title: PTP1B KO mammary gland P15 rep4

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

description: PTP1B KO mammary gland P15

hyb_protocol: Affymetrix Gene Chip Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidiscs protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affzmetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader

data_processing: Arrays were normalized and probeset-level expression values were calculated with R/Bioconductor's (v2.15) 'affy' package using the rma() function

source_name: mammary gland PTP1B KO

label_protocol: 100ng of extracted total RNA was amplified using the Ambion WT Expression kit (Ambion) and the resulting sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: PTP1B-/- mice (Klaman et al., 2000) were backcrossed to an FVB background for at least seven generations. Twelve-week-old female mice were mated and pregnancy scored by the observation of a vaginal plug and confirmed by the presence of the fertilized eggs or the embryos when mammary glands were collected at pregnancy days 3, 7 or 10. Mammary glands from nulliparous mice were collected when mice were in estrus, as determined by a vaginal plug after an overnight mating with a male.

extract_protocol: RNA was isolated by using the RNeasy Plus mini kit (Qiagen) according to the manufacturer’s instructions. RNA concentration was measured using a Nanodrop 1000.

treatment_protocol: no treatment was applied.

tag: background strain

value: FVB

tag: developmental stage

value: Pregnancy day 15

value: Mammary gland

value: PTP1B KO


title: PTP1B WT mammary gland P15 rep4

status: Public on Oct 23 2012

type: RNA

description: PTP1B WT mammary gland P15

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: mammary gland PTP1B WT

tag: tissue

tag: genotype/variation

value: PTP1B WT


title: PTP1B KO mammary gland P15 rep1

description: PTP1B KO mammary gland P15


title: MDA-MB-468, shCont L-cont, biological rep1 [expt1]

city: Jerusalem

first: Ittai

last: Ben-Porath

address: Faculty of Medicine, Ein kerem

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University of Jerusalem

description: MDA-MB-468 cells stably infected with scrambled shRNA sequence and treated with control condition medium for 8 hours

hyb_protocol: 2ug ss cDNA in 80 ul were hybridized to a Mouse Gene 1.0 ST array using Affymetrix hybridization kit materials and hybridized for 17 hours at 45° at 60rpm. Post-hyb washes were done with Affymetrix wash solutions on the FS450 station using FS450_0007 protocol.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G

data_processing: Data was quantified using Affymetrix Expression Console, applying the RMA method

label: biotin

organism: Homo sapiens

source_name: MDA-MB-468 Breast cancer cell line

label_protocol: 200ng TotalRNA were used. cDNA samples were generated and labeled using Affymetrix WT-cDNA synthesis and labeling kit

growth_protocol: Cells were grown under standard conditions as specified by the ATCC. 24 hours prior to RNA extraction cells were seeded at equal confluence. For mouse samples, mammary epithelium was isolated using enzimatic dissociation and total RNA was extracted

extract_protocol: Total RNA was extracted using the RNeasy Mini Plus kit (Qiagen). For mice samples, total RNA was extracted using TRI reagent (Sigma).

treatment_protocol: Infected cells were exposed to viral supernatants of specified vector in the presence of 6μg/ml polybrene. 48 hours post infection cells were placed under 1μg/ml puromycin selection. control or Wnt3A condition medium was collected from L-cells or L-Wnt3A cells receptively. Cells were treated for 8 hours prior to RNA extraction. For mouse samples, three transgenic mice K5-rtTA/tet-Tcf3 (or three tet-Tcf3 control mice) were induced for 2 days using doxycyclin.

tag: cell line

value: MDA-MB-468 Breast cancer cell line

value: control

tag: treatment protocol

value: control condition medium


title: PTP1B WT mammary gland P15 rep1

description: PTP1B WT mammary gland P15


title: PTP1B KO mammary gland P15 rep3

description: PTP1B KO mammary gland P15


title: PTP1B KO mammary gland P10 rep3

description: PTP1B KO mammary gland P10

value: Pregnancy day 10


title: PTP1B KO mammary gland P15 rep2

description: PTP1B KO mammary gland P15


title: PTP1B KO mammary gland P10 rep1

description: PTP1B KO mammary gland P10


title: PTP1B WT mammary gland P15 rep2

description: PTP1B WT mammary gland P15


title: NTc5

city: Paris

first: Helene

last: Perrin

address: 91 boulevard de l'hopital

country: France

institute: INSERM

description: gene expression MVA-HIVgag naive mice

hyb_protocol: Cy3 labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

source_name: naive_lymph node

label_protocol: SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology. 250 ng of each of the amplified cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

extract_protocol: Cell samples were lysed using SuperAmp Lysis Buffer following manufacturer’s instructions.

treatment_protocol: Cells sorted by flow cytometry from fresh mouse lymph node and bone marrow cell suspensions: pentamer H2kD-AMQMLKETI (HIV-gagP24) CD8+ CD3+ T cells from draining lymph nodes (LN) and bone marrow (BM ) 5 days following intradermal injection of MVA-HIV gag, CD62L Hi CD44 int CD8+CD3+ T cells from lymph node of non-injected mice (NTc).

tag: strain background

value: Balb/c

tag: injected with

value: none; naive mice (NTc)

value: lymph node

tag: cell population

value: Naive CD62L Hi CD44 int CD8 T cells


title: NTc3

description: gene expression MVA-HIVgag naive mice


title: PTP1B KO mammary gland P10 rep2

description: PTP1B KO mammary gland P10


title: PTP1B WT mammary gland P10 rep3

description: PTP1B WT mammary gland P10


title: PTP1B WT mammary gland P10 rep2

description: PTP1B WT mammary gland P10


title: NTc4

description: gene expression MVA-HIVgag naive mice


title: NTc1

description: gene expression MVA-HIVgag naive mice


title: PTP1B KO mammary gland P7 rep5

description: PTP1B KO mammary gland P7

value: Pregnancy day 7


title: BM2

description: gene expression 5 days after intradermal injection of MVA-HIV gag

source_name: MVA-HIV gag injected_bone marrow

value: modified virus Ankara (MVA)-HIV gag

tag: time point

value: 5 days after intradermal injection

value: bone marrow

value: pentamer H2kD-AMQMLKETI CD8 T cells


title: BM5


title: PTP1B KO mammary gland P7 rep4

description: PTP1B KO mammary gland P7

value: FVB


title: PTP1B WT mammary gland P10 rep1

description: PTP1B WT mammary gland P10

value: Mammary gland


title: BM3


title: PTP1B KO mammary gland P7 rep3

description: PTP1B KO mammary gland P7

value: PTP1B KO


title: NTc2

description: gene expression MVA-HIVgag naive mice


title: BM4


title: BM1


title: post_exercise_right [G031A_D07_35_9_R_T1]

city: Wageningen

first: Milene

last: Catoire

address: Bomenweg 2

department: Human Nutrition

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of Affymetrix GeneChip Human Gene 1.1 ST arrays was carried out according to standard Affymetrix protocols (Affymetrix, Santa Clara, CA).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner according to standard protocol.

data_processing: Expression estimates were calculated using RMA. Microarray analysis was performed using MADMAX pipeline for statistical analysis of microarray data.

source_name: muscle biopsy

label_protocol: One hundred nanogram of  total RNA was labelled using Ambion WT expression kit (Applied Biosystems, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Nine healthy middle-aged men (age 51.5±5.1 years, body weight 88±17 kg, body mass index 26 ± 4) participated in the study. All subjects exercised less than 4 hours per week. The study was approved by the medical ethical committee of Wageningen University and all subjects received oral and written information about the experimental procedures and provided written informed consent.

extract_protocol:
Percutaneous needle biopsies were taken before (T0) and shortly after (T1) exercise from the vastus lateralis muscle from both legs (4 biopsies in total), using the Bergström technique with suction.  All biopsies were taken from a separate incisions. After each biopsy, the collected tissue sample was carefully cleared from visible adipose tissue and blood and divided into four pieces. Three pieces were directly frozen into liquid nitrogen and one piece was embedded into Tissue-Tek O.C.T. compound (Sakura Tissue Tek, Alphen a/d Rijn, NL) and frozen in liquid-nitrogen cooled isopentane, and stored at -80C for further analysis.
Total RNA was isolated from the skeletal muscle tissue by using Trizol reagent (Invitrogen, Breda, NL). Thereafter RNA was purified using the Qiagen RNeasy Micro kit (Qiagen, Venlo, NL).

treatment_protocol: All subjects performed a single 60 minutes experimental endurance exercise bout, which was preceded by two preliminary exercise tests and two familiarization trials. During the endurance exercise bout subjects had to perform one-legged cycling on a cycle ergometer (Excalibur Sport, Lode, Groningen NL) adapted with a custom-made leg support. Subjects cycled with their dominant leg (all but subject 6 cycled with their right leg).

tag: subject

tag: ethnicity

value: Caucasian

tag: gender

value: male

tag: age

value: 55 years

tag: exercised leg

value: right

tag: time

value: post_exercise (T1)

tag: biopsied leg

value: vastus lateralis muscle


title: baseline_right [G031A_C09_33_9_R_T0]

value: baseline (T0)


title: Endometrium_d16_rep3

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

institute: University of Zurich

description: beginning of ovulatory phase

hyb_protocol: Microarray analysis was performed using Agilent 4x44k Horse Gene Expression microarrays (AMADID 021322). Labeled cRNA was hybridized to the microarrays according the manufacturer’s instructions.

scan_protocol: Hybridized and washed slides were scanned at 3 µm resolution, 20 bit option, single pass with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies).

data_processing: Image processing was performed with Feature Extraction Software 10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09 and Grid: 021322_D_F_20090727) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Equus caballus

label_protocol: Cy3-labeled cRNA was produced using the Quick Amp Labeling Kit, one-color (Agilent Technologies) according the manufacturer’s instructions.

extract_protocol: Total RNA was isolated from the 25 endometrial biopsy samples using Trizol® Reagent (Invitrogen GmbH, Karlsruhe, Germany) according to the manufacturer’s instructions. Quantity and purity of RNA were measured with a NanoDrop 1000 (PEQLAB Biotechnologie GMBH, Erlangen, Germany). Quality of total RNA was assessed by electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

treatment_protocol: Endometrial biopsy samples were collected from five normal cycling mares (Bavarian Warmblood). Follicular development and ovulation were monitored routinely by daily transrectal palpation and ultrasound examination. Samples were obtained by transcervical biopsy and taken on five different time points during the estrous cycle (days 0, 3, 8, 12, 16), where day 0 corresponded to the day of ovulation. Biopsies were collected during different cycles. When two biopsies were collected in the same cycle, the interval between biopsy collections was at least 9 days.


title: Endometrium_d16_rep5

description: beginning of ovulatory phase


title: Endometrium_d16_rep2

description: beginning of ovulatory phase


title: baseline_left [G031A_D05_34_9_L_T0]

value: left


title: PTP1B KO mammary gland P7 rep2

description: PTP1B KO mammary gland P7

tag: background strain


title: LN5

source_name: MVA-HIV gag injected_lymph node

value: Balb/c

value: lymph node


title: LN4

value: modified virus Ankara (MVA)-HIV gag


title: LN2

value: 5 days after intradermal injection


title: PTP1B KO mammary gland P7 rep1

description: PTP1B KO mammary gland P7

tag: developmental stage

value: Pregnancy day 7


title: LN3

tag: tissue

value: pentamer H2kD-AMQMLKETI CD8 T cells


title: Endometrium_d16_rep4

description: beginning of ovulatory phase


title: Endometrium_d16_rep1

description: beginning of ovulatory phase


title: Endometrium_d12_rep5

description: late luteal phase


title: post_exercise_left [G031A_D09_36_9_L_T1]


title: PTP1B WT mammary gland P7 rep4

description: PTP1B WT mammary gland P7

value: FVB

tag: genotype/variation

value: PTP1B WT


title: PTP1B WT mammary gland P7 rep2

description: PTP1B WT mammary gland P7

value: Mammary gland


title: Endometrium_d12_rep4

description: late luteal phase


title: PTP1B WT mammary gland P7 rep1

description: PTP1B WT mammary gland P7


title: PTP1B KO mammary gland P3 rep3

description: PTP1B KO mammary gland P3

value: Pregnancy day 3

value: PTP1B KO


title: PTP1B WT mammary gland P7 rep3

description: PTP1B WT mammary gland P7


title: Endometrium_d12_rep3

description: late luteal phase


title: post_exercise_right [G031A_C05_31_8_R_T1]

value: Caucasian

value: male

value: 44 years


title: baseline_left [G031A_B09_30_8_L_T0]

value: right

value: vastus lateralis muscle


title: LN1


title: post_exercise_left [G031A_C07_32_8_L_T1]

value: post_exercise (T1)

value: left


title: baseline_right [G031A_B07_29_8_R_T0]

value: baseline (T0)


title: siRNA targeted to AR exon 1 treated with ethanol, replicate 2

city: Minneapolis

first: Scott

last: Dehm

address: Mayo Mail Code 806, 420 Delaware St SE

country: USA

institute: Masonic Cancer Center, University of Minnesota

description: SAMPLE 11

hyb_protocol: 150ng of biotin-labeled cRNA was hybridized with Illumina Beadchips using the HumanHT-12 v4 Expression Beadchip Kit in accordance with the manufacturer's specifications.

scan_protocol: Hybridized Beadchips were scanned with an Illumina iScan.

data_processing: Average probe intensity data was extracted from iScan image files using the Partek Report Plug-in for Illumina GenomeStudio and then imported to Partek Genomics Suite 6.6.  Raw intensity data was log2 transformed and quantile normalized using Partek GS 6.6.

source_name: late-passage CWR-R1 prostate cancer cells

label_protocol: Total RNA was converted to amplified, biotinylated, antisense cRNA using the Illumina TotalPrep-96 RNA Amplification Kit (Life Technologies) in accordance with the manufacturer's specifications.

growth_protocol: Late-passage CWR-R1 cells were cultured in RPMI 1640 medium supplemented with penicillin/streptomycin and 5% charcoal-stripped, steroid-depleted serum for 48h following electroporation.  Cells were then switched to serum-free RPMI 1640 medium supplemented with penicillin/streptomycin containing 1nM DHT or vehicle control (ethanol) for 24h.

extract_protocol: RNA was extracted using an acid guanidinium method and cleaned using a QIAGEN RNeasy kit in accordance with the prescribed protocol provided with the kit.  Quality control was performed with an a NanoDrop 8000 spectrophotometer and Caliper LabChip GX.

treatment_protocol: 48h post-transfection with the appropriate siRNA, cells were stimulated with 1nM DHT or vehicle control (ethanol) for 24h prior to RNA extraction.

tag: cell line

value: CWR-R1 prostate cancer cells

value: 48kb intragenic deletion in AR intron 1

tag: sirna

value: AR exon 1

tag: biological replicate number

tag: agent

value: ethanol


title: siRNA targeted to AR exon CE3 treated with 1nM DHT, replicate 3

description: SAMPLE 12

value: AR exon CE3

value: DHT


title: PTP1B KO mammary gland P3 rep2

description: PTP1B KO mammary gland P3

value: FVB

value: Mammary gland


title: Endometrium_d12_rep1

description: late luteal phase


title: post_exercise_left [G031A_A07_26_7_L_T1]

value: 56 years


title: siRNA targeted to AR exon CE3 treated with ethanol, replicate 3

description: SAMPLE 10


title: Endometrium_d12_rep2

description: late luteal phase


title: baseline_left [G031A_B05_28_7_L_T0]

value: Caucasian


title: post_exercise_right [G031A_A05_25_7_R_T1]

value: male


title: PTP1B WT mammary gland P3 rep1

description: PTP1B WT mammary gland P3

value: Pregnancy day 3

value: PTP1B WT


title: Endometrium_d8_rep4

description: mid luteal phase

value: diestrus


title: PTP1B KO mammary gland P3 rep1

description: PTP1B KO mammary gland P3

value: PTP1B KO


title: siRNA targeted to AR exon 7 treated with ethanol, replicate 2

description: SAMPLE 9

value: AR exon 7


title: baseline_right [G031A_A09_27_7_R_T0]

value: right

value: baseline (T0)

value: vastus lateralis muscle


title: PTP1B KO mammary gland P0 rep4

description: PTP1B KO mammary gland P0

value: Virgin


title: siRNA targeted to AR exon CE3 treated with 1nM DHT, replicate 1

description: SAMPLE 7

value: CWR-R1 prostate cancer cells

value: 48kb intragenic deletion in AR intron 1


title: PTP1B WT mammary gland P3 rep2

description: PTP1B WT mammary gland P3


title: siRNA targeted to AR exon 1 treated with ethanol, replicate 3

description: SAMPLE 8

value: AR exon 1

value: ethanol


title: Endometrium_d8_rep2

description: mid luteal phase


title: Endometrium_d8_rep5

description: mid luteal phase


title: siRNA targeted to AR exon CE3 treated with ethanol, replicate 1

description: SAMPLE 5

value: AR exon CE3


title: PTP1B KO mammary gland P0 rep3

description: PTP1B KO mammary gland P0

value: FVB

value: Mammary gland


title: post_exercise_left [G030A_G09_21_6_L_T1]

value: Caucasian

value: male

value: 56 years

value: left

value: post_exercise (T1)


title: post_exercise_right [G030A_H09_24_6_R_T1]


title: Endometrium_d8_rep1

description: mid luteal phase

value: diestrus


title: siRNA targeted to AR exon 7 treated with ethanol, replicate 3

description: SAMPLE 6

value: AR exon 7


title: Endometrium_d8_rep3

description: mid luteal phase


title: baseline_left [G030A_H05_22_6_L_T0]

value: baseline (T0)


title: PTP1B KO mammary gland P0 rep2

description: PTP1B KO mammary gland P0

value: PTP1B KO


title: baseline_right [G030A_H07_23_6_R_T0]

value: right

value: vastus lateralis muscle


title: siRNA targeted to AR exon CE3 treated with ethanol, replicate 2

description: SAMPLE 2

value: CWR-R1 prostate cancer cells

value: 48kb intragenic deletion in AR intron 1


title: siRNA targeted to AR exon 1 treated with ethanol, replicate 1

description: SAMPLE 3

value: AR exon 1

value: ethanol


title: siRNA targeted to AR exon CE3 treated with 1nM DHT, replicate 2

description: SAMPLE 4

value: AR exon CE3

value: DHT


title: PTP1B WT mammary gland P15 rep3

description: PTP1B WT mammary gland P15

value: FVB

value: Pregnancy day 15

value: Mammary gland

value: PTP1B WT


title: Endometrium_d3_rep5

description: early luteal phase


title: Endometrium_d3_rep4

description: early luteal phase


title: PTP1B KO mammary gland P0 rep1

description: PTP1B KO mammary gland P0

value: Virgin


title: PTP1B WT mammary gland P0 rep4

description: PTP1B WT mammary gland P0


title: Endometrium_d3_rep3

description: early luteal phase


title: post_exercise_left [G030A_G07_20_5_L_T1]

value: Caucasian

value: male

value: 53 years

value: post_exercise (T1)

value: left


title: siRNA targeted to AR exon 7 treated with ethanol, replicate 1

description: SAMPLE 1

value: AR exon 7


title: post_exercise_right [G030A_G05_19_5_R_T1]

value: right

value: vastus lateralis muscle


title: PTP1B WT mammary gland P0 rep2

description: PTP1B WT mammary gland P0


title: Endometrium_d3_rep1

description: early luteal phase


title: PTP1B WT mammary gland P0 rep3

description: PTP1B WT mammary gland P0


title: PTP1B WT mammary gland P0 rep1

description: PTP1B WT mammary gland P0


title: Endometrium_d0_rep5

description: ovulatory phase shortly after ovulation

value: estrus


title: baseline_left [G030A_E07_14_4_L_T0]

value: 56 years

value: baseline (T0)


title: baseline_left [G030A_F09_18_5_L_T0]


title: PD21 Pik3cd-/- ovaries after E2 injection for 72h, biological rep1

city: Nanjing

first: Qian

last: Li

address: Hanzhong Road 140

country: China

institute: Nanjing Medical University

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Ovary RNA samples were extracted from untreatment PD21 Pik3cd+/- and Pik3cd-/- female mice; PD21 Pik3cd+/- and Pik3cd-/- female mice after PMSG injection for 44 hours; PD21 Pik3cd+/- and Pik3cd-/- female mice after E2 injection for 72 hours;

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

treatment_protocol: PMSG treatment group mice were intraperitoneally injected with single 10IU PMSG per mouse for 44 hrs; E2  treatment group mice were Intraperitoneally injected three times 0.03ml E2 per mouse every 24 hours, ovaries were dissected after 72 hours from the first injection.

tag: strain background

value: female

value: 21 days + 72 hrs old

value: ovaries

tag: injected with

value: 0.03ml E2_every 24 hr_3 times

tag: harvest time after the first injection


title: PD21 Pik3cd-/- ovaries after E2 injection for 72h, biological rep3


title: baseline_right [G030A_F07_17_5_R_T0]

tag: subject

tag: ethnicity


title: NAC4

city: Nashville

first: Philip

middle: D

last: Anderson

state: TN

department: Pathology

institute: Vanderbilt University

description: SAMPLE 7

hyb_protocol: Samples were hybridized to GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: Arrays were scanned with Affymetrix Gene Chip Scanner v. 3.2.2.

data_processing: CEL files were imported to Bioconductor for analysis using the affy package. One array failed QC (C3; not included in this submission) and was not analyzed further. The remaining seven arrays were background corrected, normalized and summarized using RMA (implemented in affy). Limma was used to identify genes changed between control and NAC treatment groups.  We used expresso (implemented in the Bioconductor affy package) to perform background correction, normalization and summarization of probes. We then used the Affymetrix Mouse Gene 1.0-ST Array Transcriptcluster Revision 5 annotation data database, implemented in Bioconductor, to remove probesets without EntrezIDs, probesets with duplicate EntrezIDs, and AFFX control probesets. A total of 20,696 probesets were used to test for differential expression between control and NAC-treated prostates.

label_protocol: RNA was quantified using the Qubit RNA assay and RNA quality was assessed with the Agilent Bioanalyzer.  cDNA was generated using the Ambion® WT Expression Kit.  After fragmentation, the cDNA was labelled and hybridized to Affymetrix Mouse Gene 1.0 ST arrays.

growth_protocol: Mice were raised to weaning age in the Vanderbilt Animal Facility

extract_protocol: Total RNA was extracted from snap-frozen mouse anterior prostate tissue according to the Trizol® manufacturer’s protocol

treatment_protocol: Mice were treated with 5 mM NAC or plain water for 13 weeks.

tag: strain

value: recombinant inbred B6/129

tag: age

value: 16 weeks

tag: treated with

value: 5 mM NAC for 13 wks

value: whole prostate


title: PD21 Pik3cd+/- ovaries after E2 injection for 72h, biological rep3

tag: gender


title: Endometrium_d0_rep4

description: ovulatory phase shortly after ovulation

tag: time point


title: post_exercise_right [G030A_E09_15_4_R_T1]

value: Caucasian

value: male

tag: exercised leg

tag: time

tag: biopsied leg


title: Endometrium_d3_rep2

description: early luteal phase


title: PD21 Pik3cd+/- ovaries after E2 injection for 72h, biological rep2

tag: genotype/variation

tag: tissue


title: PD21 Pik3cd-/- ovaries after E2 injection for 72h, biological rep2


title: post_exercise_left [G030A_F05_16_4_L_T1]

value: post_exercise (T1)

value: left


title: NAC3

description: SAMPLE 6


title: Endometrium_d0_rep3

description: ovulatory phase shortly after ovulation


title: Endometrium_d0_rep2

description: ovulatory phase shortly after ovulation


title: NAC2

description: SAMPLE 5


title: baseline_right [G030A_E05_13_4_R_T0]

value: right


title: PD21 Pik3cd+/- ovaries after E2 injection for 72h, biological rep1


title: Endometrium_d0_rep1

description: ovulatory phase shortly after ovulation


title: NAC1

description: SAMPLE 4


title: post_exercise_right [G030A_D07_11_3_R_T1]

value: 52 years

value: vastus lateralis muscle


title: Day 16 CL_AI+E2 treatment_Biological rep3

city: BANGALORE

first: SUDESHNA

last: TRIPATHY

state: KARNATAKA

address: NEW BIOLOGICAL SCIENCES BUILDING

department: MOLECULAR REPRODUCTION, DEVELOPMENT AND GENETICS

country: India

institute: INDIAN INSTITUTE OF SCIENCE

description: Day 16 CL_AI+E2 treatment

scan_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev. 3, 2001) using Affymetrix Genearray scanner 3000 series

data_processing: The processed image files (.CEL) were normalized across arrays using the robust multichip average (RMA) algorithm and log-transformed (base 2) [R version 2.12.2].

organism: Rattus norvegicus

source_name: Corpus luteum from pregnant rats post 96 h AI+E2 treatment

growth_protocol: Following retrieval of CL from the ovary, flash frozen in liquid nitrogen and stored at -70°C for the purpose of RNA isolation. The isolated RNA was labeled and hybridized to Affymetrix Rat Gene 1.0 ST Array

extract_protocol: Total RNA was isolated using Trizol reagent (Sigma Aldrich Co., St.Louis, MO) according to manufacturer’s instructions.

treatment_protocol: In the experiments with pregnant rats, during day 12 to 16 of pregnancy, E2 deprivation was brought about by AI (1mg/ kg bw orally) treatment beginning on day12 of pregnancy daily for 4 days. In the E2 supplementation experiments, together with AI, rats were treated with E2 (10µg/ day s.c.). CL tissues were collected on day 12 (no treatment; n=3 animals/ time point), day 16 (vehicle treatment; n=3 animals/ time point), day 16 (AI treatment; n=3 animals/ time point) and day 16 (AI+ E2 treatment; n=3 animals/ time point).Following retrieval of CL from the ovary, corpora lutea were flash frozen in liquid nitrogen and stored at -70C for the purpose of RNA isolation. The isolated RNA was labelled and hybridized to Affymetrix GeneChip® Rat Gene 1.0 ST arrays as per the manufacturer’s instructions.

value: Wistar

value: Corpus luteum

tag: day of pregnancy


title: Control4

description: SAMPLE 3

value: plain water for 13 wks


title: PD21 Pik3cd-/- ovaries after PMSG injection for 44h, biological rep2

value: female

value: 21 days + 44 hrs old

value: 10IU PMSG once


title: baseline_right [G030A_C09_9_3_R_T0]

value: baseline (T0)


title: baseline_left [G030A_D05_10_3_L_T0]


title: post_exercise_left [G030A_C07_8_2_L_T1]

value: 53 years


title: post_exercise_right [G030A_C05_7_2_R_T1]


title: post_exercise_left [G030A_D09_12_3_L_T1]


title: Day 16 CL_AI+E2 treatment_Biological rep1

description: Day 16 CL_AI+E2 treatment

hyb_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev. 3, 2001)


title: Day 16 CL_AI treatment_Biological rep3

description: Day 16 CL_AI treatment

source_name: Corpus luteum from pregnant rats post 96 h AI treatment

label_protocol: Standard Affymetrix protocols (Chip Expression Analysis Technical Manual rev. 3, 2001)


title: Day 16 CL_AI treatment_Biological rep2

description: Day 16 CL_AI treatment


title: Day 16 CL_AI+E2 treatment_Biological rep2

description: Day 16 CL_AI+E2 treatment


title: Normal karyotyped H1 rep2

city: Seattle

first: LI

middle: B

last: LI

state: WA

address: 1905 NE pacific st

department: Department of Hematology

institute: University of Washington

hyb_protocol: cRNA samples were hybridized onto Human HT-12 v4 Expression BeadChip (Illumina) according to manufacture's protocols.

scan_protocol: Arrays were scanned by the Genomics Resource Lab at Fred Hutchinson Cancer Center with an Illumina BeadArray Reader.

data_processing: Raw expression files were loaded into Bioconductor. The Bioconductor package 'lumi' was used to read in the GenomeStudio Probe Level from unnormalized data, and quantile normalize the data.

label: biotin, Cy3

source_name: embyonic stem cell

label_protocol: All RNA samples were amplified and labelled using Illumina's TotalPrep RNA Amplification Kit according to manufacturer's protocol.

growth_protocol: All cells were cultured on Matrigel (BD Biosciences) in mTESR media (Stem Cell Technologies)

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent 2100 Bioanalyzers and NanoDrop DN-1000 spectrophotometer.

tag: cell type

value: embyonic stem cell

tag: karyptype


title: Day 16 CL_AI treatment_Biological rep1

description: Day 16 CL_AI treatment

tag: strain background


title: Control2

description: SAMPLE 2

value: recombinant inbred B6/129

value: 16 weeks

value: whole prostate


title: Control1

description: SAMPLE 1


title: PD21 Pik3cd-/- ovaries after PMSG injection for 44h, biological rep3

value: ovaries

tag: injected with

tag: harvest time after the first injection


title: Day 16 CL_Vehicle treatment_Biological rep3

description: Day 16 CL_Vehicle treatment

source_name: Corpus luteum from pregnant rats post 96 h vehicle treatment


title: Disomic iPSC C3-5-13 derived from trisomic C3-5

description: iPSCs were made by lentiviral infection carrying OCT4, NANOG, SOX2, LIN28. Clone C3-5, C3-5-11 and C3-5-13 carry same reprogramming transgenes

source_name: iPSC from Down syndrome (DS) fibroblasts

value: IPSC

tag: number of chromosomes

value: Disomic


title: PD21 Pik3cd+/- ovaries after PMSG injection for 44h, biological rep1


title: PD21 Pik3cd-/- ovaries after PMSG injection for 44h, biological rep1


title: PD21 Pik3cd-/- ovaries, biological rep3

source_name: PD21 Pik3cd-/- ovaries

value: 21 days old


title: PD21 Pik3cd+/- ovaries after PMSG injection for 44h, biological rep3


title: PD21 Pik3cd+/- ovaries after PMSG injection for 44h, biological rep2


title: PD21 Pik3cd-/- ovaries, biological rep2


title: Normal karyotyped H1 rep1


title: baseline_left [G030A_B09_6_2_L_T0]

tag: subject

tag: ethnicity

value: Caucasian

value: male

value: right

value: left

value: vastus lateralis muscle


title: Disomic iPSC C3-5-11 derived from trisomic C3-5


title: PTP1B WT mammary gland P3 rep3

description: PTP1B WT mammary gland P3

tag: background strain

value: FVB

tag: developmental stage

value: Pregnancy day 3

value: Mammary gland

value: PTP1B WT


title: baseline_left [G030A_A07_2_1_L_T0]

tag: gender

tag: age

value: 44 years

value: baseline (T0)


title: post_exercise_right [G030A_A09_3_1_R_T1]

tag: exercised leg

tag: time

value: post_exercise (T1)


title: baseline_right [G030A_B07_5_2_R_T0]

value: 53 years

tag: biopsied leg


title: post_exercise_left [G030A_B05_4_1_L_T1]

tag: tissue


title: Day 16 CL_Vehicle treatment_Biological rep1

description: Day 16 CL_Vehicle treatment

value: Wistar

value: Corpus luteum

tag: day of pregnancy


title: Day 12 CL_No treatment_Biological rep2

description: Day 12 CL_No treatment

source_name: Corpus luteum from pregnant rats without treatment


title: Day 16 CL_Vehicle treatment_Biological rep2

description: Day 16 CL_Vehicle treatment


title: baseline_right [G030A_A05_1_1_R_T0]


title: Day 12 CL_No treatment_Biological rep3

description: Day 12 CL_No treatment


title: Day 12 CL_No treatment_Biological rep1

description: Day 12 CL_No treatment


title: PD21 Pik3cd+/- ovaries, biological rep3

source_name: PD21 Pik3cd+/- ovaries

value: female

tag: genotype/variation

value: ovaries


title: PD21 Pik3cd+/- ovaries, biological rep2

value: 21 days old


title: PD21 Pik3cd-/- ovaries, biological rep1


title: PD21 Pik3cd+/- ovaries, biological rep1


title: Trisomic iPSC C2-4

description: iPSCs were made by lentiviral infection carrying OCT4, NANOG, SOX2, LIN28. Clone C2-4, C2-4-3 and C2-4-4 carry same reprogramming transgenes

tag: cell type

value: IPSC

value: Trisomic

tag: karyptype


title: Disomic iPSC C2-4-4 derived from trisomic C2-4

value: Disomic


title: Disomic iPSC C2-4-3 derived from trisomic C2-4


title: PMN_48hr_LVS_4

status: Public on Oct 22 2012

city: Hamilton

first: Addie

last: Whitney

state: MT

address: 903 S 4th St

department: LHBP

institute: NIH/NIAID/RML

description: test PMNs

hyb_protocol: cRNA were hybridized on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2004, Affymetrix).  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix scanner.

data_processing: Affymetrix GeneChip Operating Software (GCOS v1.0, http://www.affymetrix.com) was used to perform the preliminary analysis of the custom chips (pivot table).  All *.cel files, representing individual replicates, were scaled to a trimmed mean of 500 to produce the *.chp files.  A pivot table with all samples was created including calls, call p-value and signal intensity for each gene.  Statistical and quality filters were applied as follows.  The average scaled expression must be at least 500 in at least one group.  For probe sets more highly expressed in control samples, the call must be present/marginal in at least 3 of 4 samples; for probe sets more highly expressed in LVS-treated samples, the call must be present/marginal in at least 3 of 4 samples.  At least a 2-fold change is required, and an ANOVA p-value of less than 0.05, with a multiple test correction.

source_name: polymorphonuclear leukocytes, 48hr, LVS-treated, replicate 4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ugs total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

extract_protocol: Total RNA was extracted with the Qiagen RNeasy kit according to the manufacturer's instructions.

treatment_protocol: Polymorphonuclear leukocytes (PMNs) were isolated from the blood of healthy donors.  PMNs were treated with F. tularensis subsp. holarctica live vaccine strain (LVS) at a bacteria to PMN ratio of 200:1 for 0, 3, 6, 12, 24, or 48 hours at 37C.  Untreated PMNs serve as controls.

value: polymorphonuclear leukocytes

tag: f. tularensis exposure status

value: test PMNs

value: 48 hr


title: Trisomic iPSC C3-5


title: PMN_48hr_LVS_3

description: test PMNs

source_name: polymorphonuclear leukocytes, 48hr, LVS-treated, replicate 3


title: Holstein-2_b vs Angus-4

type: genomic

city: College Station

first: Ryan

last: Doan

state: Texas

address: 4467 TAMU

institute: Texas A&M University

hyb_protocol: Cy5 and Cy3 labeled samples combined with hyb buffers were hybridized to array, washed, and scanned

scan_protocol: Scanned on an Agilent C2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Feature Extraction Software (v 10.7.1.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

organism: Bos taurus

label_protocol: 4ug DNA labeled with Bioprime Plus Kit (Invitrogen)

extract_protocol: genomic DNA isolated using standard PCI extraction

tag: breed

value: Holstein

tag: subspecies

value: taurine

value: White Blood Cells

source_name: Angus-4 [reference]

value: Angus


title: Angus-15 vs Angus-4


title: Angus-16 vs Angus-4


title: Angus-5 vs Angus-4


title: Angus-13 vs Angus-4


title: Angus-9 vs Angus-4


title: Angus-3_b vs Angus-4


title: Angus-2_b vs Angus-4


title: Angus-14 vs Angus-4


title: Angus-10 vs Angus-4


title: Brahman-1 vs Angus-4

value: Brahman

value: indicine


title: PMN_48hr_LVS_2

description: test PMNs

source_name: polymorphonuclear leukocytes, 48hr, LVS-treated, replicate 2


title: Brahman-1_b vs Angus-4


title: Brahman-2 vs Angus-4


title: Nellore-3 vs Angus-4

value: Nellore


title: Angus-7 vs Angus-4


title: Nellore-2_b vs Angus-4


title: Angus-6 vs Angus-4


title: Brahman-3 vs Angus-4


title: Angus-12 vs Angus-4


title: Angus-11 vs Angus-4


title: Nellore-3_b vs Angus-4


title: PMN_48hr_LVS_1

description: test PMNs

source_name: polymorphonuclear leukocytes, 48hr, LVS-treated, replicate 1


title: Angus-8 vs Angus-4


title: PMN_48hr_ctrl_4

description: control PMNs

source_name: polymorphonuclear leukocytes, 48hr, control, replicate 4

value: control PMNs


title: Brahman-4 vs Angus-4


title: HCV_SK7 [Illumina]

city: New Haven

first: Christopher

last: Bolen

state: CT

address: 300 George Street, Suite 505

institute: Yale University

description: Human PBMC collected from whole blood of patients chronically infected with HCV, before initiation of therapy

hyb_protocol: 1.5 µg of cRNA was combined with hybridization controls and hybridized to the array for 16 hours in a hybridization oven at 58°C. The chip was then washed and stained with streptavidin-Cy3.

scan_protocol: The array was scanned using the Illumina BeadArray reader.

data_processing: Microarray data from the validation cohort underwent quantile normalization using the Beadarray package in bioconductor.

source_name: PBMC

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out by the Yale Center for Genomic Analysis using the standard Illumina protocols.

extract_protocol: Treatment-naïve HCV patients were recruited by hepatologists in the outpatient hepatitis clinic within the Yale Liver Center. Healthy volunteers were recruited from Yale’s PhenoGenetic Cohort of Healthy controls. PBMCs were isolated from whole blood by density gradient centrifugation using Ficoll-Paque (GE Healthcare) centrifugation. Total RNA was isolated from PBMCs using an RNeasy kit (Qiagen, Valencia, CA), and the quality of total RNA was evaluated by A260/A280 ratio and by electrophoresis on an Agilent Bioanalyzer.

tag: cell

value: PBMC

tag: infection

value: HCV


title: HCV_SK5 [Illumina]


title: PMN_48hr_ctrl_3

description: control PMNs

source_name: polymorphonuclear leukocytes, 48hr, control, replicate 3


title: PMN_48hr_ctrl_2

description: control PMNs

source_name: polymorphonuclear leukocytes, 48hr, control, replicate 2


title: PMN_24hr_LVS_3

description: test PMNs

source_name: polymorphonuclear leukocytes, 24hr, LVS-treated, replicate 3

value: 24 hr


title: Nellore-4 vs Angus-4


title: Holstein-4 vs Angus-4


title: HCV_SK9 [Illumina]


title: Holstein-3 vs Angus-4


title: HCV_SK3 [Illumina]


title: Testis Stage III Ctrl 55

city: Rennes

first: Elisabeth

last: Sambroni

address: Bat 16A Campus de Beaulieu

department: PHASE

institute: INRA

hyb_protocol: Prehybridization of microarrays was performed in a hybridization buffer (5X Denhardt's, 5X SSC, 0.5% SDS) at 65°C for 4 hours. Labelled cDNA targets were denatured at 95°C for 5 minutes and incubated with microarrays for 48 hours at 65°C in the same buffer. Microarrays were then washed three times 1 hour at 68°C (0.1X SSC, 0.2% SDS).

scan_protocol: Microarrays were exposed 48 hours to phosphor-imaging plates that were scanned using a FUJI BAS 500 at 25 µm resolution. Signals acquisition was performed using the BZscan software.

data_processing: Raw expression signals were first corrected for the amount of spotted cDNA by dividing complex signals by oligonucleotide signals. To avoid the bias affecting relative gene expression levels, corrected sample signal of each spot was further multiplied by the median vector signal of all arrays for this same spot. Expression values (clones only) were then log2-transformed and submitted to a quantile-quantile normalisation using AMEN software (http://sourceforge.net/projects/amen/)

organism: Oncorhynchus mykiss

source_name: Whole testis

label_protocol: 5µg RNAs were reverse-transcribed for 2 hours at 42°C in presence of radiolabelled dNTP (30 µCi [alpha-33P] dCTP, 120 µM dCTP, 20 mM each dATP, dTTP, dGTP) using an oligo(dT) primer and 400 units Superscript II reverse transcriptase (Invitrogen).

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, Cergy Pontoise, France). Total RNA concentration was determined on an Agilent 2100 Bioanalyzer and quality-controlled on a RNA 6000 LabChip® kit (Agilent Technologies, Stockport, UK).

treatment_protocol: Testes were collected from all-male population rainbow trout and chopped in small pieces, in sterile conditions. Fragments were randomly distributed on Nunc polycarbonate membrane inserts in 24-well plates filled with 300 µL of modified L15 culture medium plus 2% Ultroser SF. Incubation were performed in six replicates for 96 hours, at 12°C, in the absence or presence of purified salmonid gonadotropins, FSH and LH (500 ng/mL). Medium was replaced after 48 h of incubation.

value: Stage III

tag: treatment

value: Control

value: 96 hours

value: testis


title: PMN_24hr_LVS_2

description: test PMNs

source_name: polymorphonuclear leukocytes, 24hr, LVS-treated, replicate 2

value: polymorphonuclear leukocytes

value: test PMNs


title: Healthy_SK59 [Illumina]

description: Human PBMC collected from whole blood of healthy volunteers

value: Healthy


title: Healthy_SK96 [Illumina]


title: Healthy_SK83 [Illumina]


title: HCV_SK1 [Illumina]


title: PMN_24hr_LVS_4

description: test PMNs

source_name: polymorphonuclear leukocytes, 24hr, LVS-treated, replicate 4


title: PMN_24hr_LVS_1

description: test PMNs

source_name: polymorphonuclear leukocytes, 24hr, LVS-treated, replicate 1


title: Holstein-2 vs Angus-4

value: Holstein

value: taurine


title: Healthy_SK35 [Illumina]


title: Nellore-2 vs Angus-4

value: White Blood Cells

value: Angus


title: Nellore-1 vs Angus-4

value: indicine


title: Testis Stage III LH 67

tag: developmental stage

value: LH 500 ng/mL


title: Healthy_SK11 [Illumina]


title: Angus-2 vs Angus-4


title: RA55

city: Jinan

first: Xiaotian

last: Chang

address: Jingshi road 18877

institute: Shandong Acedemy of medicinal sciences

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina Genomestudio V2011.1 and gene expression module (1.9.0).

source_name: rheumatoid arthritis

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

extract_protocol: Total RNA from synovial tissues was extracted using TRIzol reagent (Invitrogen) according to the supplier's recommendation. cRNA was synthesized, amplified and purified using the Illumina TotalPrep RNA Amplification Kit following manufacturer recommendations.

tag: gender

value: female

tag: age (years)

value: synovial membrane


title: Testis Stage III T0-5

value: No culture

value: 0 hour


title: Testis Stage I-II LH 32

value: Stage I-II


title: PMN_24hr_ctrl_2

description: control PMNs

source_name: polymorphonuclear leukocytes, 24hr, control, replicate 2

value: control PMNs

value: 24 hr


title: Holstein-1 vs Angus-4


title: Angus-4 vs Angus-4


title: Testis Stage III T0-4

value: Stage III

value: testis


title: PMN_24hr_ctrl_3

description: control PMNs

source_name: polymorphonuclear leukocytes, 24hr, control, replicate 3

value: polymorphonuclear leukocytes


title: Testis Stage I-II LH 33

value: 96 hours


title: RA47


title: Angus-3 vs Angus-4


title: PMN_48hr_ctrl_1

description: control PMNs

source_name: polymorphonuclear leukocytes, 48hr, control, replicate 1

value: 48 hr


title: Testis Stage III Ctrl 57

value: Control


title: PMN_24hr_ctrl_1

description: control PMNs

source_name: polymorphonuclear leukocytes, 24hr, control, replicate 1


title: RA53


title: RA51


title: PMN_12hr_LVS_3

description: test PMNs

source_name: polymorphonuclear leukocytes, 12hr, LVS-treated, replicate 3

value: test PMNs

value: 12 hr


title: RA42

value: male


title: PMN_12hr_LVS_2

description: test PMNs

source_name: polymorphonuclear leukocytes, 12hr, LVS-treated, replicate 2


title: PMN_24hr_ctrl_4

description: control PMNs

source_name: polymorphonuclear leukocytes, 24hr, control, replicate 4


title: RA27


title: RA28


title: RA37


title: Testis Stage I-II LH 34

value: LH 500 ng/mL


title: OA47

source_name: osteoarthritis


title: Testis Stage III FSH 65

value: FSH 500 ng/mL


title: RA11

value: female

value: synovial membrane


title: Testis Stage III FSH 64


title: OA27


title: RA31


title: OA26


title: Testis Stage I-II Ctrl 24


title: Testis Stage III Ctrl 58


title: OA34


title: PMN_12hr_LVS_1

description: test PMNs

source_name: polymorphonuclear leukocytes, 12hr, LVS-treated, replicate 1


title: AS44

source_name: ankylosing spondylitis


title: OA29


title: PMN_12hr_ctrl_4

description: control PMNs

source_name: polymorphonuclear leukocytes, 12hr, control, replicate 4


title: PMN_12hr_ctrl_1

description: control PMNs

source_name: polymorphonuclear leukocytes, 12hr, control, replicate 1


title: AS19


title: OA42


title: PMN_12hr_ctrl_3

description: control PMNs

source_name: polymorphonuclear leukocytes, 12hr, control, replicate 3


title: PMN_6hr_LVS_4

description: test PMNs

source_name: polymorphonuclear leukocytes, 6hr, LVS-treated, replicate 4

value: 6 hr


title: AS18


title: OA25


title: Testis Stage III Ctrl 56

source_name: Whole testis


title: PMN_12hr_ctrl_2

description: control PMNs

source_name: polymorphonuclear leukocytes, 12hr, control, replicate 2


title: Testis Stage III LH 68


title: Angus-1 vs Angus-4

value: Angus

value: taurine

value: White Blood Cells

source_name: Angus-4 [reference]


title: AS16


title: aP2Cre-derived tumor mouse 144

city: Memphis

first: David

last: Finkelstein

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description:
Gene expression data from tumors derived from aP2-expressing cells
as144

data_processing: The data were quantile normalized using BeadStudio

source_name: mouse tumor model

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain

value: mixed C57Bl/6 and 129X1/SvJ

tag: tissue type

value: tumor

tag: genotype


title: PMN_12hr_LVS_4

description: test PMNs

source_name: polymorphonuclear leukocytes, 12hr, LVS-treated, replicate 4

value: polymorphonuclear leukocytes

tag: time


title: AS11

tag: tissue


title: Testis Stage I-II LH 31

value: Stage I-II

value: 96 hours

value: testis


title: Testis Stage I-II FSH 30


title: PMN_6hr_LVS_2

description: test PMNs

source_name: polymorphonuclear leukocytes, 6hr, LVS-treated, replicate 2

value: test PMNs


title: aP2Cre-derived tumor mouse 165

description:
Gene expression data from tumors derived from aP2-expressing cells
as165


title: Testis Stage III FSH 63

value: Stage III


title: Testis Stage III LH 69


title: Testis Stage III LH 72


title: aP2Cre-derived tumor mouse 164

description:
Gene expression data from tumors derived from aP2-expressing cells
as164


title: aP2Cre-derived tumor mouse 115

description:
Gene expression data from tumors derived from aP2-expressing cells
as115


title: aP2Cre-derived tumor mouse 174

description:
Gene expression data from tumors derived from aP2-expressing cells
as174


title: PMN_6hr_ctrl_3

description: control PMNs

source_name: polymorphonuclear leukocytes, 6hr, control, replicate 3

value: control PMNs


title: Myogenin-derived tumor mouse 42

description:
Gene expression data from tumors derived from Myogenin-expressing cells
smyog42


title: PMN_6hr_ctrl_4

description: control PMNs

source_name: polymorphonuclear leukocytes, 6hr, control, replicate 4


title: Testis Stage I-II LH 36

value: LH 500 ng/mL


title: Myogenin-derived tumor mouse 41

description:
Gene expression data from tumors derived from Myogenin-expressing cells
smyog41


title: aP2Cre-derived tumor mouse 95

description:
Gene expression data from tumors derived from aP2-expressing cells
as95


title: aP2Cre-derived tumor mouse 104

description:
Gene expression data from tumors derived from aP2-expressing cells
as104


title: PMN_6hr_LVS_3

description: test PMNs

source_name: polymorphonuclear leukocytes, 6hr, LVS-treated, replicate 3


title: Myogenin-derived tumor mouse 43

description:
Gene expression data from tumors derived from Myogenin-expressing cells
smyog43


title: PMN_6hr_LVS_1

description: test PMNs

source_name: polymorphonuclear leukocytes, 6hr, LVS-treated, replicate 1


title: Testis Stage I-II Ctrl 19

value: Control


title: Testis Stage III LH 71


title: PMN_6hr_ctrl_2

description: control PMNs

source_name: polymorphonuclear leukocytes, 6hr, control, replicate 2


title: aP2Cre-derived tumor mouse 68

description:
Gene expression data from tumors derived from aP2-expressing cells
as68


title: aP2Cre-derived tumor mouse 89

description:
Gene expression data from tumors derived from aP2-expressing cells
as89


title: aP2Cre-derived tumor mouse 64

description:
Gene expression data from tumors derived from aP2-expressing cells
as64


title: Testis Stage III FSH 66

value: FSH 500 ng/mL


title: PMN_6hr_ctrl_1

description: control PMNs

source_name: polymorphonuclear leukocytes, 6hr, control, replicate 1


title: aP2Cre-derived tumor mouse 90

description:
Gene expression data from tumors derived from aP2-expressing cells
as90


title: PMN_3hr_LVS_4

description: test PMNs

source_name: polymorphonuclear leukocytes, 3hr, LVS-treated, replicate 4

value: 3 hr


title: normal muscle control, sternocleidomastoid 3

description:
Gene expression data from normal skeletal muscle
scm3

source_name: normal muscle

value: sternocleidomastoid


title: aP2Cre-derived tumor mouse 65

description:
Gene expression data from tumors derived from aP2-expressing cells
as65


title: aP2Cre-derived tumor mouse 140

description:
Gene expression data from tumors derived from aP2-expressing cells
tumor3


title: normal muscle control, sternocleidomastoid 1

description:
Gene expression data from normal skeletal muscle
scm1


title: PMN_3hr_LVS_1

description: test PMNs

source_name: polymorphonuclear leukocytes, 3hr, LVS-treated, replicate 1


title: Testis Stage III Ctrl 60


title: HCV_p10 [Affymetrix]

description: Human PBMC collected from whole blood of patients chronically infected with HCV, before initiation of therapy

hyb_protocol: Following fragmentation, 15 microg of cRNA were mixed with spike controls and 2/3 was hybridized for 17 hr at 45C on GeneChip Human Genome 133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station per manufacturer's instructions.

scan_protocol: The microarrays were scanned using a dedicated Model 3000 scanner controlled by GCOS software.

data_processing: Microarray data was normalized using the GCRMA package in bioconductor. After normalization, Principle Component Analysis (PCA) was used to identify major patterns in the data, which revealed that the HCV samples were split into two groups based on the sample preparation time. Batch correction techniques were applied to remove these effects, and the data then separated into two distinct groups representing the healthy and HCV samples.

source_name: Human PBMC collected from whole blood

label_protocol: Preparation of cDNA, cRNA, and labeling were carried out according to the protocols recommended by Affymetrix in the GeneChip® Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA)

extract_protocol: Whole blood was collected from a group of 10 patients who were infected with genotype 1 hepatitis C, before initiation of treatment at the Indiana University School of Medicine. Control blood samples were harvested from healthy student volunteers. Peripheral blood mononuclear cells (PBMCs) were isolated from the whole blood samples of the cohort using centrifugation through a 10-ml Ficoll-Hypaque gradient (Amersham/Pharmacia, Piscataway, NJ), and RNA was isolated within a few hours.

value: PBMC

value: HCV


title: HCV_p09 [Affymetrix]


title: HCV_p07 [Affymetrix]


title: HCV_p06 [Affymetrix]


title: Testis Stage III FSH 61


title: Testis Stage I-II Ctrl 21


title: PMN_3hr_LVS_2

description: test PMNs

source_name: polymorphonuclear leukocytes, 3hr, LVS-treated, replicate 2


title: normal muscle control, sternocleidomastoid 2

description:
Gene expression data from normal skeletal muscle
scm2


title: aP2Cre-derived tumor mouse 135

description:
Gene expression data from tumors derived from aP2-expressing cells
tumor2


title: PMN_3hr_LVS_3

description: test PMNs

source_name: polymorphonuclear leukocytes, 3hr, LVS-treated, replicate 3


title: aP2Cre-derived tumor mouse 128

description:
Gene expression data from tumors derived from aP2-expressing cells
tumor1


title: HCV_p04 [Affymetrix]


title: PMN_3hr_ctrl_4

description: control PMNs

source_name: polymorphonuclear leukocytes, 3hr, control, replicate 4


title: HCV_p03 [Affymetrix]


title: Testis Stage I-II LH 35

source_name: Whole testis


title: HCV_p05 [Affymetrix]


title: Testis Stage I-II Ctrl 20


title: PMN_3hr_ctrl_3

description: control PMNs

source_name: polymorphonuclear leukocytes, 3hr, control, replicate 3


title: HCV_p01 [Affymetrix]


title: PMN_3hr_ctrl_2

description: control PMNs

source_name: polymorphonuclear leukocytes, 3hr, control, replicate 2


title: PMN_3hr_ctrl_1

description: control PMNs

source_name: polymorphonuclear leukocytes, 3hr, control, replicate 1


title: Healthy_p08_OUTLIER [Affymetrix]

description: Human PBMC collected from whole blood of healthy volunteers

value: Healthy


title: Testis Stage III T0-6

value: No culture

value: 0 hour


title: Testis Stage III FSH 62


title: Testis Stage I-II T0-1


title: Testis Stage I-II Ctrl 22


title: Healthy_p06 [Affymetrix]


title: Healthy_p05 [Affymetrix]


title: PMN_0hr_LVS_3

description: test PMNs

source_name: polymorphonuclear leukocytes, 0hr, LVS-treated, replicate 3

value: polymorphonuclear leukocytes

value: 0 hr


title: PMN_0hr_LVS_2

description: test PMNs

source_name: polymorphonuclear leukocytes, 0hr, LVS-treated, replicate 2


title: PMN_0hr_LVS_1

description: test PMNs

source_name: polymorphonuclear leukocytes, 0hr, LVS-treated, replicate 1


title: HCV_p02 [Affymetrix]


title: Healthy_p07_OUTLIER [Affymetrix]


title: Healthy_p01 [Affymetrix]


title: Testis Stage I-II FSH 27

value: Stage I-II

value: 96 hours


title: Testis Stage I-II T0-3

value: testis


title: PMN_0hr_ctrl_4

description: control PMNs

source_name: polymorphonuclear leukocytes, 0hr, control, replicate 4


title: PMN_0hr_ctrl_3

description: control PMNs

source_name: polymorphonuclear leukocytes, 0hr, control, replicate 3


title: PMN_0hr_ctrl_2

description: control PMNs

source_name: polymorphonuclear leukocytes, 0hr, control, replicate 2


title: Healthy_p03 [Affymetrix]


title: Testis Stage III Ctrl 59

value: Stage III


title: Healthy_p02 [Affymetrix]


title: Healthy_p04 [Affymetrix]


title: PMN_0hr_LVS_4

description: test PMNs

source_name: polymorphonuclear leukocytes, 0hr, LVS-treated, replicate 4

value: test PMNs


title: Testis Stage III LH 70

value: LH 500 ng/mL


title: Cabinet versus Field 2005 B (Dye reverse)

first: Elizabeth

middle: A

last: Weretilnyk

state: Ontario

address: 1280 Main Street West

department: Biology

country: Canada

institute: McMaster University

description:
Three biological replicates with dye swap as technical replicates were examined for all experimental conditions
F2005-B2

hyb_protocol: Microarrays were prehybridized, hybridized and washed according to the protocol provided by the MicroArray Lab at Biotechnology Research Institute, Montreal. (http://www.bri.nrc.gc.ca/pdf/microarray_Direct_Incorporation_Labeling%20_Protocol_e.doc). An extra step of dipping the slides in isopropanol was performed prior to air-drying the slides.

scan_protocol: ScanArray confocal scanning system and QuantArray data acquisition software (Perkin Elmer, Boston, MA) were used according to the manufacturer’s instructions to capture the data.

data_processing: Data transformed using Joint Lowess method using the maanova (v0.98.8) Bioconductor package..

organism: Eutrema

label_protocol: For field samples mRNA was first amplified using the Ambion MessageAmp aRNA Amplification kit (Applied Biosystems) and the cDNA was primed with a random primer mix (Invitrogen).  A single round of RNA amplification was carried out according to the manufacturer’s protocol using 1 µg of total RNA.  For cabinet control samples mRNA was not amplified prior to cDNA synthesis. Aminoally-labeling of cDNA was done by coupling of the aminoallyl groups to either Cyanine 3 or 5 (Cy 3/Cy5) fluorescent molecules using protocol from the Institute of Genome Research (TIGR; http://www.tigr.org/tdb/microarray/protocolsTIGR.shtml).

growth_protocol: Cabinet plants of the Yukon ecotype of Thellungiella salsuginea (Pall.) O.E. Schulz (Al-Shehbaz et al., 1999; Cody, 2000) were grown in controlled environments with an irradiance of 250 mmol photons m-2 s-1; a 21 h daylength, and a day/night temperature regime of 22/10°C. Field soil and weather conditions are reported in the associated publication.

extract_protocol: Total RNA was extracted from cauline leaves using method as described by Danyluk and Sarhan (1990).

treatment_protocol: No treatments were applied to the control chamber plants. Plants in the field were exposed to ambient conditons.

tag: ecotype

value: Yukon

value: Cauline leaves from 12 wk-old chamber-grown plants

source_name: natural habitat_Field_2005

value: Cauline leaves from individual plants collected from Yukon habitat

tag: harvest year


title: Cabinet versus Field 2005 A

description:
Three biological replicates with dye swap as technical replicates were examined for all experimental conditions
F2005-A1


title: Testis Stage I-II FSH 29

value: FSH 500 ng/mL


title: Testis Stage I-II FSH 25


title: Cabinet versus Field 2005 A (Dye reverse)

description:
Three biological replicates with dye swap as technical replicates were examined for all experimental conditions
F2005-A2


title: Cabinet versus Field 2005 B

description:
Three biological replicates with dye swap as technical replicates were examined for all experimental conditions
F2005-B1


title: Cabinet versus Field 2005 C

description:
Three biological replicates with dye swap as technical replicates were examined for all experimental conditions
F2005-C1


title: Cabinet versus Field 2005 C (Dye reverse)

description:
Three biological replicates with dye swap as technical replicates were examined for all experimental conditions
F2005-C2


title: Testis Stage I-II FSH 28


title: Testis Stage I-II Ctrl 23

value: Control


title: Testis Stage I-II FSH 26


title: PMN_0hr_ctrl_1

description: control PMNs

source_name: polymorphonuclear leukocytes, 0hr, control, replicate 1

tag: cell type

value: control PMNs


title: Testis Stage I-II T0-2


title: Cabinet versus Field 2003 C

description:
Three biological replicates with dye swap as technical replicates were examined for all experimental conditions
F2003-C1

source_name: natural habitat_Field_2003


title: Cabinet versus Field 2003 B

description:
Three biological replicates with dye swap as technical replicates were examined for all experimental conditions
F2003-B1


title: Cabinet versus Field 2003 A (Dye reverse)

description:
Three biological replicates with dye swap as technical replicates were examined for all experimental conditions
F2003-A2


title: Cabinet versus Field 2003 B (Dye reverse)

description:
Three biological replicates with dye swap as technical replicates were examined for all experimental conditions
F2003-B2


title: Cabinet versus Field 2003 A

description:
Three biological replicates with dye swap as technical replicates were examined for all experimental conditions
F2003-A1

data_processing: Data transformed using Joint Lowess method using the maanova (v0.98.8) Bioconductor package.


title: Slide 186129

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 3

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of rokA mutant strain over the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: Net intensity (tr.mean) {A}

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown GM17 medium and harvested at OD600 of 0.25.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

value: rokA mutant

source_name: Net intensity (tr.mean) {B}

value: Wild type


title: Slide 185515

description: Sample 2


title: Slide 185499

description: Sample 1


title: Root non-mycorrhized rep2

city: MONTPELLIER CDX 5

first: Valérie

last: HOCHER

address: 911 av. Agropolis BP64501

department: DIADE

institute: IRD

description: Gene expression in non-inoculated roots cultivated without phophate and sampled 4 weeks regarding inoculation time (control)

hyb_protocol: The Agilent Hybridization Kit (catalog no. 5188-5242) was used . 600 ng of the labeled sample RNA was used for hybridization according to the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol. The hybridization was performed for 17 h at 65°C. Slides were them washed for 1 min at room temperature in Wash Solution 1 (catalog no. 5188-5325) and 1 min at room temperature in Wash Solution 2, prewarmed to 37°C (catalog no. 5188-5326).

scan_protocol: Scanning  was performed with the Agilent scanner (G2505B) using default parameters for 8 x 15 K formats and the one-color protocol. (scan area 61 X 21.6 mm; scan resolution 5µm; single pass; dye channel is set to green and green PMT is set to 100%).

data_processing: Data were extracted with Feature Extraction 9.1 software (Agilent Technologies) according to the 1-color Agilent protocol (GE1-v5_95_Feb protocol). This software reads and processes microarray image files to prepare them for analysis. Feature Extraction automatically assigns a grid template and a protocol, based on the barcode of the slide. It determines feature intensities, rejects outliers and calculates statistical confidence intervals. Genespring sofware was then used for data processing. Normalization was done as follows: data transformation (Set measurements less than 5.0 to 5.0), per chip : normalized to 50th percentile (probes with presence flags only), per gene : normalized to median. Data were then filtered using flag parameter (Flags (Absent, Marginal, Present) : All control -> Absent, Saturated spot -> Marginal, Spot not uniform -> Marginal, Spot not positive and not significant -> Absent, Spot not above background -> Absent, Population outlier -> Marginal) and each probe must be present for 2/3 of the tested conditions.

organism: Casuarina glauca

source_name: Root, non-inoculated (reference time)

label_protocol: Five hundred nanograms of RNA and Agilent One-Color RNA Spike-In RNA were labeled with the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color according to the manufacturer's instructions as follows: 1.2 µl of T7 Promoter Primer was added to 500 ng of RNA and 5 µl of spike-in control (in a 11.5-µl volume) and denatured at 65°C. First-Strand Buffer (to 1x), DTT (to 10 mM), dNTP (to 0.5 mM), Moloney murine leukemia virus (MMLV) reverse transcriptase (1 µl of stock provided in the kit in a 20-µl reaction), and RNaseOut (0.5 µl of stock provided in the kit in a 20-µl reaction) were added. The cDNA was synthesized during the following incubation step (2 h at 40°C). After 10-min denaturation at 65°C and the addition of Cy3-labeled CTP (to 0.3 mM), Transcription Buffer (to 1x), DTT (to 10 mM), NTP (8 µl of stock provided in the kit in a 80-µl reaction), RNaseOUT (0.5 µl of stock provided in the kit in a 80-µl reaction), inorganic phosphatase (0.6 µl of stock provided in the kit in a 80-µl reaction), and T7 RNA polymerase (0.8 µl of stock provided in the kit in a 80-µl reaction), the synthesis of the fluorescent labeled cRNA was performed during the second incubation step (2 h at 40°C). The labeled cRNA was purified with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol.

growth_protocol: Plantlets were grown in a hydroponics system containg a BD medium for 3 weeks. 22 plants were transferred to pots containing a sterile sand:soil mixture (95:5) and spores from G. intraradices isolated from root organ cultures (1 plate for 10 plants) and watered with a modified Hoagland solution containing 10uM phosphate. 16 control plants were transferred to pots containing a sterile sand:soil mixture (9:1) without any inoculum and watered with a modified Hoagland solution containing 10uM phosphate.

extract_protocol: Total RNA was purified from roots by ultracentrifugation  (Chirgwin et al., 1979).Residual DNA was removed from RNA samples using the Turbo DNA free kit (Ambion, USA), quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific, Courtaboeuf, France) and qualitatively assessed using a Bioanalyser 2100 (Agilent p/n G2938A) according to the manufacturer’s instructions (Agilent, Santa Clara, CA, USA).

treatment_protocol: The starting point of the experiment was 8 weeks after  tranfer in soil:sand mixture. Roots (control and inoculated) were sampled 8 weeks after transfer and all samples were frozen in liquid nitrogen and conserved at -80°C before RNA extraction.  The presence of AM structures was checked on a root sample of each plant.

value: Root

tag: culture condition

value: Cultivated without phosphate

value: No inoculation

value: 4 weeks post inoculation


title: Cabinet versus Field 2003 C (Dye reverse)

description:
Three biological replicates with dye swap as technical replicates were examined for all experimental conditions
F2003-C2


title: Root mycorrhized rep3

description: Gene expression in mycorrhized roots sampled 4 weeks  after inoculation with the fungus Glomus on plants cultivated without phosphate

source_name: Root mycorrhized inoculated, 4 weeks post inoculation with fungus

value: Inoculated with symbiotic Glomus fungus


title: Root non-mycorrhized rep3


title: Root non-mycorrhized rep1


title: Root mycorrhized rep2


title: Root mycorrhized rep1


title: Wildtype strain, rep1

status: Public on Oct 21 2012

city: Taipei

first: Chi

last: Yang

address: No.155, Sec.2, Linong Street

department: Institute of BioMedical Informatics

country: Taiwan

institute: National Yang-Ming University

description: Gene expression data from E. coli MG1655 wildtype under phosphate starvation condition

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit was used and its protocol was applied. (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).

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

data_processing: The data were normalized by RMA method and then analyzed by limma package to identify differentially expressed genes (bioconductor).

organism: Escherichia coli

source_name: E. coli MG1655 wildtype strain grows under phosphate starvation condition

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip® Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Cells grew in MOPS minimal medium with 0.4% glucose and 0.2 mM K2HPO4 and harvested at the OD600 value of 1.0.

tag: genotype/variation

value: wild type


title: PhoB knock-out strain, rep2

description: Gene expression data from E. coli MG1655 PhoB knock-out strain under phosphate starvation condition

source_name: E. coli MG1655 PhoB knock-out strain grows under phosphate starvation condition

value: PhoB knock-out


title: PhoB knock-out strain, rep1


title: wildtype strain, rep2


title: 4N biological repeat II

city: La Jolla

first: Ofer

last: Shoshani

state: California

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

description: Tetraploid MSC cell line

hyb_protocol: Affymetrix standard protocol.

scan_protocol: Affymetrix scanner.

data_processing: Data was analyzed using Partek Genomics Suite software.  Pre-background Ajustment: Adjust for GC Content. Background Correction: RMA Background Correction. Normalization: Quantile Normalization. Probeset Summarization: Median Polish.

source_name: Tetraploid MSC

label_protocol: Affymetrix standard protocol.

growth_protocol: Mesenchymal cells were extacted from mouse bone marow and grown in Stem Cell media (Stem Cells Tech.).

extract_protocol: TRI reagent total RNA extraction according to manufacturer's protocol.

treatment_protocol: MSCs were classified based on DNA content using propidium iodide staining and FACS analysis, and validated using SKY analysis.

value: Mesenchymal stromal cells (MSCs)

tag: ploidy

value: Tetraploid


title: 2N biological repeat I

description: Diploid MSC clone

source_name: Diploid MSC

value: Diploid


title: 2N biological repeat III

description: Diploid primary MSC


title: 2N biological repeat II

description: Diploid primary MSC


title: 4N biological repeat III

description: Artificial tetraploid MSC clone


title: Rice seedlings roots_As(V) Replicate 3

city: Tainan

first: Tsai-Lien

last: Huang

state: Taiwan

address: No.1, University Raod,

department: Life Sciences

institute: National Cheng Kung University

description: Biological replicate 3 of 3. Rice seedling roots with or without 25 μM-treated As(V)

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Rice Oligo 4×44K Microarray (Agilent Technologies, USA) at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5. Scanned images are analyzed by Feature extraction software 9.5.3 (Agilent Technologies, USA),

data_processing: An image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.

organism: Oryza sativa

source_name: Roots of rice seedlings were exposed to 25 μM As(V)

label_protocol: 0.5 μg of total RNA was amplified by a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP or Cy5-CTP (CyDye, PerkinElmer, USA) during the in vitro transcription process rice roots after As(V) treatment RNA was labeled by Cy5 and RNA from control RNA was labeled by Cy3. 0.825 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer (Agilent Technologies, USA) at 60oC for 30 minutes.

growth_protocol: 5-day-old seedlings

extract_protocol: Total RNA were extracted using QIAGEN RNeasy kit follwed by DNAse treatment. The RNA samples were further purified and concentrated by RNeasy MinElute Cleanup.

treatment_protocol: Control and rice seedlings were exposed to 25 μM As(V)

tag: cultivar

tag: age

value: 5 day

value: 25 μM As(V)

value: roots

source_name: Rice seedlings roots were exposed to water

value: water


title: Rice seedlings roots_As(V) Replicate 1

description: Biological replicate 1 of 3. Rice seedling roots with or without 25 μM-treated As(V)

tag: treatment


title: Rice seedlings roots_As(V) Replicate 2

description: Biological replicate 2 of 3. Rice seedling roots with or without 25 μM-treated As(V)


title: HSALR EDL, sample7

city: Cleveland

first: Erik

last: van Lunteren

state: OH

address: 10701 East Boulevard

department: Pulmonary 111J(W)

institute: Cleveland VA Medical Center

description: gene expression data from HSALR EDL

hyb_protocol: 15 ug of biotin-labeled cRNA was used in a 300 ul hybridization cocktail which included spiked transcript controls.  200 ul of cocktail was loaded onto Affymetrix MOE430 2.0 microarrays (Santa Clara, CA) and hybridized for 16 hr at 45o C with agitation.  Standard post-hybridization washes and double-stain protocols used an Affymetrix GeneChip Fluidics Station 400.

scan_protocol: Arrays were scanned using a Hewlett Packard Gene Array scanner.

data_processing: Affymetrix GCOS version 1.4 software

source_name: HSALR mouse EDL

label_protocol: 8 ug of RNA was used in a reverse transcription reaction (SuperScript II; Life Technologies, Rockville, MD) to generate first strand cDNA.  After second strand synthesis, double strand cDNA was used in an in vitro transcription reaction to generate biotinylated cRNA, which was purified and fragmented.

extract_protocol: Total RNA was extracted using Trizol (GibcoBRL, Rockville, MD), and the RNA pellets were resuspended at 1 ug RNA/ul DEPC-treated water.  This was followed by a cleanup protocol with a Qiagen (Valencia, CA) RNeasy Total RNA mini kit.

value: 19 weeks

value: FVB

value: transgenic HSALR line 20 b


title: HSALR EDL, sample8

description: gene expression data from HSALR EDL


title: adipose tissue at CT18, Ad-Bmal1-/- mouse, biological rep2

city: Philadelphia

first: Georgios

middle: K

last: Paschos

state: PA

address: 10-102 Translational Research Center, 3400 Civic Center Boulevard, Building 421

department: Pharmacology

institute: University of Pennsylvania, School of Medicine

hyb_protocol: 2.25 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were processed and normalized with RMA.

source_name: inguinal adipose tissue collected at CT18 from Ad-Bmal1-/- mouse

label_protocol: Fragmented and biotinylated single-stranded cDNA were prepared with the Encore Biotin Module from 50 ng total RNA amplified by the Ovation Pico WTA System (WT-Ovation Exon Module was used for generation of sense transcript cDNA) (NuGEN, 2011).

growth_protocol: Mice were crossed to the C57BL/6J background for at least 6 generations. Mice were maintained in a regular chow diet.

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

treatment_protocol: Mice were brought to constant darkness 36 hours prior to the initiation of tissue collection. Tissues were isolated at CT0, CT6, CT12, CT18 where CT0 the beginning of the subjective day. Each group of mice was fasted for 24 hours before euthanized for tissue collection.

tag: strain background

value: aP2-Cre+/- Bmal1fx/fx

value: Adipocyte-specific Bmal1 KO (Ad-Bmal1-/-)

tag: circadian time (ct)

value: inguinal adipose tissue


title: adipose tissue at CT18, control mouse, biological rep2

source_name: inguinal adipose tissue collected at CT18 from control mouse


title: adipose tissue at CT18, control mouse, biological rep3


title: adipose tissue at CT18, Ad-Bmal1-/- mouse, biological rep3


title: HSALR EDL, sample6

description: gene expression data from HSALR EDL


title: HSALR EDL, sample3

description: gene expression data from HSALR EDL


title: HSALR EDL, sample4

description: gene expression data from HSALR EDL


title: HSALR EDL, sample9

description: gene expression data from HSALR EDL


title: adipose tissue at CT18, control mouse, biological rep1


title: HCV_p08 [Affymetrix]

description: Human PBMC collected from whole blood of patients chronically infected with HCV, before initiation of therapy

source_name: Human PBMC collected from whole blood

tag: cell

value: PBMC

tag: infection

value: HCV


title: 4N biological repeat I

description: Tetraploid primary MSC


title: HSALR EDL, sample1

description: gene expression data from HSALR EDL

tag: strain


title: HSALR EDL, sample10

description: gene expression data from HSALR EDL


title: HSALR EDL, sample5

description: gene expression data from HSALR EDL


title: adipose tissue at CT12, control mouse, biological rep3

source_name: inguinal adipose tissue collected at CT12 from control mouse


title: Wild type EDL, sample8

description: gene expression data from normal wild-type EDL

source_name: Wild type EDL muscle

value: wild type


title: Wild type EDL, sample9


title: adipose tissue at CT12, control mouse, biological rep2


title: HSALR EDL, sample2

description: gene expression data from HSALR EDL


title: Wild type EDL, sample7


title: adipose tissue at CT12, Ad-Bmal1-/- mouse, biological rep1

source_name: inguinal adipose tissue collected at CT12 from Ad-Bmal1-/- mouse


title: Wild type EDL, sample4


title: Wild type EDL, sample6


title: adipose tissue at CT6, control mouse, biological rep3

source_name: inguinal adipose tissue collected at CT6 from control mouse


title: adipose tissue at CT6, Ad-Bmal1-/- mouse, biological rep1

source_name: inguinal adipose tissue collected at CT6 from Ad-Bmal1-/- mouse


title: Wild type EDL, sample5


title: adipose tissue at CT0, control mouse, biological rep3

source_name: inguinal adipose tissue collected at CT0 from control mouse


title: adipose tissue at CT0, Ad-Bmal1-/- mouse, biological rep1

source_name: inguinal adipose tissue collected at CT0 from Ad-Bmal1-/- mouse


title: adipose tissue at CT18, Ad-Bmal1-/- mouse, biological rep1


title: adipose tissue at CT6, Ad-Bmal1-/- mouse, biological rep3


title: adipose tissue at CT0, control mouse, biological rep2


title: adipose tissue at CT12, control mouse, biological rep1


title: adipose tissue at CT6, Ad-Bmal1-/- mouse, biological rep2


title: adipose tissue at CT0, Ad-Bmal1-/- mouse, biological rep2


title: adipose tissue at CT12, Ad-Bmal1-/- mouse, biological rep2


title: adipose tissue at CT6, control mouse, biological rep2


title: adipose tissue at CT0, Ad-Bmal1-/- mouse, biological rep3


title: adipose tissue at CT6, control mouse, biological rep1


title: Wild type EDL, sample3


title: Wild type EDL, sample1


title: PhoB_ChIP, rep1

description: Comparison of MG1655_PhoB_FLAG/MG1655

hyb_protocol: The instructions of the NimbleChipTM Arrays User Guide-ChIP-chip anaysis (version 2.0) for hybridization were followed and the hybrization process was done by the NimbleGen hybridization system.

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

data_processing: The R package, Ringo, was used to read the pair files and the limma package for within- and between-array normalization. ChIP-chip data were bi-weighted scaled within each array and aquantile normalized between arrays.

source_name: ChIP DNA from MG1655_PhoB_FLAG

label_protocol: The instructions of the NimbleChipTM Arrays User Guide-ChIP-chip anaysis (version 2.0) for Cy5 and Cy3 labeling were followed.

extract_protocol: Cultures were grown to the OD600 value of 1.0 and treated with 1% formaldehyde for 10 min. To quench the reaction, glycine was added at the final concentration of 0.125 M for 5 min. Cells were washed twice with lysis buffer (10 mM Tris-HCl (pH 7.4), 0.1 M NaCl, 1 mM EDTA and 0.5% Tween-20). The washed cells were then lysed with the lysis buffer containing 8 KU/ml lysozyme, 1 mM PMSF and protease inhibitor cocktail (Sigma) for 30 min at 4 ℃. The lysates were sonicated by a sonicator (Bioruptor) and this sonication resulted in the size of DNA ranged from 100 bps to 1000 bps with the average size of 500 bps. After sonication, the lysates were centrifuged at 12,000 g for 20 min at 4 ℃ and the resulting supernatant was used for immunoprecipitation. Before immunoprecipitation, the magnetic beads coated with Dynabeads Protein G (Invitrogen) were pre-incubated with 0.05 mg/ml anti-FLAG antibody (Sigma) and the lysates were also pre-cleared by incubating with the beads only. To immunoprecipitate the PhoB-FLAG-DNA complex, beads pre-incubated with antibody were added in both lysates of MG1655_PhoB_FLAG and MG1655 strains at 4 ℃ overnight. The beads were washed once with IP buffer (10 mM Tris-HCl (pH 7.4), 0.1 M NaCl, 1 mM EDTA, and 0.05% [v/v] Tween-20 and 1 mM fresh PMSF), twice with ChIP wash buffer I (10 mM Tris HCl (pH 7.4), 300 mM NaCl, 1 mM EDTA, 0.1% Tween-20 and 1 mM fresh PMSF), three times with ChIP wash buffer II (10 mM Tris-HCl (pH 7.4), 500 mM NaCl, 1 mM EDTA, 0.1% [v/v] Tween-20 and 1 mM fresh PMSF), once with ChIP wash buffer III (10 mM Tris-HCl (pH 7.4), 250 mM LiCl, 1 mM EDTA, 0.1% [v/v] Tween-20 and 1 mM fresh PMSF) and once with TE buffer (10 mM Tris-HCl (pH 7.4) and 1 mM EDTA). After removing the TE buffer, beads were incubated with elution buffer (50 mM Tris-HCl (pH 7.4), 10 mM EDTA and 1% SDS) at 65 ℃ for 15 min twice and then the resulting eluted solutions combined. After incubating with the final concentration of 10.5 U/ml proteinase K (Sigma) at 42 ℃ for 2 hours, the reverse cross-link procedure was performed by incubating at 65 ℃ overnight. Samples were then treated with the final concentration of 26 μg/ml RNase A (Sigma). The PCR purification kit (Qiagen) was used to purify DNA from the RNase A-treated samples.

source_name: ChIP DNA from MG1655 wild type strain


title: PhoB_ChIP, rep3

description: Comparison of MG1655_PhoB_FLAG/MG1655


title: PhoB_ChIP, rep2

description: Comparison of MG1655_PhoB_FLAG/MG1655


title: BT474_80%Tumor

status: Public on Oct 20 2012

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

institute: Vrije Universiteit Medical Center

hyb_protocol: Standard NimbleGen protocol.

scan_protocol: Standard NimbleGen protocol.

data_processing: Median normalization in R/Bioconductor.

source_name: BT474 80% tumor diluted with normal DNA

label_protocol: DNA labeling protocol according to Enzo Life Sciences.

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al., J Pathol. 2007 Jan;211(1):45-51 (PMID 17117405).

tag: cell line

value: breast cancer cells

tag: percent bt474

source_name: Reference DNA

tag: sample type

value: pool of 19 healthy individuals


title: BT474_60%Tumor

source_name: BT474 60% tumor diluted with normal DNA


title: BT474_50%Tumor

source_name: BT474 50% tumor diluted with normal DNA


title: soil 10 day  incubation at WHC rep3

city: Heverle

first: Tekle Tafese

last: Fida

address: Kastelpark Arenberg 220

department: Earth and environmental Science

country: Belgium

institute: KU Leuven

description: gene expression in after 10 days of incubation in soil

hyb_protocol: Sixty nanograms of labeled cDNA with an incorporation efficiency of cyanine-3-labeled dCTP between 4-5% were used for microarray analysis. The cDNA was hybridized with the array for 17 h at 65oC, washed, and scanned according to the one-color microarray-based gene expression analysis protocol of Agilent Technologies

scan_protocol: The Agilent Feature Extraction software package (version 9.5.3; Agilent Technologies) was used to extract the hybridization signal intensities from the images scanned according to the one-color microarray-based gene expression analysis protocol of Agilent Technologies

data_processing: Normalization of the signal intensities (Quantile normalization) and analysis of the data were done using the Genespring GX software package (version 11, Agilent technologies). To test for significantly differentially expressed genes, Welch’s t- test with unequal variances was first used to calculate p-values. The Benjamini and Hochberg procedure was then used to correct the p-vales for multiple hypothesis testing and convert the p-vales into false discovery rates (FDRs)

organism: Sphingomonas sp. LH128

source_name: 12 day incubation in soil at WHC_replicate1

label_protocol: The nucleic acids were labeled with Cyanin-3-labeled dCTP while reverse transcribing the RNA to cDNA using a one-color gene expression protocol of Agilent Technologies with some modifications. Briefly, the reaction was performed in 25 µl containing 4 µg of RNA, 10 mM of each dATP, dGTP and dTTP, 5 mM of unlabeled dCTP, 200 units of Superscript III reverse transcriptase (Invitrogen), 625 ng of random hexanucleotide primer (Promega), and 1.25 mM Cyanin-3-labeled dCTP (PerkinElmer). Reactions were performed by heating at 55oC for 2 h followed by 70oC for 10 min. Residual RNA was removed by alkaline hydrolysis using 100 mM of NaOH and heating at 65oC for 20 min followed by neutralization using 100 mM HCl and 300 mM sodium acetate (pH 5.2). The labeled cDNA was purified with a MiniElute PCR purification kit (Qiagen) to remove unincorporated nucleotides and salts. The quality of the labeled cDNA and the efficiency of incorporation of cyanine-3-labeled dCTP were determined using the microarray function of the NanoDrop spectrophotometer

growth_protocol: Cells were pregrown in phosphate buffered minimal medium containg 2 g per liter glucos

extract_protocol: Total RNA was extracted from triplicate samples of 2 g of soil inoculated with about 5 x 109 cells per g after 4 h and 10 days of incubation. The RNA PowerSoil Total RNA Isolation Kit (Mo Bio, Benelux, BV) was used for RNA extraction according to the manufacturer’s instructions, with minor modifications that were needed for obtaining RNA suitable for microarray analysis. Briefly, 10 μl of β-mercaptoethanol per ml of bead solution was added to the soil in the step before the cell lysis step with SR1 solution in order to avoid degradation of RNA. The samples were incubated for 30 min at room temperature instead of at 4oC after addition of the SR4 solution. The RNA was finally eluted with 100 μl of SR7 solution. In addition, total RNA was extracted from the inoculum suspension (control sample) from a volume that was identical to this added to the soil, using the RNeasy Protect Bacteria Mini Kit (Qiagen, Benelux, BV) according to the manufacturer’s instructions. Subsequent purification steps were performed to remove substances, such as humic acid, that could be co-extracted with RNA  and that affects microarray analysis. this involved the use of of illustra MicroSpin™ S-400 as well as involved purification and precipitation by using sodium acetate and ethanol precipitation method.

treatment_protocol: Sphingmonas strain LH128 was precultured in minimal medium containing 2 g l-1 of glucose till an OD600 of 0.5. Five ml of cells was washed twice with 0.01M MgSO4 with intermittent centrifugation at 5000 x g for 10 min. The cells were resuspended in 0.01M MgSO4 to appropriate cell densities and added to 2 g of soil (containing phenanthrene at concentration of 500 mg l-1) as a volume of 160 μl per tube. The samples were homogenized by gentle vortexing and incubated at 20°C for 4 h or 10 days. At each time point, triplicate tubes were sacrificed for RNA extraction and other physiological examinations.

value: phenanthrene contaminated soil inoculated

tag: time


title: BT474_25%Tumor

source_name: BT474 25% tumor diluted with normal DNA


title: BT474_70%Tumor

source_name: BT474 70% tumor diluted with normal DNA


title: BT474_30%Tumor

source_name: BT474 30% tumor diluted with normal DNA


title: BT474_40%Tumor

source_name: BT474 40% tumor diluted with normal DNA


title: BT474_85%Tumor

source_name: BT474 85% tumor diluted with normal DNA


title: BT474_75%Tumor

source_name: BT474 75% tumor diluted with normal DNA


title: BT474_12.5%Tumor

source_name: BT474 12.5% tumor diluted with normal DNA


title: 6071838104_E

city: New York

first: Camelia

last: Iancu-Rubin

state: NY

address: One Gustave Levy Place Box 1079

department: Hematology and Medical Oncology

institute: Mount Sinai School of Medicine

description: replicate 1 (RNA combined from two biological replicates)

data_processing: The data were normalized using quantile normalisation with Illumina GenomeStudio software

extract_protocol: RNA was extracted with Qiagen Rneasy  mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: SC from donor#77 treated with 100 micrograms/ml ACE-011

value: stromal

tag: days in culture

value: 7 days


title: 6071838104_D

treatment_protocol: SC from donor#77 untreated

tag: cell type


title: 6071838104_H

description: replicate 2 (RNA combined from two biological replicates)


title: BT474_100%Tumor

source_name: BT474 100% tumor not diluted


title: 6071838104_G


title: BT474_6.25%Tumor

source_name: BT474 6.25% tumor diluted with normal DNA


title: 6071838104_K

treatment_protocol: SC from donor#97 treated with 100 micrograms/ml ACE-011


title: BT474_90%Tumor

source_name: BT474 90% tumor diluted with normal DNA


title: 6071838104_F

treatment_protocol: SC from donor#97 untreated


title: 6071838104_C

source_name: HPC-T

treatment_protocol: erythroid cultures differentiated from bone marrow CD34+ cells in cultures containing conditioned media from ACE-011 treated stromal cells

value: primary erythroid


title: 6071838104_J


title: BT474_50%Tumor_replicate2


title: 6071838104_I


title: soil 10 day  incubation at WHC rep1

source_name: 10 day incubation in soil at WHC_replicate1


title: soil 10 day  incubation at WHC rep2

source_name: 11 day incubation in soil at WHC_replicate1


title: adipose tissue at CT12, Ad-Bmal1-/- mouse, biological rep3

source_name: inguinal adipose tissue collected at CT12 from Ad-Bmal1-/- mouse

tag: tissue


title: Initial inoculum rep2

description: gene expression in inoculum culture

source_name: control_inoculum_culture_ replicate2

value: culture control

value: control


title: 6071838104_B

source_name: HPC-UN

treatment_protocol: erythroid cultures differentiated from bone marrow CD34+ cells in cultures containing conditioned media from untreated stromal cells


title: soil 4h  incubation at WHC rep2

description: gene expression in after 4h of incubation in soil

source_name: 4h incubation in soil at WHC_replicate2

value: 4 h


title: Initial inoculum rep3

description: gene expression in inoculum culture

source_name: control_inoculum_culture_ replicate3


title: soil 4h  incubation at WHC rep3

source_name: 4h incubation in soil at WHC_replicate3


title: soil 4h  incubation at WHC rep1

source_name: 4h incubation in soil at WHC_replicate1


title: adipose tissue at CT0, control mouse, biological rep1

source_name: inguinal adipose tissue collected at CT0 from control mouse

tag: genotype/variation


title: Initial inoculum rep1

description: gene expression in inoculum culture

source_name: control_inoculum_culture_ replicate1


title: twin pair 17_lower IQ

city: Kobe-shi

first: Chihchieh

last: Yu

address: 7-5-1 kusunoki-cho, chuo-ku

country: Japan

institute: Kobe University

description:
twin 17B
expression profile from Twin Pair ID17, lower IQ twin

hyb_protocol: Following fragmentation, cRNA were hybridized for 17+/-1 hr at 45C on Human Genechip 1.0st arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) was used.

scan_protocol: Gene chips were scanned using Genechip Scanner 3000.

data_processing: The data were analysed using Partek Genomic Suite 6.5 (Agilent). We normalized the data according to the RMA algorithm.

label: Tdt

source_name: twin 17B_Lower_IQ

label_protocol: 300ng of total RNA was processed using Ambion WT expression Kit (Applied Biosystems) and the Affymetrix GeneChip WT Terminal Labeling Kit.

growth_protocol: B-lymphoblastoid cell lines were grown in a RPMI-1640 (WAKO) medium and supplemented with 10% FBS (Gibco) and antibiotics (Wako).

extract_protocol: total RNA was isolated using RNeasy Plus Mini Kit (Qiagen)

tag: twin pair id

tag: relative iq within twin pair

value: Lower

value: B-lymphoblastoid cell


title: twin pair 16_higher IQ

description:
twin 16A
expression profile from Twin Pair ID16, higher IQ twin

source_name: twin 16A_Higher_IQ

value: Higher


title: twin pair 15_higher IQ

description:
twin 15A
expression profile from Twin Pair ID15, higher IQ twin

source_name: twin 15A_Higher_IQ


title: twin pair 16_lower IQ

description:
twin 16B
expression profile from Twin Pair ID16, lower IQ twin

source_name: twin 16B_Lower_IQ


title: 6071838104_A

source_name: HPC

treatment_protocol: erythroid cultures differentiated from bone marrow CD34+ cells in standard conditions


title: twin pair 17_higher IQ

description:
twin 17A
expression profile from Twin Pair ID17, higher IQ twin

source_name: twin 17A_Higher_IQ


title: twin pair 15_lower IQ

description:
twin 15B
expression profile from Twin Pair ID15, lower IQ twin

source_name: twin 15B_Lower_IQ


title: BPMV empty vector - rep3

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description: treatment=BPMV empty vector rep 3 (May still include original submitter created erros/discrepancies)

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy soybean scanning protocol

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

organism: Glycine max

source_name: The top fully expanded trifoliolate leaves, petioles and stem segments. (treatment: BPMV empty vector)

label_protocol: Affymetrix one-cycle target labeling

extract_protocol: QIAGEN RNeasy Plant Mini Kit

tag: germplasm name

tag: development stage

value: leaf production ('PO:0007133')

tag: growth media

value: not specified

tag: transfection

value: BPMV empty vector

value: soybean rust


title: Twin Pair ID 17 B-A

description: twin pair ID 17 enriched in Lower IQ (compared to Higher IQ)

hyb_protocol: Labeled DNA targets were hybridized for 16 hrs at 45C on Human Promoter 1.0R arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400. GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) was used.

scan_protocol: Promoter chips were scanned using Genechip Scanner 3000.

data_processing: Data were converted to GCOS format and then normalized and analyzed with MAT software. Candidate regions sized around 600bp with p value less than 0.000001 were extracted. Annotation was done using R.

source_name: twin pair ID 17 B

label_protocol: After amplification using WGA2 kit, 7.5ug dsDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix).

extract_protocol: Genomic DNA was extracted from the blood samples using traditional methods. 1ug of gDNA was fragemeted and subjected to methylated DNA enrichment using MethylMiner Methlyated DNA Enrichment Kit (Invitrogen).

tag: twin a or twin b

value: B


title: Twin Pair ID 17 A-B

description: twin pair ID 17 enriched in Higher IQ (compared to Lower IQ)

source_name: twin pair ID 17 A

value: A


title: twin pair 13_higher IQ

description:
twin 13B
expression profile from Twin Pair ID13, higher IQ twin

source_name: twin 13B_Higher_IQ


title: twin pair 13_lower IQ

description:
twin 13A
expression profile from Twin Pair ID13, lower IQ twin

source_name: twin 13A_Lower_IQ


title: twin pair 14_lower IQ

description:
twin 14B
expression profile from Twin Pair ID14, lower IQ twin

source_name: twin 14B_Lower_IQ