title: patient 53_whole liver tissue_HCC_tumor area B_99476

description:
WLT-53-B-99476
specimen obtained from the liver of patient 53


title: patient 35_whole liver tissue_HCC_tumor area B_103076

status: Public on Dec 22 2014

type: RNA

city: Bethesda

first: Patrizia

last: Farci

state: MD

address: 50 South Drive

department: National Institute of Allergy and Infectious Diseases

country: USA

institute: National Institutes of Health

description:
WLT-35-B-103076
specimen obtained from the liver of patient 35

hyb_protocol: Following fragmentation, 10 to 18 µg (mean 12.8) of cRNA was hybridized for 16 hr at 45°C on Affymetrics Human U133 Plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using GeneArray Scanner 3000_7Gplus

data_processing: Affymetrics probeset summaries were computed using RMA algorithm.  Data were then imported to BRB-ArrayTools and subsequent data filtering, median normalization and statistical analyses were performed using this software.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole liver tissue_HCC_tumor area B

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 ng total RNA (GeneChip Expression Analysis Technical Manual, 2005-2006, Affymetrix).

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

tag: subject condition

value: HBV-associated HCC patient

tag: patient id

value: patient 35

tag: distance from the tumor center

value: tumor area B

tag: sample type

value: whole liver tissue (WLT)


title: patient 53_whole liver tissue_HCC_tumor area B_99474

description:
WLT-53-B-99474
specimen obtained from the liver of patient 53

value: patient 53


title: Normal-Tw_Chilling-effect_rep2

city: Morioka

first: Kensaku

last: Suzuki

address: 4 Akahira, Shimo-Kuriyagawa

country: Japan

institute: NARO Tohoku Agricultural Research Center

description: Biologican replicate C2: Chilled and non-chilled spikelets at the booting stage in normal-Tw rice plants (NN vs NC).

scan_protocol: Microarray slides were scanned on an Agilent G2505B DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Oryza sativa

source_name: spikelets

label_protocol: The RNA (450-ng aliquots) was labeled by using a Quick Amp Labeling Kit (Agilent Technologies) in the presence of cyanine-3 (Cy3)-CTP or cyanine-5 (Cy5)-CTP according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen), and purified using PureLink Micro-to-Midi Total RNA Purification System (Invitrogen), following manufacturer's instructions.

treatment_protocol: Low-Tw treatment, water temperature at 18°C for 2 weeks before panicle initiation; Chilling treatment, room temperature at 12°C for 5 days at the booting stage.

tag: treatment before panicle inititation

value: normal water temperature

tag: treatment at booting stage

value: not chilled

tag: cultivar

value: Hayayuki

tag: developmental stage

value: spikelet

tag: tissue

value: whole plant

tag: treatment before panicle initiation

value: chilled


title: patient 35_whole liver tissue_HCC_tumor area B_103075

description:
WLT-35-B-103075
specimen obtained from the liver of patient 35


title: patient 35_whole liver tissue_HCC_tumor area B_103067

description:
WLT-35-B-103067
specimen obtained from the liver of patient 35


title: patient 35_whole liver tissue_HCC_tumor area B_99463

description:
WLT-35-B-99463
specimen obtained from the liver of patient 35


title: Normal-Tw_Chilling-effect_rep3

description: Biologican replicate C3: Chilled and non-chilled spikelets at the booting stage in normal-Tw rice plants (NN vs NC).

hyb_protocol: according to the manufacturer’s instructions


title: Normal-Tw_Chilling-effect_rep4

description: Biologican replicate C4: Chilled and non-chilled spikelets at the booting stage in normal-Tw rice plants (NN vs NC).


title: patient 35_whole liver tissue_HCC_tumor area B_103074

description:
WLT-35-B-103074
specimen obtained from the liver of patient 35


title: patient 92_whole liver tissue_HCC_tumor area A_103102

description:
WLT-92-A-103102
specimen obtained from the liver of patient 92

source_name: whole liver tissue_HCC_tumor area A

value: patient 92

value: tumor area A


title: patient 35_whole liver tissue_HCC_tumor area B_99462

description:
WLT-35-B-99462
specimen obtained from the liver of patient 35


title: patient 98_whole liver tissue_HCC_tumor area A_104644

description:
WLT-98-A-104644
specimen obtained from the liver of patient 98

value: patient 98


title: Tw-effect_Not-chilled_rep3

description: Biological replicate B3: Non-chilled spikelets at the booting stage in normal- and low-Tw rice plants (NN vs LN).

value: low water temperature


title: Tw-effect_Not-chilled_rep4

description: Biological replicate B4: Non-chilled spikelets at the booting stage in normal- and low-Tw rice plants (NN vs LN).


title: patient 110_whole liver tissue_HCC_tumor area B_106730

description:
WLT-110-B-106730
specimen obtained from the liver of patient 110

value: patient 110


title: patient 35_whole liver tissue_HCC_tumor area B_99461

description:
WLT-35-B-99461
specimen obtained from the liver of patient 35


title: patient 35_whole liver tissue_HCC_tumor area B_99449

description:
WLT-35-B-99449
specimen obtained from the liver of patient 35


title: Tw-effect_Not-chilled_rep2

description: Biological replicate B2: Non-chilled spikelets at the booting stage in normal- and low-Tw rice plants (NN vs LN).


title: patient 111_whole liver tissue_HCC_tumor area A_112258

description:
WLT-111-A-112258
specimen obtained from the liver of patient 111

value: patient 111


title: patient 110_whole liver tissue_HCC_tumor area A_106729

description:
WLT-110-A-106729
specimen obtained from the liver of patient 110

value: HBV-associated HCC patient


title: Normal-Tw_Chilling-effect_rep1

description: Biologican replicate C1: Chilled and non-chilled spikelets at the booting stage in normal-Tw rice plants (NN vs NC).


title: patient 125_whole liver tissue_HCC_tumor area A_106735

description:
WLT-125-A-106735
specimen obtained from the liver of patient 125

value: patient 125


title: patient 53_whole liver tissue_HCC_tumor area A_99473

description:
WLT-53-A-99473
specimen obtained from the liver of patient 53


title: patient 105_whole liver tissue_HCC_tumor area A_112251

description:
WLT-105-A-112251
specimen obtained from the liver of patient 105

value: patient 105


title: Tw-effect_Chilled_rep4

description: Biological replicate A4: Chilled spikelets at the booting stage in normal- and low-Tw rice plants NC vs LC).


title: patient 35_whole liver tissue_HCC_tumor area A_103073

description:
WLT-35-A-103073
specimen obtained from the liver of patient 35

value: patient 35

value: whole liver tissue (WLT)


title: IBD18 colon biopsy

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

description: colon biopsy, (U of A/Cedars-Sinai)

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

source_name: colon biopsy

label_protocol: Total RNA (0.3µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

growth_protocol: All human colon biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: The immunosuppressive treatment of the patients before the biopsy was based on individual treatment regiments; the treatment after the biopsy was adjusted based on the histopathological diagnosis.

tag: diagnosis (ibdu, uc, nomoa)

value: NOMOA


title: patient 33_whole liver tissue_HCC_tumor area A_99468

description:
WLT-33-A-99468
specimen obtained from the liver of patient 33

value: patient 33


title: patient 33_whole liver tissue_HCC_tumor area A_99446

description:
WLT-33-A-99446
specimen obtained from the liver of patient 33


title: patient 35_whole liver tissue_HCC_tumor area A_99460

description:
WLT-35-A-99460
specimen obtained from the liver of patient 35


title: Tw-effect_Not-chilled_rep1

description: Biological replicate B1: Non-chilled spikelets at the booting stage in normal- and low-Tw rice plants (NN vs LN).

value: normal water temperature

value: not chilled

value: Hayayuki


title: Tw-effect_Chilled_rep1

description: Biological replicate A1: Chilled spikelets at the booting stage in normal- and low-Tw rice plants NC vs LC).

value: chilled

value: spikelet

value: whole plant


title: Tw-effect_Chilled_rep2

description: Biological replicate A2: Chilled spikelets at the booting stage in normal- and low-Tw rice plants NC vs LC).


title: IBD16 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

value: UC


title: IBD17 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: IBD13 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: IBD15 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: IBD11 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: OCP4 replicate 4

city: Rockville

first: Anju

last: Aingh

address: 9800 Medical Center DRive

department: DPI

institute: NIH

description: Mouse Gene 1.0 ST array

hyb_protocol: Following fragmentation cRNA were hybridized onto Mouse Gene ST 1.0 array for 16 hours at 45°C. Posthybridization staining and washing were performed according to manufacturer's protocols using the Fluidics Station 450 instrument (Affymetrix)

scan_protocol: The gene chps were scanned using the  GeneChip Scanner 3000.

data_processing:
Microarray was performed using Mouse Gene 1.0 ST array at the Microarray Core Facility, Dana-Farber Cancer Institute. All MoGene 1.0 ST arrays were processed using the 'oligo' BioConductor package, quality-controlled with arrayQualityMetrics and corrected for batch effects with ComBat after RMA normalization. Differentially expressed genes were identified using limma.
Matrix supplementary file shows log fold changes relative to OCP2, average expression and p values
Matrix supplementary file - the data represents 3 biological replicates for OCP1 and OCP2 and 4 replicates for OCP3 and OCP4

organism: Mus musculus

source_name: CD9+CD73+Thy1+ embryonic bone cells

label_protocol: Biotin labeled cRNA was prepared from 1 μg of total RNA

growth_protocol: Embryonic limbs were dissected from mouse embryos at E 16.5

extract_protocol: RNAeasy isolation kit from Qiagen

treatment_protocol: samples were digested with collagenase and dispase, RBS lysed and FACS sorted after staining with flurochrome conjugated antibodies

tag: strain

value: embryonic 16.5


title: IBD14 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

value: IBDU


title: patient 33_whole liver tissue_HCC_tumor area A_99447

description:
WLT-33-A-99447
specimen obtained from the liver of patient 33

value: tumor area A


title: Aggressive fibromatosis - 212nsp

city: toronto

first: benjamin

last: alman

state: ontario

address: 555 university avenue

department: Developmental and stem cell biology

institute: Hospital for Sick Children

description: Cells were isolated from a human aggressive fibromatosis, and RNA isolated for gene profiling analysis.  The cells were not maintained in culture but used immediately for RNA extraction.

hyb_protocol: The cRNA labeling and hybridizations were then performed according to Affymetrix GeneChip Protocol (Affymetrix Inc., Santa Clara, CA).

scan_protocol: The chips were scanned for fluorescence signal detection. Affymetrix - GeneChip® Human U133 Plus 2.0 Array was utilized.

data_processing: Expression console software (Affymetrix)

source_name: aggressive fibromatosis tumor

label_protocol: RNA was converted to double-stranded cDNA using Superscript (Gibco-Invitrogen) with a T7-(dT)24 primer, which was then transcribed to biotinylated complementary RNA (cRNA) by incorporating biotin-CTP and biotin-UTP using Enzo BioArray High Yield RNA labeling kit (Enzo Diagnostics, New York, NY).

extract_protocol: RNA was extracted using Trisol as per the manufacturer's instructions. RNA was converted to double-stranded cDNA using Superscript (Gibco-Invitrogen) with a T7-(dT)24 primer

tag: array expression from an aggressive fibromatosis tumor


title: OCP4 replicate 2

description: Mouse Gene 1.0 ST array


title: aggressive fibromatosis - 213sp


title: WT MEFs  treated with 1μM thapsigargin for 12hr Replicate 3

city: San Francisco

first: Feroz

last: Papa

state: CA

address: 1700 4th Street

institute: University of California, San Francisco

description: WT MEFs  treated with 1μM thapsigargin for 12hrs hybed against not treated WT MEFs. Replicate 3

hyb_protocol: Scanned on an Axon scanner.

scan_protocol: Images were quantified using GenePix 6.0.

data_processing: LOWESS normalized.

label_protocol: Oligo dT and mouse Cot-1 DNA were added to the labeled and purified cDNA with the presence of 3xSSC,0.25mg/mL polyA, 0.25mg/mL yeast tRNA,25mM Hepes, and 0.25%SDS. Samples were applied to microarrays enclosed in Maui hybridization chamber and hybed at 42oC overnight. After hybridization, slides were washed sequentially with 2xSSC 0.03% SDS, 1XSSC,0.2XSSC.

growth_protocol: cells were kept in DMEM media supplemented with 10% FBS.

extract_protocol: 10 µg of total RNA were reverse transcribed with 400U superscript II RTase (invitrogen) and labeled with NHS-ester Cy3 or Cy5 dye (Amersham RPN5661) at RT for 1hr.

treatment_protocol: When treated, cells are ~50-60% density. Cells are treated with  1μM thapsigargin or left untreated for the 12hr and harvested with Trizol.

tag: cell line

value: MEF

tag: cell type

value: mouse embryonic fibroblast

source_name: Total RNA from not treated WT MEFs


title: IRE1α-/- MEFs  treated with 1μM thapsigargin for 12hr Replicate 2

description: IRE1α-/- MEFs  treated with 1μM thapsigargin for 12hrs hybed against not treated IRE1α-/- MEFs. Replicate 2

source_name: Total RNA from not treated IRE1α-/- MEFs


title: IRE1α-/- MEFs  treated with 1μM thapsigargin for 12hr Replicate 3

description: IRE1α-/- MEFs  treated with 1μM thapsigargin for 12hrs hybed against not treated IRE1α-/- MEFs. Replicate 3


title: Tw-effect_Chilled_rep3

description: Biological replicate A3: Chilled spikelets at the booting stage in normal- and low-Tw rice plants NC vs LC).

value: low water temperature


title: OCP4 replicate 3

description: Mouse Gene 1.0 ST array


title: WT MEFs  treated with 1μM thapsigargin for 12hr Replicate 2

description: WT MEFs  treated with 1μM thapsigargin for 12hrs hybed against not treated WT MEFs. Replicate 2


title: IRE1α-/- MEFs  treated with 1μM thapsigargin for 12hr Replicate 1

description: IRE1α-/- MEFs  treated with 1μM thapsigargin for 12hrs hybed against not treated IRE1α-/- MEFs. Replicate 1


title: OCP4 replicate 1

description: Mouse Gene 1.0 ST array


title: IBD10 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: IBD9 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: aggressive fibromatosis - 212sp


city: Ramat-Gan

first: Hiba

last: Waldman Ben-Asher

address: Ramat-Gan

department: Life-Sciences

country: Israel

institute: Bar-Ilan University

description: 32°C treatment (T2) vs. 34°C control (T3). Technical replicates

hyb_protocol: Equal amounts of labeled RNA were then hybridized on the chip, per the Agilent protocol, at 60 degrees overnight. The hybridization mixes were prepared using the Gene Expression Hybridization Kit from Agilent following the manufacturer’s protocol. After hybridization, the slide was washed first with Gene Expression Wash Buffer 1(Agilent) and then Gene Expression Wash Buffer 2(Agilent). This was followed by a acetonitrile wash and finally the slides were placed in Stabilization& Drying Solution (Agilent). The washed slides were scanned on on an Agilent G2565BA scanner. Feature extraction was performed using the Feature extraction software from Agilent

scan_protocol: Scanned on an Agilent G2565BA microarray scanner

data_processing: The data from all arrays were first subjected to background correction and LOESS within-array normalization using Agilent Feature Extraction software (version 9.5.1.1 Agilent Technologies, Santa Clara, CA). The rest of the analysis was performed in Partek® Genomics Suite software, version 6.6 Copyright © 2012 Partek Inc., St. Louis, MO, USA.The log expression ratios that were produced during the normalization step were analyzed.

organism: Stylophora pistillata

label_protocol: 200 ng of total RNA, in the presence of control RNAs (RNA spike-in kit; Agilent), for each sample was labeled with either Cy-3 or Cy-5 using the Low Input Quick Amp Labeling Kit, two-color (Agilent) following the manufacturer’s protocol.

extract_protocol: Total RNA extracted using Trizol ,the samples were further purified using an RNA Clean and Concentrator kit (Zymo Research).

treatment_protocol: The experimental aquarium was subjected to an increase of 1°C per day, from 24°C to 34°C.

tag: temperature


title: OCP3 replicate 4

description: Mouse Gene 1.0 ST array

source_name: CD9+CD73-Thy1+ embryonic bone cells


title: OCP3 replicate 3

description: Mouse Gene 1.0 ST array


title: WT MEFs  treated with 1μM thapsigargin for 12hr Replicate 1

description: WT MEFs  treated with 1μM thapsigargin for 12hrs hybed against not treated WT MEFs. Replicate 1


title: IBD8 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: IBD7 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


description: 32°C treatment (T2) vs. 28°C control (T1). Technical replicates


title: aggressive fibromatosis - 213nsp


title: INS1 cells expressing sXBP1  treated with dox and 1NMPP1 for 24hr Replicate 3

description: INS1 cells expressing sXBP1  treated with dox and 1NMPP1 for 24hrs hybed against INS1 cells harboring sXBP1  transgene. Replicate 3

hyb_protocol: Oligo dT and mouse Cot-1 DNA were added to the labeled and purified cDNA with the presence of 3xSSC,0.25mg/mL polyA, 0.25mg/mL yeast tRNA,25mM Hepes, and 0.25%SDS. Samples were applied to microarrays enclosed in Maui hybridization chamber and hybed at 65oC overnight. After hybridization, slides were washed sequentially with 2xSSC 0.03% SDS, 1XSSC,0.2XSSC.

scan_protocol: Scanned on an Axon scanner. Images were quantified using GenePix 6.0.

organism: Rattus norvegicus

label_protocol: 10 µg of total RNA were reverse transcribed with 400U superscript II RTase (invitrogen) and labeled with NHS-ester Cy3 or Cy5 dye (Amersham RPN5661) at RT for 1hr.

growth_protocol: cells were kept in RPMI media supplemented with 10% FBS, 1mM sodium pyruvate, 10mM Hepes, 2mM glutamine, 50μM β-mercaptoethonal.

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

treatment_protocol: When treated, cells are ~50-60% density. Cells are treated with either 0.1μg/mL doxycycline and 5μM 1NMPP1 or left untreated for the indicated time and harvested with Trizol.

value: rat pancreatic beta cells

source_name: Total RNA from not treated INS1 cells harboring sXBP1  transgene


title: IBD6 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: OCP3 replicate 1

description: Mouse Gene 1.0 ST array


description: 34°C treatment (T3) vs. 28°C control (T1). Technical replicates


title: INS1 cells expressing sXBP1  treated with dox and 1NMPP1 for 24hr Replicate 2

description: INS1 cells expressing sXBP1  treated with dox and 1NMPP1 for 24hrs hybed against INS1 cells harboring sXBP1  transgene. Replicate 2


title: 24°C control (C1) vs. 34°C treatment (T3), 2

description: 24°C control (C1) vs. 34°C treatment (T3). Technical replicates


title: OCP3 replicate 2

description: Mouse Gene 1.0 ST array


title: OCP2 replicate 2

description: Mouse Gene 1.0 ST array

source_name: CD9+CD73-Thy1- embryonic bone cells


title: INS1 cells expressing N906A IRE1α treated with dox and 1NMPP1 for 24hr Replicate 3

description: INS1 cells expressing N906A IRE1α treated with dox and 1NMPP1 for 24hrs hybed against INS1 cells harboring N906A IRE1α transgene. Replicate 3

source_name: Total RNA from not treated INS1 cells harboring N906A IRE1α transgene


title: IBD5 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: 34°C treatment (T3) vs. 24°C control (C3), 3

description: 34°C treatment (T3) vs. 24°C control (C3). biological replicate 3 of 3


title: IBD2 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: patient 53_whole liver tissue_HCC_tumor area B_99475

description:
WLT-53-B-99475
specimen obtained from the liver of patient 53

value: HBV-associated HCC patient

value: patient 53

value: tumor area B

value: whole liver tissue (WLT)


title: INS1 cells expressing N906A IRE1α treated with dox and 1NMPP1 for 24hr Replicate 1

description: INS1 cells expressing N906A IRE1α treated with dox and 1NMPP1 for 24hrs hybed against INS1 cells harboring N906A IRE1α transgene. Replicate 1


title: INS1 cells expressing sXBP1  treated with dox and 1NMPP1 for 24hr Replicate 1

description: INS1 cells expressing sXBP1  treated with dox and 1NMPP1 for 24hrs hybed against INS1 cells harboring sXBP1  transgene. Replicate 1


title: INS1 cells expressing N906A IRE1α treated with dox and 1NMPP1 for 24hr Replicate 2

description: INS1 cells expressing N906A IRE1α treated with dox and 1NMPP1 for 24hrs hybed against INS1 cells harboring N906A IRE1α transgene. Replicate 2


title: IBD4 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: patient 4_whole liver tissue_HCC_tumor area A_99440

description:
WLT-4-A-99440
specimen obtained from the liver of patient 4A

value: patient 4A


title: IBD3 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: IBD25 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

value: NOMOA


title: 34°C treatment (T3) vs. 24°C control (C3), 2

description: 34°C treatment (T3) vs. 24°C control (C3). biological replicate 2 of 3


title: 34°C treatment (T3) vs. 24°C control (C3), 1

description: 34°C treatment (T3) vs. 24°C control (C3). biological replicate 1 of 3


title: OCP1 replicate 3

description: Mouse Gene 1.0 ST array

source_name: CD9+CD73+Thy1- embryonic bone cells


title: OCP1 replicate 1

description: Mouse Gene 1.0 ST array


title: IBD24 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: OCP2 replicate 1

description: Mouse Gene 1.0 ST array


title: TREx 293 cells expressing I642G IRE1α treated with dox and 1NMPP1 for 24hr Replicate 3

hyb_protocol: Oligo dT and mouse Cot-1 DNA were added to the labeled and purified cDNA with the presence of NExterion Hyb hybe buffer (Schott). Samples were applied to microarrays enclosed in Maui hybridization chamber and hybed at 65oC overnight. After hybridization, slides were washed sequentially with 2xSSC 0.03% SDS, 1XSSC,0.2XSSC.

source_name: TREx 293 cells expressing I642G IRE1α  treated with dox and 1NMPP1 for 24hrs

label_protocol: 20 µg of total RNA were reverse transcribed with 400U superscript II RTase (invitrogen) and labeled with NHS-ester Cy3 or Cy5 dye (Amersham RPN5661) at RT for 1hr.

treatment_protocol: When treated, cells are ~50-60% density. Cells are treated with either 1μg/mL doxycycline and 5μM 1NMPP1 or left untreated for the indicated time and harvested with Trizol.

value: TREx 293

value: human embrionic kidney cells

source_name: Total RNA from not treated TREx 293 cells harboring I642G IRE1α transgene

value: human embryonic kidney cells


title: IBD22 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

value: UC


title: OCP2 replicate 3

description: Mouse Gene 1.0 ST array

value: embryonic 16.5


title: OCP1 replicate 2

description: Mouse Gene 1.0 ST array


title: TREx 293 cells expressing I642G IRE1α treated with dox and 1NMPP1 for 8hr Replicate 3

source_name: TREx 293 cells expressing I642G IRE1α  treated with dox and 1NMPP1 for 8hrs


title: 32°C treatment (T2) vs. 24°C control (C2), 3

description: 32°C treatment (T2) vs. 24°C control (C2). biological replicate 3 of 3


title: TREx 293 cells expressing I642G IRE1α not treated Replicate 2

source_name: Total RNA pool from not treated TREx 293 cells harboring I642G IRE1α transgene and TREx 293 cells expressing I642G IRE1α for 24hrs.


title: IBD23 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: 28°C treatment (T1) vs. 24°C control (C1), 3

description: 28°C treatment (T1) vs. 24°C control (C1). biological replicate 3 of 3


title: INS1 cells expressing I642G IRE1α treated with dox and 1NMPP1 for 24hr Replicate 2

description: INS1 cells expressing I642G IRE1α treated with dox and 1NMPP1 for 24hrs hybed against INS1 cells harboring I642G IRE1α transgene. Replicate 2

source_name: Total RNA from not treated INS1 cells harboring I642G IRE1α transgene


title: INS1 cells expressing I642G IRE1α treated with dox and 1NMPP1 for 24hr Replicate 1

description: INS1 cells expressing I642G IRE1α treated with dox and 1NMPP1 for 24hrs hybed against INS1 cells harboring I642G IRE1α transgene. Replicate 1


title: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 24hr Replicate 3

description: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 24hrs hybed against INS1 cells harboring WT IRE1α transgene. Replicate 3

source_name: Total RNA from not treated INS1 cells harboring WT IRE1α transgene


title: 32°C treatment (T2) vs. 24°C control (C2), 2

description: 32°C treatment (T2) vs. 24°C control (C2). biological replicate 2 of 3


title: INS1 cells expressing I642G IRE1α treated with dox and 1NMPP1 for 24hr Replicate 3

description: INS1 cells expressing I642G IRE1α treated with dox and 1NMPP1 for 24hrs hybed against INS1 cells harboring I642G IRE1α transgene. Replicate 3


title: IBD12 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: 24°C control (C1) vs. 34°C treatment (T3), 1

description: 24°C control (C1) vs. 34°C treatment (T3). Technical replicates


title: TREx 293 cells expressing I642G IRE1α treated with dox and 1NMPP1 for 24hr Replicate 1


title: 28°C treatment (T1) vs. 24°C control (C1), 2

description: 28°C treatment (T1) vs. 24°C control (C1). biological replicate 2 of 3


title: IBD1 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 16hr Replicate 2

description: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 16hrs hybed against INS1 cells harboring WT IRE1α transgene. Replicate 2


title: TREx 293 cells expressing I642G IRE1α not treated Replicate 1

source_name: TREx 293 cells harboring I642G IRE1α transgene


title: TREx 293 cells expressing I642G IRE1α treated with dox and 1NMPP1 for 24hr Replicate 2


title: IBD19 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

source_name: colon biopsy


title: 32°C treatment (T2) vs. 24°C control (C2), 1

description: 32°C treatment (T2) vs. 24°C control (C1). biological replicate 1 of 3


title: 28°C treatment (T1) vs. 24°C control (C1), 1

description: 28°C treatment (T1) vs. 24°C control (C1). biological replicate 1 of 3


title: TREx 293 cells expressing I642G IRE1α treated with dox and 1NMPP1 for 8hr Replicate 2


title: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 16hr Replicate 3

description: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 16hrs hybed against INS1 cells harboring WT IRE1α transgene. Replicate 3


title: IBD21 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: TREx 293 cells expressing I642G IRE1α treated with dox and 1NMPP1 for 8hr Replicate 1


title: TREx 293 cells expressing WT IRE1α treated with dox and 1NMPP1 for 24hr Replicate 3

source_name: TREx 293 cells expressing WT IRE1α  treated with dox and 1NMPP1 for 24hrs

source_name: Total RNA from not treated TREx 293 cells harboring WT IRE1α transgene


title: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 24hr Replicate 1

description: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 24hrs hybed against INS1 cells harboring WT IRE1α transgene. Replicate 1


title: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 24hr Replicate 2

description: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 24hrs hybed against INS1 cells harboring WT IRE1α transgene. Replicate 2


title: TREx 293 cells expressing WT IRE1α treated with dox and 1NMPP1 for 24hr Replicate 1

source_name: Total RNA pool from not treated TREx 293 cells harboring WT IRE1α transgene and TREx 293 cells expressing WT IRE1α for 24hrs.


title: TREx 293 cells expressing WT IRE1α not treated Replicate 2

source_name: TREx 293 cells harboring WT IRE1α transgene


title: TREx 293 cells expressing WT IRE1α treated with dox and 1NMPP1 for 24hr Replicate 2


title: TREx 293 cells expressing WT IRE1α not treated Replicate 1


title: TREx 293 cells expressing WT IRE1α treated with dox and 1NMPP1 for 8hr Replicate 2

description: TREx 293 cells expressing WT IRE1α treated with dox and 1NMPP1 for 8hr hybed against TREx cells harboring WT IRE1α transgene. Replicate 2

source_name: TREx 293 cells expressing WT IRE1α  treated with dox and 1NMPP1 for 8hrs


title: IBD20 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: TREx 293 cells expressing WT IRE1α not treated Replicate 3

source_name: Total RNA pool from not treated TREx 293 cells harboring WT IRE1α transgene and TREx 293 cells expressing WT IRE1α for 8hrs.


title: TREx 293 cells expressing WT IRE1α treated with dox and 1NMPP1 for 8hr Replicate 3


title: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 8hr Replicate 2

description: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 8hrs hybed against INS1 cells harboring WT IRE1α transgene. Replicate 2


title: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 8hr Replicate 3

description: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 8hrs hybed against INS1 cells harboring WT IRE1α transgene. Replicate 3


title: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 16hr Replicate 1

description: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 16hrs hybed against INS1 cells harboring WT IRE1α transgene. Replicate 1


title: IBD47 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: IBD42 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: INS1 CAT cells  treated with 1μM thapsigargin for 6hr Replicate 2

description: INS1 CAT cells  treated with 1μM thapsigargin for 6hrs hybed against not treated INS1 CAT cells . Replicate 2

label_protocol: Oligo dT and mouse Cot-1 DNA were added to the labeled and purified cDNA with the presence of 5xSSC,0.1%SDS,25%formamide. Samples were applied to microarrays enclosed in Maui hybridization chamber and hybed at 42oC overnight. After hybridization, slides were washed sequentially with 2xSSC 0.03% SDS, 1XSSC,0.2XSSC.

treatment_protocol: When treated, cells are ~50-60% density. Cells are treated with 1μM thapsigargin for the indicated time and harvested with Trizol.

source_name: Total RNA from not treated INS1 CAT cells


title: INS1 CAT cells  treated with 1μM thapsigargin for 6hr Replicate 3

description: INS1 CAT cells  treated with 1μM thapsigargin for 6hrs hybed against not treated INS1 CAT cells . Replicate 3


title: IBD44 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: IBD46 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: IBD49 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: IBD48 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

value: IBDU


title: IBD41 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 8hr Replicate 1

description: INS1 cells expressing WT IRE1α treated with dox and 1NMPP1 for 8hrs hybed against INS1 cells harboring WT IRE1α transgene. Replicate 1


title: IBD50 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: IBD43 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: IBD39 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: TREx 293 cells expressing WT IRE1α treated with dox and 1NMPP1 for 8hr Replicate 1

description: TREx 293 cells expressing WT IRE1α treated with dox and 1NMPP1 for 8hr hybed against TREx cells harboring WT IRE1α transgene. Replicate 1


title: Male chicken BC2 n°6561 (from the sire BC1 n°1998)

city: Rennes

first: Le MIGNON

last: Guillaume

address: 65 rue de Saint Brieuc

country: France

institute: INRA

description: For each gene, the fluorescence ratio represents the relative abundance of the hepatic mRNA of the animal of interest  compared with the RNA pool reference.

hyb_protocol: The microarray was hybridized for 8 h at 42°C with Cy5-labeled chicken cDNA sample  and an aliquot of the Cy3-labeled reference cDNA using automatic hybridization chamber (Discovery from Ventana Medical System, Inc). Slides were washed in increasing stringency using salt sodium citrate.

scan_protocol: The microarray slides were scanned using a laser scanner (GenePix 4000A from Axon Instrument, CA) at 550 nM for Cy3 and 640 nM for Cy5 to generate two TIFF images for each slide.

data_processing:
The two images from each slide were analyzed with GenepixPro 4.0 software (Axon instruments, Inc., Union City, CA). Pre-processing and normalization of data were accomplished using the R-project statistical and Bioconductor environment (http://www.r-project.org) (http://www.bioconductor.org).
For the normalization step, data were filtered according to 3 criterions based on 1) the genepix flag automatically performed by GenepixPro 4.0; 2) the SNR 3) the asymmetry spot (see Desert et al. 2008). The ratio Cy5/Cy3 used was expressed as the Log(base 2) of the ratio of median pixel intensity of the two red and green spots. Log2 median ratio values were then normalized by “Lowess fitness”.

organism: Gallus gallus

label_protocol:
Five µg of each mRNA sample were reverse-transcribed and Cy5 fluorescent-
labelled using the ChipShot™ Direct Labeling kit (Promega, Charbonnieres, France).

growth_protocol: Standard broiler chicken growth protocol. Livers were rapidly excised, frozen in liquid nitrogen and stored at –75 °C until RNA extraction

extract_protocol: Total RNA was extracted from liver using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

value: male

tag: protocol

value: fed ad libitum during 4 hours minimum

tag: age

value: 9 weeks

value: Liver

source_name: Reference

label_protocol:
Five µg of each mRNA sample were reverse-transcribed and Cy3 fluorescent-
labeled using the ChipShot™ Direct Labeling kit (Promega, Charbonnieres, France).

tag: sample

value: Total liver RNA pool obtained from the 45 Male broiler chickens	(sire BC1 n°1998)


title: INS1 CAT cells  treated with 1μM thapsigargin for 6hr Replicate 1

description: INS1 CAT cells  treated with 1μM thapsigargin for 6hrs hybed against not treated INS1 CAT cells . Replicate 1

tag: cell line

tag: cell type

value: rat pancreatic beta cells


title: Male chicken BC2 n°6562 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: tissue

extract_protocol:
Total RNA was extracted  from liver using TRIzol reagent according to the
manufacturer’s instructions (Invitrogen, Carlsbad, CA)


title: INS1 CAT cells  treated with 1μM thapsigargin for 4hr Replicate 2

description: INS1 CAT cells  treated with 1μM thapsigargin for 4hrs hybed against not treated INS1 CAT cells . Replicate 2

tag: cell line

tag: cell type


title: IBD40 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

tag: diagnosis (ibdu, uc, nomoa)


title: Male chicken BC2 n°6443 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: sample


title: IBD37 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

tag: diagnosis (ibdu, uc, nomoa)


title: IBD38 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: Male chicken BC2 n°6565  (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: tissue


title: Male chicken BC2 n°6446 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: sample


title: INS1 CAT cells  treated with 1μM thapsigargin for 4hr Replicate 1

description: INS1 CAT cells  treated with 1μM thapsigargin for 4hrs hybed against not treated INS1 CAT cells . Replicate 1

tag: cell line

tag: cell type


title: INS1 CAT cells  treated with 1μM thapsigargin for 2hr Replicate 1

description: INS1 CAT cells  treated with 1μM thapsigargin for 2hrs hybed against not treated INS1 CAT cells . Replicate 1


title: Male chicken BC2 n°6560 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: tissue


title: IBD34 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

tag: diagnosis (ibdu, uc, nomoa)


title: Akita cells vs ct14 cells 4

description: Akita cells  vs ct14 celss . Replicate 4

hyb_protocol: Oligo dT and mouse Cot-1 DNA were added to the labeled and purified cDNA with the presence of 5xSSC,0.1%SDS,25%formamide. Samples were applied to microarrays enclosed in Maui hybridization chamber and hybed at 42oC overnight. After hybridization, slides were washed sequentially with 2xSSC 0.03% SDS, 1XSSC,0.2XSSC.

source_name: Akita cells

growth_protocol: cells were kept in DMEM media supplemented with 15% FBS, 125μM β-mercaptoethonal.

treatment_protocol: Cells are plated at 60% confluency and RNA is harvested by Trizol 24hr after plating.

tag: cell line

tag: cell type

value: Akita mouse pancreatic beta cells

source_name: Total RNA from ct14 cells

value: wild type mouse pancreatic beta cells


title: Male chicken BC2 n°6445 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: sample


title: Male chicken BC2 n°6438 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: tissue


title: Male chicken BC2 n°6440 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: sample


title: Male chicken BC2 n°6432 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: tissue


title: Male chicken BC2 n°6437 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: sample


title: IBD36 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

tag: diagnosis (ibdu, uc, nomoa)


title: IBD33 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: Male chicken BC2 n°6435 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: tissue


title: Akita cells vs ct14 cells 3

description: Akita cells  vs ct14 celss . Replicate 3

tag: cell line

tag: cell type


title: Akita cells vs ct14 cells 2

description: Akita cells  vs ct14 celss . Replicate 2


title: IBD32 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

tag: diagnosis (ibdu, uc, nomoa)


title: IBD30 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: Akita cells vs ct14 cells 1

description: Akita cells  vs ct14 celss . Replicate 1


title: Male chicken BC2 n°6425 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: sample


title: Male chicken BC2 n°6434 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: tissue


title: IBD27 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

tag: diagnosis (ibdu, uc, nomoa)


title: IBD29 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: Male chicken BC2 n°6424 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: sample


title: IBD31 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

tag: diagnosis (ibdu, uc, nomoa)


title: Male chicken BC2 n°5702 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: tissue


title: Phaeodactylum_Red light_24h_rep2

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

hyb_protocol: 1650 ng cRNA from each sample was fragmented and hybridized on 4x44K P. tricornutum whole-genome 60-mer oligonucleotide microarrays (Agilent Technologies) in an Agilent G2545A Hybridization rotary oven (10 rpm, 65°C, 17.5 h). Hybridization was performed with the Gene Expression Hybridization Kit (Agilent p/n 5188-5242). The slides were washed with buffer 1 & 2 from Gene Expression Wash Buffer kit (Agilent p/n 5188-5327)

scan_protocol: The microarray sides were scanned twice at 5 µm resolution on a laser scanner (G2505 B from Agilent Technologies), using the “dynamic range expander” option in the scanner software. The resulting images were processed using Agilent Feature Extraction software v9.5.

data_processing: The median signal intensities (gMedianSignal) were normalized using the quantile method, and no background subtraction was performed. Spots identified as feature outliers were excluded from analysis, and weak or non-detected spots were given reduced weight (0.5). Genes with statistically significant differential expression were identified using the Limma package (version 3.2.3) and R (version 2.10.1).

organism: Phaeodactylum tricornutum

source_name: Phaeodactylum, Red light, 24 h

label_protocol: Total RNA (83 - 200 ng) was reverse transcribed, amplified and labelled with Cy3-CTP using the Low Input Quick Amp Labelling Kit, One-Color (Agilent p/n 5190-2305)

growth_protocol: Cultures were grown in f/2 medium made with 0.2 μm-filtered and autoclaved local seawater supplemented with f/2 vitamins and inorganic nutrients, filter sterilized and added after autoclaving. Continuous, axenic culturing of P. tricornutum was done as described in Nymark et al. (2009). The cultures were incubated at 15°C under cool white fluorescent light (Philips TLD 36W/96) providing a scalar irradiance (EPAR) of 100 μmol m-2 s-1 under continuous white light (CWL) conditions.

extract_protocol: Diatom cultures were centrifuged at 4000 g for 10 min at 15°C. The supernatant was removed and the cell pellet was resuspended in 1 ml f/2 medium. The suspension was transferred to 2 ml tubes and centrifuged at 18000 g for 1 min at 4°C. Supernatants were removed and the cell pellets were flash frozen in liquid nitrogen and stored at -80°C. Precooled (-80°C) 5 mm stainless steel beads (QIAGEN) were added to the tubes with frozen cell pellets, and the samples were mechanically disrupted and homogenized using the TissueLyser system (QIAGEN). Disruption was carried out for 2 x 2 min at 25 Hz. The samples were placed in a precooled (-80°C) adapter set for the first shaking step. Before the second shaking step, the samples were transferred to a room temperate adapter set and 0.5 ml lysis buffer (SpectrumTM Plant Total RNA kit, Sigma-Aldrich) was added to each tube. Total RNA was isolated from the homogenized lysate using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich). On-column digestion of DNA with DNase I (QIAGEN) was included for all RNA preparations. The concentration of the RNA was determined by measuring the absorbance at 260 nm with the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies), and the purity of the RNA was estimated by the OD260/OD280 nm absorption ratio (all ratios were > 2.0). The integrity of the RNA was verified by denaturing agarose gel electrophoresis and ethidium bromide staining following the protocol described in the RNeasy Mini handbook (QIAGEN).

treatment_protocol: Upon the onset of the experiment the cultures were synchronized by 48 h dark-treatment (D48). Thereafter the algae were exposed to blue light (BL), green light (GL) or red light (RL) provided by a waveband specific LED panel (SL3500, Photon Systems Instruments). The algae were exposed to 0.5 h, 6 h or 24 h of: 1) 230 μmol m-2 s-1 of RL, 2) 100 μmol m-2 s-1 of GL, 3) 50 μmol m-2 s-1 of BL or 4) 100 μmol m-2 s-1 of WL respectively. Three biological replicas for each of the treatments were harvested. Data for the white light exposure and 48h dark treatment is described in GSE42039, PMID: 23520530.

tag: clone

value: clone Pt 1 8.6 (CCMP632)

tag: treatment

value: Re-exposure to 24h red light (230 µmol m-2 s-1) after 48h dark treatment


title: Male chicken BC2 n°6429 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: sample


title: IBD56 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

tag: diagnosis (ibdu, uc, nomoa)


title: Male chicken BC2 n°5699 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: tissue


title: Engineered Methylobacterium methanol batch exponential

city: Cambridge

first: HSIN-HUNG

last: CHOU

state: MA

address: 16 Divinity Avenue, Biolab 3079

department: Organismic and Evolutionary Biology

institute: Harvard University

description: Comparison of global transcription profiles of an engineered Methylobacterium strain versus the WT strain

hyb_protocol: Hybridization was performed according to the Agilent 60-mer oligo microarray processing protocol (Sure-Hyb chamber/SSPE wash with the Agilent Stabilization and Drying Solution) except that a microhybridization oven (Bellco Biotechnology, Vienland, NJ) was used. The appropriate amount of labeled cDNA to use for hybridizations was examined by generating a Ratio-Intensity (RI) plot. The condition in which the majority of the values of [1/2 log2(R*G)] showed 10 to 12 (1024 to 4096) was selected to strike a good balance between intensities that are too close to background and those that approach the limits of the dynamic range of the assay. Alexa Fluor 555- and Alexa Fluor 647-labeled cDNAs (40 pmol) were cohybridized. After hybridized slides had been washed and dried, they were kept in a nitrogen-purged SmartDesiccator (Terra Universal, Fullerton, CA) until scanning. Unused array slides were also kept under the nitrogen purged SmartDesiccator.

scan_protocol: Microarray slides were sent to the Mogene (Saint Louis, MO) and scanned using an Agilent G2565AA microarray scanner. Scanned images were processed by Agilent Feature Extraction software Ver. 7.5.1 using the default settings for Agilent arrays, the Linear & Lowess method for normalization, and PMT settings of 10, 50, and 100 to obtain usable signal intensities from weak through strong signals. These results showed that for most of the probes, data from the 100 PMT setting were optimal. However, data from the 10-PMT setting were used for the signals (g and r mean) whose intensities were >50,000 at the 100-PMT setting.

data_processing: Initial data processing was done using Microsoft Excel, Array Assistant (a custom-designed program, Tom Lorimor, developer—available on the Lidstrom laboratory Website,  http://depts.washington.edu/mllab/research.htm), and TIGR MEV software (t-test and SAM analysis). The Array Assistant program was used to: (1) replace rMean or gMean values >50,000 from the PMT100 scan with the values derived from the PMT10 scan, (2) average duplicate probes, (3) remove noncenter/alternate probes, (4) add p-values to the data processed using TIGR’s MEV microarray analysis software, and (5) add annotations from an existing spreadsheet to the processed data. Six arrays (three sets of dye swap) were used to analyze each condition. Self–self hybridizations among the biological replicates were also performed as a control. After deletion of dye control probes and replacement of saturated probe data with PMT10 values, data from duplicate probes were averaged, the alternate probe (noncenter, additional probes) data were deleted, the resulting log ratios and log p-values from each data set were averaged and then uploaded into MEV as tab delimited, multiple sample files (TDMS). For t-test analysis, data analysis was run using equal variance assumptions (unequal and equal variance assumptions gave identical results) with or without Bonferroni corrections using an overall alpha (critical p-value) of 0.01. For SAM analysis, default settings (oneclass, testing against a mean of 0, SO parameters selected using the method of Tusher et al., imputation engine-K-nearest neighbors) and delta values of 0.5–5 were used. From this list of resulting significant genes, genes with a fold difference of >1.45 and an initial average p-value of <e 2 (from all six replicates) were chosen for further analysis. Because of the use of Alexa Fluor dyes, differences in gene expression levels of >1.3-fold were previously shown to be significant. Correlation coefficients were run both across and within the dye swaps. No pattern indicated any difference in ratios across the dye swaps suggesting that the dye swaps are not a blocking factor (data not shown). The data in the VALUE column in the table were computed by taking the Log10 of the ratio of the normalized Alexa_647 signal (rDyeNormSignal) divided by the normalized Alex_555 signal (gDyeNormSignal) for each spot.

label: Alexa Fluor 555

organism: Methylorubrum extorquens AM1

source_name: strain CM702

label_protocol: The cDNA synthesis and labeling reactions were carried out by using an Amino Allyl cDNA Labeling Kit (Ambion) and Alexa Fluor 555 and Alexa Fluor 647 Reactive Dyes (Invitrogen Corporation, Carlsbad, CA) according to the manufacture’s manual with the following modifications: 5 ug DNaseI-treated total RNA and 4 ug random decamers were used for cDNA synthesis. Ethanol precipitated cDNA incorporating amino allyl dUTP was incubated overnight at  80°C and microcentrifuged for 45 min at 20,800 g at 4°C. Precipitated cDNA was coupled to either Alexa Fluor 555 or Alexa Fluor 647 reactive dye dissolved in 3 uL high-quality DMSO. Dye-labeled cDNA was purified using a QIAquick PCR Purification Kit (QIAGEN) following the instructions in the kit except for performing three washes instead of one. cDNA samples were eluted into 50 uL Nuclease-free water. The incorporation of dyes, the nucleic acid concentration, and the labeling efficiency of dye-labeled cDNA were measured and calculated as described above.

growth_protocol: 10 uL frozen culture were inoculated in 9.6 mL Hypho media supplemented with 15 mM of methanol. The culture was incubated at 30 °C with 225 rpm shaking for 4 days. 0.15 mL culture was then transferred to 9.45 mL of fresh Hypho media and grown under the same conditions for 4 days. From this acclimated culture, 6.25 mL was inoculated into 393.75 mL fresh Hypho media in a 2 liter flask and grown under the same conditions. Bacterial cells were harvested at mid log phase (OD600~0.13).

extract_protocol:
To obtain individual replicates for RNA extraction, samples from cultures were harvested under exponential growth phase and taken as rapidly as possible to limit any potential changes in transcript profiles. A culture volume of 50 mL was sampled directly from the 400 mL batch culture into a conical tube containing 1/10th the culture volume of ice-cold “Stop Solution” (5% water saturated phenol (pH 7.0), 95% absolute ethanol). Cultures were immediately harvested by centrifugation at 4500 g for 8 min at 4°C. Total RNA was extracted from M. extorquens AM1 pellets using the RNeasy Mini Kit (QIAGEN) according to the manufacture’s Yeast III protocol. Lysis was achieved by 3 min of bead-beating in the Mini-Beadbeater 8 (BioSpec Products, Bartlesville, OK) with 600 uL of 0.1-mm zirconium-silica beads (BioSpec Products). SUPERase•In (Ambion, Austin, TX) was added at a final concentration of 1 U/uL to prevent RNA degradation after the elution of RNA with RNase-free water. RNA concentration and purity were determined by using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). RNA integrity was assessed by using a Bioanalyzer (Agilent Technologies) as per manufacturer’s instructions. Residual DNA was removed from isolated RNA samples by treating 60 ug RNA with 36 units of RNasefree DNaseI (Ambion) in a 300-uL reaction volume for 1 h at 37°C. DNaseI-treated total RNA samples were purified by using the RNeasy Mini Kit (QIAGEN) according to the manufacture’s RNA cleanup protocol with a slight modification. Briefly, 1050 uL Buffer RLT and 750 uL ethanol were added to the 300
uL RNA samples and subsequently loaded onto an RNeasy mini column and centrifuged. The remaining RNA sample was successively loaded onto the same column and processed until the rest of the RNA sample was collected on the column. The column was washed three times with 700 uL buffer RW1, and then three times with 500 uL RPE buffer. DNaseI-treated total RNA was eluted with 30 uL of RNase-free water. RNA concentration, purity, and integrity were determined as above. The presence of DNA contamination was examined by PCR. DNaseI-treated total RNA (100 ng) was used as a template in a 50-uL reaction. PCR was done using Taq DNA polymerase (Promega, Madison, WI) with 40 cycles. Only RNA that did not result in a PCR product was used for cDNA synthesis and labeling.

tag: strain cm702 strain is distingished from the wt by the following genetic characteristics

value: deletion of the mptG gene, carrying the the disrupted crtI502 allele, and expressing flhA and fghA genes from Paracoccus denitrificans

label: Alexa Fluor 647

source_name: strain CM502

growth_protocol: 10 uL frozen culture were inoculated in 9.6 mL Hypho media supplemented with 15 mM of methanol. The culture was incubated at 30 °C with 225 rpm shaking for 4 days. 0.15 mL culture was then transferred to 9.45 mL of fresh Hypho media and grown under the same conditions for 4 days. From this acclimated culture, 6.25 mL was inoculated into 393.75 mL fresh Hypho media in a 2 liter flask and grown under the same conditions. Bacterial cells were harvested at mid log phase (OD600~0.26).

tag: strain CM502 is isogenic to WT Methylobacterium extorquens AM1 except for carrying a disrupted allele crtI502, whose activity is required to generate the pink carotenoid


title: IBD55 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

tag: diagnosis (ibdu, uc, nomoa)


title: IBD54 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: Phaeodactylum_Red light_24h_rep3

tag: clone

tag: treatment


title: IBD28 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: Phaeodactylum_Red light_24h_rep1


title: IBD53 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: Phaeodactylum_Green light_24h_rep3

source_name: Phaeodactylum, Green light, 24 h

value: Re-exposure to 24h green light (100 µmol m-2 s-1) after 48h dark treatment


title: Male chicken BC2 n°5697 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: sample


title: Male chicken BC2 n°5698 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: tissue


title: Male chicken BC2 n°5696 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: sample


title: Wildtype_LPStreated_rep3

first: Charlie

last: Kim

address: 1001 Potrero Ave

description: Gene expression in wild type macrophages, treated with LPS

hyb_protocol: 1.5 ug of Cy3-labeled aRNA was fragmented and hybridized to Agilent 8x60k mouse gene expression microarrays as per manufacturer instructions.

scan_protocol: Arrays were scanned on an Agilent scanner at 3 um resolution as 20-bit TIFF images.

data_processing: Features were extracted using Agilent Feature Extraction software. Non-background subtracted raw Cy3 intensities were taken as gene expression values and quantile normalized.

source_name: Wild type, LPS-treated, rep3

label_protocol: Aminoallyl-incorporated aRNA was conjugated to Cy3 dye (Life Technologies) for 1 h in sodium bicarbonate buffer and cleaned up on a spin column.

growth_protocol: Macrophages were derived from mouse bone marrow differentiated in MCSF for one week.  Macrophages were plated at 1 million per well in 6-well dishes.

extract_protocol: RNA was isolated with the RNAqueous Micro kit (Life Technologies).  Isolated RNA was amplified using the Aminoallyl MessageAmp II kit (Life Technologies).

treatment_protocol: LPS was administered at 100 ng/ml for 4 h.

tag: genotype

tag: treatment

value: 100 ng/ml LPS 4 h

tag: cell type

value: macrophage

tag: genetic background


title: Male chicken BC2 n°5694 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: tissue


title: Male chicken BC2 n°5693 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: sample


title: Male chicken BC2 n°5683 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: tissue


title: Phaeodactylum_Blue light_24h_rep3

source_name: Phaeodactylum, Blue light, 24 h

tag: clone

tag: treatment

value: Re-exposure to 24h blue light (50 µmol m-2 s-1) after 48h dark treatment


title: Phaeodactylum_Blue light_24h_rep2


title: Phaeodactylum_Green light_24h_rep2


title: Male chicken BC2 n°5680 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: sample


title: Phaeodactylum_Blue light_24h_rep1

tag: clone

tag: treatment


title: Wildtype_LPStreated_rep2

source_name: Wild type, LPS-treated, rep2

tag: genotype

tag: cell type

tag: genetic background


title: IBD35 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

source_name: colon biopsy

tag: diagnosis (ibdu, uc, nomoa)

value: UC


title: Male chicken BC2 n°5687 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: tissue


title: IBD52 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

tag: diagnosis (ibdu, uc, nomoa)


title: Wildtype_untreated_rep4

description: Gene expression in wild type macrophages, untreated

source_name: Wild type, untreated, rep4

tag: genotype

tag: treatment

tag: cell type

tag: genetic background


title: Wildtype_LPStreated_rep1

source_name: Wild type, LPS-treated, rep1


title: Phaeodactylum_Red light_6h_rep3

source_name: Phaeodactylum, Red light, 6 h

tag: clone

value: Re-exposure to 6h red light (230 µmol m-2 s-1) after 48h dark treatment


title: Wildtype_LPStreated_rep4

source_name: Wild type, LPS-treated, rep4


title: IBD51 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)


title: Wildtype_untreated_rep3

source_name: Wild type, untreated, rep3


title: JunbKO_LPStreated_rep4

description: Gene expression in Junb knockout macrophages, treated with LPS

source_name: Knockout, LPS-treated, rep4

value: Junb-fl/fl Lyz2-Cre+/+


title: Male chicken BC2 n°5679 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

value: male

tag: protocol

value: fed ad libitum during 4 hours minimum

tag: age

source_name: Reference

tag: sample


title: Male chicken BC2 n°5678 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

value: 9 weeks

tag: tissue

value: Liver


title: Wildtype_untreated_rep2

source_name: Wild type, untreated, rep2

tag: genotype

tag: treatment

tag: cell type

tag: genetic background


title: IBD26 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

tag: diagnosis (ibdu, uc, nomoa)


title: Phaeodactylum_Red light_6h_rep1

tag: clone


title: Phaeodactylum_Green light_6h_rep3

source_name: Phaeodactylum, Green light, 6 h

value: Re-exposure to 6h green light (100 µmol m-2 s-1) after 48h dark treatment


title: Phaeodactylum_Red light_6h_rep2


title: Wildtype_untreated_rep1

source_name: Wild type, untreated, rep1


title: Phaeodactylum_Green light_24h_rep1


title: Phaeodactylum_Green light_6h_rep1


title: IBD45 colon biopsy

description: colon biopsy, (U of A/Cedars-Sinai)

value: NOMOA


title: Phaeodactylum_Green light_6h_rep2


title: Male chicken BC2 n°5676 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: sample

value: Total liver RNA pool obtained from the 45 Male broiler chickens	(sire BC1 n°1998)


title: JunbKO_LPStreated_rep3

source_name: Knockout, LPS-treated, rep3

tag: genotype

tag: treatment

tag: cell type

tag: genetic background


title: Male chicken BC2 n°5675 (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: tissue


title: Male chicken BC2 n°5671  (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: sample


title: JunbKO_untreated_rep4

description: Gene expression in Junb knockout macrophages, untreated

source_name: Knockout, untreated, rep4

tag: genotype

tag: treatment

tag: cell type

tag: genetic background


title: JunbKO_LPStreated_rep2

source_name: Knockout, LPS-treated, rep2


title: JunbKO_untreated_rep3

source_name: Knockout, untreated, rep3


title: Phaeodactylum_Blue light_6h_rep2

source_name: Phaeodactylum, Blue light, 6 h

tag: clone

value: clone Pt 1 8.6 (CCMP632)

value: Re-exposure to 6h blue light (50 µmol m-2 s-1) after 48h dark treatment


title: JunbKO_untreated_rep2

source_name: Knockout, untreated, rep2


title: O_sativa_japonica_cigalon_B510inoculated_rep2

city: Villeurbanne

first: Benoît

last: DROGUE

state: Rhône-Alpes

address: Boulevard du 11 novembre

department: Université Lyon 1

institute: Université de Lyon

description: This sample is the second replicate Oriza sativa japonica cv. Cigalon inoculated with Azospirillum sp. B511

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

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

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185)
Intensity values were summarized using median polish algorithm. The median value was used for the replicate method.

organism: Oryza sativa Japonica Group

source_name: Oriza sativa japonica cultivar Cigalon inoculated with strain B510

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

growth_protocol: Before inoculation, Azospirillum cells were grown overnight in Nfbm medium (Vial et al. J. Bacteriol. 108:5364-75). Bacterial cells were harvested in the late-exponential phase (at OD580 around 1.2), centrifuged and resuspended in a defined volume of 0.8% NaCl to obtain 2 x109 cells mL-1. Then, 109 cells were mixed with 50 ml plant agar (8 g l-1) and introduced into 120 × 120 × 17 mm square plates. Rice seed sterilization was performed as previously described by Drogue et al. 2014 (FEMS Microbiol. Ecol.). Four plant were added in each square plate. All the plates were incubated vertically, for 7 d in a growth chamber (MLR350, SANYO, UK) with a photoperiod of 16 h at 28°C (light 150 μE m-2 s-1), and 8 h at 22°C in the dark.

extract_protocol: For each experiment, 30 plant root systems were pooled and frozen using liquid nitrogen. Root cell lysis was performed by grinding root systems with a mortar and pestle under liquid nitrogen. Total RNA was isolated using the TRIzol method (Invitrogen, Carlsbad, CA, USA). RNA samples were purified using RNeasy plant mini kit (Qiagen, Courtaboeuf, France) according to the manufacturer’s protocol. RNA integrity was assessed using Agilent RNA 6000 Pico Kit (Agilent Technologies, Waldbronn, Germany) and the Agilent 2100 Bioanalyzer (Agilent Technologies) device. In order to increase mRNA representation in RNA samples, total RNA were digested with mRNA ONLYTM Procaryotic mRNA isolation kit (Epicentre Biotechnologies, Madison, WI, USA) according to the provided protocol.  The microarray cDNA (three independent samples per condition) was synthesized with the SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen), using a mix (1:1) of random primers (Promega Corporation, Madison, WI, USA) and Oligo-dT(15) primers (Promega).

tag: cultivar

value: Cigalon

tag: tissue

value: root

tag: pathogen

value: Azospirillum strain B510

tag: days post inoculation


title: JunbKO_untreated_rep1

source_name: Knockout, untreated, rep1

value: macrophage


title: O_sativa_japonica_cigalon_B510inoculated_rep3

description: This sample is the third replicate Oriza sativa japonica cv. Cigalon inoculated with Azospirillum sp. B512


title: Male chicken BC2 n°5670  (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)


title: Phaeodactylum_Red light_0.5h_rep2

source_name: Phaeodactylum, Red light, 0.5 h

tag: clone

tag: treatment

value: Re-exposure to 30 min red light (230 µmol m-2 s-1) after 48h dark treatment


title: Phaeodactylum_Red light_0.5h_rep3


title: Phaeodactylum_Blue light_6h_rep1


title: Phaeodactylum_Red light_0.5h_rep1


title: Phaeodactylum_Blue light_6h_rep3


title: Male chicken BC2 n°4159  (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: tissue

tag: sample


title: O_sativa_japonica_cigalon_4Binoculated_rep2

description: This sample is the second replicate Oriza sativa japonica cv. Cigalon inoculated with Azospirillum lipoferum 4B

source_name: Oriza sativa japonica cultivar Cigalon inoculated with strain 4B

tag: cultivar

tag: pathogen

value: Azospirillum lipoferum strain 4B

tag: days post inoculation


title: O_sativa_japonica_cigalon_4Binoculated_rep3

description: This sample is the third replicate Oriza sativa japonica cv. Cigalon inoculated with Azospirillum lipoferum 4B


title: O_sativa_japonica_cigalon_B510inoculated_rep1

description: This sample is the first replicate Oriza sativa japonica cv. Cigalon inoculated with Azospirillum sp. B510


title: Male chicken BC2 n°5672  (from the sire BC1 n°1998)

description: For each gene, the fluorescence ratio represents the relative abundance of the hepatic mRNA of the animal of interest  compared with the RNA pool reference.

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)


title: Male chicken BC2 n°4166  (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: tissue

tag: sample


title: Male chicken BC2 n°4165  (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)


title: Phaeodactylum_Green light_0.5h_rep3

source_name: Phaeodactylum, Green light, 0.5 h

tag: clone

tag: treatment

value: Re-exposure to 30 min green (100 µmol m-2 s-1) light after 48h dark treatment


title: Male chicken BC2 n°4158  (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: tissue

tag: sample


title: Male chicken BC2 n°4169  (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)


title: Male chicken BC2 n°4163  (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: tissue

tag: sample


title: Male chicken BC2 n°4150  (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)


title: Male chicken BC2 n°4154  (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

tag: tissue

tag: sample


title: O_sativa_japonica_nipponbare_B510inoculated_rep3

description: This sample is the third replicate Oriza sativa japonica cv. Nipponbare inoculated with Azospirillum sp. B512

source_name: Oriza sativa japonica cultivar Nipponbare inoculated with strain B510

tag: cultivar

value: Nipponbare

tag: pathogen

tag: days post inoculation


title: O_sativa_japonica_cigalon_4Binoculated_rep1

description: This sample is the first replicate Oriza sativa japonica cv. Cigalon inoculated with Azospirillum lipoferum 4B


title: Phaeodactylum_Green light_0.5h_rep2

tag: clone

tag: treatment


title: O_sativa_japonica_cigalon_noninoculated_rep3

description: This sample is the third replicate of non-inoculated roots of Oriza sativa japonica cv. Cigalon

source_name: Oriza sativa japonica cultivar Cigalon non inoculated


title: O_sativa_japonica_cigalon_noninoculated_rep1

description: This sample is the first replicate of non-inoculated roots of Oriza sativa japonica cv. Cigalon


title: Phaeodactylum_Blue light_0.5h_rep3

source_name: Phaeodactylum, Blue light, 0.5 h

value: Re-exposure to 30 min blue light (50 µmol m-2 s-1) after 48h dark treatment


title: Phaeodactylum_Green light_0.5h_rep1


title: O_sativa_japonica_nipponbare_B510inoculated_rep2

description: This sample is the second replicate Oriza sativa japonica cv. Nipponbare inoculated with Azospirillum sp. B511


title: Male chicken BC2 n°4151  (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker mcw0020 (alleles)

tag: marker adl0328 (alleles)

tag: marker lei0043 (alleles)

tag: marker mcw0083 (alleles)

tag: marker seq0352 (alleles)

tag: marker huj0006 (alleles)

tag: marker mcw0150 (alleles)

tag: marker lei0032 (alleles)

tag: marker lei0161 (alleles)

tag: marker mcw0193 (alleles)

tag: marker adl0292 (alleles)

tag: marker mcw0214 (alleles)

tag: marker mcw0210 (alleles)

tag: marker mcw0238 (alleles)

tag: marker lei0064 (alleles)

tag: marker adl0326 (alleles)

value: male

value: fed ad libitum during 4 hours minimum

source_name: Reference


title: Male chicken BC2 n°4148  (from the sire BC1 n°1998)

tag: marker lei0101 (alleles)

tag: marker adl0314 (alleles)

tag: marker mcw0068 (alleles)

tag: marker lei0217 (alleles)

tag: marker lei0088 (alleles)

tag: marker adl0313 (alleles)

tag: marker mcw0036 (alleles)

tag: marker lei0106 (alleles)

tag: marker mcw0181 (alleles)

tag: marker lei0079 (alleles)

tag: marker seq0291 (alleles)

tag: marker lei0061 (alleles)

tag: marker adl0122 (alleles)

tag: marker seq0296 (alleles)

tag: marker seq0353 (alleles)

tag: marker mcw0178 (alleles)

tag: gender

tag: protocol

tag: age

value: 9 weeks

tag: tissue

value: Liver

tag: sample


title: Phaeodactylum_Blue light_0.5h_rep1

tag: clone

tag: treatment


title: O_sativa_japonica_cigalon_noninoculated_rep2

description: This sample is the second replicate of non-inoculated roots of Oriza sativa japonica cv. Cigalon

tag: cultivar

tag: days post inoculation


title: Phaeodactylum_Blue light_0.5h_rep2


title: O_sativa_japonica_nipponbare_4Binoculated_rep3

description: This sample is the third replicate Oriza sativa japonica cv. Nipponbare inoculated with Azospirillum lipoferum 4B

source_name: Oriza sativa japonica cultivar Nipponbare inoculated with strain 4B

tag: pathogen


title: O_sativa_japonica_nipponbare_B510inoculated_rep1

description: This sample is the first replicate Oriza sativa japonica cv. Nipponbare inoculated with Azospirillum sp. B510


title: R6_W

status: Public on Dec 21 2014

type: genomic

city: Singapore

first: Gourvendu

last: Saxena

state: Singapore (General)

address: #05-02, 28 Medical Drive

department: The Singapore Centre on Environmental Life Sciences Engineering

country: Singapore

institute: National University of Singapore

hyb_protocol: Arrays were hybridized overnight at 48degC and 60 rpm and then washed and stained using standard Affymetrix buffers/reagents.

scan_protocol: Images were captured on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: CEL files were converted to CELa files and then processed using proprietary software (PhyCA).

molecule: genomic DNA

organism: mixed sample

source_name: Surface water from concrete paved waterways

label_protocol: TDT enzyme (Promega; Madison, WI) and GeneChip Labeling Reagent (Affymetrix; Santa Clara, CA) were used to label fragmented amplicons.

extract_protocol:
Genomic DNA was extracted from the about 5gm (wet weight) of sediment and 1.2L of water samples immediately after the samples were brought to the lab. Sediments were dewatered and DNA was extracted by a combination of mechanical, chemical and thermal lysis and chloroform-isoamyl alcohol purification using protocol from Zhou et al., 1996 (1). Water samples were filtered through sterile Millipore 0.22µm membrane filter (Thermo Fisher Scientific Inc.) to collect the biomass, followed by the DNA extraction protocol similar to the DNA extraction protocol for sediment samples. Humic substances were removed using OneStep™ PCR Inhibitor Removal Kit from Zymo Research Corporation (USA). The DNA quality and quantity was measured with PicoGreen using a FLUOstar Optima (BMG Labtech, Jena, Germany) before loading onto microarrays.
amplification protocol: 0.5 - 1 ng template was used in each of 8 PCR tubes (8 different annealing temperatures were used). 300 nM primers (27F and 1492R for 16S rRNA amplicons), 200 uM each dNTP, 1 ug/uL BSA, and 1.25 U ExTaq (Takara) enzyme were used in the amplifications (95C for 3 min., 30 cycles of 95 (30 sec) ,48 - 58 C annealing temp. (30 sec), 72 C (2 min), followed by 72 C for 10 min., hold at 4 C).

tag: phase

value: Water

tag: land-use type

value: Residential

tag: land-use region


title: R10_W


title: R9_W


title: R2_W


title: I6_W

value: Industrial


title: R0_W


title: R11_W


title: R3_W


title: R8_W