title: ILC2_Media_24 hour_rep2

description:
SAM3461521
Human ILC2 cells treated with media for 24 hours.


title: Rat_liver_HW_10_TCDD_19_hours_rep_3 [NanoString]

status: Public on Dec 31 2013

type: RNA

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

description: Treated

data_processing: Raw NanoString data (absolute molecule counts) were loaded into the R statistical environment (v2.12.2). Data was normalized for hybridization efficiency using the positive, spike-in controls, negative controls and reference genes Eef1a1, Gapdh, Hprt1, Ppia and Sdha and log2 transformed. Fold-changes calculated using the mean of the biological replicates (Treated - Control).

label: FAM

molecule: total RNA

organism: Rattus norvegicus

source_name: liver, Han/Wistar, 10 TCDD, 19 hour exposure

growth_protocol: Animals were housed in suspended, stainless-steel wire-mesh cages in groups of 4 rats with a 12h/12h light/dark cycle and with pelleted R36 feed and tap water. The temperature was maintained at  21 +/- 1 degree Celcius with relative humidity 50% +/- 10%.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini kits according to the manufacturer’s instructions (Qiagen, Mississauga, Canada). RNA was quantified using a NanoDrop UV spectrophotometer (Thermo Scientific, Mississauga, ON) and RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Animals were treated with either TCDD or corn oil vehicle alone by oral gavage.

tag: gender

value: Male

tag: tissue

value: Liver

tag: strain

value: Han/Wistar

tag: age

value: 10-12 weeks

tag: treatment

value: 10 ug/kg

tag: exposure

value: 19 hours


title: Sabre_PBMC_14

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

country: Germany

institute: Leibniz Institute for Farm Animal Biology (FBN)

description: Gene expression data from PBMC sample of adults

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42°C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

label: biotin

organism: Sus scrofa

source_name: Leukocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: status of aggressiveness

value: high

tag: Sex

value: m

tag: breed

value: German Landrace


title: ILC2_Media_24 hour_rep1

city: South San Francisco

first: Alex

last: Abbas

state: CA

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech, Inc.

description:
SAM3461520
Human ILC2 cells treated with media for 24 hours.

hyb_protocol: cRNA was hybridized on Agilent-026652 Whole Human Genome Microarray 4x44K v2.

scan_protocol: Chips were scanned using the Agilent SureScan Microarray Scanner.

data_processing: The data were processed with Agilent Feature Extraction software, version 10.7.3.1, using default settings, including linear and Lowess normalization.

organism: Homo sapiens

source_name: ILC2 cells, media, 24 hr

label_protocol: Biotinylated cRNA were prepared according to the standard Agilent protocol.

growth_protocol: Purified ILC2s were expanded in vitro in the presence of IL-2, IL-7, IL-33 and IL-25 (each at 50 ng/ml) for 7-10 days and then rested for 2 days in the presence of 1 ng/ml IL-2 and IL-7.

extract_protocol: RNeasy Mini Kit (Qiagen).

treatment_protocol: Cells were treated in the presence of 1 ng/ml IL-2 and IL-7 with either media control, IL-25 (50 ng/ml), IL-33 (50 ng/ml), and/or TSLP (50 ng/ml) in combination, for 6 or 24 hours.

tag: cell type

value: ILC2 (Lineage negative, CRTH2+, CD161+, CD127+)

tag: cytokine treatment

value: media

tag: time point

value: 24 hours

extract_protocol: Stratagene Universal Human Reference RNA (catalog number 740000).

tag: sample type

value: reference


title: ILC2_IL-33 IL-25_6 hour_rep4

description:
SAM798419
Human ILC2 cells treated with IL-33/IL-25 for 6 hours.

source_name: ILC2 cells, IL-33/IL-25, 6 hr

value: 6 hours

source_name: Stratagene Universal Human Reference RNA


title: Sabre_PBMC_11

value: low

value: f


title: Sabre_PBMC_12


title: Sabre_PBMC_10


title: Sabre_PBMC_9


title: ILC2_IL-33 IL-25_6 hour_rep3

description:
SAM798418
Human ILC2 cells treated with IL-33/IL-25 for 6 hours.


title: Rat_liver_HW_100_TCDD_19_hours_rep_1 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 19 hour exposure

value: 100 ug/kg


title: Sabre_PBMC_7


title: Rat_liver_HW_10_TCDD_19_hours_rep_2 [NanoString]

description: Treated

value: Male


title: Sabre_PBMC_8


title: ILC2_IL-33 IL-25_6 hour_rep2

description:
SAM798417
Human ILC2 cells treated with IL-33/IL-25 for 6 hours.


title: ILC2_IL-33 IL-25_6 hour_rep1

description:
SAM798416
Human ILC2 cells treated with IL-33/IL-25 for 6 hours.


title: Rat_liver_HW_1_TCDD_19_hours_rep_3 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 1 TCDD, 19 hour exposure

value: Liver

value: 1 ug/kg


title: Rat_liver_HW_1_TCDD_19_hours_rep_2 [NanoString]

description: Treated

value: Han/Wistar

value: 10-12 weeks


title: Sabre_PBMC_5


title: Rat_liver_HW_1_TCDD_19_hours_rep_4 [NanoString]

description: Treated

value: 19 hours


title: Rat_liver_HW_1_TCDD_19_hours_rep_1 [NanoString]

description: Treated


title: Rat_liver_HW_10_TCDD_19_hours_rep_1 [NanoString]

description: Treated

value: 10 ug/kg


title: ILC2_IL-33_6 hour_rep4

description:
SAM798414
Human ILC2 cells treated with IL-33 for 6 hours.

source_name: ILC2 cells, IL-33, 6 hr


title: Rat_liver_HW_0.1_TCDD_19_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 0.1 TCDD, 19 hour exposure

value: 0.1 ug/kg


title: ILC2_IL-33_6 hour_rep5

description:
SAM798415
Human ILC2 cells treated with IL-33 for 6 hours.


title: ILC2_IL-33_6 hour_rep3

description:
SAM798413
Human ILC2 cells treated with IL-33 for 6 hours.


title: Sabre_PBMC_6

value: high

value: m

value: German Landrace


title: ILC2_IL-25_6 hour_rep4

description:
SAM798409
Human ILC2 cells treated with IL-25 for 6 hours.

source_name: ILC2 cells, IL-25, 6 hr

value: ILC2 (Lineage negative, CRTH2+, CD161+, CD127+)


title: ILC2_IL-33_6 hour_rep1

description:
SAM798411
Human ILC2 cells treated with IL-33 for 6 hours.

value: reference


title: ILC2_IL-25_6 hour_rep5

description:
SAM798410
Human ILC2 cells treated with IL-25 for 6 hours.

value: 6 hours


title: Sabre_PBMC_4

value: low


title: Rat_liver_HW_0.1_TCDD_19_hours_rep_3 [NanoString]

description: Treated


title: Sabre_PBMC_3


title: ILC2_IL-33_6 hour_rep2

description:
SAM798412
Human ILC2 cells treated with IL-33 for 6 hours.


title: DT40_Pax5KO_rep3

city: Stockholm

first: Pekka

middle: Juhani

last: Kohonen

address: Nobelsväg 13, Box 210

department: IMM Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

hyb_protocol: According to manufacturer's instructions.

data_processing: The dataset was log2 transformed as part of the RMA protocol (Irizarry RA et al. 2003). All results were combined to a single data table.

organism: Gallus gallus

source_name: B cell, cell line, DT40, gene knock out,  Pax5 deficient

growth_protocol: DT40 B cells were maintained in RPMI 1640 supplemented with 10% FCS, 1% chicken serum, 50 micromolar beta-mercaptoethanol, 2 micromolar L-glutamine, penicillin and streptomycin. The cells were cultured at +40 degrees Celsius in a humified atmosphere with 5% CO2.<br>(Parameters: time unit = seconds, min temperature = 40, temperature unit = C)

extract_protocol: The RNA was isolated from DT40 wt and Pax5-/- cells using TRIzol reagent (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) using RNA cleanup protocol according to manufacturers instructions  The RNA was isolated from DT40 wt and Bcl6-/- cells using TRIzol reagent (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) using RNA cleanup protocol according to manufacturers instructions.<br>(Parameters: Extracted product = total_RNA, Amplification = none)

treatment_protocol: In the gene-targeting construct Pax5-neo, the selection cassette was flanked by 2.0 and 2.5 kb of the chicken Pax5 sequence in the 5' and 3' sides, respectively. In the Pax5-bsr construct, the selection cassette was flanked by 3.0 and 4.0 kb of the Pax5 sequence on the 50 and 30 sides, respectively. The Pax5-neo and Pax5-bsr were introduced into DT40 cells by electroporation. Stable transfectant cloneswere selected.  flanked by 2.0 and 2.5 kb of the chicken Pax5 sequence in the 50 and 30  sides, respectively

tag: cell line

tag: developmental stage

value: adult

tag: genetic modification

value: gene knock out

tag: genotype

tag: organism part

value: bursa of Fabricius

value: female

tag: targeted cell type

value: B cell


title: ILC2_IL-25_6 hour_rep1

description:
SAM798406
Human ILC2 cells treated with IL-25 for 6 hours.


title: Rat_liver_HW_0.1_TCDD_19_hours_rep_2 [NanoString]

description: Treated

tag: gender

value: Male

tag: tissue

value: Liver

tag: strain

value: Han/Wistar


title: Rat_liver_HW_0.01_TCDD_19_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 0.01 TCDD, 19 hour exposure

tag: age

value: 10-12 weeks

tag: treatment

tag: exposure

value: 19 hours


title: Rat_liver_HW_0.1_TCDD_19_hours_rep_1 [NanoString]

description: Treated

value: 0.1 ug/kg


title: Sabre_PBMC_2

tag: status of aggressiveness

value: high

tag: Sex

value: m

tag: breed


title: ILC2_IL-25_6 hour_rep2

description:
SAM798407
Human ILC2 cells treated with IL-25 for 6 hours.

tag: cell type

value: ILC2 (Lineage negative, CRTH2+, CD161+, CD127+)

tag: cytokine treatment

tag: time point


title: Sabre_PBMC_1

value: f

value: German Landrace


title: DT40_Pax5KO_rep1

scan_protocol: According to manufacturer's instructions.

tag: cell line

tag: developmental stage


title: ILC2_Media_6 hour_rep4

description:
SAM798404
Human ILC2 cells treated with media for 6 hours.

source_name: ILC2 cells, media, 6 hr

value: media

value: 6 hours

tag: sample type

value: reference


title: Rat_liver_HW_0.01_TCDD_19_hours_rep_3 [NanoString]

description: Treated


title: Rat_liver_HW_0.01_TCDD_19_hours_rep_2 [NanoString]

description: Treated


title: Rat_liver_HW_0.01_TCDD_19_hours_rep_1 [NanoString]

description: Treated


title: DT40_WildType_rep3

source_name: B cell, cell line, DT40, gene knock out,  wild type

label_protocol: According to manufacturer's instructions.

value: adult

tag: genetic modification

value: gene knock out

tag: genotype

value: wild type

tag: organism part

value: bursa of Fabricius


title: Rat_liver_HW_0.001_TCDD_19_hours_rep_3 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 0.001 TCDD, 19 hour exposure

tag: gender

value: Male

tag: tissue

value: Liver


title: DT40_Pax5KO_rep2

value: female

tag: targeted cell type

value: B cell


title: Rat_liver_HW_0.001_TCDD_19_hours_rep_1 [NanoString]

description: Treated

tag: strain

value: Han/Wistar

tag: age

value: 10-12 weeks

tag: treatment

value: 19 hours


title: L2868_b

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

country: France

institute: INRA

description: Gene expression in sample L2868, biological rep 2

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 038619 completed with the regions A, B and C + KHR1 + MPR1 from the new regions of EC1118  (Agilent Technologies, Santa Clara, CA, USA). A quantity of 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plate were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software PRO7

data_processing: Data normalization and statistical analysis were performed using R 2.14.2 software and the limma package. Normalization was done by the quantile method considering all arrays

organism: Saccharomyces cerevisiae

source_name: L2868 repetition 2

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific)

growth_protocol: For each strain, RNAs were isolated from fermenting cells, at 45g/L of CO2 production (50% fermentation progress on a nitrogen limited medium containing 100mg.l-1 assimilable nitrogen).

extract_protocol: Total RNA extraction were perform with Trizol reagent (Gibco BRL, Life Technologies), purified by isopropanol precipitation then with RNeasy kit (Qiagen).

treatment_protocol: For each condition, 10E9 cells were sampled, pelleted, washed with DEPC-treated water and freeze in methanol at -80°C.

tag: array

tag: block

tag: nitrogen requirements

value: HNR


title: Rat_liver_HW_0.001_TCDD_19_hours_rep_2 [NanoString]

description: Treated

tag: exposure


title: ILC2_IL-25_6 hour_rep3

description:
SAM798408
Human ILC2 cells treated with IL-25 for 6 hours.

tag: cell type

value: ILC2 (Lineage negative, CRTH2+, CD161+, CD127+)

tag: cytokine treatment

tag: time point


title: s4CAR1_b

description: Gene expression in sample 4CAR1, biological rep 2

source_name: s4CAR1 repetition 2


title: Zymasil_b

description: Gene expression in sample Zymasil, biological rep 2

source_name: Zymasil repetition 2

value: Zymasil


title: ILC2_Media_6 hour_rep5

description:
SAM798405
Human ILC2 cells treated with media for 6 hours.

value: media

tag: sample type


title: DT40_WildType_rep2

tag: cell line

tag: developmental stage

tag: genetic modification

tag: Sex


title: Rat_liver_HW_0.001_TCDD_19_hours_rep_4 [NanoString]

description: Treated

tag: gender

tag: tissue


title: EC1118_b

description: Gene expression in sample EC1118, biological rep 2

source_name: EC1118 repetition 2

tag: strain


title: K1M_b

description: Gene expression in sample K1M, biological rep 2

source_name: K1M repetition 2

value: LNR


title: ILC2_Media_6 hour_rep2

description:
SAM798402
Human ILC2 cells treated with media for 6 hours.

value: 6 hours

value: reference


title: ILC2_Media_6 hour_rep1

description:
SAM798401
Human ILC2 cells treated with media for 6 hours.


title: MTF1782_b

description: Gene expression in sample MTF1782, biological rep 2

source_name: MTF1782 repetition 2


title: Rat_liver_HW_Corn_oil_19_hours_rep_6 [NanoString]

description: Control

source_name: liver, Han/Wistar, Corn oil treated, 19 hour exposure

tag: age

value: Corn Oil vehicle


title: ILC2_Media_6 hour_rep3

description:
SAM798403
Human ILC2 cells treated with media for 6 hours.

source_name: Stratagene Universal Human Reference RNA


title: DT40_WildType_rep1

value: adult

value: gene knock out

tag: genotype

value: wild type

tag: organism part

tag: targeted cell type


title: Fermiflor_b

description: Gene expression in sample Fermiflor, biological rep 2

source_name: Fermiflor repetition 2

value: Fermiflor

tag: array

tag: block

tag: nitrogen requirements


title: MTF1782_a

description: Gene expression in sample MTF1782, biological rep 1

source_name: MTF1782 repetition 1


title: Rat_liver_HW_Corn_oil_19_hours_rep_7 [NanoString]

description: Control

value: Male

value: Liver

tag: treatment

tag: exposure


title: L2868_a

description: Gene expression in sample L2868, biological rep 1

source_name: L2868 repetition 1


title: s7013_a

description: Gene expression in sample 7013, biological rep 1

source_name: s7013 repetition 1


title: s7013_b

description: Gene expression in sample 7013, biological rep 2

source_name: s7013 repetition 2


title: Rat_liver_HW_Corn_oil_19_hours_rep_3 [NanoString]

description: Control

value: Han/Wistar


title: EC1118_a

description: Gene expression in sample EC1118, biological rep 1

source_name: EC1118 repetition 1


title: Rat_liver_HW_Corn_oil_19_hours_rep_2 [NanoString]

description: Control

value: 10-12 weeks


title: Human Embryonic stem cells

city: Baltimore

first: Xiaosong

last: Huang

state: Maryland

address: 733 North Broadway, Rm780

department: Medicine/Hematology

institute: Johns Hopkins University

description:
Human Embryonic stem cells
ESC

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip® Expression Wash, Stain and Scan User Manual (www.affymetrix.com).

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
Image analysis used the Affymetrix Command Console version 3 (AGCC v3.0) software, processed with the Expression Console PLIER algorithm and the manufacturer’s specifications.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.na33.1.hg19.probeset.csv, HuGene-1_0-st-v1.na33.1.hg19.transcript.csv
RMA Log2 values from the Partek Genomics Suite, using all probesets, were summarized for gene-level analysis.

source_name: Human Embryonic stem cells

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter engineered random primers for cDNA synthesis, and Ambion® WT Expression Kit (www.affymetrix.com).

growth_protocol: pCBE19: After thawing, frozen CB MNCs (5x106/ml) were cultivated in serum-free medium (SFM; 50% IMDM with 50% Ham’s F12 (Invitrogen), synthetic lipids (Invitrogen), insulin-transferrin-selenium supplement (Invitrogen) and 5 mg/ml BSA (Sigma), 50 ug/ml of ascorbic acid (Sigma) and 2 mM glutamax ) supplemented with Epo (2 U/mL; R&D systems), Dexamethasone (1 µM; Sigma), insulin-like growth factor 1 (IGF-1; 40 ng/mL), stem cell factor (SCF; 100 ng/mL), and holo-transferrin (100 µg/ml; Sigma), termed “erythroblast expansion medium” in gelatin-coated wells. Primary cultures of erythroblasts established after several days were kept less than 1x106 cells/ml by daily cell counting and partial medium changes. iE2: Grow in the erythroblast expansion medium. After the culture cells become proliferating constantly, only partial medium change and cell passaging every 2 or 3 days are performed to keep cell density at or below 5 × 105 cells/ml. CD34+: primary cells isolated by magenetic beads binding to CD34 cell surface marker. TF-1: RPMI-1640+10% FBS+ 3U/ml hEPO. iPSC and ESC: standard ESC medium and on MEF feeder.

extract_protocol: RNeasy according to manufacture's protocol

treatment_protocol: no treatment

tag: tissue of origin

value: blastocyst

tag: expansion days

value: passage 51

tag: genetic factors

value: no genetic factors


title: Human induced pluripotent stem cells derived from adult blood cells (Large T antigen)

description:
Human induced pluripotent stem cells derived from adult blood cells
iPSC2

value: adult blood

value: passage 36

value: OCT4, SOX2, KLF4, C-MYC, LIN28, Large T antigen


description:
Human induced pluripotent stem cells derived from adult blood cells
iPSC1

value: passage 37

value: OCT4, SOX2, KLF4, C-MYC, LIN28


title: Human induced pluripotent stem cells derived from mesenchymal stromal cells

description:
Human induced pluripotent stem cells derived from adult mesenchymal stromal cells
iPSC4

value: adult mesenchymal stromal cells

value: passage 29


description:
Human erythroleukemia cell line TF-1 cultured with Epo for 8 days
TF-1

value: bone marrow

value: years


title: s4CAR1_a

description: Gene expression in sample 4CAR1, biological rep 1

source_name: s4CAR1 repetition 1

value: HNR


title: Rat_liver_HW_100_TCDD_10_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 10 hour exposure

value: Male

value: 100 ug/kg

value: 10 hours


description:
Human induced pluripotent stem cells derived from adult mesenchymal stromal cells
iPSC3

value: passage 38


title: Rat_liver_HW_Corn_oil_19_hours_rep_5 [NanoString]

description: Control

value: Liver

value: Han/Wistar

value: 10-12 weeks

value: Corn Oil vehicle

value: 19 hours


title: Zymasil_a

description: Gene expression in sample Zymasil, biological rep 1

source_name: Zymasil repetition 1

value: Zymasil


title: Rat_liver_HW_Corn_oil_19_hours_rep_1 [NanoString]

description: Control


title: Rat_liver_HW_Corn_oil_19_hours_rep_4 [NanoString]

description: Control


title: Rat_liver_HW_100_TCDD_10_hours_rep_3 [NanoString]

description: Treated


title: Rat_liver_HW_100_TCDD_10_hours_rep_2 [NanoString]

description: Treated


title: Human fetal liver isolated CD34+ cells

description:
Human fetal liver isolated CD34+ cells
FL CD34+

source_name: Human fetal liver isolated CD34+ cells

value: fetal liver

value: 4 days

value: no genetic factors


title: Rat_liver_HW_100_TCDD_10_hours_rep_1 [NanoString]

description: Treated


title: K1M_a

description: Gene expression in sample K1M, biological rep 1

source_name: K1M repetition 1

value: LNR


title: Rat_liver_HW_100_TCDD_6_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 6 hour exposure

value: 6 hours


title: Fermiflor_a

description: Gene expression in sample Fermiflor, biological rep 1

source_name: Fermiflor repetition 1

value: Fermiflor


title: Rat_liver_HW_100_TCDD_6_hours_rep_3 [NanoString]

description: Treated


title: Rat_liver_HW_100_TCDD_6_hours_rep_2 [NanoString]

description: Treated


title: Rat_liver_HW_100_TCDD_3_hours_rep_4 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 3 hour exposure

value: 3 hours


title: Rat_liver_HW_100_TCDD_6_hours_rep_1 [NanoString]

description: Treated

value: Male


title: primary CB-derived erythroblasts at day 19 of expansion culture (donor b) (subset CD235a-)

description:
gene expression data from primary erythroblasts at day 19 expansion culture (FACS sorted subset CD235a-CD45+) from CB MNCs (donor b) in serum-free medium supplemented with SCF, IL-3, IGF-1, EPO and Dexamethasone
pCBE19b2

source_name: day 19 expansion culture of primary erythroblasts from human cord blood mononuclear cells (donor b)(subset CD235a-)

value: cord blood

value: 19 days


title: Rat_liver_HW_100_TCDD_3_hours_rep_2 [NanoString]

description: Treated

value: 100 ug/kg


title: immortalized erythroblasts (donor b) at day 40 of expansion culture (after viral transduction)

description:
immortalized erythroblasts at day 40 of expansion culture (after viral transduction) in serum-free medium supplemented with SCF, IL-3, IGF-1, EPO and Dexamethasone
iE2(d40)

value: Sox2, Klf4, c-Myc and p53shRNA


title: Human adult blood isolated CD34+ cells

description:
Human adult blood isolated CD34+ cells
CD34+

source_name: Human adult blood isolated CD34+ cells

value: adult blood


title: Rat_liver_HW_100_TCDD_3_hours_rep_3 [NanoString]

description: Treated

value: Liver

value: Han/Wistar

value: 10-12 weeks


title: immortalized erythroblasts (donor b) at day 141 of expansion culture (after viral transduction)

description:
immortalized erythroblasts at day 141 of expansion culture (after viral transduction) in serum-free medium supplemented with SCF, IL-3, IGF-1, EPO and Dexamethasone
iE2(d141)


title: primary CB-derived erythroblasts at day 19 of expansion culture (donor b) (subset CD235a+)

description:
gene expression data from primary erythroblasts at day 19 expansion culture (FACS sorted subset CD235a+CD45+) from CB MNCs (donor b) in serum-free medium supplemented with SCF, IL-3, IGF-1, EPO and Dexamethasone
pCBE19b1

source_name: day 19 expansion culture of primary erythroblasts from human cord blood mononuclear cells (donor b)(subset CD235a+)


title: Rat_liver_HW_100_TCDD_1.5_hours_rep_3 [NanoString]

description: Treated

source_name: liver, Han/Wistar, 100 TCDD, 1.5 hour exposure

value: 1.5 hours


title: Rat_liver_HW_100_TCDD_3_hours_rep_1 [NanoString]

description: Treated


title: primary CB-derived erythroblasts at day 19 of expansion culture (donor b)

description:
gene expression data from primary erythroblasts at day 19 expansion culture from CB MNCs (donor b) in serum-free medium supplemented with SCF, IL-3, IGF-1, EPO and Dexamethasone
pCBE19b

source_name: day 19 expansion culture of primary erythroblasts from human cord blood mononuclear cells (donor b)


title: Rat_liver_HW_100_TCDD_1.5_hours_rep_1 [NanoString]

description: Treated


title: Rat_liver_HW_100_TCDD_1.5_hours_rep_2 [NanoString]

description: Treated


title: Rat_liver_HW_Corn_oil_1.5_hours_rep_3 [NanoString]

description: Control

source_name: liver, Han/Wistar, Corn oil treated, 1.5 hour exposure

value: Corn Oil vehicle


title: Rat_liver_HW_Corn_oil_1.5_hours_rep_2 [NanoString]

description: Control


title: Rat_liver_HW_Corn_oil_1.5_hours_rep_1 [NanoString]

description: Control


title: CB70BS2 ANG2+TGF

city: Epalinges

first: Marie-Agnès

last: Doucey

address: Biopôle 3; Ch. des Boveresses 155

country: Switzerland

description: Gene expression data from human Cord-blood derived monocytes treated with Ang-2 and TGF

hyb_protocol: Affymetrix Human Gene 1.0 ST arrays (Affymetrix, Santa Clara , CA, USA) were hybridized with 2.7 microg of biotinylated target, at  45°C for 17 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007).

scan_protocol: The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).

data_processing: Background subtraction, RNA normalization and probeset summarization were performed using the Affymetrix Power Tools software package

source_name: Cord-blood derived monocytes

label_protocol: For each sample, 100ng of total RNA were amplified using the WT sense strand Target Labelling kit (Affymetrix, Cat.no. 900223); 5.5 microg of the resulting sense cDNA was fragmented by UDG (uracil DNA glycosylase) and APE 1 (apurinic/apyrimidic endonuclease 1) and biotin-labelled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip® WT Terminal labelling kit (Affymetrix Cat.no. 900671, Santa Clara, USA).

growth_protocol: TEM were differentiated in vitro from CD34+ cord-blood precursors using SCF (Stem Cell Factor), Interleukine-6, TPO (Thrombopoietin), Flt-3 ligand and MCF-7 conditioned medium as previously reported (Laurent et al., Cancer Res. 2011 Jun 1;71(11):3781-91)

extract_protocol: Total RNAs from 10 000 monocytes were isolated and purified with the Qiagen RNeasy micro plus extraction kit.

treatment_protocol: TEM  were exposed for 2 hours to the treatments (100 ng/ml excepted TNF 20ng/ml), washed, kept for 30 h in culture and used for RNA extraction.

tag: cell type

value: Cord-blood derived monocytes


title: CB79 ANG2+TGF


title: primary CB-derived erythroblasts at day 19 of expansion culture (donor a)

description:
gene expression data from primary erythroblasts at day 19 expansion culture from CB MNCs (donor a) in serum-free medium supplemented with SCF, IL-3, IGF-1, EPO and Dexamethasone
pCBE19a

source_name: day 19 expansion culture of primary erythroblasts from human cord blood mononuclear cells (donor a)

value: no genetic factors


title: normal pancreas - Patient Sample 17

status: Public on Dec 30 2013

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

country: Italy

institute: Consiglio Nazionale delle Ricerche (CNR)

description: sample retrieved during surgery, placed in RNA Later stabilization fluid and then kept at minus 80 until required. Small RNA preparation was performed using 100ng of total RNA in 10ul volume per sample and performed according to manufacturer's instructions (NanoString Technologies).

hyb_protocol: Resulting material is hybridized with a panel of miRNA:tag-specific nCounter capture and bar-coded reporter probes. Hybridization reactions were performed according to manufacturer's instructions. Hybridized probes were purified using the nCounter Prep Station (NanoString Technologies).

scan_protocol: A high-density scan was performed for each assay. Data collection was carried out on the nCounter Digital Analyzer (NanoString Technologies) following manufacturer's instructions.

data_processing: NanoString Expression Data Analysis guide recommendations were followed.

source_name: Fresh patient tissue from surgery

label_protocol: All sample preparation was performed according to manufacturer's instructions (NanoString Technologies). Small RNA preparation was performed using 100ng of total RNA in 10ul volume per sample. Sample preparation involves a multiplexed annealing of specific tags to their target miRNAs, a ligation reaction, and an enzymatic purification step to remove unligated material.

growth_protocol: Fresh patients tissue samples were used

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

treatment_protocol: No treatment given

tag: patient

value: normal pancreas


title: normal pancreas - Patient Sample 16


title: CB79 PIGF+TGF

description: Gene expression data from human Cord-blood derived monocytes treated with PIGF and TGF

value: PIGF+TGF


title: CB80 NT

description: Gene expression data from untreated human Cord-blood derived monocytes

value: untreated


title: normal pancreas - Patient Sample 18


title: normal pancreas - Patient Sample 13


title: Chat_hb_ip_3

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

description: Trap'd MHb cholinergic neuron RNA, biological replicate 3

hyb_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform

data_processing: GCRMA normalization within biological replicate groups.  Performed with R / Bioconductor.   Entrez CDFs, version 14.

label: Biotin

organism: Mus musculus

label_protocol: Affymetrix two cycle amplification kit, starting with 20 ng of total RNA

extract_protocol: TRAP affinity purification of ribosomes from BAC transgenic mice(see PMID:19013282), followed by Trizol extraction, DNAse treatment, and RNeasy-Minelute Cleanup

value: Dissected habenula

value: adult (6-12 weeks)

value: Chat DW167

tag: sample type

value: TRAP RNA


title: Chat_hb_ub_1

description: Total tissue RNA (unbound) from Replicate 1

scan_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform

tag: tissue

value: cytoplasmic polysomal RNA, unbound


title: CB67 NT


title: normal pancreas - Patient Sample 14


title: CB70B NT


title: normal pancreas - Patient Sample 15


title: CB80 PIGF+TGF


title: Chat_hb_ip_2

description: Trap'd MHb cholinergic neuron RNA, biological replicate 2

tag: strain


title: CB61 NT


title: CB70B VEGF+TNF

description: Gene expression data from human Cord-blood derived monocytes treated with VEGF and TNF

value: VEGF+TNF


title: normal pancreas - Patient Sample 12


title: CB61 VEGF+TNF


title: Chat_hb_ub_3

description: Total tissue RNA (unbound) from Replicate 3

tag: age


title: CB80 PIGF+TNF

description: Gene expression data from human Cord-blood derived monocytes treated with PIGF and TNF

value: PIGF+TNF


title: Chat_hb_ip_1

description: Trap'd MHb cholinergic neuron RNA, biological replicate 1


title: CB70BS2 NT


title: CB79 NT


title: Chat_hb_ub_2

description: Total tissue RNA (unbound) from Replicate 2


title: pancreatic ductal adenocarcinoma - Patient Sample 09

value: pancreatic ductal adenocarcinoma


title: normal pancreas - Patient Sample 10


title: CB67 PIGF+TGF


title: pancreatic ductal adenocarcinoma - Patient Sample 08


title: Dam_only-1

type: genomic

city: Heidelberg

first: nati

last: ha

address: Im Neuenheimer Feld, 267

institute: COS, University of Heidelberg

hyb_protocol: Affymetrix Processing of DamID DNA to GeneChip Drosophila Tiling Array, was performed as in http://www.flychip.org.uk/protocols/chip/affy_chip.php

data_processing:
rMAT R package
Results file reports Abd-B binding regions throughout the genome.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: L3 testis, control DamID, expt 1

growth_protocol:
Dam was fused to the N terminus of Abd-B and transgenic flies were generated. As a control for nonspecific Dam activity, transgenic flies expressing the Dam alone were used (Choksi et al., 2006).
Plasmid construction & generation of transgenic flies for DamID:    To express the Abd-B-Dam fusion protein, we first generated a pNDam-Myc-Abd-B construct by cloning Abd-B in the pNDam-Myc vector (van Steensel et al., 2001) and then subcloned the NDam-Myc-AbdB fragment into the pUAST-attB. The Abd-B cDNA (m-form) was amplified using the following primers: 5’-CTA TAT GCG GCC GCC TCA GCA GCA CCA TCT GCA GCA GCA G-3’ (forward) and 5’-CTA TAT GCG GCC GCT CAC TGG TGC ATC TTG GCG GCA TGG-3’ (reverse) (blue, additional nucleotides; red, NotI restriction site; black, Abd-B cDNA). Generation of transgenic flies using the PhiC31-integrase system (Bischof et al. 2007) and balancing of the stock was done by BestGene Inc. (Chino Hills, CA, U.S.A.). Plasmid DNA (pUAST-Dam-Myc-Abd-B-attB) was injected into embryos of strain attP40 (cytogenetic location of attP-landing site: 25C7). Transgenic flies were balanced over CyO.

extract_protocol:
Isolation of genomic DNA (gDNA) for DamID:   Genomic DNA was extracted from L3 testes, expressing either the Dam-Abd-B fusion protein or the Dam protein alone using a specific protocol (Tolhuis et al., 2011); and van Steensel personal communication). Testes from Dam-Myc (control), Dam-Myc-Abd-B transgenic and wt flies were dissected in PBS and transferred to a glass well on ice containing ice-cold PBS. Around 200 testes were pooled in 100 μl of lysis (TENS) buffer. 2 μl of Proteinase K (20 μg ml-1) (Roche) were added and incubated for 7 hours at 65°C. Tubes were mixed every 60 min by gentle tapping. RNAs were degraded by RNase A treatment: 1 μl RNase A (100 μg ml-1) (Qiagen) were added and incubated for 30 min at 37°C. An equal volume (200 μl) of phenol: chloroform: isoamyl alcohol (25:24:1, v/v, Invitrogen) was added and mixed well by inversion until a homogenous solution was acquired. Mixture was then applied onto spin phase lock gel light 1.5 ml tube (5PRIME, Inc.) for efficient separation of the two phases. Tubes were prepared by centrifugation for 1 min at 14,000 (Eppendorf Centrifuge-5424). Spin phase lock gel light tubes containing homogenous mixture of aqueous and organic solution were then spun for 5 min at 14,000 rpm. The gel inside the spin phase lock gel light tube then separated the aqueous and organic solution and the upper aqueous solution containing gDNA was transferred to a clean 1.5 ml tube, followed by DNA precipitation. Absence of DNA degradation and of RNA was verified on a 1% agarose gel.
Digestion and PCR amplification of Dam-methylated DNA:    DNA digestion and PCR amplification was done essentially as previous described (Greil et al., 2003). To cut methylated GATC sequences, gDNA (2.5 μg) from each genotype (Dam-Myc, Dam-Myc-Abd-B and wt) was digested with DpnI in a total volume of 10 μl (1x buffer 4, NEB) at 37°C o/n in a PCR machine with a heated lid to avoid evaporation and condensation. For PCR amplification of the DpnI cut DNA sequences, adaptors were ligated to those fragments. Double-stranded adaptors were generated by mixing equal volumes of oligo AdRt (100 μM) (5’-CTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAGGA-3’) and oligo AdRb (100 μM) (5’-TCCTCGGCCG-3’) (Vogel et al., 2007) and heating to 100°C for 1 min. Adaptors were then allowed to cool down in about 20 min at RT. 5 μl of DpnI digested DNA (1.25 μg) and 2 μM of adaptors and 5 units of T4 Ligase in a final volume of 20 μl (1x T4 ligase buffer, Fermentas) were incubated for 3 hours at 16°C in a PCR machine. The ligase was inactivated at 65 °C for 10 min. To avoid amplification of fragments between two neighboring methylated GATC, which was not bound by the fusion construct itself, ligated fragments were cut at unmethlyted GATC sites using DpnII. 20 μl of ligation product (1.25 μg) were mixed with 5 units of DpnII enzyme in a final volume of 80 μl (1x DpnII buffer, NEB) and incubated for 2 hours at 37°C in a PCR machine with heated lid to avoid evaporation and condensation. The enzyme was not inactivated and digested DNA was directly used for PCR reaction or stored at -20°C. DpnII digested DNA was amplified using following PCR program. The primer (5’-GGTCGCGGCCGAGGATC-3’) was designed to fit to the adaptor (Vogel et al., 2007). Reaction mix contained approximately 313 ng DNA, 0.2 mM dATP, dCTP, dGTP, 0.16 mM dTTP, 0.04 mM dUTP (needed for fragmentation of the DNA when Affymetrix microarrays are used), 1 μM primer and 1.6 μl of Advantage cDNA Polymerase Mix in a total volume of 80 μl (1x Advantage Polymerase Mix Buffer, Clontech). The PCR product was purified using the QIAquick PCR Purification Kit according to manufacturer’s instruction and eluted in 50 μl ddH2O. Successful amplification was verified by running a small aliquot on a 1% agarose gel containing a final concentration of 0.5 μg/ml ethidium bromide.

treatment_protocol: For identifying Abd-B targets in the Drosophila testis the fusion protein was expressed from the uninduced minimal Hsp70 promoter of the UAS vector pUAST .

tag: developmental stage

value: larval testis

tag: genotype/variation

value: control DamID


title: Dam_AbdB-1

scan_protocol: Affymetrix Processing of DamID DNA to GeneChip Drosophila Tiling Array, was performed as in http://www.flychip.org.uk/protocols/chip/affy_chip.php

source_name: L3 testis, Abd-B  DamID, expt1

value: Abd-B  DamID


title: Dam_only-2

source_name: L3 testis, control DamID, expt 2

label_protocol: Affymetrix Processing of DamID DNA to GeneChip Drosophila Tiling Array, was performed as in http://www.flychip.org.uk/protocols/chip/affy_chip.php


title: Dam_AbdB-2

source_name: L3 testis, Abd-B  DamID, expt 2


title: CB58 VEGF+TNF


title: CB58 NT


title: pancreatic ductal adenocarcinoma - Patient Sample 07


title: pancreatic ductal adenocarcinoma - Patient Sample 01


title: pancreatic ductal adenocarcinoma - Patient Sample 03


title: pancreatic ductal adenocarcinoma - Patient Sample 02


title: pancreatic ductal adenocarcinoma - Patient Sample 06


title: pancreatic ductal adenocarcinoma - Patient Sample 04


title: pancreatic ductal adenocarcinoma - Patient Sample 05


title: MS2 + let-7b-5p

city: Seattle

first: Lucas

last: Dennis

state: WA

address: 530 Fairview Ave N

institute: NanoString Technologies

description: Prepared by miRQC Consortium

hyb_protocol: After enzymatic purification of unligated miRtags, prepared samples were hybridized with an nCounter Human (V2) miRNA Expression Assay CodeSet overnight at 65°C.

scan_protocol: Unhybridized CodeSet was removed via an automated purification performed on an nCoutner Prep Station and resulting target:probe complexes were deposited and bound to a imaging surface as previously described (Geiss et al, 2008 PMID: 18278033). Reporter counts were tabulated for each sample by the nCounter Digital Analyzer.

data_processing: Raw data was imported into nSolver (www.nanostring.com). Internal negative control probes included in each assay were used to determine a background threshold (3 standard deviations above the mean negative control probe count value) for each sample.  Background was subtracted from raw count values for each probe and set to 1 for all probes at or below the background threshold. Positive control count values were then used to normalize samples for any differences in sample preparation, hybridization and Prep Station processing efficiency.

source_name: Phage + Spike-In

label_protocol: 2uL of each sample was prepared per the nCounter miRNA Expression Assay Manual (www.nanostring.com). Mature miRNAs were ligated to a species-specific tag sequence (miRtag) via a thermally controlled splinted ligation.

extract_protocol: All samples were supplied by the miRQC Consortium.

tag: sample id

value: MS2 + let-7b-5p

value: MS2 + let-7b-5p Phage + Spike-In


title: MS2 + let-7d-5p

description: Prepared by miRQC Consortium

value: MS2 + let-7d-5p

value: MS2 + let-7d-5p Phage + Spike-In


title: liver + miR-302d

description: Prepared by miRQC Consortium

source_name: Liver + Spike-In

value: liver + miR-302d

value: liver + miR-302d Liver + Spike-In

value: liver


title: MS2 + let-7a-5p

description: Prepared by miRQC Consortium

value: MS2 + let-7a-5p

value: MS2 + let-7a-5p Phage + Spike-In


title: MS2 + let-7c

description: Prepared by miRQC Consortium

value: MS2 + let-7c

value: MS2 + let-7c Phage + Spike-In


title: miRQC D

description: Prepared by miRQC Consortium

source_name: Total RNA

value: miRQC D

value: miRQC D Total RNA Universal Human miRNA Reference RNA (UHmiRR, A) + human brain RNA (HBR, B)


title: miRQC C repeat

description: Prepared by miRQC Consortium

value: miRQC C repeat

value: miRQC C repeat Total RNA Universal Human miRNA Reference RNA (UHmiRR, A) + human brain RNA (HBR, B)


title: Synovial tissue after to Methotrexate therapy, repl 8

city: Brussels

first: Bernard

middle: Robert

last: Lauwerys

address: Avenue Hippocrate 10

department: Institut de Recherches Expérimentales et Cliniques

country: Belgium

institute: Université catholique de Louvain

description: MTX8 T12

hyb_protocol: GeneChip® HGU133 Plus 2.0 arrays were hybridized overnight at 45°C with 10 µg fragmented biotinylated cRNA. The slides were then washed and stained using EukGE-WS2v5 fluidics protocol on the GeneChip® Fluidics station 450.

scan_protocol: The slides were scanned on the GeneChip® Scanner 3000 (Affymetrix, UK).

data_processing: Statistical analyses of microarray data were performed using GeneSpring software (Agilent Technologies). Fluorescence intensity data were normalized by robust multiarray analysis.

source_name: Knee synovial biopsies, obtained by needle arthroscopy, 12 weeks after initiation of Methotrexate therapy (15 mg, q1w)

label_protocol: Complementary RNA (cRNA) was synthetized and biotin-labeled according to a standard Affymetrix procedure (GeneChip® 3’ IVT express kit, Affymetrix, High Wycombe, UK), as previously described. Briefly, total RNA was first reverse transcribed into single-stranded complementary DNA (cDNA) using T7 oligo(dT) primer. The second-strand cDNA is then synthetized using DNA polymerase and Rnase H to simultaneously degrade RNA. The double-stranded cDNA served as template for the in vitro transcription reaction, which was performed for 16 hours in the presence of a biotinylated ribonucleotide analog mix. At the end of the procedure, biotinylated cRNA was purified and fragmented to prepare the target for hybridization to GeneChip® Human Genome U133 Plus 2.0 arrays (Affymetrix, UK)

extract_protocol: Total RNA was extracted from the synovial biopsy samples using the Nucleospin® RNA II extraction kit (Macherey-Nagel, Düren, Germany), including DNase treatment of the samples. At least 2 µg total RNA could be extracted for further processing from 12 and 8 paired samples at T0 and T12 in TCZ- and MTX-treated groups, respectively. RNA quality was assessed using an Agilent 2100 Bioanalyzer and RNA nanochips (Agilent Technologies, Santa Clara, CA). All samples had a RNA integrity number (RIN) > 6.5

treatment_protocol:
All patients included in the protocol met the American College of Rheumatology 1987 revised classification criteria for RA. They were all methotrexate (MTX) naive at inclusion and 3 of them were treated with low-dose glucocorticoids (prednisone ≤ 7.5 mg/day). All patients presented knee synovitis at inclusion. Patients were randomized into 2 groups: 12 received intravenous 8 mg/kg/month tociliuzumab (TCZ) therapy during 6 months, and 8 were treated with MTX that was administered orally at a 15 mg/week dose. Disease activity at baseline and at 3 months was evaluated using Disease Activity Score (DAS)-28CRP.
Synovial biopsy samples from 20 patients (12 in TCZ-treated group, 8 in MTX-treated group) were obtained by needle mini-arthroscopy of the affected knee at baseline (T0) and 12 weeks (T12) after initiation of therapy. For each procedure, 4–8 synovial samples were kept overnight at 4°C in an RNA stabilizing solution (RNALater; Ambion) and then stored at –80°C for later RNA extraction.The same amount of tissue was snap-frozen in liquid nitrogen and kept at –80°C for immunostaining experiments on frozen sections. The remaining material was fixed in 10% formaldehyde and embedded in paraffin for conventional optical evaluation and immunostaining of selected markers. All the experiments (RNA extraction, histology, immunohistochemistry) were performed on at least 4 biopsy samples harvested during every procedure in order to correct for variations related to the potential heterogeneous distribution of synovial inflammation. The study was approved by the ethics committee of the Université catholique de Louvain, and informed consent was obtained from all patients.

tag: gender

value: M

tag: disease activity score (das)-28crp


title: EPC rep2

city: Tampa

first: Jeff

last: Russell

state: FL

address: 12902 Magnolia Drive

department: Head and Neck/Endocrine

institute: Moffitt Cancer Center

description:
F; replicate B
8924929066_F.AVG_Signal

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: EPC

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

growth_protocol: Primary EPC harvested passage 3-6, EPC_acLDL cells harvest passage 3-6, EPC_late harvested passage 16-20; grown in Mouse Endothelial Medium w/20% FBS

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

treatment_protocol: EPC_acLDL cells were labeled with Flourescent acLDL then sorted and only positive cells replated

value: athymic nude

value: lung

value: Endothelial Progenitor Cell (EPC)

tag: identifier

value: primary EPC

tag: passage

value: passage 3-6


title: liver + miR-302b

description: Prepared by miRQC Consortium

value: liver + miR-302b

value: liver + miR-302b Liver + Spike-In


title: liver + miR-302c

description: Prepared by miRQC Consortium

value: liver + miR-302c

value: liver + miR-302c Liver + Spike-In

value: liver


title: EPC_acLDL rep2

description:
G; replicate C
8924929066_G.AVG_Signal

value: acLDL + staining


title: miRQC D repeat

description: Prepared by miRQC Consortium

value: miRQC D repeat

value: miRQC D repeat Total RNA Universal Human miRNA Reference RNA (UHmiRR, A) + human brain RNA (HBR, B)


title: Synovial tissue after to Methotrexate therapy, repl 7

description: MTX7 T12


title: liver + miR-302a

description: Prepared by miRQC Consortium

value: liver + miR-302a

value: liver + miR-302a Liver + Spike-In


title: Synovial tissue after to Methotrexate therapy, repl 5

description: MTX5 T12

value: F


title: Synovial tissue prior to Methotrexate therapy, repl 8

description: MTX8 T0

source_name: Knee synovial biopsies, obtained by needle arthroscopy, in untreated patient with early rheumatoid arthritis (< 1 year disease duration)

value: M


title: miRQC C

description: Prepared by miRQC Consortium

value: miRQC C

value: miRQC C Total RNA Universal Human miRNA Reference RNA (UHmiRR, A) + human brain RNA (HBR, B)


title: Synovial tissue prior to Methotrexate therapy, repl 5

description: MTX5 T0


title: Synovial tissue prior to Methotrexate therapy, repl 7

description: MTX7 T0


title: Synovial tissue prior to Methotrexate therapy, repl 6

description: MTX6 T0


title: EPC_Late rep1

description:
D; Sample D
8924929066_D.AVG_Signal

value: athymic nude

value: lung

value: Endothelial Progenitor Cell (EPC)

value: high passage

value: passage 16-20


title: EPC_Late rep2

description:
H; replicate D
8924929066_H.AVG_Signal


title: Synovial tissue after to Methotrexate therapy, repl 4

description: MTX4 T12


title: miRQC B repeat

description: Prepared by miRQC Consortium

value: miRQC B repeat

value: miRQC B repeat Total RNA 100% human brain RNA (HBR, B)

value: brain


title: EPC_acLDL rep1

description:
C; Sample C
8924929066_C.AVG_Signal

value: acLDL + staining

value: passage 3-6


title: EPC rep1

description:
B; Sample B
8924929066_B.AVG_Signal

value: primary EPC


title: Synovial tissue after to Methotrexate therapy, repl 6

description: MTX6 T12


title: miRQC B

description: Prepared by miRQC Consortium

value: miRQC B

value: miRQC B Total RNA 100% human brain RNA (HBR, B)


title: Synovial tissue prior to Methotrexate therapy, repl 4

description: MTX4 T0

value: F


title: miRQC A

description: Prepared by miRQC Consortium

value: miRQC A

value: miRQC A Total RNA 100% Universal Human miRNA Reference RNA (UHmiRR, A)


title: Synovial tissue after to Methotrexate therapy, repl 3

description: MTX3 T12


title: miRQC A repeat

description: Prepared by miRQC Consortium

value: miRQC A repeat

value: miRQC A repeat Total RNA 100% Universal Human miRNA Reference RNA (UHmiRR, A)


title: Synovial tissue prior to Methotrexate therapy, repl 2

description: MTX2 T0


title: immature DC, iDC16

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using Lowess normalization with oneChannelGUI 1.16.0 in R.

source_name: immature DC

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

extract_protocol: Total RNA was extracted and purified from iDC, mDC and TLF-DC as described in the mirVANA miRNA isolation kit procedure (Applied Biosystem, California, USA).

treatment_protocol: Human peripheral blood mononuclear cells (PBMCs) were obtained from buffy coats of healthy donors by sedimentation over Histopaque (Sigma-Aldrich, S. Louis, MO). CD14+ cells were isolated from fresh PBMCs by positive immunoselection with magnetic beads (Miltenyi Biotec, Bergisch Gladbach, Germany). Immature DCs (i-DC) were generated in 6-well plates at 37°C in 5% humidified CO2 5 x 10^6 CD14+ cells in 3 ml RPMI 1640 medium (Invitrogen Life Technologies, Grand Island, NY) supplemented with 100 unit of penicillin, 0.1 mg/ml streptomycin, 50µM β-mercaptoethanol, 10% heat-inactivated qualified foetal bovine serum (FBS, Invitrogen Life Technologies), 100 ng/ml of granulocyte-macrophage colony stimulating factor (GM-CSF) and 50 ng/ml of IL-4 (both from PeproTech, Rocky Hill, NY) (complete medium, CM). On day 3, 2 ml of fresh CM containing GM-CSF and IL-4 were added.  On day 6, cells were harvested, resuspended as 1 x 10^6 cells/ml of CM in order to have i-DC or in CM further supplemented with 50 ng/ml of Tumor Necrosis Factor (TNF) -alfa and 50 ng/ml IL-1beta (both from Thermo Scientific, Rockford, IL) to obtain conventionally matured DC (m-DC), or with 1000 microg/ml of a Food and Drug Administration-approved, GMP level recombinant TLF generated in eukaryotic cells  (batch # C667034/E/A, # X803560A, Agennix, Houston, TX) to obtain TLF-DC.  After 24 hour culture, cells were harvested and analyzed.

value: peripheral blood

value: immature dendritic cells


title: TLF matured DC, TLF21

source_name: mature DC, TLF

value: talactoferrin-matured DC


title: TLF matured DC, TLF18


title: TNF/IL1 matured DC, mDC20

source_name: mature DC

value: conventionally matured dendritic cells


title: Synovial tissue after to Methotrexate therapy, repl 1

description: MTX1 T12


title: TNF/IL1 matured DC, mDC17


title: Synovial tissue after to Methotrexate therapy, repl 2

description: MTX2 T12


title: immature DC, iDC10


title: immature DC, iDC19


title: Synovial tissue after to Tocilizumab therapy, repl 12

description: TCZ12 T12

source_name: Knee synovial biopsies, obtained by needle arthroscopy, 12 weeks after initiation of Tocilizumab therapy (8 mg/kg, q1m)


title: TNF/IL1 matured DC, mDC11


title: Synovial tissue prior to Tocilizumab therapy, repl 12

description: TCZ12 T0


title: TLF matured DC, TLF12


title: immature DC, iDC7


title: Synovial tissue prior to Methotrexate therapy, repl 1

description: MTX1 T0


title: TNF/IL1 matured DC, mDC8


title: TLF matured DC, TLF9


title: VEGF-induced CAM 3

city: Talence

first: Martin

last: Hagedorn

address: Av des Facultes

department: Biology

institute: University Bordeaux 1

description: A pool of three normal chick-chorio-allantoic membrane fragements were compared to three individual CAMs treated with 3 micrograms of human recombinant VEGF for 24h (VEGF dried on a Thermanox disc).

hyb_protocol: Hybridization and washing was carried out on a GeneChip (Affymetrix) station, washing according to the manufacturer’s protocol.

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

data_processing: Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.

source_name: CAM was isolated from a chick embryo at developmental day 14

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) 'small sample protocol'

growth_protocol: Chick embryos were incubated at 37.8ºC and 75% humidity.

extract_protocol:
CAMs were immediately snap-frozen in liquid nitrogen after excision. Total
RNA was isolated using RNeasy mini kits (Qiagen) according to the
manufacturer's  instructions  and  quantified  using  a  NanoDrop
spectrophotometer.

treatment_protocol: Thermanox discs were deposited on the surface of the intact CAM on E13. CAM areas under the disc were excised on E14 and snap-frozen in liquid nitrogen prior to mRNA isolation

tag: 'tissue

value: chorio-allantoic membrane' 'Embryo age:E14'


title: Synovial tissue prior to Tocilizumab therapy, repl 11

description: TCZ11 T0


title: Synovial tissue prior to Methotrexate therapy, repl 3

description: MTX3 T0


title: Escherichia coli_Biofilm_bioreplicate2_techreplicate_1

city: Ann Arbor

first: Dongjuan

last: Dai

state: MI

address: 109 Observatory St

department: Environmental Health Sciences

institute: University of Michigan

description: A and B correspond to Cy3 and Cy5 channels, respectively, in .mev files.

hyb_protocol: Microarray slides were pre-hybridized with 1 mg/ml BSA in prehybridization buffer for 4 h. Slide washing, hybridization and washing were performed according to the manufacturer's protocol (Corning Epoxide Coated Slides instructions, Lowell, MA). Hybridization was at 42 °C water bath for 16 h.

scan_protocol: Microarray slides were scanned with a Virtek ChipReader (Virtek Vision, Waterloo, ON, Canada). Spots on scanned images were recognized and pixel intensity for each spot was quantified using the TIGR software Spotfinder (v3.1.1).

data_processing: Data was analyzed in the software Acuity 4.0 (Molecular Devices, Sunnyvale, CA). Hybridized spots for E. coli K12 having a high QC (quality control) value >0.1, good flag tags (A, B and C) in both Cy3/Cy5 channels were chosen for analysis. LOWESS normalization was performed with three iterations using a smoothing factor of 0.4.  One sample t-tests were performed across replicates. P-value of 0.05 was chosen as the significant level.

organism: Escherichia coli K-12

source_name: E. coli cells from biofilm 2

label_protocol: RNA was reversely transcribed into cDNA using random hexamers (pd(N)6) (GE Healthcare, Piscataway, NJ) and labeled with Amersham CyDye Post-Labeling Reactive Dye (Amersham Biosciences, Piscataway, NJ) following the manufacturer's protocol provided by the Amino Allyl cDNA Labeling Kit (Ambion, Austin, TX). The two biological replicates were labeled with dye swapping.

growth_protocol: Cells for inoculation were from overnight planktonic culture in 10% Luria-Bertani broth at 30 degree Celsius. Cells were washed in equal volume of fresh 10% LB broth before inoculation. Planktonic cultures were conducted in flasks with 30 ml 10% LB, inoculated with 300 ul E. coli overnight culture. Flasks were set on a shaker (250 rpm) at room temperature (20 C) for 18 h. Biofilms were cultivated in static disposable petri dishes (60 mm x 15 mm) with 5 ml 10% LB, inoculated with 50 ul E. coli overnight culture. The petri dishes were set static at room temperature (20 C) for 18 h.

extract_protocol: RNAlater was removed from cells by filtration. Total RNA was extracted from cells using a hot SDS/phenol protocol (http://www.genome.wisc.edu/pub/reprints/) with an additional 1-min bead-beating. Chemical extractions were performed in phase lock gels (Fisher Scientific, Pittsburgh, PA).

treatment_protocol: Planktonic cultures of E. coli were harvested and resuspended in RNAlater and kept in 4C fridge overnight. Suspended cells were removed from petri dishes and biofilms were washed three times with fresh 10% LB before being craped from the bottom surface of petri dishes. Biofilms were also re-suspeded into RNAlater and kept at 4C overnight. Both planktonic and biofilm samples were homogenized for 2 min on ice with an Omni TH homogenizer. Cells were then aliquoted into vials containing around 2x10^8 cells. Cells in each vial were then re-suspended in nuclease-free phosphate buffered saline, incubated with anti-E. coli antibody and microbeads, followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater.

tag: culture time

tag: culture temperature

value: room temperature (20 C)

tag: culture media

value: 10% Luria broth

tag: culture system

value: static petri dish (disposable)

tag: treatment

value: with homogenization and separation

source_name: E. coli cells from planktonic culture 2

value: flask with continuous shaking (250 rpm)


title: Synovial tissue after to Tocilizumab therapy, repl 11

description: TCZ11 T12


title: Escherichia coli_Biofilm_bioreplicate2_techreplicate_2


title: Escherichia coli_MixedSpeciesPlanktonic_bioreplicate2_techreplicate_1

source_name: sorted E. coli cells from mono-species pure planktonic culture 2

growth_protocol: Cells for inoculation were from overnight planktonic culture in 10% Luria-Bertani broth at 30 degree Celsius. Cells were washed in equal volume of fresh 10% LB broth before inoculated into 30 ml 10% LB in a flask. 300 ul E. coli culture was inoculated for mono-species pure culture. 150 ul E. coli and 60 ul S. maltophilia were mixed and inoculated for mixed-species cultures. Flasks were set on a shaker (250 rpm) at room temperature (20 C) for 18 h.

treatment_protocol: Cells were harvested and resuspended in RNAlater and kept in 4C fridge overnight. Cells were aliquoted into vials containing around 2x10^8 cells. Cells in each vial were then re-suspended in nuclease-free phosphate buffered saline, incubated with anti-E. coli antibody (ViroStat) and microbeads (Miltenyi), followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater until RNA extraction.

source_name: sorted E. coli cells from dual-species planktonic culture 2

value: flask with continous shaking (250 rpm)


title: Escherichia coli_MixedSpeciesPlanktonic_bioreplicate2_techreplicate_2


title: VEGF-induced CAM 2


title: VEGF-induced CAM 1


title: Escherichia coli_Biofilm_bioreplicate1_techreplicate_1

source_name: E. coli cells from biofilm 1

source_name: E. coli cells from planktonic culture 1


title: Escherichia coli_Biofilm_bioreplicate1_techreplicate_2


title: Synovial tissue after to Tocilizumab therapy, repl 10

description: TCZ10 T12

value: M


title: Synovial tissue prior to Tocilizumab therapy, repl 9

description: TCZ9 T0

value: F


title: 35S:RPS4 rrs1-11, 24h, rep1

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

country: China

institute: Huazhong Agricultural University

description: Gene expression data at 24h in the rrs1 mutant background

hyb_protocol: After amplification and fragmentation, 12.5 μg of cRNA was hybridized for 16 h at 45°C on GeneChip ATH1-121501 Genome Array. GeneChips were washed and stained with Fluidics Script FS450-004 in the Affymetrix Fluidics Station 450.

scan_protocol: Chips were scanned using a GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the affy package in the R environment and expression values were normalized by the GC-RMA method with the gcrma package.

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA was prepared according to a standard Ambion protocol from 1 μg total RNA (MessageAmp II-Biotin Enhanced Kit; Ambion).

growth_protocol: Plants were grown for 3,5 weeks at 28°C

extract_protocol: Total RNA were extracted using the Qiagen Rneasy kit, according to the manufacturer's instructions.

treatment_protocol: Plants were shifted from 28°C to 19°C for 8h before collecting and freezing the samples. T0 samples were not shifted.

value: leaves

tag: genotype

value: Col-0 35S:RPS4-HS rrs1-11

value: 3,5 week-old


title: 35S:RPS4 rrs1-11, 24h, rep2

tag: tissue


title: 35S:RPS4 rrs1-11, 24h, rep3


title: Normal control CAM at E14

source_name: A pool of three normal chick chorio-allantoic membrane fragments

value: chorio-allantoic membrane'

tag: 'embryo age


title: normal pancreas - Patient Sample 11

source_name: Fresh patient tissue from surgery

tag: patient

value: normal pancreas


title: Synovial tissue prior to Tocilizumab therapy, repl 10

description: TCZ10 T0

tag: age


title: Escherichia coli_MixedSpeciesPlanktonic_bioreplicate1_techreplicate_2

source_name: sorted E. coli cells from mono-species pure planktonic culture 1

source_name: sorted E. coli cells from dual-species planktonic culture 1


title: Synovial tissue after to Tocilizumab therapy, repl 8

description: TCZ8 T12


title: 35S:RPS4 rrs1-11, 8h, rep1

description: Gene expression data at 8h in the rrs1 mutant background


title: 35S:RPS4 rrs1-11, 2h, rep2

description: Gene expression data at 2h in the rrs1 mutant background


title: 35S:RPS4 rrs1-11, 2h, rep3


title: DKO, biological rep2

city: Houston

first: Orla

last: Conneely

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on a GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: bone marrow cells from DKO mice

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

growth_protocol: We generated DKO mice in a C57BL/6 and 129SvJ hybrid background by breeding previously generated Nr4a3–/–Nr4a1+/+ and Nr4a3+/+Nr4a1–/– mice.

extract_protocol: We extracted RNA according to the RNeasy Micro method (Qiagen) optimized for small amounts of RNA according to the manufacturer's instructions.

treatment_protocol: Bone marrow cells were flushed from both tibias and femurs and suspended in cold 1X Hank’s buffered saline solution (HBSS) with 2% fetal bovine serum. HSC-enriched cells (lin-Sca1+) were purified by FACS.

tag: strain

value: C57BL/6 and 129SvJ hybrid

value: Nr4a1 Nr4a3 double knockout (DKO)

value: bone marrow

tag: cell type

value: Lin-Sca1+ hematopoietic stem cells

value: 2-3 weeks


title: Synovial tissue after to Tocilizumab therapy, repl 9

description: TCZ9 T12

tag: gender


title: 35S:RPS4 rrs1-11, 8h, rep2


title: Escherichia coli_MixedSpeciesBiofilm_bioreplicate2_techreplicate_2

source_name: sorted E. coli cells from mono-species biofilms 2

growth_protocol: Cells for inoculation were from overnight planktonic culture in 10% Luria-Bertani broth at 30 degree Celsius. Cells were washed in equal volume of fresh 10% LB broth before inoculation and were inoculated into 5 ml 10% LB in a disposable petri dish (60 mm x 15 mm). 50 ul E. coli culture was inoculated for mono-species pure culture. 50 ul E. coli and 10 ul S. maltophilia were mixed and inoculated for mixed-species culture. Petri dishes were set static at room temperature (20 C) for 18 h for biofilm growth.

treatment_protocol: Suspended cells were then removed and biofilms were washed 3 times with 1 ml 10% LB broth. Biofilms from each petri dish were then scraped into a vial containing 1 ml 10% LB. Scraped biofilms in each vial were concentrated from 1 ml into 50 ul by centrifugation. 500 ul RNAlater was added and mixed well. Samples in RNAlater were kept in 4C fridge overnight.  Each vial was homogenized with OMNI TH homogenizer for 2 min on ice and further aliquoted into small vials. Cells in each vial were then re-suspended in nuclease-free phosphate buffered saline, incubated with anti-E. coli antibody (ViroStat) and microbeads (Miltenyi), followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater until RNA extractions.

value: room temperature (20 C)

value: 10% Luria broth

source_name: sorted E. coli cells from dual-species biofilms 2


title: Escherichia coli_MixedSpeciesBiofilm_bioreplicate2_techreplicate_1

value: static petri dish (disposable)

value: with homogenization and separation


title: Escherichia coli_MixedSpeciesBiofilm_bioreplicate1_techreplicate_3

source_name: sorted E. coli cells from mono-species biofilms 1

source_name: sorted E. coli cells from dual-species biofilms 1


title: 35S:RPS4 rrs1-11, 2h, rep1


title: Escherichia coli_MixedSpeciesPlanktonic_bioreplicate1_techreplicate_1

value: flask with continuous shaking (250 rpm)

value: flask with continous shaking (250 rpm)


title: DKO, biological rep3


title: DKO, biological rep1


title: Synovial tissue prior to Tocilizumab therapy, repl 8

description: TCZ8 T0

source_name: Knee synovial biopsies, obtained by needle arthroscopy, in untreated patient with early rheumatoid arthritis (< 1 year disease duration)

value: F

tag: disease activity score (das)-28crp


title: Synovial tissue prior to Tocilizumab therapy, repl 6

description: TCZ6 T0


title: Synovial tissue after to Tocilizumab therapy, repl 7

description: TCZ7 T12

source_name: Knee synovial biopsies, obtained by needle arthroscopy, 12 weeks after initiation of Tocilizumab therapy (8 mg/kg, q1m)


title: Synovial tissue after to Tocilizumab therapy, repl 6

description: TCZ6 T12


title: Synovial tissue prior to Tocilizumab therapy, repl 7

description: TCZ7 T0


title: wild type, biological rep2

source_name: bone marrow cells from wild type mice

value: WT


title: Synovial tissue after to Tocilizumab therapy, repl 5

description: TCZ5 T12

value: M


title: Escherichia coli_MixedSpeciesBiofilm_bioreplicate1_techreplicate_2


title: wild type, biological rep3


title: Whole blood, Stage 4 colon cancer patients, biological rep3

city: Kuala Lumpur

first: Yong

middle: Fung

last: Lin

address: Faculty of Medicine, University of Malaya

department: Surgery

country: Malaysia

institute: University of Malaya

description: MicroRNA gene expression

hyb_protocol: The samples were hybridized to GeneChip miRNA 2.0 arrays at 48C and 60 rpm for 16hours in the Affymetrix Hybridization Oven 640. The arrays were washed and stained on Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using GeneSpring GX 12.0 software (Agilent Technologies, Santa Clara, CA). ). Robust multichip averaging (RMA) algorithm was applied and the normalized data were filtered at p value and fold change cut off of 0.05 and 1.5, respectively

source_name: Whole blood from stage 4 colon cancer patients

label_protocol: Total RNA (1 ug) was biotin-labeled using Flashtag Biotin HSR RNA Labeling Kit (Genisphere, Hatfield, PA).

extract_protocol: Ribopure Blood RNA Isolation Kit  (Ambion, Austin, TX) and Qiagen miRNeasy Mini Kit (Qiagen, Valencia, CA) were used in the extraction of total RNA from whole blood and tissue samples, respectively.

treatment_protocol: Whole blood and paired tumor tissues and adjacent normal mucosa were obtained from healthy controls/colorectal cancer patients admitted to University of Malaya Medical Centre.

value: Whole blood

tag: affected site

value: Colon

tag: disease state

value: Stage 4 colon cancer


title: 35S:RPS4 rrs1-11, T0, rep2

description: Gene expression data at TO in the rrs1 mutant background

value: leaves

value: Col-0 35S:RPS4-HS rrs1-11

value: 3,5 week-old


title: Escherichia coli_MixedSpeciesBiofilm_bioreplicate1_techreplicate_1


title: 35S:RPS4 eds1-2, 24h, rep3

description: Gene expression data at 24h in the eds1 mutant background

value: Col-0 35S:RPS4-HS eds1-2


title: 35S:RPS4 rrs1-11, 8h, rep3


title: 35S:RPS4 eds1-2, 24h, rep2


title: 35S:RPS4 rrs1-11, T0, rep3


title: Synovial tissue prior to Tocilizumab therapy, repl 4

description: TCZ4 T0


title: Synovial tissue after to Tocilizumab therapy, repl 4

description: TCZ4 T12


title: 35S:RPS4 rrs1-11, T0, rep1


title: 35S:RPS4 eds1-2, 8h, rep3

description: Gene expression data at 8h in the eds1 mutant background


title: IDA T-DNA knockout vs.Arabidopsis thaliana (Col-0) control: replica 4

city: Oslo

first: Reidunn

middle: B.

last: Aalen

address: P.O.Box 1066 Blindern

department: Department of Biosciences

country: Norway

institute: University of Oslo

description: Two color microarray. Biological replicas are dye-swaped between slides.

hyb_protocol: Hybridizations were performed in a Slide Booster Hybridization Station (Advalytix, Brunnthal, Germany), and the slides were washed according to the manufacturers’ descriptions (Genisphere and Advalytix).

scan_protocol: The slides were scanned at 10 mm resolution on a G2505B Agilent DNA microarray scanner (Agilent Technologies,Palo Alto, CA, USA). The resulting image files were processed using GenePix 5.1 software (Axon Instruments, Union City, CA, USA).

data_processing: Spots identified as not found or which were manually flagged out as bad were filtered out. The data sets were log-transformed and normalized using the printtip-loess approach. Within-array replicated measurements for the same gene were merged by taking the average between the replicates. The data were then scaled so that all array data sets had the same median absolute deviation. No background normalization was done. The differentially expressed genes were identified using the Limma software package. References: Smyth, G. K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3 (2004)

source_name: Abscission zone regions of siliques position 4 to 8, control (biological replica 4)

label_protocol: Total RNA (15 mg) and Super-Script III reverse transcriptase (Invitrogen, Carlsbad, CA,USA) were used in a reverse transcription reaction.  Microarray slides were printed by the Norwegian Microarray Consortium (Trondheim, Norway). A 3DNA Array 350 kit with Cy3- and Cy5-labelled dendrimers (Genisphere,Inc., Hatfield, PA, USA) was used for labelling.

growth_protocol: Fill in the details, example: Arabidopsis thaliana (ecotype Colombia-0) seeds were sown into 6-cm-diameter pots filled with a sterile soil mix (1.0 part soil and 0.5 part horticultural perlite). Plants were kept in growth chambers Vötsch VB 1514 (Vötch Industrietechnik GmbH, Germany) with a 16/8 h (light/dark) photoperiod at 22/18 °C, 40/70% relative humidity, and 70/0 mmol m-2 s-1 light intensity.

extract_protocol: Total RNA was isolated with the Spectrum Plant Total RNA Kit (Sigma, St. Louis,MO,USA) and was quantified with NanodropND 1000 (Nanodrop Technologies, Wilmington, DE, USA).

value: wild type

tag: ecotype

source_name: Abscission zone regions of siliques position 4 to 8, IDA T-DNA knockout (biological replica 4)

value: IDA T-DNA knockout


title: 35S:RPS4 eds1-2, 8h, rep2


title: IDA T-DNA knockout vs.Arabidopsis thaliana (Col-0) control: replica 3

source_name: Abscission zone regions of siliques position 4 to 8, IDA T-DNA knockout (biological replica 3)

source_name: Abscission zone regions of siliques position 4 to 8, control (biological replica 3)


title: Whole blood, Stage 4 rectal cancer patients

description: MicroRNA gene expression

source_name: Whole blood from stage 4 rectal cancer patients

value: Rectum

value: Stage 4 rectal cancer


title: Whole blood, Stage 4 colon cancer patients, biological rep2

description: MicroRNA gene expression


title: 35S:RPS4 eds1-2, 24h, rep1


title: Synovial tissue prior to Tocilizumab therapy, repl 5

description: TCZ5 T0


title: Whole blood, Stage 3 colon cancer patients, biological rep2

description: MicroRNA gene expression

source_name: Whole blood from stage 3 colon cancer patients

value: Stage 3 colon cancer


title: Whole blood, Stage 3 rectal cancer patients

description: MicroRNA gene expression

source_name: Whole blood from stage 3 rectal cancer patients

value: Stage 3 rectal cancer


title: Synovial tissue after to Tocilizumab therapy, repl 3

description: TCZ3 T12


title: 35S:RPS4 eds1-2, 2h, rep3

description: Gene expression data at 2h in the eds1 mutant background


title: wild type, biological rep1

value: bone marrow

value: Lin-Sca1+ hematopoietic stem cells

value: 2-3 weeks


title: Synovial tissue after to Tocilizumab therapy, repl 2

description: TCZ2 T12

value: M


title: IDA T-DNA knockout vs.Arabidopsis thaliana (Col-0) control: replica 2

description: Two color microarray. Biological replicas are dye-swaped between slides

source_name: Abscission zone regions of siliques position 4 to 8, control (biological replica 2)

source_name: Abscission zone regions of siliques position 4 to 8, IDA T-DNA knockout (biological replica 2)


title: Synovial tissue prior to Tocilizumab therapy, repl 3

description: TCZ3 T0

value: F


title: IDA T-DNA knockout vs.Arabidopsis thaliana (Col-0) control: replica 1

source_name: Abscission zone regions of siliques position 4 to 8, IDA T-DNA knockout (biological replica 1)

source_name: Abscission zone regions of siliques position 4 to 8, control (biological replica 1)


title: hae hsl2 double mutant vs.Arabidopsis thaliana (Col-0) control: replica 4

source_name: Abscission zone regions of siliques position 4 to 8, hae hsl2 double mutant (biological replica 1)

value: hae hsl2 double mutant


title: Synovial tissue prior to Tocilizumab therapy, repl 2

description: TCZ2 T0


title: Whole blood, Stage 3 colon cancer patients, biological rep1

description: MicroRNA gene expression

value: Whole blood

value: Colon


title: hae hsl2 double mutant vs.Arabidopsis thaliana (Col-0) control: replica 3

value: Abscission zone regions of siliques position 4 to 8


title: Synovial tissue after to Tocilizumab therapy, repl 1

description: TCZ1 T12


title: 35S:RPS4 eds1-2, 2h, rep1

value: leaves

value: 3,5 week-old


title: Sampada

city: Lucknow

first: Ashutosh

middle: K

last: Shukla

state: Uttar Pradesh

address: P.O. CIMAP

department: Biotechnology Division

country: India

institute: CSIR-Central Institute of Medicinal and Aromatic Plants

hyb_protocol: 10.0 µg of the labeled aRNA in 75 µl of Ocimum's Hyb buffer was used for hybridization with the CA1001 custom array chip for Papaver somniferum designed and printed at Ocimum Biosolutions, Hyderabad. Hybridized chips were scanned using Affymetrix 428TMarray scanner at three different PMT gains and the data was analyzed using Genowiz software from Ocimum Biosolutions.

scan_protocol: Arrays were scanned using an Affymetrix 428 scanner at three PMT settings 40,50 and 60.

data_processing: Image analysis was carried out using Imagene, version 5.6.1. The signal values obtained at three PMT settings 40,50 and 60 were averaged, to get the signal mean for further analysis. Replicate genes were also averaged before normalization. Thus obtained signal values from each channel were log2 transformed and normalized using LOWESS algorithm and MAD scaling. For each sample, Cy3 and Cy5 intensities related to that sample were averaged, and were further used to compare the samples.

label: Cy3, Cy5

organism: Papaver somniferum

source_name: Capsule wall

label_protocol: Five microgram of total RNA was used for amplification using Amino Allyl MessageAmp™ II aRNA Amplification Kit from Ambion by linear transcription based RNA amplification system to produce cRNA. Briefly, mRNA was reverse transcribed with a oligo (dT) primer bearing T7 promoter at 42°C for 2 hrs and second strand cDNA synthesis was carried out at 16°C for 2 hrs. The resulting cDNA was then purified and was then transcribed with T7 RNA polymerase to generate multiple copies of aminoallyl antisense RNA (aRNA) at 37°C for 16 hrs. aRNA was then labelled with Cy3TM/Cy5TM post-labelling reactive dye pack (GE Healthcare, UK) at room temperature and unincorporated Cy3/Cy5  molecules were removed by purification process. Samples were purified using QIAGEN PCR purification kit before hybridization.

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. RNA concentration was determined by measuring its absorbance at 260 and 280 nm using a NanoDrop (NanoDrop, USA) and RNA quality was evaluated by electrophoretic analysis with Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Total RNA that met the quality standards was released for probe generation.

value: Capsule wall

value: Sampada

label: Cy5, Cy3


title: hae hsl2 double mutant vs.Arabidopsis thaliana (Col-0) control: replica 2

value: wild type


title: Whole blood, Stage 2 colon cancer patients, biological rep3

description: MicroRNA gene expression

source_name: Whole blood from stage 2 colon cancer patients

value: Stage 2 colon cancer


title: 35S:RPS4 eds1-2, 8h, rep1

value: Col-0 35S:RPS4-HS eds1-2


title: 35S:RPS4 eds1-2, 2h, rep2


title: Sujata

description: For each sample, Cy3 and Cy5 intensities related to that sample were averaged, and were further used to compare the samples

value: Sujata


title: Whole blood, Stage 2 colon cancer patients, biological rep1

description: MicroRNA gene expression


title: Synovial tissue prior to Tocilizumab therapy, repl 1

description: TCZ1 T0

source_name: Knee synovial biopsies, obtained by needle arthroscopy, in untreated patient with early rheumatoid arthritis (< 1 year disease duration)


title: 35S:RPS4 eds1-2, T0, rep2

description: Gene expression data at TO in the eds1 mutant background


title: Whole blood, Stage 4 colon cancer patients, biological rep1

description: MicroRNA gene expression

value: Stage 4 colon cancer


title: hae hsl2 double mutant vs.Arabidopsis thaliana (Col-0) control: replica 1


title: Whole blood, Stage 2 rectal cancer patients

description: MicroRNA gene expression

source_name: Whole blood from stage 2 rectal cancer patients

value: Rectum

value: Stage 2 rectal cancer


title: 35S:RPS4 eds1-2, T0, rep3


title: 35S:RPS4, 24h, rep3

description: Gene expression data 24h upon RPS4 activation

value: Col-0 35S:RPS4-HS


title: normal pancreas - Patient Sample 18

description: sample retrieved during surgery, placed in RNA Later stabilization fluid and then kept at minus 80 until required

hyb_protocol: Affymetrix GeneChip Human Gene 1.0 ST arrays were hybridized with 11 µg of labeled sense DNA, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual

scan_protocol: The GeneChip Scanner 3000 7G was used for array image acquisition according to the manufacturer's instructions.

data_processing:
Affymetrix data were extracted, normalized, and summarized with the robust multi-average (RMA) method implemented in the xps R/Bioconductor package by calling the function 'rma'. Present/Absent calls and pvalues were obtained applying function 'dabg.call' from the same R/bioconductor package.
The following transcript clusters were selected for processing using cdf for 28926 selected probeset_ids from the original affymetrix cdf file ('HuGene-1_0-st-v1.na32.hg19.transcript.csv'). Selection: core+affx [Included Affymetrix Categories:main (N=28536); --- (N=333); control->affx (N=57)].

source_name: Fresh patient tissue from surgery

label_protocol: For each sample, 100 ng of total RNA were amplified and labeled using the Affymetrix Whole-Transcript (WT) Sense Target Labeling Protocol.

value: normal pancreas


title: 35S:RPS4 eds1-2, T0, rep1


title: Whole blood, Stage 1 rectal cancer patients

description: MicroRNA gene expression

source_name: Whole blood from stage 1 rectal cancer patients

value: Stage 1 rectal cancer


title: Whole blood, healthy controls, biological rep6

description: MicroRNA gene expression

source_name: Whole blood from healthy controls

value: Whole blood

value: healthy


title: Whole blood, healthy controls, biological rep3

description: MicroRNA gene expression


title: Whole blood, healthy controls, biological rep4

description: MicroRNA gene expression


title: normal pancreas - Patient Sample 16


title: Whole blood, healthy controls, biological rep5

description: MicroRNA gene expression


title: 35S:RPS4, 24h, rep1


title: 35S:RPS4, 24h, rep2


title: Whole blood, Stage 1 colon cancer patients

description: MicroRNA gene expression

source_name: Whole blood from stage 1 colon cancer patients

value: Colon

value: Stage 1 colon cancer


title: monocytes_ctrl_biorep3

city: Sydney

first: Nitin

last: Saksena

state: new south wales

address: Darcy Road

department: Center for Virus Research

country: Australia

institute: Westmead Millennium Institute,Westmead Hospital

description:
C3
HIV- healthy controls

data_processing: Data normalization was performed using log2 transform and a robust spline normalization (RSN) implemented in the lumi package for R/Bioconductor

source_name: peripheral blood

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

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit, followed by on-column DNase treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: viral load

value: not applicable

tag: disease status

value: HIV sero-negative healthy controls

value: peripheral blood

value: primary monocytes


title: 35S:RPS4, 8h, rep3

description: Gene expression data 8h upon RPS4 activation

value: leaves

value: 3,5 week-old


title: monocytes_ctrl_biorep1

description:
C1
HIV- healthy controls


title: normal pancreas - Patient Sample 12


title: Whole blood, healthy controls, biological rep2

description: MicroRNA gene expression


title: normal pancreas - Patient Sample 17


title: monocytes_ctrl_biorep2

description:
C2
HIV- healthy controls


title: normal pancreas - Patient Sample 10


title: Whole blood, healthy controls, biological rep1

description: MicroRNA gene expression


title: monocytes_VIR_biorep2

description:
V2
HIV+ patients on highly active antiretroviral therapy

value: 787 copies/ml

value: virological failure


title: monocytes_ctrl_biorep4

description:
C4
HIV- healthy controls


title: Normal tissue, Stage 4 colon cancer patients

description: MicroRNA gene expression

source_name: Normal tissue from stage 4 colon cancer patients

value: Normal tissue

value: Stage 4 colon cancer


title: monocytes_BDL_biorep4

description:
B4
HIV+ patients on highly active antiretroviral therapy

value: <40 copies/ml

value: sustained virus suppression


title: monocytes_VIR_biorep1

description:
V1
HIV+ patients on highly active antiretroviral therapy

value: 87 copies/ml


title: monocytes_VIR_biorep4

description:
V4
HIV+ patients on highly active antiretroviral therapy

value: 177 copies/ml


title: monocytes_VIR_biorep3

description:
V3
HIV+ patients on highly active antiretroviral therapy

value: 194 copies/ml


title: monocytes_VIR_biorep5

description:
V5
HIV+ patients on highly active antiretroviral therapy

value: 169 copies/ml


title: monocytes_BDL_biorep5

description:
B5
HIV+ patients on highly active antiretroviral therapy


title: 35S:RPS4, 8h, rep2

value: Col-0 35S:RPS4-HS


title: pancreatic ductal adenocarcinoma - Patient Sample 08

value: pancreatic ductal adenocarcinoma


title: 35S:RPS4, 2h, rep2

description: Gene expression data 2h upon RPS4 activation


title: Normal tissue, Stage 3 colon cancer patients

description: MicroRNA gene expression

source_name: Normal tissue from stage 3 colon cancer patients

value: Colon

value: Stage 3 colon cancer


title: pancreatic ductal adenocarcinoma - Patient Sample  09


title: 35S:RPS4, 2h, rep3


title: 35S:RPS4, 8h, rep1


title: pancreatic ductal adenocarcinoma - Patient Sample 07


title: Normal tissue, Stage 2 colon cancer patients

description: MicroRNA gene expression

source_name: Normal tissue from stage 2 colon cancer patients

value: Stage 2 colon cancer


title: monocytes_BDL_biorep3

description:
B3
HIV+ patients on highly active antiretroviral therapy

value: peripheral blood

value: primary monocytes


title: 35S:RPS4, 2h, rep1

value: leaves

value: 3,5 week-old


title: monocytes_BDL_biorep2

description:
B2
HIV+ patients on highly active antiretroviral therapy


title: Cancer tissue, Stage 4 colon cancer patients

description: MicroRNA gene expression

source_name: Cancer tissue from stage 4 colon cancer patients

value: Cancer tissue


title: NoAbvTI

status: Public on Dec 29 2013

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

institute: University of Canberra

description:
test CEL file: No Antibody 1 mouse promoter 20090209.CEL
test CEL file: No Antibody 2 mouse promoter 20090216.CEL
test CEL file: No Antibody 3 mouse promoter 20090217.CEL
ctrl CEL file: Total Input 1 mouse promoter 20090209.CEL
ctrl CEL file: Total Input 2 mouse promoter 20090216.CEL
ctrl CEL file: Total Input 3mouse promoter 20090217.CEL
Significant regions more in No antibody samples than total input

hyb_protocol: As per manufacturers instructions

scan_protocol: As per manufacturers instructions

data_processing:
Data is mapped against mm8. ANOVA was used to compare either c-Rel or RelA samples against total genomic DNA (total input) or samples immunoprecipitated in the absence of antibody (no antibody). First significant probes  were identified and then statistically significant enriched regions (Partek Genomics Suite (6.4)). The follow parameters were used; a minimum of 7 probes in a significant region, fraction of the lowest 10% and highest 10% of the probes excluded from calculation of mean, and a maximum bandwidth of 500 bp.
Results file descriptions:  Bed files show genomic regions identifed as having significantly higher signal in c-Rel, RelA or mock immunoprecipitated samples than either total genomic DNA or mock immunoprecipitated samples

source_name: Mock ChIP DNA from stimulated EL4 cells

label_protocol: ChIP-enriched DNA fragments were labeled using The GeneChip® WT (Whole Transcript) Terminal Labeling Kit (Affymetrix).

growth_protocol: EL4 cells were cultured in RPMI 1640 media containing 10% fetal calf serum (FCS), 16 μg/ml gentamycin (Sigma), 120 μg/ml penicillin (Sigma-Aldrich, St. Louis, MO), and 10 mM HEPES.

extract_protocol: Briefly, cells were harvested and proteins were directly cross-linked to DNA by adding 1% formaldehyde final concentration for 15 min at room temperature with shaking. The incubation was stopped by the addition of glycine to a final concentration of 0.125 M followed by shaking for 10 min at room temperature. Cross-linked cells were washed twice with PBS and resuspended in nucleus extraction buffer (20 mM TrisHCl pH 8.0, 85 mM KCl, and 0.5% NP40) containing protease inhibitors for 10 min on ice. After washing, counted nuclei were lysed in buffer (50 mM Tris-Cl pH 8.0, 10 mM EDTA, and 1% SDS) for 10 min on ice and sonicated to shear chromatin using the Bioruptor (Diagenode) for 10 min for EL4 T cells and 15 min for CD4+ T cells on a setting of 30 sec on/off intervals to give a range of DNA fragments from 100 bp to 1 kb in length. The Upstate Technologies Protein A agarose kit was then used as per manufacturers instructions.

treatment_protocol: Cells were stimulated for various times at a density of 1 x 106 cells/ml with 10 ng/ml of phorbol 12-myristate 13-acetate (PMA; Sigma) and 1 μM of calcium ionophore (I; Sigma) for 2h (RelA) or 8h (c-Rel)

value: stimulated EL4 cells

tag: chip antibody

value: mock IP (No antibody)

source_name: Total genomic DNA from stimulated EL4 cells

value: input


title: pancreatic ductal adenocarcinoma - Patient Sample 05


title: normal pancreas - Patient Sample 11

value: normal pancreas


title: RelAvNoAb

description:
test CEL file: p65 2h 1 mouse promoter 20090209.CEL
test CEL file: p65 2h 2 mouse promoter 20090216.CEL
test CEL file: p65 2h 3 mouse promoter 20090217.CEL
ctrl CEL file: No Antibody 1 mouse promoter 20090209.CEL
ctrl CEL file: No Antibody 2 mouse promoter 20090216.CEL
ctrl CEL file: No Antibody 3 mouse promoter 20090217.CEL
Significant regions more in c-Rel samples than No antibody

source_name: RelA ChIP DNA from stimulated EL4 cells

value: RelA (Santa Cruz, sc-372)


title: cRelvNoAb

description:
test CEL file: cRel 8h 1 mouse promoter 20090209.CEL
test CEL file: cRel 8h 2 mouse promoter 20090216.CEL
test CEL file: cRel 8h 3 mouse promoter 20090217.CEL
ctrl CEL file: No Antibody 1 mouse promoter 20090209.CEL
ctrl CEL file: No Antibody 2 mouse promoter 20090216.CEL
ctrl CEL file: No Antibody 3 mouse promoter 20090217.CEL
Significant regions more in c-Rel samples than No antibody

source_name: c-Rel ChIP DNA from stimulated EL4 cells

value: c-Rel (Santa Cruz, sc-71)


title: RelAvTI

description:
test CEL file: p65 2h 1 mouse promoter 20090209.CEL
test CEL file: p65 2h 2 mouse promoter 20090216.CEL
test CEL file: p65 2h 3 mouse promoter 20090217.CEL
ctrl CEL file: Total Input 1 mouse promoter 20090209.CEL
ctrl CEL file: Total Input 2 mouse promoter 20090216.CEL
ctrl CEL file: Total Input 3mouse promoter 20090217.CEL
Significant regions more in ReAl samples than total input


title: cRelvTI

description:
test CEL file: cRel 8h 1 mouse promoter 20090209.CEL
test CEL file: cRel 8h 2 mouse promoter 20090216.CEL
test CEL file: cRel 8h 3 mouse promoter 20090217.CEL
ctrl CEL file: Total Input 1 mouse promoter 20090209.CEL
ctrl CEL file: Total Input 2 mouse promoter 20090216.CEL
ctrl CEL file: Total Input 3mouse promoter 20090217.CEL
Significant regions more in c-Rel samples than total input


title: pancreatic ductal adenocarcinoma - Patient Sample 06

description: sample retrieved during surgery, placed in RNA Later stabilization fluid and then kept at minus 80 until required


title: Cancer tissue, Stage 3 colon cancer patients

description: MicroRNA gene expression

source_name: Cancer tissue from stage 3 colon cancer patients


title: pancreatic ductal adenocarcinoma - Patient Sample 02


title: Cancer tissue, Stage 2 colon cancer patients

description: MicroRNA gene expression

source_name: Cancer tissue from stage 2 colon cancer patients


title: 35S:RPS4, T0, rep3

description: Gene expression data before pathway activation


title: Whole blood, Stage 2 colon cancer patients, biological rep2

description: MicroRNA gene expression

source_name: Whole blood from stage 2 colon cancer patients

value: Whole blood


title: 35S:RPS4, T0, rep2

value: Col-0 35S:RPS4-HS


title: rice at the four-leaf stage [R109 1]

city: Nanjing

first: Zhang

last: Lei

state: Jiangsu

address: Weigang 1

institute: Nanjing Agricultural University

description: Gene expression data from leaves of rice at the four-leaf stage

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

organism: Oryza sativa

source_name: leaves of rice at the four-leaf stage

growth_protocol: Three T3 progeny of the transgenic NJH12 used in this study were grown in a sterile incubator at 28 ℃ in the greenhouse with a 16 h light/8 h dark cycle.

extract_protocol: Total RNA was extracted with TRIZOL reagent (Invitrogen, Gaithersburg, MD) according to the manufacturer's instructions.

treatment_protocol: Rice leaves were collected at the four-leaf stage and stored in liquid nitrogen prior to RNA extraction.

tag: transgenic rice line

value: wildtype

tag: cultivar

tag: developmental stage

value: four-leaf stage


title: monocytes_BDL_biorep1

description:
B1
HIV+ patients on highly active antiretroviral therapy

value: <40 copies/ml

value: sustained virus suppression

tag: tissue


title: rice at the four-leaf stage [R109 3]


title: rice at the four-leaf stage [R109 2]


title: rice at the four-leaf stage [NJH12 2]


title: rice at the four-leaf stage [NJH12 1]


title: 35S:RPS4, T0, rep1

tag: genotype


title: rice at the four-leaf stage [NJH12 3]


title: Whole blood, Stage 3 colon cancer patients, biological rep3

description: MicroRNA gene expression

source_name: Whole blood from stage 3 colon cancer patients

value: Colon

value: Stage 3 colon cancer


title: SHYG-IOE+Est

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP

description: SHYG-IOE lines were treated with 10µM Est for 5h

hyb_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

data_processing: Raw data (CEL files) obtained from RNA hybridisation experiments were normalized with the affyPLM package from the Bioconductor software project (Gentleman et al., 2004) using the GCRMA that uses GC content of probes in normalization with RMA (Robust Multiple array Average) and  gives one value for each probe set instead of keeping probe level information (Wu et al., 2004). The transcriptional changes were determined by subtracting the normalized signal intensity of the control samples from that of induced samples.

source_name: Arabidopsis WT-Col-0 Seedlings treated with Est

growth_protocol:
for IOE: Seeds were surface-sterilized for 1 min in 70% ethanol and then in sterilisation solution (20% sodium hypochlorite) for 30 min. After sterilization, the seeds were sown on half-strength MS medium (Murashige and Skoog, 1962), supplemented with 1% (w/v) sucrose and solidified with 0.7% (w/v) phytoagar and appropriate antibiotics. After imbibition, the seeds were stratified at 4°C for 3 days. The seeds were germinated at 22°C under a 16-h day (140 µmol m-2 s-1) / 8-h night regime. The two-week-old Arabidopsis seedlings were carefully removed from plates  subjected to Est/Mocktreatments.
for_plants_used_for_protoplast_preparation: Col-0 seeds were directly sown on soil and plants were grown under long day (16 h light / 8 h dark) conditions.

extract_protocol: RNeasy Plant Mini Kit

treatment_protocol: After two weeks, seedlings were transferred to MS liquid medium while shaking. β-estradiol (Sigma-Aldrich) was added to the medium to a final concentration of 10 μM. Subsequently, seedlings were harvested at 5h after estradiol addition.

value: Seedling

value: two-week-old

tag: treatment

value: with 10µM Est for 5h


title: SHYG-IOE+Mock

description: SHYG-IOE lines were treated with 0.01/ EtOH for 5h

scan_protocol: Labelling, hybridisation, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

source_name: Arabidopsis WT-Col-0 Seedlings treated with EtOH

tag: age

value: with 0.01/ EtOH for 5h


title: Pax3Zic1-injected animal cap, stage 12, treated with Chx, induced with Dex, replicate 3

status: Public on Dec 28 2013

city: Orsay

first: Anne-Helene

last: Monsoro-Burq

address: Bat 110

department: Université Paris Sud

institute: Institut Curie

description: PZC3; targets_3H.CEL

hyb_protocol: Hybridization was completed using the standard affymetrix protocol

scan_protocol: Scanning was completed using an Affymetrix Genechip scanner 3000 7G

data_processing: The data was analysed with R (v.2.14.2) and the Bioconductor Biobase (v.2.14.0) affy library (v.1.32.1 package) with default settings.

organism: Xenopus laevis

source_name: Pax3Zic1-injected animal cap_stage 12_treated with Chx_induced with Dex

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

growth_protocol: Xenopus laevis 2-4 cells stage embryos were injected with inducible Pax3-GR+/-Zic1-GR constructs and then grown at 15°C in 1/3 MMR until stage 9

extract_protocol: Total RNA was isolated using the standard trizol protocol and eppendorf phase-lock gel tubes, followed by proteinase K digestion, and Qiagen Rneasy columns

treatment_protocol: Cycloheximide (0,1mg/ml) was then applied to the healed animal caps, from stage 10 to 10.5 (i.e. for 30 min at 23*C), then dexamethasone was added at stage 10.5 to the cycloheximide-containing medium. Explants were rinced and lysed after two additional hours at 23*C, i.e. when sibling embryos reached stage 11.5-12.

value: Xenopus laevis animal cap explant, stage 12

tag: dex treatment

value: yes

tag: pax3 injection

tag: zic1 injection

tag: chx treatment

tag: biological eplicate


title: Pax3Zic1-injected animal cap, stage 12, treated with Chx, induced with Dex, replicate 2

description: PZC2; targets_2T.CEL


title: Control animal cap, stage 12, replicate 3

description: pzc3; targets_3E.CEL

source_name: Control animal cap_stage 12

value: no