title: CM rAd_rAd 91

description:
CM CD8+ T cells arising from rAd_rAd vaccination
4514990071_C


title: p53-, Myc+, rep2

status: Public on Aug 01 2013

type: RNA

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

country: USA

institute: Thomas Jefferson University

hyb_protocol: Arrays were hybridized with fragmented and biotin-labeled target (2.5 µg) in 110 µl of hybridization cocktail. Target denaturation was performed at 99oc for 2 min. and then 45oc for 5 min., followed by hybridization for 18 hrs. Arrays then were washed and stained using GeneChip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000, using Command Console Software.

data_processing: Raw intensity files from the Affymetrix Mouse Gene 1.0 ST GeneChip arrays were processed using Affymetrix Expression Console version 1.1.  Gene-level expression measurements were computed using the iterPLIER algorithm on the core probesets and exported with annotation release 32, dated June 23rd, 2011.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mammary epithelial cells, p53- Myc+

label_protocol: Labeling was performed by the WT-Ovation Pico RNA amplification system (NuGen Technologies, Inc.)

growth_protocol: Mammary epithelial cells were isolated from 8-week-old female mice and sub-cultured in DMEM/F12 media supplemented with 5% horse serum, 20ng/mL EGF, 10μg/ml insulin, 1ng/ml cholera toxin, 100μg/ml hydrocortisone, 100 U/ml penicillin/streptomycin and 2mM L-glutamine at 37oC in 5% CO2.

extract_protocol: RNA was harvested from proliferating cell populations using the RNeasy Blood and Tissue kit (Qiagen, Inc., Valencia, CA) according to the manufacturer's suggested protocols, and quantified on a Nanodrop ND-100 spectrophotometer. RNA quality was assessed by analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Adenoviral expression of Cre-recombinase was used to delete the RB and/or p53 genes, and retrovirus was used to achieve MYC overexpression.

tag: cell type

value: mammary epithelial cells

tag: gender

value: female

tag: age

value: 8 weeks

tag: myc

value: OE

value: KO

tag: rb

value: WT


title: H1N1 infected patient 39

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

description: array version 16

hyb_protocol: Hybridization on miRCURY LNA™ Arrays, using MAUI® hybridization system.

scan_protocol: Hybridization images were scanned and digitized using InnoScan 700 microarray scanner (Innopsys, France).

data_processing: miRNA microarray data were analyzed by subtracting the background signal (B532nm) from the test signal (F532nm).

organism: Homo sapiens

source_name: Blood samples

label_protocol: LNA-modified oligonucleotide (Exiqon, Denmark) probes for human, mouse and rat miRNAs annotated in miRBase version 16.0 were used in the microarray. Total RNA (1 µg) was 3′-end –labeled with Hy3 dye using the miRCURY LNA™ Power Labeling Kit (Exiqon, Denmark).

growth_protocol: Primary cultures of cortical neurons were established from E15 Swiss albino mouse brains. The cortices were dissected from E15 mouse embryos and washed with Hanks’ balanced salt solution (HBSS, 14025-092, Gibco, Invitrogen, USA). The cortical slices was dissociated with 0.05% (w/v) trypsin in HBSS without Ca2+/Mg2+ (14175-095, Gibco, Invitrogen, USA) for 30 min at 37 °C and neutralized with 1mg/ml trypsin inhibitor (T6522, Sigma, USA). Single cells were obtained by gentle trituration in Neurobasal medium (21103-049, Gibco, Invitrogen, USA) supplemented with B27 (17504-044, Invitrogen, USA), L-glutamine and Penicillin-streptomycin (Gibco, Invitrogen, USA). The cells were counted by trypan blue exclusion and seeded on to poly-d-lysine coated 24 well plates at a density of 120, 000 cells/cm2. Cultures were maintained at 37 °C with 5% CO2 in a tissue culture incubator. Cells were harvested on Days 2, 4, 6, 8.

extract_protocol: Total RNA (+ microRNA) was extracted from cells by Ribopure Kit (Ambion, USA) according to the manufacturers’ protocol. The concentration and integrity of the RNA were determined using Nanodrop ND-2000c spectrophotometry (Nanodrop Tech, Rockland, Del) and denaturing polyacrylamide gel electrophoresis, respectively.

tag: tissue

value: blood

tag: infection status

value: Influenza A H1N1 infection


title: H1N1 infected patient 41

description: array version 16


title: H1N1 infected patient 42

description: array version 16


title: H1N1 infected patient 40

description: array version 16


title: p53-, Rb-, rep2

source_name: mammary epithelial cells, p53- Rb-


title: p53-, Rb-, rep3


title: CM rAd_rAd 89

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description:
CM CD8+ T cells arising from rAd_rAd vaccination
4514990071_A

hyb_protocol: The biotinylated cRNA was hybridized onto Illumina Mouse Chips at 58 °C  for 20 h.

scan_protocol: The arrays were scanned using an Illumina BeadStation 500GX scanner and Illumina BeadStudio v3 software. Illumina probe data were exported from BeadStudio as raw data and screened for quality. Samples failing chip visual inspection and control examination were removed.

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation. Technical replicates were averaged.

label: Biotin

source_name: CD8+ T cells from mouse spleen

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct Hybridization protocol

extract_protocol: Quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using the Experion automated electrophoresis system (Bio-Rad Laboratories). Total RNA was then amplified and labeled using the Illumina TotalPrep RNA Amplification kit, which is based on the Eberwine amplification protocol. This protocol involves a first cDNA synthesis step followed by in vitro transcription for cRNA synthesis.

value: spleen

value: CD8+ T cells

tag: subset

value: CM

tag: vaccine


title: CM rAd_LCMV 86

description:
CM CD8+ T cells arising from rAd_LCMV vaccination
4514990069_F


title: p53-, Myc+, rep1


title: p53-, Rb-, rep1


title: H1N1 infected patient 38

description: array version 16


title: H1N1 infected patient 37

description: array version 16


title: H1N1 infected patient 35

description: array version 16


title: H1N1 infected patient 36

description: array version 16


title: p53-, rep2

source_name: mammary epithelial cells, p53-


title: p53-, rep3


title: CM rAd_rAd 88

description:
CM CD8+ T cells arising from rAd_rAd vaccination
4514990069_H


title: CM rAd_LCMV 85

description:
CM CD8+ T cells arising from rAd_LCMV vaccination
4514990069_E


title: p53-, rep1


title: H1N1 infected patient 32

description: array version 16


title: H1N1 infected patient 34

description: array version 16


title: CM DNA_rAd 87

description:
CM CD8+ T cells arising from DNA_rAd vaccination
4514990069_G


title: C_NT_DOX_03

city: Valbonne

first: Enzo

last: LALLI

address: 660 route des Lucioles

department: CNRS UMR 7275

country: France

institute: IPMC

description: Gene expression data from H295R/TR SF-1 cells treated with doxycycline for 72 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 Plus 2.0 arrays. Arrays 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 GC-RMA

source_name: H295R/TR SF-1 cells, treated with doxycycline (1 ug/mL) for 72 hours

label_protocol: Biotinylated cRNA were prepared according to the GeneChip 3' IVT Express Affymetrix protocol from 2 ug total RNA

growth_protocol: H295R/TR SF-1 cells were grown in DMEM/F12 (Invitrogen) containing antibiotics, 2% NuSerum (BD Biosciences) an 1% ITS+ culture supplement (BD Biosciences) in 6-well plates

extract_protocol: RNeasy Mini kit (Qiagen) following the manufacturer's procedures

treatment_protocol: Sample H295R/TR SF-1 Dox was treated with doxycycline (Dox; 1 ug/mL)

value: adrenal cortex

tag: cell line

value: H295R/TR SF-1 cell line

tag: treatment


title: WT, rep3

source_name: mammary epithelial cells, WT


title: WT, rep2


title: CM rAd_rAd 81

description:
CM CD8+ T cells arising from rAd_rAd vaccination
4514990069_A


title: CM rAd_rAd 79

description:
CM CD8+ T cells arising from rAd_rAd vaccination
4514990050_G


title: CM rAd_rAd 82

description:
CM CD8+ T cells arising from rAd_rAd vaccination
4514990069_B


title: C_NT_02

description: Gene expression data from H295R/TR SF-1 cells cultured in basal conditions for 72 hours

source_name: H295R/TR SF-1 cells, cultured in basal conditions for 72 hours


title: WT, rep1


title: C_NT_DOX_04

value: treated with doxycycline (1 ug/mL) for 72 hours


title: C_NT_01

value: cultured in basal conditions for 72 hours


title: H1N1 infected patient 31

description: array version 16


title: H1N1 infected patient 30

description: array version 16


title: CM rAd_rAd 78

description:
CM CD8+ T cells arising from rAd_rAd vaccination
4514990050_F


title: H1N1 infected patient 33

description: array version 16


title: EFF rAd_LCMV 75

description:
EFF CD8+ T cells arising from rAd_LCMV vaccination
4514990050_C

value: EFF


title: CM rAd_LCMV 84

description:
CM CD8+ T cells arising from rAd_LCMV vaccination
4514990069_D


title: H1N1 infected patient 28

description: array version 16


title: CM rAd_rAd 80

description:
CM CD8+ T cells arising from rAd_rAd vaccination
4514990050_H


title: CD45+CD34+CD38+ cells from engrafted Lin- cord blood located in trabecular bone area, biological rep 2

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

description: Gene expression data from sorted CD45+CD34+CD38+ CB cells

hyb_protocol: In accordance with manufacturer's protocols

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

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm and baseline transformation to the median of all samples using GeneSpring 12.5 software.

source_name: Purified cells from engrafted cord blood cells

growth_protocol: Xenografted primary human tissue

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions. Total RNA was amplified following the standard protocol at London Regional Genomics Centre.

value: cord blood


title: EFF rAd_LCMV 73

description:
EFF CD8+ T cells arising from rAd_LCMV vaccination
4514990050_A


title: CD45+CD34+CD38+ cells from engrafted Lin- cord blood located in long bone area, biological rep 1

label_protocol: In accordance with manufacturer's protocols


title: CD45+CD34+CD38+ cells from engrafted Lin- cord blood located in long bone area, biological rep 2


title: H1N1 infected patient 29

description: array version 16


title: CD45+CD34+CD38+ cells from engrafted Lin- cord blood located in trabecular bone area, biological rep 1


title: H1N1 infected patient 24

description: array version 16


title: H1N1 infected patient 25

description: array version 16


title: CD45+CD34+CD38- cells from engrafted Lin- cord blood located in long bone area, biological rep 1

description: Gene expression data from sorted CD45+CD34+CD38- CB cells


title: CM DNA_rAd 77

description:
CM CD8+ T cells arising from DNA_rAd vaccination
4514990050_E


title: EFF rAd_rAd 70

description:
EFF CD8+ T cells arising from rAd_rAd vaccination
4514990004_F


title: EFF rAd_LCMV 74

description:
EFF CD8+ T cells arising from rAd_LCMV vaccination
4514990050_B


title: CD45+CD34+CD38- cells from engrafted Lin- cord blood located in long bone area, biological rep 2


title: EFF rAd_LCMV 71

description:
EFF CD8+ T cells arising from rAd_LCMV vaccination
4514990004_G


title: CD45+CD34+CD38- cells from engrafted Lin- cord blood located in trabecular bone area, biological rep 2


title: H1N1 infected patient 27

description: array version 16


title: H1N1 infected patient 22

description: array version 16


title: H1N1 infected patient 26

description: array version 16


title: H1N1 infected patient 23

description: array version 16


title: H1N1 infected patient 20

description: array version 16


title: H1N1 infected patient 21

description: array version 16


title: H1N1 infected patient 19

description: array version 16


title: EFF rAd_LCMV 72

description:
EFF CD8+ T cells arising from rAd_LCMV vaccination
4514990004_H


title: EFF rAd_rAd 69

description:
EFF CD8+ T cells arising from rAd_rAd vaccination
4514990004_E


title: EFF rAd_rAd 67

description:
EFF CD8+ T cells arising from rAd_rAd vaccination
4514990004_C


title: EDL933_BSIC_M9_replicate_2

city: Saint-Genes-Champanelle

first: Yolande

last: BERTIN

address: Centre INRA de Clermont-Ferrand-Theix

institute: Institut National de Recherche Agronomique

hyb_protocol: - Labeled cDNA (200 pmol each) were mixed, dried, resuspended in 50 μl hybridization buffer (5 x SSC, 0.1% SDS, 50% deionized formamide, 0.2g L-1 salmon sperm DNA) and denatured at 95°C for 5 minutes before cooled for 5 min at room temperature. - The mixed probes was then applied to microarray slide, covered with Hybri-Slip cover slips, placed in hybridization chambers and hybridized overnight at 42°C.

scan_protocol: The slides were scanned with a SYS-SN-ARRAY Aligent Microarray Scanner (10-µm resolution) using the GenePix Pro 6.0 software (Axon Instruments).

data_processing:
- Background correction (normexp + offset=50) on log2 red and green signal and background intensities.
- Global lowess and median block effect within array normalizations followed by median-abolute-deviation standardization between arrays.

organism: Escherichia coli

source_name: RNA obtained in BSIC

label_protocol:
- 8 µg of total RNA were reverse transcribed to Cy3- or Cy5-labeled cDNA using BD-Atlas PowerScript Fluorescent labeling kit (Invitrogen) and Cy-dye Post-Labelling Reactive Dye Pack (Amersham) following the manufacturer’ instructions.
- Unincorporated Cy-dye was removed using the QIAquick PCR purification kit (Qiagen).

growth_protocol:
-Broth cultures were started from a single colony in Luria-Bertani (LB) broth and grown 8 hours at 37°C with aeration.
-The bacterial cells were then diluted 50-fold in sterile BSIC and M9-Glc respectively and cultured overnight without aeration at 39°C.
- BSIC and M9 medium were inoculated by overnight BSIC or M9 broth cultures respectively.
-The bacterial suspensions were then incubated at 39°C without shaking until the EHEC strain reached the stationary growth phase
(4h 15 and 7h30 in BSIC and M9 medium respectively).

extract_protocol:
- Bacterial suspensions were centrifuged at 10,000 x g for 15 min and the pellets were rapidly resuspended in two volumes of RNAprotect Bacteria reagent (Qiagen).
- The suspension was then centrifuged at 10,000 x g for 15 min and total RNA was purified from the bacterial pellet using the NucleoSpin RNA II kit (Macherey-Nagel).
- DNA contaminations were digested using an RNAse-free DNAse I column during the RNA preparation as described by the manufacturer (Macherey-Nagel).

tag: strain

tag: growth medium

value: bovine small intestine content (BSIC)

source_name: RNA obtained in M9 medium

value: M9 medium


title: CD45+CD34+CD38- cells from engrafted Lin- cord blood located in trabecular bone area, biological rep 1


title: EDL933_BSIC_M9_replicate_4


title: EFF rAd_rAd 68

description:
EFF CD8+ T cells arising from rAd_rAd vaccination
4514990004_D


title: Exercise_258

city: Durham

first: Jeff

last: Jasper

state: NC

department: Pharmacology and Cancer Biology

institute: Duke University

hyb_protocol: Gene Chip hG-133 plus 2.0 (Affymetrix)

scan_protocol: Affymetrix GeneChip® Scanner 7G

data_processing:
Raw data was background corrected with RMA, Log2 transformed, quantile normalized and summarized by median polish using the Affy package (v.1.36.1) in Bioconductor(v.2.15.2).
Log2 RMA, quantile normalization, and summarized by median polish using Bioconductor (2.15.2).

source_name: MDA-MB-231_exercise serum

label_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA, hybridized to Affymetrix Human Genome U133 Plus 2.0 GeneChip®  arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

growth_protocol: MDA-MB-231 cells were plated at 250,000 cells/well with 10% FBS in 6-well plates and left overnight to adhere. Media was suctioned off and replaced with serum free media. Patient serum was then added to the wells at a 10% final concentration and RNA was harvested using Qiagen RNeasy kit after 4 days.

extract_protocol: Total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA)) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE).

value: human breast adenocarcinoma cells

tag: treated with

value: serum from breast cancer patients exposed to aerobic training


title: Control_275

source_name: MDA-MB-231_control serum

treatment_protocol: Patient serum was then added to the wells at a 10% final concentration and RNA was harvested using Qiagen RNeasy kit after 4 days.

value: serum from sedentary control breast cancer patient


title: EFF DNA_rAd 64

description:
EFF CD8+ T cells arising from DNA_rAd vaccination
4514990003_H


title: Exercise_245


title: H1N1 infected patient 15

description: array version 16


title: Control_256


title: H1N1 infected patient 16

description: array version 16


title: Exercise_298


title: Control_234


title: EFF DNA_rAd 65

description:
EFF CD8+ T cells arising from DNA_rAd vaccination
4514990004_A


title: EFF rAd_rAd 66

description:
EFF CD8+ T cells arising from rAd_rAd vaccination
4514990004_B


title: EFF rAd_rAd 59

description:
EFF CD8+ T cells arising from rAd_rAd vaccination
4514990003_C


title: EFF rAd_LCMV 60

description:
EFF CD8+ T cells arising from rAd_LCMV vaccination
4514990003_D


title: si_SF1_13

description: Gene expression data from H295R/TR SF-1 cells nucleofected with SF-1-specific siRNA

hyb_protocol: According to the GeneChip WT labeling and hybridization (Affymetrix) kit, using the manufacturer's procedures

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A and the Affymetrix AGCC 3.01 software

label_protocol: RNA was labeled using the WT Expression (Ambion) and the GeneChip WT labeling and hybridization (Affymetrix) kits, using the manufacturers' procedures

treatment_protocol: Cells were nucleofected (Lonza) with control (medium GC; Invitrogen), NRSF/REST-specific (Invitrogen) and SF-1-specific (Invitrogen) siRNAs, as indicated. Samples indicated with DOX were treated with doxycycline (Dox; 1 ug/mL) for 72 hours.

value: SF-1-specific siRNA


title: si_SF1_14

source_name: H295R/TR SF-1 cells nucleofected with SF-1-specific siRNA


title: EFF rAd_rAd 58

description:
EFF CD8+ T cells arising from rAd_rAd vaccination
4514990003_B


title: EDL933_BSIC_M9_replicate_3


title: H1N1 infected patient 18

description: array version 16

value: blood


title: EFF DNA_rAd 63

description:
EFF CD8+ T cells arising from DNA_rAd vaccination
4514990003_G


title: H1N1 infected patient 17

description: array version 16

value: Influenza A H1N1 infection


title: si_R2_DOX_12

description: Gene expression data from H295R/TR SF-1 cells nucleofected with NRSF/REST-specific siRNA in the presence of an increased SF-1 dosage


title: H1N1 infected patient 9

description: array version 16


title: EFF DNA_rAd 56

description:
EFF CD8+ T cells arising from DNA_rAd vaccination
4514990001_H

value: spleen


title: EFF DNA_rAd 54

description:
EFF CD8+ T cells arising from DNA_rAd vaccination
4514990001_F

value: CD8+ T cells


title: EDL933_BSIC_M9_replicate_1


title: H1N1 infected patient 14

description: array version 16


title: si_R2_10

description: Gene expression data from H295R/TR SF-1 cells nucleofected with NRSF/REST-specific siRNA

value: NRSF/REST-specific siRNA


title: EFF rAd_LCMV 62

description:
EFF CD8+ T cells arising from rAd_LCMV vaccination
4514990003_F


title: si_C_DOX_08

description: Gene expression data from H295R/TR SF-1 cells nucleofected with control siRNA in the presence of an increased SF-1 dosage

value: adrenal cortex


title: H1N1 infected patient 7

description: array version 16


title: H1N1 infected patient 13

description: array version 16


title: H1N1 infected patient 12

description: array version 16


title: H1N1 infected patient 11

description: array version 16


title: J558LuM-PAX5-Δ2-6-#3

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

description: Transduction#6, Isolation batch 1, plate batch 2

hyb_protocol: Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array.  GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: The data were extracted analyzed with bioconductor and RMA

source_name: J558LuM transduced with PAX5 Δ2-6 construct

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

extract_protocol: Trizol

tag: genotype/variation

value: transduced with PAX5 Δ2-6 construct


title: H1N1 infected patient 8

description: array version 16


title: si_C_DOX_07

source_name: H295R/TR SF-1 cells nucleofected with control siRNA in the presence of an increased SF-1 dosage

value: H295R/TR SF-1 cell line


title: EFF DNA_rAd 55

description:
EFF CD8+ T cells arising from DNA_rAd vaccination
4514990001_G


title: si_R2_09

source_name: H295R/TR SF-1 cells nucleofected with NRSF/REST-specific siRNA


title: J558LuM-PAX5-Δ2-6-#6

description: Transduction#57, Isolation batch 2, plate batch 2


title: EFF rAd_rAd 57

description:
EFF CD8+ T cells arising from rAd_rAd vaccination
4514990003_A


title: J558LuM-PAX5-P80R-#6

description: Transduction#52, Isolation batch 2, plate batch 2

source_name: J558LuM transduced with PAX5 P80R construct

value: transduced with PAX5 P80R construct


title: H1N1 infected patient 10

description: array version 16

source_name: Blood samples


title: H1N1 infected patient 4

description: array version 16


title: H1N1 infected patient 6

description: array version 16


title: si_C_C_06

description: Gene expression data from H295R/TR SF-1 cells nucleofected with control siRNA

value: control siRNA


title: H1N1 infected patient 3

description: array version 16


title: si_R2_DOX_11

source_name: H295R/TR SF-1 cells nucleofected with NRSF/REST-specific siRNA in the presence of an increased SF-1 dosage


title: H1N1 infected patient 5

description: array version 16


title: si_C_C_05

source_name: H295R/TR SF-1 cells nucleofected with control siRNA


title: Braf 2

city: Glasgow

middle: D.

last: Adams

address: Switchback Rd, Bearsden

country: United Kingdom

institute: University of Glasgow, Beatson Institute for Cancer Research

description: Gene expression data from primary human melanocytes with activated BRAFV600E

hyb_protocol: Subsequent labelling and hybrisation to HG_U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA) using the FL-Ovation cDNA Biotin Module v2.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 running GCOS software.

data_processing: The data were analyzed with GCRMA (Bioconductor) using Affymetrix default analysis settings and quantile normalisation as normalization method.

molecule: polyA RNA

source_name: Braf 2

label_protocol: 40ng of RNA was amplified using the WT-Ovation Pico RNA Amplification system (NuGEN, San Carlos, CA).

growth_protocol: Cells were infected with respective lentiviruses and RNA was isolated 2 weeks post infection when cells were confirmed fully senescent

extract_protocol: RNA was extracted using RNA easy mini kit

treatment_protocol: No treatment other then lentiviral infection

value: Primary human epidermal melanocytes (neonatal)


title: H1N1 infected patient 2

description: array version 16


title: Braf 1

source_name: Braf 1


title: Braf 3

source_name: Braf 3


title: H1N1 infected patient 1

description: array version 16


title: J558LuM-PAX5-P80R-#3

description: Transduction#3, Isolation batch 1, plate batch 2


title: HEP-sh3

city: Worcester

first: Junhao

last: Mao

state: MA

address: 364 Plantation Street, LRB 417

institute: University of Massachusetts Medical School

description: Gene expression data from human HepG2 liver cancer cell line.

hyb_protocol: 13.5 mg of fragmented biotinylated cRNA was fragmented and hybridized for 16 hr at 45C on human genechip 1.0 st arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with the GeneChip Scanner 3000 7G

data_processing: Data were analyzed by dChIP

source_name: HepG2 cells infected with lentiviral shRNA-FoxA1/2, biological rep3

label_protocol: 300 ng of total RNA were labeled for each sample using the GeneChip WT cDNA Synthesis and Amplification Kit and WT Terminal Labeling Kit (Affymetrix, 900673 and 900671).

growth_protocol: LS174T and HepG2 cells were cultured in DMEM supplemented with 10% FBS. HepG2 cells were grown on the cell cultured dishes coated with collegan I.

extract_protocol: Total RNA was isolated using TRIZOL Reagent (Invitrogen, 15596-026) and purified by RNeasy Mini Kit (QIAGEN, 74104).

treatment_protocol: LS174T and HepG2 cells were infected by lentivirus expressing shRNAs aganist FoxA1 and FoxA2. Cells were undergone Puromycin selection for 4 days before RNA extraction.

value: HepG2 cells

tag: expression

value: infected with lentiviral shRNA-FoxA1/2


title: Uninfected 3

description: Gene expression data from Uninfected primary human melanocytes

source_name: Uninfected 3


title: TaxR_no treatment

city: Sacramento

first: allen

last: Gao

state: California

address: 4645 2nd Ave Research 3

institute: UC Davis

description: Gene expression data from docetaxel resistant TaxR cells

hyb_protocol: 2.5 ug of fragmented and labeled DNA target were hybridized to the Affymetrix Genechip Human Gene 1.0 ST arrays using using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes then centrifuge at max speed for 1 minute . • Transfer 80μl of hyb solution to each array, then tape holes. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneSpring GX 12.0 software.  Probe summarization and calculation of normalized expression signals from Affymetrix CEL files was performed with the RMA16 algorithm (Irizarry et al., 2003).
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

source_name: Docetaxel resistant prostate cancer cell line TaxR, without any treatment

label_protocol: 100ng of total RNA were amplified using the Ambion WT Expression Kit.  Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Both were cultured in RPMI-1640 medium containing 10% complete fetal bovine serum (FBS) 100 units/mL penicillin and 0.1 mg/mL streptomycin and maintained at 37C in a humidified incubator with 5% CO2.

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

treatment_protocol: No treatment on either cell lines.

value: In vitro prostate cancer cell line TaxR

tag: response to docetaxel

value: resistant


title: EmptyVector 3

description: Gene expression data from primary human melanocytes with Empty Vector infection

source_name: EmptyVector 3

tag: cell type


title: J558LuM-PAX5-G183V-#6

description: Transduction#49, Isolation batch 2, plate batch 2

source_name: J558LuM transduced with PAX5 G183V construct

value: transduced with PAX5 G183V construct


title: EmptyVector 1

source_name: EmptyVector 1


title: C4-2B_no treatment

description: Gene expression data from docetaxel sensitive C4-2B cells

source_name: Docetaxel sensitive prostate cancer cell line C4-2B, without any treatment

value: In vitro prostate cancer cell line C4-2B

value: sensitive


title: J558LuM-PAX5-G183V-#7

description: Transduction#50, Isolation batch 2, plate batch 2


title: J558LuM-PAX5-G183S-#6

description: Transduction#65, Isolation batch 2, plate batch 2

source_name: J558LuM transduced with PAX5 G183S construct

value: transduced with PAX5 G183S construct


title: J558LuM-PAX5-G183S-#7

description: Transduction#66, Isolation batch 2, plate batch 2


title: HEP-sh1

source_name: HepG2 cells infected with lentiviral shRNA-FoxA1/2, biological rep1


title: HEP-sh2

source_name: HepG2 cells infected with lentiviral shRNA-FoxA1/2, biological rep2


title: J558LuM-PAX5-G183V-#3

description: Transduction#9, Isolation batch 1, plate batch 2


title: Uninfected 2

source_name: Uninfected 2


title: J558LuM-PAX5-WT-#7

description: Transduction#63, Isolation batch 2, plate batch 2

source_name: J558LuM transduced with PAX5 WT construct

value: transduced with PAX5 WT construct


title: 6-ONS76 Mock_c

city: Essen

first: Alexander

last: Schramm

address: Hufelandstr. 55

department: Childrens Hospital

country: Germany

institute: University Hospital Essen

hyb_protocol: Hybridisation to human arrays was performed according to the manufacturer's recommendations (Affymetrix).

scan_protocol: Scanning of chips was performed using a GeneArray scanner (Agilent).

data_processing: Signal intensities were normalized using the RMA normalization feature in Partek Genomics Suite (Partek, Inc.).

source_name: ONS76, mock control

label_protocol: Biotin labelling was performed according to the manufacturer's recommendations (Affymetrix).

growth_protocol: ONS76 cells were cultivated as described (Kuenkele et al., Neuro Oncol, 2012 (PMID 22591662)).

extract_protocol: QIAGEN RNeasy mini kit.

treatment_protocol:
KDM5A/LSD1 knockdown by siRNA was performed according to a published protocol (Schulte et al., Cancer Research, 2009 (PMID 19223552)).
Cells were harvested 48 h after KDM5A/LSD1 knockdown.

value: medulloblastoma

value: mock control

tag: transfectant


title: HEP-wt3

source_name: Control HepG2 cells, biological rep3

value: expressing control plasmids


title: EmptyVector 2

source_name: EmptyVector 2


title: J558LuM-PAX5-WT-#3

description: Transduction#40, Isolation batch 1, plate batch 2


title: J558LuM-PAX5-G183S-#3

description: Transduction#44, Isolation batch 1, plate batch 2


title: HEP-wt1

source_name: Control HepG2 cells, biological rep1


title: J558LuM-PAX5-WT-#4

description: Transduction#43, Isolation batch 1, plate batch 2


title: HEP-wt2

source_name: Control HepG2 cells, biological rep2


title: LS-sh3

description: Gene expression data from human LS174T colon cancer cell line

source_name: LS174T cells infected with lentiviral shRNA-FoxA1/2, biological rep3

value: LS174T cells


title: 5-ONS76 Mock_b


title: LS-sh2

source_name: LS174T cells infected with lentiviral shRNA-FoxA1/2, biological rep2


title: J558LuM-MIR-#3

description: Transduction#37, Isolation batch 1, plate batch 2

source_name: J558LuM transduced with MIR construct

value: transduced with MIR construct


title: J558LuM-MIR-#7

description: Transduction#60, Isolation batch 2, plate batch 2


title: pancreatic non tumor, sample 6

city: Ulm

first: Karlheinz

last: Holzmann

address: Helmholtzstreet 8/1

department: Medical Faculty

institute: Ulm University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute • Transfer 200μl of hyb solution to each array, then tape holes • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing:
Normalization of the core probeset intensity values with RMA was done using oneChannelGUI/easyExon and Affymetrix Power Tools. No further filtering was applied.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.hg18.extended.mps

source_name: pancreatic tissue

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Sample RNA was isolated using RNA/DNA Mini Kit (QIAGEN) according to the manufacturer's protocol

tag: diseae state

value: pancreatic non tumor

tag: cell line manufacturer

value: Pancreatic Sample A, received from http://www.affymetrix.com/support/technical/sample_data/exon_array_data.affx


title: 4-ONS76 Mock_a


title: pancreatic non tumor, sample 5

value: Ambion

tag: catalog


title: 3-ONS76_c

source_name: ONS76, KDM5A siRNA

value: KDM5A siRNA


title: J558LuM-MIR-#4

description: Transduction#38, Isolation batch 1, plate batch 2


title: LS-sh1

source_name: LS174T cells infected with lentiviral shRNA-FoxA1/2, biological rep1

value: infected with lentiviral shRNA-FoxA1/2


title: pancreatic non tumor, sample 4

value: BioChain


title: pancreatic non tumor, sample 3

value: Stratagene


title: LS-wt2

source_name: Control LS174T cells, biological rep2


title: pancreatic non tumor, sample 2

value: Clontech

tag: lot


title: 2-ONS76_b


title: LS-wt3

source_name: Control LS174T cells, biological rep3


title: H295R/TR SF-1 cells, cultured in basal conditions for 72 hours

description: Gene expression data from H295R/TR SF-1 cells cultured in basal conditions for 72 hours

source_name: H295R/TR SF-1 cell line

value: control


title: 1-ONS76_a


title: HEP-d4

description: Gene expression data from human HepG2 liver cancer cell line.

source_name: FACS-isolated HepG2 cells expressing dominant negative TCF4 GFP expression plasmids, rep4

growth_protocol: LS174T and HepG2 cells were cultured in DMEM supplemented with 10% FBS. HepG2 cells were grown on cell cultured dishes coated with collegan I.

treatment_protocol: LS174T and HepG2 cells were transciently transfected with a DN-TCF4 GFP-expression vector using Lipofectamine 2000, and cells with high-level GFP expression were isolated 48 hours post transfection using flow cytometry.

value: HepG2 liver cancer


title: LS-wt1

source_name: Control LS174T cells, biological rep1


title: Uninfected 1

description: Gene expression data from Uninfected primary human melanocytes

source_name: Uninfected 1

value: Primary human epidermal melanocytes (neonatal)


title: pancreatic non tumor, sample 1


title: J558LuM-PAX5-Δ2-6-#5

description: Transduction#56, Isolation batch 2, plate batch 2

source_name: J558LuM transduced with PAX5 Δ2-6 construct

value: transduced with PAX5 Δ2-6 construct


title: J558LuM-PAX5-Δ2-6-#4

description: Transduction#53, Isolation batch 2, plate batch 2


title: J558LuM-PAX5-P80R-#5

description: Transduction#51, Isolation batch 2, plate batch 2

source_name: J558LuM transduced with PAX5 P80R construct

value: transduced with PAX5 P80R construct


title: J558LuM-PAX5-Δ2-6-#1

description: Transduction#4, Isolation batch 1, plate batch 2


title: J558LuM-PAX5-Δ2-6-#2

description: Transduction#5, Isolation batch 1, plate batch 2


title: H295R/TR SF-1 cells, treated with doxycycline (1 ug/mL) for 72 hours

description: Gene expression data from H295R/TR SF-1 cells treated with doxycycline for 72 hours

value: SF-1 overexpression


title: pancreatic ductal adenocarcinoma, sample 14

source_name: pancreatic ductal adenocarcinoma

value: pancreatic ductal adenocarcinoma


title: HEP-d3

source_name: FACS-isolated HepG2 cells expressing dominant negative TCF4 GFP expression plasmids, rep3


title: SDC1-silenced group, replicate 3

first: George

middle: W

last: Yip

address: 4 Medical Drive, Block MD10

description: Gene expression data from MDA-MB-231 cells transfected with SDC1-siRNA

hyb_protocol: Fragmented cRNA was hybridised at 45°C for 16 hours to Affymetrix HG U133 Plus 2.0 GeneChips, followed by washing and staining in an Affymetrix FS450 fluidics station.

scan_protocol: GeneChips were scanned using a GCOS 7000 7G scanner.

data_processing: Data were analysed using GeneSpring GX11.0 with RMA normalisation to median signal intensity.

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 3.6 µg of total RNA.

growth_protocol: MDA-MB-231 cells were cultured at 37°C in a humidified atmosphere with 5% carbon dioxide.

extract_protocol: Total RNA extracted using the Qiagen RNeasy Kit.

treatment_protocol: Cells were transfected with SDC1-siRNA or a negative control siRNA.

value: Breast cancer cells

tag: group

value: SDC1-silenced group


title: HEP-d2

source_name: FACS-isolated HepG2 cells expressing dominant negative TCF4 GFP expression plasmids, rep2


title: pancreatic ductal adenocarcinoma, sample 13


title: SDC1-silenced group, replicate 2

source_name: MDA-MB-231 cells transfected with SDC1-siRNA


title: pancreatic ductal adenocarcinoma, sample 12


title: SDC1-silenced group, replicate 1


title: pancreatic ductal adenocarcinoma, sample 15


title: pancreatic ductal adenocarcinoma, sample 10


title: Control group, replicate 3 [GY_Con3]

description: Gene expression data from MDA-MB-231 cells transfected with negative control siRNA

value: Control group


title: J558LuM-PAX5-P80R-#4

description: Transduction#48, Isolation batch 2, plate batch 2


title: HEP-d1

source_name: FACS-isolated HepG2 cells expressing dominant negative TCF4 GFP expression plasmids, rep1


title: HEP-c2

source_name: FACS-isolated HepG2 cells expressing control plasmids, rep2

value: control plasmids


title: J558LuM-PAX5-P80R-#2

description: Transduction#2, Isolation batch 1, plate batch 2


title: pancreatic ductal adenocarcinoma, sample 9


title: Control group, replicate 1 [GY_Con1]

source_name: MDA-MB-231 cells transfected with negative control siRNA


title: pancreatic ductal adenocarcinoma, sample 11


title: J558LuM-PAX5-P80R-#1

description: Transduction#1, Isolation batch 1, plate batch 2


title: HEP-c3

source_name: FACS-isolated HepG2 cells expressing control plasmids, rep3


title: J558LuM-PAX5-G183V-#4

description: Transduction#46, Isolation batch 2, plate batch 1

source_name: J558LuM transduced with PAX5 G183V construct

value: transduced with PAX5 G183V construct


title: pancreatic ductal adenocarcinoma, sample 8


title: HEP-c1

source_name: FACS-isolated HepG2 cells expressing control plasmids, rep1


title: pancreatic ductal adenocarcinoma, sample 7


title: LS-d3

description: Gene expression data from human LS174T colon cancer cell line

source_name: FACS-isolated LS174T cells expressing dominant negative TCF4 GFP expression plasmids, rep3

value: LS174T colon cancer


title: Control group, replicate 2 [GY_Con2]


title: J558LuM-PAX5-G183V-#5

description: Transduction#47, Isolation batch 2, plate batch 1


title: J558LuM-PAX5-G183V-#2

description: Transduction#8, Isolation batch 1, plate batch 1


title: B16F10r 16h JEV infection

city: Bengaluru

last: Rangarajan

state: karnataka

address: New biological science building

country: India

institute: Indian Institute of Science

description: Gene expression of B16F10r cell line 16h post JEV infection

hyb_protocol: The labeled cRNA samples were hybridized on to an Agilent Custom Mouse Whole Genome 8x60k Gene expression designed by Genotypic Technology Private Limited.(AMADID No: 026986).600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software

data_processing: The normalization was done using GeneSpring GX 11 Software. 75th Percentile Shift Normalization

source_name: B16F10r 16h JEV indection

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

growth_protocol: Cells were grown in DMEM( high glucose) supplemented with 10% FBS

extract_protocol: RNA Isolation was done using TRI reagent(Sigma), following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: JEV infection

value: murine melanoma cell

value: JEV infection


title: B16F10r 8h JEV infection

description: Gene expression of B16F10r cell line 8h post JEV infection

source_name: B16F10r 8h JEV indection


title: B16F10r uninfected

description: Gene expression of uninfected B16F10r cell line

source_name: B16F10r uninfected

value: uninfected


title: pancreatic ductal adenocarcinoma, sample 6


title: pancreatic ductal adenocarcinoma, sample 5


title: J558LuM-PAX5-G183V-#1

description: Transduction#7, Isolation batch 1, plate batch 1


title: J558LuM-PAX5-G183S-#5

description: Transduction#64, Isolation batch 2, plate batch 1

source_name: J558LuM transduced with PAX5 G183S construct

value: transduced with PAX5 G183S construct


title: J558LuM-PAX5-G183S-#1

description: Transduction#41, Isolation batch 1, plate batch 1


title: J558LuM-PAX5-WT-#5

description: Transduction#61, Isolation batch 2, plate batch 1

source_name: J558LuM transduced with PAX5 WT construct

value: transduced with PAX5 WT construct


title: LS-c3

source_name: FACS-isolated LS174T cells expressing control plasmids, rep3


title: pancreatic ductal adenocarcinoma, sample 4

source_name: pancreatic ductal adenocarcinoma


title: HEP-c4

description: Gene expression data from human HepG2 liver cancer cell line.

source_name: FACS-isolated HepG2 cells expressing control plasmids, rep4

value: HepG2 liver cancer


title: LS-d1

source_name: FACS-isolated LS174T cells expressing dominant negative TCF4 GFP expression plasmids, rep1


title: LS-d2

source_name: FACS-isolated LS174T cells expressing dominant negative TCF4 GFP expression plasmids, rep2


title: J558LuM-PAX5-WT-#6

description: Transduction#62, Isolation batch 2, plate batch 1


title: nt S. aureus 11

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

description: gene expression of S. aureus infected HepG2 nt cells

hyb_protocol: standard affymetrix hybridisation protocol

scan_protocol: standard affymetrix scanning protocol with affymetrix 3000 7G Scanner

data_processing: The data were analyzed with GCOS version 1.1.1.052 using Affymetrix default analysis settings and GeneSpring 9.3 software package

source_name: triplicate 2 of S. aureus infected HepG2 nt cells

label_protocol: standard affymetrix labeling protocol

growth_protocol: HepG2 nt and HIF-1-/- cells were infected with S. aureus 8325-4 (MOI: 20) for four hours (5 % CO2, 96 % humidity and 37 °C)

extract_protocol: standard qiagen isolation protocol

treatment_protocol: four hours upon infection RNA was isolated with the mRNeasy Mini Kit of Qiagen

value: Heptaocellular carcinoma cell line (non-target control cells)


title: LS-c2

source_name: FACS-isolated LS174T cells expressing control plasmids, rep2


title: B16F10 8h JEV infection

description: Gene expression of B16F10 cell line 8h post JEV infection

source_name: B16F10 8h JEV indection


title: LS-c1

source_name: FACS-isolated LS174T cells expressing control plasmids, rep1


title: B16F10 16h JEV infection

description: Gene expression of B16F10 cell line 16h post JEV infection

source_name: B16F10 16h JEV indection


title: J558LuM-PAX5-G183S-#4

description: Transduction#45, Isolation batch 2, plate batch 1


title: J558LuM-PAX5-WT-#1

description: Transduction#36, Isolation batch 1, plate batch 1


title: nt S. aureus 12

source_name: triplicate 3 of S. aureus infected HepG2 nt cells


title: B16F10 unifected

description: Gene expression of uninfected B16F10 cell line

source_name: B16F10 unifected


title: J558LuM-MIR-#6

description: Transduction#59, Isolation batch 2, plate batch 1

source_name: J558LuM transduced with MIR construct

value: transduced with MIR construct


title: J558LuM-PAX5-WT-#2

description: Transduction#39, Isolation batch 1, plate batch 1


title: J558LuM-PAX5-G183S-#2

description: Transduction#42, Isolation batch 1, plate batch 1


title: pancreatic ductal adenocarcinoma, sample 3


title: pancreatic ductal adenocarcinoma, sample 1


title: pancreatic ductal adenocarcinoma, sample 2


title: J558LuM-MIR-#5

description: Transduction#58, Isolation batch 2, plate batch 1


title: nt control 9

description: gene expression of uninfected HepG2 nt cells

source_name: triplicate 3 of uninfected HepG2 nt cells


title: nt S. aureus 10

source_name: triplicate 1 of S. aureus infected HepG2 nt cells


title: nt control 7

source_name: triplicate 1 of uninfected HepG2 nt cells


title: J558LuM-MIR-#2

description: Transduction#35, Isolation batch 1, plate batch 1


title: HIF-1-/- S. aureus 6

description: gene expression of S. aureus infected HepG2 HIF-1-/- cells

source_name: triplicate 3 of S. aureus infected HepG2 HIF-1-/- cells

value: Heptaocellular carcinoma cell line with HIF-1alpha knockdown


title: Lin- CD45- CD31- Sca1- CD51+ cells from mouse bone marrow located in long bone area, biological rep 2

description: Gene expression data from sorted Lin- CD45- CD31- Sca1- CD51+ OB cells

source_name: Bone marrow

growth_protocol: Primary mouse tissue

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

tag: tissue

value: bone marrow

tag: mouse strain


title: J558LuM-MIR-#1

description: Transduction#34, Isolation batch 1, plate batch 1

tag: cell line


title: Lin- CD45- CD31- Sca1- CD51+ cells from mouse bone marrow located in long bone area, biological rep 1


title: KT49

city: Palo Alto

first: Dedeepya

last: Vaka

address: 265 Campus Drive

department: Pediatrics

institute: Stanford

hyb_protocol: RNA from isolated from tumor samples or cell lines (15µg per sample) was used to create target for hybridization to DNA microarrays. First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95° C for 35 minutes. 15micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma, St. Louis) to Affymetrix (Santa Clara, CA) MG_U74Av2 arrays (for tumors ) or U133A (for cell lines) at 45°C for 16 hours. Mu_U74A  arrays contains 12,143 probes,  ~6,000 for known genes and ~6,000 for expressed sequence tags. U133A arrays contain approximately 22,000 probes.

scan_protocol: Scans were performed on Affymetrix scanners.

data_processing: Average differences (expression values) were calculated using GeneChip MAS4 Software (Affymetrix). Criteria for scan rejection included fewer than 1000 genes receiving “Present” calls or visible microarray artifacts. No scans met criteria for exclusion. The raw expression data as obtained from Affymetrix’s GeneChip were scaled to account for differences in chip intensities. We calculated the mean expression level (E) for all genes on each array. All scans within an experiment were scaled to the array with the median E value (all expression values are multiplied by Emedian/E).

source_name: KrasLA lung tumor

label_protocol: Arrays were washed and stained with streptavidin-phycoerythrin (SAPE, Molecular Probes). Signal amplification was performed using a biotinylated anti-streptavidin antibody (Vector Laboratories, Burlingame, CA) at 3 µg/ml. This was followed by a second staining with SAPE. Normal goat IgG (2 mg/ml) was used as a blocking agent.

growth_protocol: none (mouse spontaneous primary tumor samples)

extract_protocol: Tumor fragments were placed in Trizol reagent (Invitrogen) and homogenized by using first a KontesTM disposable pestle and then a polytron homogenizer.  RNA and DNA were extracted from Trizol using the manufacturer’s instructions.  RNA was further purified by using a Quiagen RNAeasy column.  Quality of RNA was assessed by gel electrophoresis.  Samples with high quality RNA were then used to prepare cRNA for hybridization to Affymetrix oligonucleotide arrays.

treatment_protocol: Mice bearing the KrasLA latent allele were allowed to develop to 5-6 month of age and sacrificed by cervical dislocation. Lungs were removed and placed in RNAlaterTM solution (Ambion).  Individual tumors large enough to be easily dissected (3mm-8mm) were removed and cut into 2 pieces. One piece was placed in formalin to be used for histological analysis while the other piece was stored at -80 for RNA/DNA extraction.

value: Lung

tag: genotype

tag: age


title: normal5

source_name: Normal lung

value: wild-type


title: HIF-1-/- S. aureus 5

source_name: triplicate 2 of S. aureus infected HepG2 HIF-1-/- cells


title: nt control 8

source_name: triplicate 2 of uninfected HepG2 nt cells


title: normal3


title: HIF-1-/- S. aureus 4

source_name: triplicate 1 of S. aureus infected HepG2 HIF-1-/- cells


title: HIF-1-/- control 3

description: gene expression of uninfected HepG2 HIF-1-/- cells

source_name: triplicate 3 of uninfected HepG2 HIF-1-/-  cells


title: Lin- CD45- CD31- Sca1- CD51+ cells from mouse bone marrow located in trabecular bone area, biological rep 1


title: KT112


title: KT102


title: HIF-1-/- control 2

source_name: triplicate 2 of uninfected HepG2 HIF-1-/- cells


title: Lin- CD45- CD31- Sca1- CD51+ cells from mouse bone marrow located in trabecular bone area, biological rep 2


title: E12 distal retina progenitors_mutant_rep 1

city: Tel Aviv

first: Ruth

last: Ashery-Padan

state: Select a State or Province

address: Tel Aviv University

department: Department of Human Molecular Genetics and Biochemistry

country: Israel

institute: Tel-Aviv University

description: Mutant_Pax6 flox alpha-Cre_E12_r1

hyb_protocol: according to the instruction manual, as described in the Affymetrix website

data_processing: RMA normalization, summarization by mean (using Affymetrix expression console)

source_name: Pax6 negative retinal progenitors

growth_protocol: alpha-Cre or Pax6 flox alpha-Cre female ICR mice were time mated with wildtype or Pax6 flox ICR males respectively. 12 days after vaginal plug detection pregnant dames were euthanized and embryos dissected out. Eye were taken out and dissociated.

treatment_protocol: Eye dissociation was preformed with 25 units/ml papain for 30 minutes followed by mechanical dissociation. Dissociated cells were resuspended in HBSS.

tag: strain background

value: ICR

value: Pax6 flox alpha-cre

tag: developmental stage

value: Embryonic retina/optic cup


title: HIF-1-/- control 1

source_name: triplicate 1 of uninfected HepG2 HIF-1-/- cells


title: H295R/TR SF-1 cells, nucleofected with NRSF/REST-specific siRNA and treated with doxycycline (1 ug/mL) for 72 hours

description: Gene expression data from H295R/TR SF-1 cells nucleofected with NRSF/REST-specific siRNA in the presence of an increased SF-1 dosage

data_processing: Affymetrix AGCC 3.01 software.  The data were analyzed with GC-RMA

tag: treatment


title: H295R/TR SF-1 cells, nucleofected with SF-1-specific siRNA

description: Gene expression data from H295R/TR SF-1 cells nucleofected with SF-1-specific siRNA

value: nucleofected with SF-1-specific siRNA


title: E12 distal retina progenitors_mutant_rep 3

description: Mutant_Pax6 flox alpha-Cre_E12_r3

scan_protocol: according to the instruction manual, as described in the Affymetrix website

tag: genotype/variation


title: E12 distal retina progenitors_mutant_rep 2

description: Mutant_Pax6 flox alpha-Cre_E12_r2

label_protocol: according to the instruction manual, as described in the Affymetrix website


title: E12 distal retina progenitors_control_rep 3

source_name: control retinal progenitors

value: alpha-cre


title: KT77


title: H295R/TR SF-1 cells, nucleofected with NRSF/REST-specific siRNA

description: Gene expression data from H295R/TR SF-1 cells nucleofected with NRSF/REST-specific siRNA


title: KT88


title: H295R/TR SF-1 cells, nucleofected with control siRNA

description: Gene expression data from H295R/TR SF-1 cells nucleofected with control siRNA

value: nucleofected with control siRNA


title: KT111


title: H295R/TR SF-1 cells, nucleofected with control siRNA and treated with doxycycline (1 ug/mL) for 72 hours

description: Gene expression data from H295R/TR SF-1 cells nucleofected with control siRNA in the presence of an increased SF-1 dosage


title: KT78


title: KT50


title: Intellectual_Disability_PN09-1085_250knsp

type: genomic

city: Nijmegen

first: Joep

last: de Ligt

address: Geert Grooteplein 10, 848

department: Human Genetics

country: Netherlands

institute: UMCN St Radboud

description: Hybridized to 250K_Nsp

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

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

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.0 and Copy Number Analyzer for Affymetrix GeneChip mapping (CNAGT 2.0) software. The inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAG2.0. Regions of homozygosity (LCSH/LOH) were determined with a likelihood based algorithm implemented in CNAG2.0.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

molecule: genomic DNA

source_name: peripheral (EDTA) blood

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: No culture but direct isolation from peripheral blood

extract_protocol: Genomic DNA was isloated with a Chemagen/Hamilton magnetic bead DNA isolation robot

tag: gender

value: male


title: KT90


title: KT86


title: Intellectual_Disability_PN08-1060_250knsp

description: Hybridized to 250K_Nsp

value: female


title: TKO UI 0h_3

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

institute: Weill Cornell Medical College

description: gene expression data after treatment

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: Background and PM/MM corrections were performed by Affymetrix Microarray Suite 5.0, (MAS5.0) and expression summary values for each probe set were calculated in Bioconductor (http://www.bioconductor.org/). In addition, hierarchical clustering was performed in dchip (http://biosun1.harvard.edu/ complab/dchip/) for both microarray studies to assess similarities and differences in gene expression among samples

source_name: uninfected 0hr

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

growth_protocol: 10% FBS with 1% antibiotics in DMEM

treatment_protocol: cell were treated with 100nM 4OHT for indicated hours

value: TKO

tag: sample type

value: telomere dysfunctional cells

value: uninfected

tag: time

value: 0 h


title: KT80


title: KT99


title: KT83


title: E12 distal retina progenitors_control_rep 2


title: TKO p53 OHT 4h_3

description: gene expression data after treatment

source_name: p53ER expressing 4hr OHT treated

value: p53ER expressing OHT treated

value: 4 h


title: TKO UI veh 4h_3

description: gene expression data after treatment

source_name: uninfected 4hr vehicle treated

value: uninfected vehicle treated


title: TKO p53 0h_3

description: gene expression data after treatment

source_name: p53ER expressing 0hr

value: p53ER expressing


title: TKO UI OHT 4h_3

description: gene expression data after treatment

source_name: uninfected 4hr OHT treated

value: uninfected OHT treated


title: TKO UI veh 4h_2

description: gene expression data after treatment


title: Intellectual_Disability_PN08-2549_250knsp

description: Hybridized to 250K_Nsp


title: TKO p53 veh 4h_3

description: gene expression data after treatment

source_name: p53ER expressing 4hr vehicle treated

value: p53ER expressing vehicle treated


title: E12 distal retina progenitors_control_rep 1

value: ICR


title: Intellectual_Disability_PN08-2713_250knsp

description: Hybridized to 250K_Nsp


title: Intellectual_Disability_PN07-2380_250knsp

description: Hybridized to 250K_Nsp


title: Intellectual_Disability_PN09-2317_250knsp

description: Hybridized to 250K_Nsp


title: normal16

value: Lung

value: wild-type


title: normal14


title: KT85

source_name: KrasLA lung tumor


title: TKO UI OHT 4h_2

description: gene expression data after treatment


title: Intellectual_Disability_PN09-1706_250knsp

description: Hybridized to 250K_Nsp


title: normal20

source_name: Normal lung


title: Intellectual_Disability_PN09-1649_250knsp

description: Hybridized to 250K_Nsp


title: TKO p53 veh 4h_2

description: gene expression data after treatment


title: normal19


title: normal18


title: normal15


title: Piringer3

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

data_processing:
Statistical analysis was done with the statistical computing environment R [version 2.15.1 (2012-06-22)]. Additional software packages (affy [version 2.10], geneplotter, multtest, and vsn [version 2.10]) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
probe group file: Unsupported Human Gene 1.0 ST Array CDF Files
meta-probeset file: HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

source_name: Piringer epithelioid cells

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

extract_protocol: RNA was amplified directly from cells using the One-direct-Kit from NUGEN applied for 250 microdissected cells

treatment_protocol: Cells were microdissected from HE stained kryosections

tag: cell type

value: Piringer epithelioid cells


title: Piringer4


title: TKO p53 OHT 4h_2

description: gene expression data after treatment


title: TKO UI 0h_2

description: gene expression data after treatment


title: TKO UI OHT 4h_1

description: gene expression data after treatment


title: Sarcoidosis5

source_name: Sarcoidosis epithelioid cells

value: Sarcoidosis epithelioid cells


title: TKO UI 0h_1

description: gene expression data after treatment


title: Intellectual_Disability_PN06-2719_250knsp

description: Hybridized to 250K_Nsp


title: Piringer5


title: Piringer2


title: TKO UI veh 4h_1

description: gene expression data after treatment


title: normal9


title: normal8


title: TKO p53 0h_2

description: gene expression data after treatment


title: normal11


title: normal7


title: Sarcoidosis3


title: Sarcoidosis2


title: TKO p53 0h_1

description: gene expression data after treatment


title: Sarcoidosis1


title: normal1


title: KT35


title: normal6


title: KT39


title: normal10


title: Piringer1


title: CC9311_MC-shock_replicate 5

city: Sydney

first: Sasha

last: Tetu

state: NSW

address: North Ryde

department: CMBS

country: Australia

institute: Macquarie University

hyb_protocol: Microarray slides were immersed in pre-hybridization buffer (1 % BSA, 5X SSC, 0.1 % SDS, 0.45 mm-filtered) before hybridization. Slides were washed with sterile water (4x) and isopropanol (3x), spin-dried and covered with lifterslip. cDNA probes were dried using Speedvac and then resuspended in hybridization buffer (50 % formamide, 5X SSC, 0.1 % SDS, 0.45 mm-filtered). Probes were heated at 95 °C (15 min) before applying to the slides. Hybridization was performed overnight at 42°C.

scan_protocol: Slides were scanned at 10-um resolution using an Axon 4000B scanner with GenePix 4.0 software

data_processing: Processing of the TIFF images from hybridized arrays was performed using TIGR-Spotfinder (www.tigr.org/software), and the datasets normalized by applying the LOWESS algorithm, using block mode and a smooth parameter of 0.33, available in the TIGR-MIDAS package (www.tigr.org/software). Statistical analysis was performed on the mean of log2-transformed signal ratios of the replicate spots using the Statistical Analysis of Microarrays (SAM) algorithms  with a false discovery rate of less than 1%.

organism: Synechococcus sp. CC9311

source_name: Synechococcus sp. CC9311, MC treated

label_protocol: Reverse transcription of RNA samples was performed using the SuperScript Plus Indirect cDNA Labeling System (Invitrogen) with random hexamer primers.  Approximately 4 µg of total RNA was used for indirect labelling, leading to the production of approximately 4 µg of cDNA with approximately 200 pmol of dye molecule incorporated per microgram of cDNA synthesized.

growth_protocol: Axenic Synechococcus sp. WH8102 and Synechococcus sp. CC9311 cultures were maintained in either SN medium or in an artificial seawater medium (SOW) with 9.0 mM NaNO3 standard.  For growth assays, batch cultures were grown in glass flasks, gently stirred, or in glass tubes, at 25 °C under 30 μEinstein m-2 s-1 continuous white light.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions, RNA was resuspended in 100 μl of DEPC-treated water, further processed using RNeasy Mini kit (Qiagen) following the manufacturer’s protocol, twice digested with DNase I (Qiagen), then eluted from the columns.

treatment_protocol: Duplicate 1.5-liter batch cultures of WH8102 and CC9311 were grown up to the early exponential phase and half the culture was spun down at room temperature, resuspended in Trizol reagent (Invitrogen), and frozen at -80°C for RNA extraction in parallel with treated cells, taking care that the harvesting time stayed under 30 min. EB (final concentration 2 μg/mL) or MC (final concentration 0.5 μg/mL) were added to the remaining culture. After a two hour incubation, these cells were harvested and suspended in Trizol reagent as above.

tag: strain

value: MC treated

source_name: Synechococcus sp. CC9311, no treatment

value: no treatment


title: CC9311_MC-shock_replicate 4


title: Sarcoidosis4


title: CC9311_MC-shock_replicate 6


title: normal2


title: NIR_LGR5lo_ISC_5

first: Hans

last: Kestler

address: Albert-Einstein-Allee 11

department: Research Group Bioinformatics and Systems Biology

institute: University of Ulm

description: gene expression non-irradiated

hyb_protocol: Cy3-labelled cRNA was fragmented and blocked following manufacturer's instructions.

scan_protocol: Slides were scanned using one color scan setting for GE 8x60K slides with the scanner (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). Further processing (background correction, normalization, summarization) was done following Agilent's quickstart guided workflow.

source_name: NIR, LGR5lo, ISC

label_protocol: 50ng of each sample was labeled with the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to manufacturer's instructions.

extract_protocol: RNA was prepared using the MagMAX-96 Viral RNA Isolation kit (Ambion) following manfacturer's instructions.

treatment_protocol: LGR5-GFPki mice were 12Gy gamma-irradiated or non-irradiated. LGR5hi and LGR5lo ISCs were FACS sorted 3 hours after irradiation.

value: male

tag: stress

value: non-irradiated

value: intestinal stem cells (ISCs)

tag: facs-sortedcell type


title: normal13


title: CC9311_MC-shock_replicate 3


title: TKO p53 OHT 4h_1

description: gene expression data after treatment

value: TKO

value: telomere dysfunctional cells


title: CC9311_MC-shock_replicate 2


title: CC9311_MC-shock_replicate 1


title: TKO p53 veh 4h_1

description: gene expression data after treatment

value: 4 h


title: IR_LGR5hi_ISC_4

description: gene expression irradiated

source_name: IR, LGR5hi, ISC

value: female

value: irradiated


title: KT10


title: NIR_LGR5lo_ISC_4

description: gene expression non-irradiated


title: normal12


title: CC9311_EB-shock_replicate 4

source_name: Synechococcus sp. CC9311, EB treated

value: EB treated


title: CC9311_EB-shock_replicate 6


title: NLPHL_AD_M8

source_name: NLPHL epithelioid cells

value: NLPHL epithelioid cells


title: CC9311_EB-shock_replicate 5


title: CC9311_EB-shock_replicate 3


title: NLPHL_AD_M7


title: NLPHL_AD_M9


title: IR_LGR5lo_ISC_3

description: gene expression irradiated

source_name: IR, LGR5lo, ISC


title: normal17


title: KT14


title: NIR_LGR5hi_ISC_4

description: gene expression non-irradiated

source_name: NIR, LGR5hi, ISC


title: IR_LGR5hi_ISC_3

description: gene expression irradiated


title: IR_LGR5lo_ISC_4

description: gene expression irradiated


title: KT16


title: KT11


title: NLPHL_AD_M6


title: NIR_LGR5hi_ISC_3

description: gene expression non-irradiated


title: NIR_LGR5lo_ISC_3

description: gene expression non-irradiated


title: IR_LGR5lo_ISC_2

description: gene expression irradiated


title: CC9311_EB-shock_replicate 1


title: CC9311_EB-shock_replicate 2


title: IR_LGR5hi_ISC_2

description: gene expression irradiated


title: KT6


title: Patient 81, 2 wks

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Hu81mu Pα+2w

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

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

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

source_name: PDGFRa+ cells from patient 81, induced for 2 wks

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

growth_protocol: PDGFRa+ mesenchymal progenitors were isolated by FACS and grown in growth medium consisting of DMEM supplemented with 20% FBS, 1% penicillin-streptomycin, and 2.5 ng/ml bFGF at 37˚C in 5% CO2 and 3% O2.

extract_protocol: RNA samples were extracted from cells using the miRNeasy Mini Kit (Qiagen).

treatment_protocol: Cells were seeded at a density of 4.2 X 10^3 cells/cm2 and incubated at 37˚C in 5% CO2 and 21% O2. At 50-70% confluency, osteogenesis was induced using osteogenic differentiation medium consisting of 10% FBS-αMEM supplemented with dexamethasone, ascorbate-phosphate, and β-glycerophosphate.

value: gluteus medius muscle

value: PDGFRa+ mesenchymal progenitor cells

tag: passage

value: osteogenic induction

tag: time after induction

value: 2 wks

tag: patient identifier


title: Patient 81, 1 wk

description: Hu81mu Pα+1w

source_name: PDGFRa+ cells from patient 81, induced for 1 wk

tag: tissue

value: 1 wk


title: KT1

value: Lung

tag: genotype


title: KT5

tag: age


title: Patient 80, 2 wks

description: Hu80mu Pα+2w

source_name: PDGFRa+ cells from patient 80, induced for 2 wks


title: Patient 81, 0 wk

description: Hu81mu Pα+pre

source_name: PDGFRa+ cells from patient 81, uninduced


title: KT15


title: NIR_LGR5lo_ISC_2

description: gene expression non-irradiated


title: Patient 80, 1 wk

description: Hu80mu Pα+1W

source_name: PDGFRa+ cells from patient 80, induced for 1 wk


title: NLPHL_AD_M4


title: NLPHL_AD_M5


title: Patient 80, 0 wk

description: Hu80mu Pα+pre

source_name: PDGFRa+ cells from patient 80, uninduced


title: KT13

source_name: KrasLA lung tumor


title: KT3


title: NLPHL_AD_M1


title: NIR_LGR5hi_ISC_2

description: gene expression non-irradiated


title: NIR_LGR5lo_ISC_1

description: gene expression non-irradiated


title: IR_LGR5hi_ISC_1

description: gene expression irradiated


title: IR_LGR5lo_ISC_1

description: gene expression irradiated


title: KT8


title: KT17


title: NLPHL_AD_M2


title: KT9


title: NIR_LGR5hi_ISC_1

description: gene expression non-irradiated


title: KT12


title: S.coelicolor germination_time 5.5 h_replicate 2

city: Prague

first: Jiri

last: Vohradsky

address: Videnska 1083

country: Czech Republic

institute: Institute of Microbiology Czech Academy of Sciences

hyb_protocol: Bacterial RNA Amplification Protocol for Gene Expression by Oxoford Gene Technology

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C and images were quantified using  Agilent Feature Extraction software.

data_processing: For background subtraction and LOWESS normalization was used Agilent Feature Extraction software. The GeneSpring software was used to filter out signal intensities < 200.

organism: Streptomyces coelicolor A3(2)

source_name: S.coelicolor germination time 5.5 h

growth_protocol: Dormant spores germiantion was activated by mechanical disruption and 10min heat shock (50°C), than cultivated in rich AM liquid medium at 37°C. Samples collected at 30 min intervals.

extract_protocol: The cells were mechanicaly disrupted and total RNA was extracted using phenol-chlorophorm RNA extraction.

source_name: proportional mixture of RNA samples from all time points


title: spinal cord control 3

city: Melbourne

first: Victoria

middle: Mary

last: Perreau

state: Victoria

address: Parkville

department: Center for Neuroscience

institute: University of Melbourne

description: Gene expression data from mouse spinal cord control sample.

hyb_protocol: Labeled RNA was then hybridized onto the murine MG U74Av2 microarray, Affymetrix®, Santa Clara CA, following manufactures instructions.

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

data_processing: Expression data was analysed using Partek® genomics suite, Missouri, USA. Affymetrix® annotation library MG_U74Av2.na31.annot.csv was used and Data was normalized using RMA (Bolstad et al 2003) and quantile normalization and adjusted for GC content.  Expression values were log transformed using base2 prior to differential expression analysis.using a 2 way ANOVA on treatment and batch.

source_name: mouse spinal cord control batch 3

label_protocol: 5ug of total RNA from spinal cords of two animals were pooled prior to the labeling reaction. Biotinylated cRNA were prepared according to the standard Affymetrix protocol).

growth_protocol: Animals were group housed.

extract_protocol: RNA was extracted using an RNeasy mini kit (QIAGEN Pty Ltd. Vic, AUS) as per manufacturer’s instructions.

treatment_protocol: EAE was induced in 8-12 week old animals with a subcutaneous flank injection of the PLP peptide. Control animals were given an injection of vechicle only. Animals were sacrificed at EAE disease score 2.5-3.0 with age and sex matched healthy controls killed on the same day. EAE animals also had an intravenous injection of murine serum ambumin MSA (0.1% in 100ul of PBS) 3 hours prior to sacrifice. The MSA treatment is due to the fact that these animals are part of a larger unpublished study for which the MSA treatment was a control group to compare with a drug treatment.  Only the control group was used in this analysis.

value: SJL/J

value: control

tag: eae grade (average)

tag: eae day

value: 8-12 weeks

tag: processing date

tag: batch

tag: number of animals pooled per array


title: spinal cord EAE 5

description: Gene expression data from mouse spinal cord after EAE treatment.

source_name: mouse spinal cord after EAE treatment batch 5

tag: treatment

value: EAE

tag: gender


title: BPA/inf female 1

city: College Station

first: Candice

last: Brinkmeyer-Langford

state: TX

address: TAMU MS4458

institute: Texas A&M University

hyb_protocol: standard Agilent protocol

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: spinal cord

label_protocol: 150-300ng total RNA for each sample was labeled with the Agilent LowInput QuickAmp two-color labeling kit and hybridized to the Agilent SurePrint G3 Unrestricted GE 8x60K mouse genome expression array (G4858A) according to the manufacturer’s protocol.

extract_protocol: Total RNA from 25 spinal cords was extracted in TRI Reagent (Life Technologies, Carlsbad, CA) and purified using Qiagen RNeasy Mini kit columns, according to manufacturer’s instructions (Qiagen, Valencia, CA).

tag: infection

value: Theiler's virus

value: spinal cord

value: BPA

tag: bpa exposed

value: Y

tag: viral infection

value: F

tag: genetic background

value: SJL

value: N


title: KZM5

source_name: Germinal center macrophages

tag: cell type

value: Germinal center macrophages


title: spinal cord control 2

source_name: mouse spinal cord control batch 2

tag: strain

value: female


title: S.coelicolor germination_time 5 h_replicate 3

source_name: S.coelicolor germination time 5 h

label_protocol: Bacterial RNA Amplification Protocol for Gene Expression by Oxoford Gene Technology


title: S.coelicolor germination_time 5 h_replicate 2


title: S.coelicolor germination_time 5.5 h_replicate 3


title: spinal cord control 1

source_name: mouse spinal cord control batch 1


title: BPA/non-inf male

value: M


title: BPA/inf female 2


title: non-BPA/non-inf female


title: non-BPA/inf female


title: S.coelicolor germination_time 5 h_replicate 1


title: S.coelicolor germination_time 5.5 h_replicate 1


title: BPA/inf female 3


title: spinal cord EAE 4

source_name: mouse spinal cord after EAE treatment batch 4


title: KT4


title: non-BPA/inf male


title: spinal cord EAE 3

source_name: mouse spinal cord after EAE treatment batch 3


title: dMV_1 with array type SUNFLOWER from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

institute: inra

description: It concerns the interaction between ROS and hormones in dormancy release in sunflower seeds. ABA is responsible for dormancy maintenance, while GA and ethylene promote seed germination. Based on our results, ROS could represent good candidate to shift from a hormone signalling to another determining the dormancy state in sunflower seeds.

hyb_protocol: labelled extract quantity: 10ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).  We take a subset of probes because we want the results only for Helianthus annuus specific probes.

organism: Helianthus annuus

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: embryonic axis - In the field Month of the period of cultivation Apr. 2009 May 2009 June. 2009 July. 2009 Aug. 2009 Sept. 2009 Total Sunshine duration (hours)  278 188 207 243 207 230  1353 Précipitations (mm) 16 168 104 120 118 57 583 Average temperatures (°C) 15.9 17.0 20.0 20.9 20.1 16.5 18.4

treatment_protocol: Name:MV - environmental treatment - methylviologen, pro-oxidant addition,mannitol,ros application:time 24hour . Oracz et al., Plant Physiology. (2009)150(1):494-505.

tag: state

value: dormant

value: MV

tag: developmental stage

value: (boyes et al. plant cell 2001):seed


title: S.coelicolor germination_time 4.5 h_replicate 2

source_name: S.coelicolor germination time 4.5 h


title: Total RNA Kb3

city: Charleston

first: Frances

middle: M

last: Van Dolah

state: SC

address: 219 Fort Johnson Rd

institute: Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research

hyb_protocol: 480 ng of Cy3 labeled targets were hybridized to the array for 17 hours at 60°C.  After hybridization, arrays were washed according to the manufacturer’s protocol (Agilent, Santa Clara, CA).

scan_protocol: Microarrays were imaged using an Agilent microarray scanner using extended dynamic range scanning

data_processing: Images were extracted with Agilent Feature Extraction version 9.5.3.1 using a rank consistency filter and a combination linear and LOWESS normalization algorithm.

organism: Karenia brevis

source_name: Karenia brevis, total RNA

label_protocol: Total RNA (100 ng) , pre-existing RNA (100 ng), and newly synthesized RNA (25 ng) were independently amplified and labeled with Cy3 dye using the Low Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA).  The amplified, labeled RNA was quantified using a NanoDrop ND-1000.

growth_protocol: Karenia brevis, Wilson isolate, was grown in 1 L batch cultures in autoclaved, 20 µm filtered seawater at 36 ‰ enriched with f/2 medium at 25 °C  on a 16 h:8 h light:dark cycle with illumination from cool white lights at 150 µE m-2 sec-1

extract_protocol: Six replicate cultures were independently harvested by centrifugation.  Total RNA from each sample was prepared using TriReagent.  Following precipitation in ethanol, the RNA was resuspended and purified using a Qiagen RNeasy column.  Total RNA was quantified using a NanoDrop ND-1000 and qualified on an Agilent 2100.  Total RNA was biotinylated with Pierce EZ-link Biotin-HPDP, precipitated in ethanol, and quantified using a NanoDrop ND-1000.  This RNA was then separated into pre-exisiting (non-biotinylated) and newly synthesized (biotinylated) RNA pools using streptavidin coated magnetic beads.  Once separated, each fraction was precipitated with isopropanol and quantified using a NanoDrop ND-1000 and qualified on an Agilent 2100.

treatment_protocol: 0.2 mM 4-thiouracil in DMSO was added to cultures to biosynthetically label newly synthesized RNA.  Cultures were harvested 2 h post 4-thiouracil addition

tag: rna pool

value: total RNA

tag: isolate

value: Wilson Isolate


title: dMV_2 with array type SUNFLOWER from Affymetrix


title: spinal cord EAE 1

source_name: mouse spinal cord after EAE treatment batch 1

value: SJL/J

tag: eae grade (average)

tag: age

value: 8-12 weeks


title: apinal cord EAE 2

source_name: mouse spinal cord after EAE treatment batch 2

value: EAE

tag: eae day

tag: processing date


title: dABA_1 with array type SUNFLOWER from Affymetrix

treatment_protocol: Name:ABA - environmental treatment - hormone addition,hormone,abscissic acid:time 24hour . Corbineau and Côme (2003) in biology and biotechnology of the plant hormone ethylene, F. Romojaro eds

value: ABA


title: NDABA_2 with array type SUNFLOWER from Affymetrix

value: non-dormant


title: dCH3_1 with array type SUNFLOWER from Affymetrix

treatment_protocol: Name:ETH - environmental treatment - hormone addition,ethylene,earthworms:time 24hour . Corbineau and Côme (2003) in biology and biotechnology of the plant hormone ethylene, F. Romojaro eds


title: S.coelicolor germination_time 4 h_replicate 3

source_name: S.coelicolor germination time 4 h


title: S.coelicolor germination_time 4 h_replicate 2


title: S.coelicolor germination_time 4 h_replicate 1


title: S.coelicolor germination_time 3.5 h_replicate 3

source_name: S.coelicolor germination time 3.5 h


title: NDABA_1 with array type SUNFLOWER from Affymetrix


title: NDH2O_1 with array type SUNFLOWER from Affymetrix

treatment_protocol: Name:H20 - environmental treatment - water,imbibition:time 24hour . Oracz et al., Plant Physiology. (2009)150(1):494-505.


title: dH20_2 with array type SUNFLOWER from Affymetrix


title: Pre-Existing RNA Kb1

source_name: Karenia brevis, pre-existing RNA

value: pre-existing RNA


title: New RNA Kb1

source_name: Karenia brevis, newly synthesized RNA

value: newly synthesized RNA


title: Pre-Existing RNA Kb2


title: Total RNA Kb2


title: Arabidopsis root_Dosed with gold_rep3

city: York

first: Elizabeth

middle: L

last: Rylott

address: Wentworth Way

department: Department of Biology

institute: University of York

description: Root gene expression data from hydroponically-grown Arabidopsis treated with gold

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis ATH1 array.

scan_protocol: GeneChips were scanned using an Affyimetrix GCS3000 scanner with Command Console Software (AGCC)

data_processing: Data was processed using GeneSpring GX10 Expression software (Agilent Technologies) and global scaling as normalisation method.   Differentially expressed genes were identified using a two-class t-test (p< 0.05 significance level).   Genes that were up or down-regulated more than 2-fold were selected

organism: Arabidopsis thaliana

source_name: Arabidopsis roots 0.125 mM gold 24 h

label_protocol: The cDNA was labelled using a MessageAmp™ II-Biotin Enhanced Kit (Ambion)

growth_protocol: For the microarray experiment, Arabidopsis was grown according to the method described by Kumari et al. (Kumari et al. 2008). Rafts were made from circular lightweight plastic, 75 mm diameter and 6 mm thick. Approximately 100 holes (3-4 mm diameter) were drilled into each disk. These rafts were sterilised by autoclaving and the holes were plugged with ½MS(A). Sterile Arabidopsis seeds, which had been stratified for two nights in the dark at 4 ºC, were pipetted onto each plugged hole. Rafts were transferred to liquid Richard’s medium (pH 5.7). Plants were grown in sealed sterile jars for 14 days at 22 ºC / 19 ºC day / night temperatures on a 16 hour light (80 μmol.m-2.s-1) / 8 hour dark cycle.

extract_protocol: Total RNA was extracted usign Qiagen RNAeasy kit for plants. RNA quality was tested using a Bioanalyser (Agilent Technologies)

treatment_protocol: 0.125 mM KAuCl4 was prepared in  water and pH adjusted to pH 5.7 using NaOH. 1/2 Murashige and Skoog (1962) liquid growth medium was replaced with 0.125 mM KAuCl4 solution for six hours, and plants grown at 80 μmol.m-2.s-1 21 oC for 6 hours. then roots harvested, snap frozen in liquid nitrogen and total RNA extracted.

tag: ecotype

value: Col 0

tag: tissue

value: roots

value: 0.125 mM gold 24 h


title: S.coelicolor germination_time 4.5 h_replicate 3

source_name: proportional mixture of RNA samples from all time points


title: New RNA Kb2


title: S.coelicolor germination_time 4.5 h_replicate 1


title: Arabidopsis root_Dosed with gold_rep1

tag: treatment


title: S.coelicolor germination_time 3.5 h_replicate 2


title: S.coelicolor germination_time 3.5 h_replicate 1


title: Arabidopsis root_no gold_rep2

description: Root gene expression data from hydroponically-grown Arabidopsis not treated with gold

source_name: Arabidopsis roots untreated 24 h

value: untreated


title: dCH3_2 with array type SUNFLOWER from Affymetrix


title: S.coelicolor germination_time 3 h_replicate 2

source_name: S.coelicolor germination time 3 h


title: Total RNA Kb1


title: S.coelicolor germination_time 2.5 h_replicate 2

source_name: S.coelicolor germination time 2.5 h


title: Arabidopsis root_No gold_rep1


title: S.coelicolor germination_time 3 h_replicate 3


title: Arabidopsis root_no gold_rep3


title: Arabidopsis root_Dosed with gold_rep2


title: IBM1R_2 with array type ATH1 from Affymetrix

description: Epigenetic informations include histone post-translational modifications such as acetylation and methylation. The jumoni proteins can remove the methyl group from lysine or arginine residues of histones. The aim of this project is to compare gene expression levels between mutants of two jumonji genes and wild type at seedling stage (12 d old).

hyb_protocol: labelled extract quantity: 15ug

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label_protocol: labelling Biotin indirect, amplification=yes, ssDNA 5.5 ug.

growth_protocol: aerial - MS 0,5X - Hygrometry 60% - Long Day (16h 20 °C, 8h 18°C) - 120 μmol.m-2.s-1

treatment_protocol: no treatment

tag: genotype/variation

value: IBM1 knockout


title: dABA_2 with array type SUNFLOWER from Affymetrix

value: dormant


title: JMJ24R_2 with array type ATH1 from Affymetrix

growth_protocol: aerial - - MS 0,5X - Hygrometry 60% - Long Day (16h 20 °C, 8h 18°C) - 120 μmol.m-2.s-1

value: JMJ24 knockout


title: COLOR_2 with array type ATH1 from Affymetrix

value: WT


title: NDH2O_2 with array type SUNFLOWER from Affymetrix

value: (boyes et al. plant cell 2001):seed


title: JMJ24IBMR_2 with array type ATH1 from Affymetrix

growth_protocol: aerial - - MS 0,5X - Hygrometry 60% - Long Day (16h 20 °C, 8h 18°C) - 120 μmol.m-2.s-

value: JMJ24-IBM1 double knockout


title: dH20_1 with array type SUNFLOWER from Affymetrix


title: S.coelicolor germination_time 2 h_replicate 3

source_name: S.coelicolor germination time 2 h


title: S.coelicolor germination_time 3 h_replicate 1


title: COLOR_1 with array type ATH1 from Affymetrix


title: JMJ24IBMR_1 with array type ATH1 from Affymetrix


title: CHES1 rep3

city: Montréal

first: Mathieu

last: Vernier

state: Quebec

address: 2900 Edouard Montpetit

department: Biochemistry

institute: Université de Montréal

description: Gene expression data from H1299 infected with a vector expressing CHES3

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

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G/4 Color Early Access.

data_processing: The data were analyzed with the affymetrix Expression Console software using Affymetrix default analysis settings and RMA as normalization method. Transcripts with a fold change higher or equal to 1.5 and a p-value˂ 0.05 according to the two-sample student's t-test were selected for final determination.

source_name: H1299 infected with a vector expressing CHES1, 5 days post-infection

label_protocol: Biotinylated cRNA were prepared according to the protocol from the Ambion® WT Expression kit for Affymettrix® GeneChip®Whole Transcrpit (WT) Expression Arrays

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle medium (DMEM; Wisent, Montréal, QC) supplemented with 10% fetal bovine serum (FBS; Wisent) and 1% penicillin G/streptomycin sulfate (Wisent).

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

treatment_protocol: Cells were infected with an empty retrovirus or a retrovirus expressing CHES1 and selected during three days with 5 µg/ml puromycin before RNA extraction.

tag: cell line

tag: vector

value: expressing CHES1


title: zebrafish mycobacterium yolk injection embryos experiment 2

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

institute: Leiden University

description: Single sample

hyb_protocol: The dual colour hybridization of the microarray chips was performed at the Microarray Department (MAD) of the University of Amsterdam (Amsterdam, The Netherlands) using the standard Agilent protocol.

scan_protocol: The arrays were scanned with DNA Microarray Scanner G2565CA from Agilent Technologies. The arrays were scanned twice with 10% PMT and 100% PMT laser power.

data_processing: Microarray data was processed from raw data image files with Feature Extraction Software 9.5.3.1 (Agilent Technologies). The XDR function was used to extend the dynamic range. Processed data were subsequently imported into Rosetta Resolver 7.0 (Rosetta Biosoftware, Seattle, Washington) and subjected to default ratio error modelling. The Agilent Feature Extraction files contain the final log ratio data. The algorithms that were used to normalize the feature signal and calculate the log ratios are described in the Reference Guide for Agilent Feature Extraction Software v9.5. The standard settings as described for the GE2-v5_95 protocol in the Reference Guide were used. In order to calculate the normalized signal, the Rank Consistency Probes method was used and the Linear&LOWESSDyeNormFactor (= DyeNormalSignal/(BGSubSignal x LinearDyeNormFactor) was calculated as described on page 231 of the Reference Guide. The dye normalized signal was calculated as follows (page 232): DyeNormSignal = BGSubSignal x DyeNormFactor. The log10 ratio was subsequently calculated as follows (page 232): LogRatio = Log(rProcessedSignal/gProcessedSignal), where rProcessedSignal and gProcessedSignal are signals post dye normalization and post surrogate processing in the red and green channels, respectively. The surrogate values are calculated and used as the lowest limit of detection to replace the dye normalized signal when either the mean feature signal is less than the background signal or not significant when compared to the background signal, or when the mean signal is less than its background standard deviation (page 226).

organism: Danio rerio

source_name: D.rerio_infected_experiment 2

label_protocol: Amino Allyl modified aRNA was synthesized in one amplification round from 1 ug of total RNA using the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion). Subsequently, 6 ug of Amino Allyl modified aRNA was used for coupling of monoreactive Cy3 or Cy5 dye (GE Healthcare) and column purified.

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol: Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Zebrafish embryos were either untreated or micro-injected into the yolk (2hpf) with 12 CFU (+/- 7) of Mycobacterium strain E11 mCherry bacteria suspended in PVP (Polyvinylpyrrolidone),  At 5 days post fertilization embryos were snap frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

value: 5 days post fertilisation embryos

tag: agent

value: Mycobacterium marinum

value: none (control)


title: IBM1R_1 with array type ATH1 from Affymetrix


title: zebrafish mycobacterium yolk injection embryos experiment 1

description: Single sample

source_name: D.rerio_infected_experiment 1


title: S.coelicolor germination_time 2.5 h_replicate 1


title: S.coelicolor germination_time 2 h_replicate 2


title: S.coelicolor germination_time 2 h_replicate 1


title: CHES1 rep1

description: Gene expression data from H1299 infected with a vector expressing CHES1


title: zebrafish control embryos 1

description: Single sample


title: S.coelicolor germination_time 1.5 h_replicate 3

source_name: S.coelicolor germination time 1.5 h


title: zebrafish control embryos 2

description: Single sample


title: Non-Pregnant_Endometrium_Sow, biological replicate 4

city: Hamilton

first: Jocelyn

last: Wessels

address: 1280 Main Street West

department: Obstetrics and Gynecology

institute: McMaster University

description:
Non-Pregnant Endometrium 4
Experimental replicate 4 of 4 (Non-Pregnant Endometrium).

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer-defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing:
Microarray assay was performed by LC Sciences.
Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.
Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system-related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193]. A transcript to be listed as detectable must meet at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.
T-test is performed between control and test sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using a hierarchical method and is performed with average linkage and Euclidean distance metric.
All data processes, except clustering plot, are carried out using in-house-developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

organism: Sus scrofa

source_name: Mesometrial endometrium from a non-pregnant sow, mid-estrus, sow #4

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 2 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore), and the small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3/Cy5 dye staining.

growth_protocol: None. Gestation Day 20 sows (Yorkshire breed).

extract_protocol: Total RNA was extracted using the miRNeasy mini kit (Qiagen).

treatment_protocol: None.

tag: breed

value: Yorkshire

tag: gender

value: female

value: endometrium

tag: pregnancy status

value: non-pregnant

tag: sow identifier


title: Non-Pregnant_Endometrium_Sow, biological replicate 3

description:
Non-Pregnant Endometrium 3
Experimental replicate 3 of 4 (Non-Pregnant Endometrium).

source_name: Mesometrial endometrium from a non-pregnant sow, mid-estrus, sow #3


title: JMJ24R_1 with array type ATH1 from Affymetrix


title: CHES1 rep2

description: Gene expression data from H1299 infected with a vector expressing CHES2


title: S.coelicolor germination_time 1.5 h_replicate 1

tag: strain