Slide07: Phosphate-deprived roots at 30 min vs hosphate-deprived roots at 2 hrs

source_name: Phosphate-deprived medium, 30 min


title: temporal_cortex_47_control

description:
temporal_cortex_47_control
6229076096_R01C01

value: male

value: brain

value: control

tag: sampletype


title: inflamed_no drug_rep3

description:
Sample name: INF no drug3
from patient with ulcerative colitis

source_name: rectal mucosa biopsy cultured ex vivo_inflamed_no drug


title: inflamed_5-ASA_rep1

description:
Sample name: INF +5ASA1
from patient with ulcerative colitis


title: temporal_cortex_116_control

description:
temporal_cortex_116_control
6229076096_R01C02


title: inflamed_no drug_rep1

description:
Sample name: INF no drug1
from patient with ulcerative colitis


title: Phosphate-enriched roots at 30 min vs phosphate-deprived roots at 30 min

description: Slide05: Phosphate-enriched roots at 30 min vs hosphate-deprived roots at 30 min

tag: cultivar


title: inflamed_no drug_rep2

description:
Sample name: INF no drug2
from patient with ulcerative colitis


title: Phosphate-deprived roots at 10 min vs phosphate-deprived roots at 30 min

description: Slide03: Phosphate-deprived roots at 10 min vs hosphate-deprived roots at 30 min

tag: time course period


title: Osteocyte_WT, biological rep3

description: Gene expression data from control osteocytes

tag: strain

tag: gender

tag: cell type

value: Calvarial osteocytes

tag: genotype/variation


title: prefrontal_cortex_61_autism

description:
prefrontal_cortex_61_autism
6264496103_R05C02

value: prefrontal cortex

value: autism


title: prefrontal_cortex_91_control

description:
prefrontal_cortex_91_control
6264496108_R01C01


title: Phosphate-enriched roots at 10 min vs phosphate-deprived roots at 10 min

description: Slide01: Phosphate-enriched roots at 10 min vs hosphate-deprived roots at 10 min


title: Phosphate-deprived roots at 10 min vs phosphate-enriched roots at 10 min

description: Slide02: Phosphate-deprived roots at 10 min vs hosphate-enriched roots at 10 min


title: Phosphate-deprived roots at 30 min vs phosphate-enriched roots at 30 min

description: Slide06: Phosphate-deprived roots at 30 min vs hosphate-enriched roots at 30 min


title: bsgs_861

status: Public on Dec 11 2013

first: Joseph

middle: E

last: Powell

state: Qld

address: St lucia

department: Queensland Brain Institute

hyb_protocol: 750ng of cRNA was hybridised to Illumina HT12-v4.0 beadarray according to the whole-genome gene expression direct hybridization assay guide

scan_protocol: samples were scanned using an Illumina bead array reader

data_processing: preprocessing was done using genomestudio and included correction for chip background effects, removal of outlier beads and computation of average bead signal and detection p-values.

source_name: whole blood, healthy

label_protocol: not provided

extract_protocol: Total RNA extracted using the WB gene RNA purification kit.

treatment_protocol: Whole blood collected into PAXgene tubes. Quality assessed using agilent bioanalyzer.

value: F

tag: twin

value: 48 yrs


title: bsgs_860

value: DZ

value: 14 yrs


title: bsgs_857

value: M


title: bsgs_856

value: 49 yrs


title: prefrontal_cortex_88_control

description:
prefrontal_cortex_88_control
6264496103_R04C02


title: bsgs_853

value: 15 yrs


title: bsgs_859

value: 41 yrs


title: bsgs_852

value: 51 yrs


title: bsgs_855

value: 44 yrs


title: bsgs_849

value: 12 yrs


title: bsgs_858


title: bsgs_851

value: MZ


title: prefrontal_cortex_34_autism

description:
prefrontal_cortex_34_autism
6264496048_R01C01

value: female

value: brain

value: postmortem brain tissue


title: prefrontal_cortex_73_autism

description:
prefrontal_cortex_73_autism
6264496108_R03C01

value: male

value: prefrontal cortex


title: bsgs_850

value: 13 yrs


title: prefrontal_cortex_115_control

description:
prefrontal_cortex_115_control
6229076096_R05C02

value: control


title: bsgs_862

value: 46 yrs


title: prefrontal_cortex_46_control

description:
prefrontal_cortex_46_control
6229076096_R03C02


title: bsgs_847

value: F


title: prefrontal_cortex_67_control

description:
prefrontal_cortex_67_control
6264496103_R06C01


title: bsgs_848

value: M

value: DZ


title: bsgs_842

value: 15 yrs


title: bsgs_844

value: 14 yrs


title: bsgs_841


title: bsgs_845


title: bsgs_843


title: bsgs_846


title: bsgs_838


title: bsgs_839


title: bsgs_837


title: bsgs_836

value: 16 yrs


title: prefrontal_cortex_43_autism

description:
prefrontal_cortex_43_autism
6229076096_R03C01

value: autism


title: bsgs_834


title: bsgs_840


title: bsgs_835

value: 45 yrs


title: bsgs_831

value: 49 yrs


title: bsgs_832


title: bsgs_829

value: 51 yrs


title: bsgs_824

value: 11 yrs


title: bsgs_826

value: 43 yrs


title: bsgs_833

value: 17 yrs


title: bsgs_854

value: 42 yrs


title: bsgs_823

value: MZ

value: 13 yrs


title: bsgs_817


title: bsgs_827


title: bsgs_822

value: 12 yrs


title: bsgs_828

value: 40 yrs


title: bsgs_830

value: F

value: 19 yrs


title: bsgs_818

value: M


title: bsgs_813


title: bsgs_821

value: 14 yrs


title: bsgs_819

value: 48 yrs


title: bsgs_810

value: 21 yrs


title: bsgs_815

value: 18 yrs


title: bsgs_816

value: 16 yrs


title: bsgs_825


title: bsgs_820


title: bsgs_806


title: bsgs_807


title: bsgs_811

value: DZ


title: bsgs_808


title: bsgs_814


title: bsgs_809


title: bsgs_812


title: bsgs_805


title: bsgs_804


title: bsgs_801


title: bsgs_797


title: bsgs_795


title: prefrontal_cortex_85_autism

description:
prefrontal_cortex_85_autism
6229076096_R05C01

value: male

value: brain

value: prefrontal cortex

value: autism

value: postmortem brain tissue


title: bsgs_800