title: CD4-131-A


title: CD4-441-D

status: Public on Mar 03 2012

type: RNA

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

hyb_protocol: cRNA was hybridized to the Illumina Whole Genome 6 (version 3) BeadChip (Illumina, San Diego, non-RA inflammatory arthritisA), following the manufacturer’s protocol.

scan_protocol: Each BeadChip measured the expression of 48,804 genes (annotation file at http://www.illumina.com/support/annotation_files.ilmn) and was imaged using the Illumina BeadArray Reader.

data_processing:
Phases 1 and 2 of the study were independently normalized in 2 steps: each probe measurement was first divided by the 50th percentile of all measurements in its array, before being centred around its own median expression measurement accross all samples in the phase. The within-phase batch-effect related to RNA labelling was corrected in the R statistical computing environment (http://www.r-project.org/) using the empirical Bayes method of Johnston et al. (2007) before phases were combined.  Phases were then combined and residual between-phase batch effect corrected by the same method.

Non-normalized data is available in 'GSE20098_non-normalized.txt', which is linked to the Series GSE20098 record as a supplementary file.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: ex-vivo peripheral blood CD4 T-cells, non-RA/non-inflammatory arthritis

label_protocol: 250ng RNA was reverse transcribed into cRNA, and biotin-UTP labeled, using the Illumina TotalPrep RNA Amplification Kit (Ambion, Texas).

extract_protocol: Monocytes were first depleted by immunorosetting (Rosettesep Human Monocyte depletion cocktail, Stemcell Technologies Inc., Vancouver, non-RA inflammatory arthritisanada), and remaining cells underwent positive selection using Easisep whole blood CD4+ positive selection kit reagents in conjunction with the Robosep automated cell separator (Stemcell). CD4+ T-cell purity was determined using standard flow cytometry techniques; FITC-conjugated anti-CD4 and PE-conjugated anti-CD14 antibodies were used (Beckton Dickinson, New Jersey, USA). RNA was immediately extracted from CD4+ T-cell isolates using RNeasy MINI kits (Qiagen GmbH, Germany), incorporating an “on-column” DNA digestion step.

treatment_protocol: Between 1300hrs and 1630hrs during the clinic appointment, 15ml peripheral whole blood was drawn into EDTA tubes (Greiner Bio-One, ACPA- RAustria) and stored at room temperature for a maximum of 4 hours before processing.

tag: tissue

value: peripheral blood

tag: cell type

value: CD4+ T-cells

tag: outcome

value: D

tag: classification

value: training

tag: phase batch

tag: labelling batch


title: CD4-388-A

source_name: ex-vivo peripheral blood CD4 T-cells, ACPA- RA

value: A


title: CD4-387-C

source_name: ex-vivo peripheral blood CD4 T-cells, non-RA inflammatory arthritis

value: C


title: CD4-406-C


title: CD4-405-D

value: UA


title: CD4-391-C


title: CD4-401-A


title: CD4-439-A


title: CD4-369-A


title: CD4-358-B

source_name: ex-vivo peripheral blood CD4 T-cells, ACPA+ RA

value: B


title: CD4-364-A


title: CD4-366-A


title: CD4-351-C


title: CD4-354-C


title: CD4-389-A


title: CD4-350-A


title: CD4-353-C


title: CD4-340-D


title: CD4-346-D


title: CD4-359-B


title: CD4-355-D


title: CD4-315-B


title: CD4-314-C


title: CD4-326-C


title: CD4-307-C


title: CD4-336-A


title: CD4-322-A


title: CD4-334-D


title: CD4-313-C


title: CD4-302-A


title: CD4-304-C


title: CD4-320-C


title: CD4-311-C


title: CD4-305-A


title: CD4-328-D


title: CD4-306-B


title: CD4-296-A


title: CD4-286-D


title: CD4-272-C


title: CD4-283-D


title: CD4-263-C


title: CD4-260-D


title: CD4-273-A


title: CD4-266-C


title: CD4-294-B


title: CD4-261-B


title: CD4-253-A


title: CD4-247-B


title: CD4-264-B


title: CD4-254-A


title: CD4-220-A


title: CD4-218-B


title: CD4-203-B


title: CD4-210-C


title: CD4-188-C


title: CD4-232-A


title: CD4-204-B


title: CD4-221-B


title: T cells-BDC2.5/B6g7 lymph node-rep1

status: Public on Apr 17 2004

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

description:
Antigen-specific T cells from the pancreatic lymph nodes of mice developping an aggressive form of insulitis (BDC2.5 on C57Bl/6.H2g7 background at 25 days)
jos1158

organism: Mus musculus

source_name: pancreatic lymph nodes

extract_protocol: total RNA was extracted using Trizol reagent and was submitted to two rounds of amplification.

tag: genetic background

tag: transgene

value: BDC2.5 T cell receptor genes.

tag: isolation

value: FACS on CD4+, BDC2.5 clonotype high, Hoechst- (viable) cells.

tag: age

value: 25 days.


title: CD4-239-B


title: NK cells-C57Bl/6.H2g7-rep1

description:
Splenic NK cells from mice on C57Bl/6H2g7 genetic background.
jos1786

data_processing: RMA

source_name: spleen

extract_protocol: RNA isolated with Trizol reagent and amplified twice.

value: None.

value: 6 weeks.

value: spleen.

value: FACS on on Asialo GM1+ cd45+ Hoechst- (viable) cells.


title: NK cells-C57Bl/6.H2g7-rep2

description: Splenic NK cells from mice on C57Bl/6.H2g7 genetic background.

value: 3 weeks.


title: 1day_Mtnf-ya1-1_3 with array type Medicago from Affymetrix

status: Public on Nov 01 2011

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description: MtNF-YA1 is a transcription factor involved in the regulation of nitrogen fixing nodule organogenesis. Mtnf-ya1-1 mutant has been shown to be more resistant to Aphanomyces euteiches (Ae), a root pathogen, than the A17 wild type (WT) line. In this study we want to compare both WT and mutant plant responses, 1 and 6 days post inoculation (dpi) between WT and the Mtnf-ya1-1 mutant, in order to identify MtNF-YA1-dependent gene networks during infection. Data about non inoculated A17 control plants and infected A17 at 1 dpi have been already obtained in another experiment in which the conditions of in vitro culture of M. truncatula plants and ofA.euteiches(Ae) inoculation were exactly the same than the ones used in these experiments.

hyb_protocol: labelled extract quantity: 15ug

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

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

label: Biotin

organism: Medicago truncatula

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

growth_protocol: roots - - In vitro conditions on M medium - 16h light 8h dark 22°C

extract_protocol: 1day_Mtnf-ya1-1_3:136ng. RNeasy Qiagen kit

treatment_protocol: Name:A_euteiches_1dpi - time course study - pathogen infection,ae 1dpi:time 24hour . inoculation with A. euteiches Reference protocol or description Sample treatment protocol : Djebali et al, MPMI, 2009.

tag: strain

value: medicago truncatula (a17)

tag: genotype/variation

value: mutant (Mtnf-ya1-1)

tag: harvest date

tag: treatment name

tag: treatment time


title: 1day_Mtnf-ya1-1_1 with array type Medicago from Affymetrix

extract_protocol: 1day_Mtnf-ya1-1_1:142ng. RNeasy Qiagen kit

value: A_euteiches_1dpi - time course study - pathogen infection,ae 1dpi


title: 6days_Mtnf-ya1-1_3 with array type Medicago from Affymetrix

extract_protocol: 6days_Mtnf-ya1-1_3:132ng. RNeasy Qiagen kit

treatment_protocol: Name:water_A_euteiches - with euteiches,inoculation - mock infiltration,ae 6d:time 6day . Factor value : Mtnf-ya1-1 Reference protocol or description Sample treatment protocol : Djebali et al, MPMI, 2009.


title: CD4-184-B

value: peripheral blood

value: CD4+ T-cells


title: ctrl_Mtnf-ya1-1_1 with array type Medicago from Affymetrix

extract_protocol: ctrl_Mtnf-ya1-1_1:364ng. RNeasy Qiagen kit

treatment_protocol: Name:water - inoculation - mock infiltration,mock_water:time 24hour . Mtnf-ya1-1 Reference protocol or description Sample treatment protocol : Djebali et al, MPMI, 2009.


title: 1day_Mtnf-ya1-1_2 with array type Medicago from Affymetrix

extract_protocol: 1day_Mtnf-ya1-1_2:300ng. RNeasy Qiagen kit


title: CD4-196-A

value: A

value: training


title: 6days_Mtnf-ya1-1_2 with array type Medicago from Affymetrix

extract_protocol: 6days_Mtnf-ya1-1_2:123ng. RNeasy Qiagen kit

value: water_A_euteiches - with euteiches,inoculation - mock infiltration,ae 6d


title: ctrl_Mtnf-ya1-1_3 with array type Medicago from Affymetrix

extract_protocol: ctrl_Mtnf-ya1-1_3:178ng. RNeasy Qiagen kit

value: water - inoculation - mock infiltration,mock_water


title: worker/queen_hindleg_PP2

status: Public on Feb 15 2012

city: Piracicaba

first: Ana

middle: Durvalina

last: Bomtorin

state: São Paulo

address: R Ajudante Albano 847

country: Brazil

institute: Universidade de Sao Paulo

description: Analysis used RNA from hind leg imaginal discs of workers at prepupal as a control to compare with RNA provenient form hind leg imaginal discs of queens at prepupal stages

hyb_protocol: For hybridization, probes [in 40µL of hybridization solution (0.98mL of formamide, 0.98mL SSC 20X, 39.2µLSDS 10%)] were pre-heated at 55°C during at 3 min and placed on microarrays under lifter-slip cover glasses (22x60, 31.25µL). Microarrays slides were placed in single slide hybridization chambers which were incubated in a water bath for hybridization for 22h, at 42°C. Washing procedure included twice the following steps: SSC 2X, SDS 0,1%; SSC 0,5X, SDS 0,01%; SSC 2X; SSC 0,1X; deionized water, shaking manually for 30s and for the last incubated in isopropanol before centrifuging for 3min at 2000rpm.

scan_protocol: Slides were scanned by using  Axon GenePix 4000B at default parameters. For images quantitation we used ScanAlyze 2.35 (http://rana.lbl.gov/EisenSoftware.htm) with default parameters.

data_processing: Background correction was performed in a manner we could avoid the correction of negative or zero intensities (offset correction) by adding to the background-corrected intensities a positive constant (=50). It restrains spurious variation in log-ratios, particularly at low intensity spots. The “print-tip loess” normalization was used to correct for within-array dye and spatial effects and single channel normalization was used to facilitate comparison between arrays. After normalization we determined a log2 ratio (Queen´s sample intensity/Worker´s sample intensity), for each probe on each array. The fold-change in expression and its standard error for each gene were calculated by fitting a linear regression to the normalized expression data. A Bayesian smoothing procedure was used to shrink the estimated standard errors, with which we calculated the moderated t-statistic for each gene.

organism: Apis mellifera

source_name: hind leg imaginal discs of Apis mellifera worker at prepupal stages

label_protocol: RNA amplification (from 1μg of total RNA) and probe synthesis (from 10μg of amplified RNA) were done with and according to Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion).

growth_protocol: Bees were obtained from the Experimental Apiary of the University of São Paulo at Ribeirão Preto

extract_protocol: Total RNA was extracted using GenElute™ Mammalian Total RNA Kit (Sigma) solution (Invitrogen) following Invitrogen’s protocol and purified using RNeasy Mini Kit (QIAGEN).

treatment_protocol: workers and queens were reared under natural conditions

tag: developmental stages

value: prepupae

tag: bee type

value: worker

value: hind leg imaginal discs

source_name: hind leg imaginal discs of Apis mellifera queen at prepupal stages

value: queen


title: T cells-BDC2.5/B6g7 lymph node-rep2

description:
Antigen-specific T cells from the pancreatic lymph nodes of mice developping an aggressive form of insulitis (BDC2.5 on C57Bl/6.H2g7 background at 22 days).
jos1634

value: BDC2.5 T cell receptor genes.

value: FACS on CD4+, BDC2.5 clonotype high, Hoechst- (viable) cells.

value: 22 days.


title: ctrl_Mtnf-ya1-1_2 with array type Medicago from Affymetrix

extract_protocol: ctrl_Mtnf-ya1-1_2:168ng. RNeasy Qiagen kit


title: 6days_a17_1 with array type Medicago from Affymetrix

growth_protocol: roots - -In vitro condition on M medium - 16h light 8h dark 22°C

extract_protocol: 6days_a17_1:158ng. RNeasy Qiagen kit

treatment_protocol: Name:A_euteiches_6dpi - inoculation - pathogen infection,ae 6dpi:time 6day . Factor value : WT Reference protocol or description Sample treatment protocol : Djebali et al, MPMI, 2009.

value: mutant (wt)


title: 6days_Mtnf-ya1-1_1 with array type Medicago from Affymetrix

extract_protocol: 6days_Mtnf-ya1-1_1:106ng. RNeasy Qiagen kit

value: medicago truncatula (a17)


title: 6days_a17_3 with array type Medicago from Affymetrix

extract_protocol: 6days_a17_3:166ng. RNeasy Qiagen kit

value: A_euteiches_6dpi - inoculation - pathogen infection,ae 6dpi


title: 6days_a17_2 with array type Medicago from Affymetrix

extract_protocol: 6days_a17_2:95ng. RNeasy Qiagen kit


title: CD4-316-C

tag: tissue

value: C