title: RNA_NK_12_6h_rep1

status: Public on Oct 28 2020

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

data_processing:
FastATAC-seq reads from two biological replicates for each sample were mapped to the mouse genome (mm9 assembly) using Bowtie 0.12.8.
FastATAC-seq: Redundant reads were removed using fastquniq (Xu et al., 2012). Only one mapped read to each unique regions of the genome that was less than 175 base pairs was kept and used  in peak calling. Regions of open chromatin were identified by MACS (version 1.4.2)(Zhang et al., 2008) using a P-value threshold of 1 x 10-5. Only regions called in both replicates were used in downstream analysis.
RNA-Seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of sequentially varying length were mapped to the mouse genome mm9 using TopHat 2.0. Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Cufflinks 2.0.
RNA-Seq: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Cufflinks 2.0.
ChIP-seq: Reads of 50 bases were aligned to the mouse genome build mm9 with Bowtie 0.12.8, allowing two mismatches. Uniquely mapped and non-redundant reads were retained and used for peak calling.
ChIP-seq: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958).
scRNA-seq: Sequence reads from all samples were processed and aggregated using Cell Ranger. Aggregated data was further analyzed by Seurat(Macosko et al., 2015).Downstream analyses and heatmap generation were performed with R using Rstudio. To
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for ATAC-seq, RNA-seq and transcription factor ChIP-seq; bedgraph for histone modification ChIP-seq

growth_protocol:
cell isolation protocol: Cells from spleen were obtained by mechanical disruption. Peritoneal cells were obtained by  washing of the peritoneal cavity with cold PBS. Isolated cells were further sorted as based on their surface markers.
in vitro culture protocol: All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10 ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.

extract_protocol:
FastATAC-Seq: FastATAC-Seq was performed according to a published protocol(Corces et al., 2016)
RNA-Seq: RNA-seq was performed as described previously with slight modification (Hirahara et al., 2015). Total RNA was prepared from approximately 30-50,000 cells by using TRIzol  following manufacture’s protocol (Life Technologies).
RNA-Seq: Total RNA was subsequently processed to mRNA-seq library using TruSeq SR mRNA sample prep kit (FC-122-1001, Illumina).
RNA-Seq: The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.
ChIP-seq: Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.
ChIP-seq: Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of NEBNext adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with NEBNext index primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen).
ChIP-Seq (size fractionation). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.
scRNA-seq: Freshly sorted NK cells (13,000 cells each) were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics). Indexed libraries were multiplexed and sequenced on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
scRNA-seq: The generated scRNA-Seq libraries were sequenced using a 50 cycle (paired-end) with a HiSeq 3000 (Illumina).

treatment_protocol: Toxoplasma gondii infection protocol: Mice of at least 8 weeks of age were inoculated with an average of 15 cysts of type II avirulent T.gondii strain ME-49 by intraperitoneal injection

tag: strain

value: Spleen

value: Natural killer cells

tag: surface marker

tag: culture condition

value: ex vivo

tag: description for exp id


title: RNA_NK_2_6h_rep1

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type


title: RNA_NK_untreated_rep1


title: RNA_NK_12_6h_rep2


title: RNA_NK_untreated_rep2


title: RNA_NK_IL2_12_6h_rep3


title: RNA_NK_2_6h_rep3


title: 8858-1_5_hSS_125_Baseline

status: Public on Oct 20 2021

city: Los Angeles

first: Aaron

last: Gordon

state: CA

address: 695 Charles E. Young Drive South, Gonda 2306, Los Angeles, CA  90095-1761

department: Neurology

institute: UCLA

data_processing:
Paired end reads were mapped using STAR to hg38 with Gencode v25 annotations.
Gene expression levels were quantified using rsem (v1.3.0)
Genome_build: hg38
Supplementary_files_format_and_content: csv file containing raw counts

organism: Homo sapiens

source_name: human subpalial spheroids

growth_protocol: hCS and hSS differentiations from hiPSCs grown on MEF feeders were performed as previously described (Birey et al., 2017; Sloan et al., 2018).

extract_protocol:
RNA was extracted from hSS and hCS using the Quick-RNA Miniprep kit (Zymo Research, R1054).
For library construction, non-stranded cDNA libraries were constructed using poly(A) mRNA enrichment and the NEBNext Ultra™ II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, E7770S).

tag: Sex

value: M

tag: iPSc line

value: CTRL

tag: region

value: hSS

tag: differntiation

tag: differentiation day

tag: genetic ancestry pc1

tag: genetic ancestry pc2

tag: activation with kcl

value: Baseline

tag: reprogramming method

value: Episomal


title: RNA_NK_12_6h_rep3


title: RNA_NK_2_6h_rep2


title: RNA_NK_exvivo_rep3


title: RNA_NK_exvivo_rep4


title: wt_brain_K27me3_(20170605_KA_DmSc_420_BdiC_187)

status: Public on May 01 2019

city: Seattle

first: Kamran

last: Ahmad

state: WA

address: Fred Hutchinson Cancer Center, 1100 Fairview Ave North, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Center

description: Chromatin immunocleavage and release

library_source: genomic

data_processing:
Genome_build: UCSC dm6
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC dm6. 2. We used bowtie 2.2.5 with options "--local --very-sensitive-local --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700" to map the same 25bp paired-end Illumina reads to UCSC sacCer3. 3. We extracted properly paired reads from the marked alignments to both genomes. 4. We used the bedtools 2.17.0 genomecov command with a scaling factor of 10000/(number of fragments mapped to S.cervisiae) to create a spike-in calibrated track file (Supplementary file .bedgraph.gz).

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: wt larval brains K27me3

extract_protocol:
G021_disc_CUT&RUN.pdf
PMID 25827087

tag: tissue/genotype

value: wt larval brains

tag: antibody

value: anti-K27me3 Cell Signalling#9733


title: R5_wing_Pc_(20180222_KA_DmSc_772PX)

description: Chromatin immunocleavage and release

source_name: vg dPRE deletion wing discs Pc

value: vgR5 mutant wing discs

value: anti-Pc (antibody 100)


title: S2_K27me3_(20160706_AS_DmSc_235_AB187_B1)

description: Chromatin immunocleavage and release

source_name: S2 cells K27me3

tag: cell line

value: S2 cells


title: wt_wing_Pc_(20170420_AS_DmSc_390_WDiC_A100)

description: Chromatin immunocleavage and release

source_name: wt wing discs Pc

value: wt wing discs


title: R5_wing_K27me3_(20180222_KA_DmSc_711X)

description: Chromatin immunocleavage and release

source_name: vg dPRE deletion wing discs K27me3

value: vg dPRE deletion wing discs


title: S2_Pc_(20160920_AS_DmSc_247_S2iCA100)

description: Chromatin immunocleavage and release

source_name: S2 cells Pc


title: wt_wing_K27me3_(20170605_KA_DmSc_421_WdiC_187)

description: Chromatin immunocleavage and release

source_name: wt wing discs K27me3


title: DJR_wing_K27me3_(20180222_KA_DmSc_709X)

description: Chromatin immunocleavage and release

source_name: vg pPRE dPRE deletion wing discs K27me3

value: vg pPRE dPRE deletion wing discs


title: DJR_wing_Pc_(20180424_KA_DmSc_834PX)

description: Chromatin immunocleavage and release

source_name: vg pPRE dPRE deletion wing discs Pc

value: vgDJ vgR22 mutant wing discs


title: COT2_wing_FACS_K27me3_(20180424_KA_DmSc_909PX)

description: Chromatin immunocleavage and release

source_name: FACS isolated GFP-positive wing disc pouch cells K27me3

value: P[attPB,y+,w+,vgQ]CO-B P[UAS-GFP,w+]T2 FACS-isolated GFP-positive wing disc pouch cells


title: CL1_wing_Pc_(20180424_KA_DmSc_878S)

description: Chromatin immunocleavage and release

source_name: vg pPRE deletion wing discs Pc

value: vgCL1 wing discs


title: HD_rep 2 (human)

status: Public on Aug 11 2021

city: Gaithersburg

first: Timothy

last: Break

address: 16020 Industrial Dr.

institute: MesoScale Diagnostics

description:
HD-APECED_CPM_TMM_counts.txt
HD-APECED_RawCountFile.txt

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCh38.v25 human genome using STAR v2.5.2a in  single-pass mode. With the following parameters:  --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.25 --outFilterScoreMinOverLread 0.25 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCh38 v25 genome annotation GTF which included ERCCs.
An expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Genome_build: GRCh38.v25
Supplementary_files_format_and_content: Tab delimited files include a raw counts and TMM-normalized expression matrices.

source_name: Oral mucosal tissue

extract_protocol:
Oral mucosal tissue was homogenized using Miltenyi Gentlemacs M tube and total RNA was extracted from whole tissue using Trizol Reagent
Sequencing libraries were prepared by the Illumina Nextera method, following manufacturer's recommendations and sequenced in a NextSeq500 instrument in 150 bp end mode

value: Oral mucosal gingival tissue

tag: age

value: 43 years old

value: Female

tag: disease state

value: Healthy donor


title: HD_rep 3 (human)

value: 23 years old


title: M2_BMDM_scRNAseq

status: Public on Apr 24 2019

city: Avon

first: Beiyan

last: Zhou

state: Connecticut

address: 263 Farmington Ave, Immunology

department: Immunology

institute: UCONN Health

description: For dietary feeding studies, mice were fed with a standard chow diet (18% fat calories, 24% protein calories, and 58% of carbohydrate calories;  Cat No. 2918, Envigo. Teklad.) for 12 weeks. bone marrow cells were collected from femur and tibia bone followed by erythrocyte lysis with ammonium chloride solution (8.3 g/L ammonium chloride, 1.0 g/L potassium bicarbonate, and 0.009% EDTA) and seeded in tissue culture plates at a concentration of 0.15 x 106/cm2. Cells were induced for differentiation to monocytes in BMDM growth medium (Iscove's Modified Dulbecco's Medium (IMDM) + 10% FBS + 15% L-929 cell (ATCC, CCL-1)) culture supernatant for 7 days; fresh BMDM growth medium was replaced on day 3. Maturation and purity of BMDMs were evaluated on day 7 using flow cytometry analysis with fluorescence conjugated antibodies against CD11b and F4/80. To induce polarization, BMDMs were stimulated 20 ng/mL IL4 and 20 ng/mL IL13 and collected as M2 activation state.

data_processing:
The amplified cDNA from each channel of the Chromium System was used to construct an Illumina sequencing library and sequenced on a HiSeq 4000 with 150 cycle sequencing (asymmetric reads per 10x Genomics).
Illumina basecall files (*.bcl) were converted to FASTQs using CellRanger v1.3 (10X Genomics), which uses bcl2fastq v2.17.1.14.
FASTQ files were then aligned to mm10 mouse reference genome and transcriptome using the CellRanger v1.3 software pipeline with default parameters , which demultiplexes the samples and generates a gene versus cell expression matrix based on the barcodes and assigned unique molecular identifiers (UMIs) that enable determining from which individual cell RNA molecule originated.
Genome_build: mm10
Supplementary_files_format_and_content: Market Exchange Format (MEX) matrices (.mtx) containing the UMI counts for each cell;  TSV files (.tsv) with genes and barcode sequences corresponding to row and column indices of the MEX file, respectively

source_name: bone marrow derived macrophages

growth_protocol: Male mice (C57BL6/j) were housed in a 12/12-hour light: dark cycle and provided ad libitum access to food and water for the duration of the study unless stated otherwise. Male mice of 5-6 weeks of age were used for feeding analyses.

extract_protocol:
refer to the description column of the SAMPLES section
Single-cell gel beads in emulsion (GEMs) macrophages were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3' Reagent Kit v2 (10x Genomics) according to manufacturer's protocol.

tag: strain

value: bone marrow

value: 17~18 weeks


title: M1_BMDM_scRNAseq

description: For dietary feeding studies, mice were fed with a standard chow diet (18% fat calories, 24% protein calories, and 58% of carbohydrate calories;  Cat No. 2918, Envigo. Teklad.) for 12 weeks. bone marrow cells were collected from femur and tibia bone followed by erythrocyte lysis with ammonium chloride solution (8.3 g/L ammonium chloride, 1.0 g/L potassium bicarbonate, and 0.009% EDTA) and seeded in tissue culture plates at a concentration of 0.15 x 106/cm2. Cells were induced for differentiation to monocytes in BMDM growth medium (Iscove's Modified Dulbecco's Medium (IMDM) + 10% FBS + 15% L-929 cell (ATCC, CCL-1)) culture supernatant for 7 days; fresh BMDM growth medium was replaced on day 3. Maturation and purity of BMDMs were evaluated on day 7 using flow cytometry analysis with fluorescence conjugated antibodies against CD11b and F4/80. To induce polarization, BMDMs were stimulated with 100 ng/mL LPS and 50 ng/ml IFNγ and  collected as M1 activation state.

treatment_protocol: refer to the description column of the SAMPLES section

tag: tissue


title: M0_BMDM_scRNAseq

description: For dietary feeding studies, mice were fed with a standard chow diet (18% fat calories, 24% protein calories, and 58% of carbohydrate calories;  Cat No. 2918, Envigo. Teklad.) for 12 weeks. Bone marrow cells were collected from femur and tibia bone followed by erythrocyte lysis with ammonium chloride solution (8.3 g/L ammonium chloride, 1.0 g/L potassium bicarbonate, and 0.009% EDTA) and seeded in tissue culture plates at a concentration of 0.15 x 106/cm2. Cells were induced for differentiation to monocytes in BMDM growth medium (Iscove's Modified Dulbecco's Medium (IMDM) + 10% FBS + 15% L-929 cell (ATCC, CCL-1)) culture supernatant for 7 days; fresh BMDM growth medium was replaced on day 3. Maturation and purity of BMDMs were evaluated on day 7 using flow cytometry analysis with fluorescence conjugated antibodies against CD11b and F4/80. The unstimulated BMDMs were collected as M0 state.


title: wt_brain_Pc_(20170420_AS_DmSc_389_BiC_A100)

description: Chromatin immunocleavage and release

source_name: wt larval brains Pc

value: wt larval brains


title: lnATM_scRNAseq

description: For dietary feeding studies, mice were fed with a standard chow diet (18% fat calories, 24% protein calories, and 58% of carbohydrate calories;  Cat No. 2918, Envigo. Teklad.) for 12 weeks. The visceral adipose tissues were mechanically dissected, digested, and filtered. The filtered cells were suspended in red blood cell lysis buffer to remove red blood cells. Macrophages in the dissociated cells were separated as CD45.2+ CD11b+F4/80+ on a BD Biosciences FACS Aria II cell sorter.

source_name: adipose tissue macrophages

value: adipose tissue


title: obATM_scRNAseq

description: For dietary feeding studies, mice were fed with a high-fat diet (HFD; 60% fat calories, 20% protein calories, and 20% carbohydrate calories; Cat. No. D12492, Research Diets, Inc.) for 12 weeks. The visceral adipose tissues were mechanically dissected, digested, and filtered. The filtered cells were suspended in red blood cell lysis buffer to remove red blood cells. Macrophages in the dissociated cells were separated as CD45.2+ CD11b+F4/80+ on a BD Biosciences FACS Aria II cell sorter.


title: CL1_wing_K27me3_(20170313_AS_DmSc_353_WDiC_187)

description: Chromatin immunocleavage and release

source_name: vg pPRE deletion wing discs K27me3

value: vgCL1 mutant wing discs

value: anti-K27me3 Cell Signalling#9733


title: sample 47_RNA_Sp_NK_rpt1

status: Public on May 05 2016

first: Yuka

last: Kanno

address: 10 Center Drive, Rm13C120

department: NIAMS

institute: NIH

data_processing:
alignment, ATAC-seq: ATAC-seq reads from two biological replicates for each sample were mapped to the mouse genome (mm9 assembly) using Bowtie 0.12.8.
peak-calling, ATAC-seq: Redundant reads were removed using fastquniq (Xu et al., 2012). Only one mapped read to each unique regions of the genome that was less than 175 base pairs was kept and used for peak calling with MACS (version 1.4.2)(Zhang et al., 2008) using a P-value threshold of 1 x 10-5. Peaks called from replicates of the same cell type were merged using the mergePeaks module in HOMER. Only peaks called in both replicates were used to generate a bed file for a cell type.
alignment, RNA-seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of sequentially varying length were mapped to the mouse genome mm9 using TopHat 2.0.
bw file, RNA-seq: Intron-less bigWig files were generated using USCS genome browser’s program bedGraphToBigWig, from bedGraph files made with the BEDtools package (Quinlan and Hall, Bioinformatics:26(6):841-2, 2010).
alignment, ChIP-seq: Reads of 50 bases were aligned to the mouse genome build mm9 with Bowtie 0.12.8, allowing two mismatches. Uniquely mapped and non-redundant reads were retained and used for peak calling.
peaks, ChIP-seq: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958 for histone mark K27Ac. Peak detection was performed with MACS1.4.2 with the default parameters and a p value <1.0E-05 fortransscription factors p300 and Tbet.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for ATAC-seq, RNA-seq and transcription factor ChIP-seq (p300, Tbet); bedgraph for histone modification ChIP-seq (K27Ac). bed file for common ATAC-seq peaks of replicates (linked as supplementary files on Series record).

source_name: Natural killer cells

growth_protocol:
cell isolation protocol: Cells from bone marrow, liver, and spleen were obtained by mechanical disruption. Cells from lung were isolated after incubating lungfragments with 0.5 mg/ml Liberase TL for 1h followed by purification with 40% Percoll (GE Healthcare) (Meylan et al., 2013). Cells from siLP were isolated after incubating fine-cut intestine in HBSS solution with 0.5 mg/ml DNase I (Roche) and 0.25 mg/ml  Liberase TL (Roche) followed by filtering with 100 μm cell strainer and purification with 40% Percoll (Sciumé et al., 2012). NK cells were isolated from spleen and liver; ILC1s were isolated from liver; Treg, IL17GFP+Th17, ILC2s, CD4+ILC3 and NCR+ILC3 were isolated from siLP; HSC, CLP, NKp, immature NK, and ILC2p were isolated from bone marrow; Nippo-infected ILC2 and Th2 cells were isolated from lung. Isolated cells were further sorted as based on their surface markers.
in vitro culture protocol: All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10 ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.
Nippostrongylus brasiliensis infection protocol: Mice of at least 8 weeks of age were infected with 500 infective third-stage N. brasiliensis by subcutaneous injection. Cells from lungs were isolated after 10 days of infection.

extract_protocol:
RNA-seq was performed as described previously with slight modification (Hirahara et al., Immunity 2015). Total RNA was prepared from approximately 30-50,000 cells by using TRIzol following manufacture’s protocol (Life Technologies).
RNA-seq: Total RNA was subsequently processed to mRNA-seq library using TruSeq SR mRNA sample prep kit (FC-122-1001, Illumina).
ChIP-seq: Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.
ATAC-seq was performed according to published protocol (Buenrostro et al., 2013) with minor modification. 50,000 cells were pelleted and washed with 50ul 1xPBS, followed by treatment with 50ul lysis buffer (10mM Tris-HCl, pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% of IGEPAL CA-630). After pelleting the nuclei by centrifuging at 500x g for 10min, the pellets were re-suspended in 40ul transposition reaction with 2ul Tn5  transposase (Illumina Cat# FC-121-1030) to tag and fragmentalize accessible chromatin. The reaction was incubated at 37ºC with shaking at 300rpm for 30min. The fragmentalized DNAs were then purified using Qiagen MinElute Kit and amplified with 10-11 cycles of PCR based on the amplification curve. Once the libraries are purified using Qiagen PCR Cleanup Kit, they were further sequenced for 50 cycles (paired-end reads) on HiSeq2500.
RNA-Seq: The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.
ChIP-seq: Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt-ended, then phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of NEBNext adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with NEBNext index primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen).
ChIP-Seq (size fractionation). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on GAII, HiSeq 2000 or 2500 following the manufacturer's protocols.

value: Spleen

tag: surface marker

tag: culture condition

value: ex vivo

tag: cell type

value: Natural killer cells


title: sample 48_RNA_Sp_NK_rpt2


title: sample 58_RNA_Sp_NK_IL2_IL12_rpt2

value: in vitro culture for 6 hours w/ IL2 +IL12


title: sample 57_RNA_Sp_NK_IL2_IL12_rpt1


status: Public on Jul 22 2010

type: RNA

city: Sapporo

first: Masanao

last: Sato

state: Hokkaido

address: Kita 9 jo Nishi 9 chome, Kita-ku, Sappro

country: Japan

institute: Hokkaido University

description: pad4-1sag101-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

hyb_protocol: Labeled RNA was suspended in hybridization buffer (50% Formamide, 5xSSC, 0.1% SDS, 10 ug Sheared Salmon Sperm DNA (Eppendorf), 50pg calbation oligo)

scan_protocol: Slide was scaned using Genepix4000B with low and high voltages of photomultiplier at 532nm and constant voltage at 635nm.

data_processing: The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray. The residual Eij is assumed to be independent and normally distributed. Stable genes-based quantile normalization was applied for slide-to-slide comparisons. mutant-group00_set1_Col-0_Pst-aR2_6h, mutant-group00_set1_noa1_Pst-aR2_6h, mutant-group00_set1_ein2-1_Pst-aR2_6h, mutant-group00_set1_ein3-1_Pst-aR2_6h, mutant-group00_set1_mpk3_Pst-aR2_6h, mutant-group00_set1_npr1-1_Pst-aR2_6h, mutant-group00_set1_pad4-1_Pst-aR2_6h, mutant-group00_set1_rbohD_Pst-aR2_6h, mutant-group00_set2_Col-0_Pst-aR2_6h, mutant-group00_set2_noa1_Pst-aR2_6h, mutant-group00_set2_ein2-1_Pst-aR2_6h, mutant-group00_set2_ein3-1_Pst-aR2_6h, mutant-group00_set2_mpk3_Pst-aR2_6h, mutant-group00_set2_npr1-1_Pst-aR2_6h, mutant-group00_set2_pad4-1_Pst-aR2_6h, mutant-group00_set2_rbohD_Pst-aR2_6h, mutant-group01_set1_Col-0_Pst-aR2_6h, mutant-group01_set1_ein2-1_Pst-aR2_6h, mutant-group01_set1_ndr1-1_Pst-aR2_6h, mutant-group01_set1_ndr1-1b_Pst-aR2_6h, mutant-group01_set1_pad4-1_Pst-aR2_6h, mutant-group01_set1_pbs2-1_Pst-aR2_6h, mutant-group01_set1_rps2-101C_Pst-aR2_6h, mutant-group01_set1_sid2-2_Pst-aR2_6h, mutant-group01_set2_Col-0_Pst-aR2_6h, mutant-group01_set2_ein2-1_Pst-aR2_6h, mutant-group01_set2_ndr1-1_Pst-aR2_6h, mutant-group01_set2_ndr1-1b_Pst-aR2_6h, mutant-group01_set2_pad4-1_Pst-aR2_6h, mutant-group01_set2_pbs2-1_Pst-aR2_6h, mutant-group01_set2_rps2-101C_Pst-aR2_6h, mutant-group01_set2_sid2-2_Pst-aR2_6h, mutant-group01_set3_Col-0_Pst-aR2_6h, mutant-group01_set3_ein2-1_Pst-aR2_6h, mutant-group01_set3_ndr1-1_Pst-aR2_6h, mutant-group01_set3_ndr1-1b_Pst-aR2_6h, mutant-group01_set3_pad4-1_Pst-aR2_6h, mutant-group01_set3_pbs2-1_Pst-aR2_6h, mutant-group01_set3_rps2-101C_Pst-aR2_6h, mutant-group01_set3_sid2-2_Pst-aR2_6h, mutant-group02_set1_Col-0_Pst-aR2_6h, mutant-group02_set1_noa1_Pst-aR2_6h, mutant-group02_set1_nia2_Pst-aR2_6h, mutant-group02_set1_rbohDF_Pst-aR2_6h, mutant-group02_set1_rbohD_Pst-aR2_6h, mutant-group02_set1_rbohF_Pst-aR2_6h, mutant-group02_set2_Col-0_Pst-aR2_6h, mutant-group02_set2_noa1_Pst-aR2_6h, mutant-group02_set2_nia2_Pst-aR2_6h, mutant-group02_set2_rbohDF_Pst-aR2_6h, mutant-group02_set2_rbohD_Pst-aR2_6h, mutant-group02_set2_rbohF_Pst-aR2_6h, mutant-group02_set3_Col-0_Pst-aR2_6h, mutant-group02_set3_noa1_Pst-aR2_6h, mutant-group02_set3_nia2_Pst-aR2_6h, mutant-group02_set3_rbohDF_Pst-aR2_6h, mutant-group02_set3_rbohD_Pst-aR2_6h, mutant-group02_set3_rbohF_Pst-aR2_6h, mutant-group03_set1_Col-0_Pst-aR2_6h, mutant-group03_set1_dde2-2_Pst-aR2_6h, mutant-group03_set1_ein3-1_Pst-aR2_6h, mutant-group03_set1_jar1-1_Pst-aR2_6h, mutant-group03_set1_jin1-1_Pst-aR2_6h, mutant-group03_set1_mpk3_Pst-aR2_6h, mutant-group03_set1_mpk6-2_Pst-aR2_6h, mutant-group03_set1_npr1-1_Pst-aR2_6h, mutant-group03_set2_Col-0_Pst-aR2_6h, mutant-group03_set2_dde2-2_Pst-aR2_6h, mutant-group03_set2_ein3-1_Pst-aR2_6h, mutant-group03_set2_jar1-1_Pst-aR2_6h, mutant-group03_set2_jin1-1_Pst-aR2_6h, mutant-group03_set2_mpk3_Pst-aR2_6h, mutant-group03_set2_mpk6-2_Pst-aR2_6h, mutant-group03_set2_npr1-1_Pst-aR2_6h, mutant-group03_set3_Col-0_Pst-aR2_6h, mutant-group03_set3_dde2-2_Pst-aR2_6h, mutant-group03_set3_ein3-1_Pst-aR2_6h, mutant-group03_set3_jar1-1_Pst-aR2_6h, mutant-group03_set3_jin1-1_Pst-aR2_6h, mutant-group03_set3_mpk3_Pst-aR2_6h, mutant-group03_set3_mpk6-2_Pst-aR2_6h, mutant-group03_set3_npr1-1_Pst-aR2_6h, mutant-group04_set1_Col-0_Pst-aR2_6h, mutant-group04_set1_coi1-1_Pst-aR2_6h, mutant-group04_set1_nho1-2_Pst-aR2_6h, mutant-group04_set1_pad4-1sag101-2_Pst-aR2_6h, mutant-group04_set1_pen2-1_Pst-aR2_6h, mutant-group04_set1_pmr4-1_Pst-aR2_6h, mutant-group04_set1_sag101-2_Pst-aR2_6h, mutant-group04_set1_vpe_Pst-aR2_6h, mutant-group04_set2_Col-0_Pst-aR2_6h, mutant-group04_set2_coi1-1_Pst-aR2_6h, mutant-group04_set2_nho1-2_Pst-aR2_6h, mutant-group04_set2_pad4-1sag101-2_Pst-aR2_6h, mutant-group04_set2_pen2-1_Pst-aR2_6h, mutant-group04_set2_pmr4-1_Pst-aR2_6h, mutant-group04_set2_sag101-2_Pst-aR2_6h, mutant-group04_set2_vpe_Pst-aR2_6h, mutant-group04_set3_Col-0_Pst-aR2_6h, mutant-group04_set3_coi1-1_Pst-aR2_6h, mutant-group04_set3_nho1-2_Pst-aR2_6h, mutant-group04_set3_pad4-1sag101-2_Pst-aR2_6h, mutant-group04_set3_pen2-1_Pst-aR2_6h, mutant-group04_set3_pmr4-1_Pst-aR2_6h, mutant-group04_set3_sag101-2_Pst-aR2_6h, mutant-group04_set3_vpe_Pst-aR2_6h, samples published previously (GSE8273 and GSE14237), and unpublished samples were normalized together (total sample number: 564; ndr1-1b is a blindly chosen ndr1-1). Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu). Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana pad4-1sag101-2, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h

label_protocol: Following procedure was performed with Amino Allyl MessageAmp aRNA Amplification Kit II (Ambion).First, cDNA was synthesized from 1ug of total RNA.  Next, RNA was in vitro transcribed.  The RNA was then labeled with Alexa555 in coupling reaction.

growth_protocol: Plants were grown in pots with BM-2 soil (Berger Peat Moss Ltd, Quebec, Canada) at a density of 9 plants per pot and kept at 22 degrees Celsius and75% humidity with a 12 hour day length.

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

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2 and harvested 6h later.

tag: genotype

value: leaves

value: 4 week-old

tag: treatment

tag: time point


title: mutant-group04_set3_pen2-1_Pst-aR2_6h

description: pen2-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana pen2-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group04_set3_sag101-2_Pst-aR2_6h

description: sag101-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana sag101-2, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group04_set3_Col-0_Pst-aR2_6h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group04_set3_nho1-2_Pst-aR2_6h

description: nho1-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana nho1-2, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group04_set3_pmr4-1_Pst-aR2_6h

description: pmr4-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana pmr4-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group04_set3_vpe_Pst-aR2_6h

description: vpe infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana vpe, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h

value: vpe


title: mutant-group04_set3_coi1-1_Pst-aR2_6h

description: coi1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana coi1-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group04_set2_vpe_Pst-aR2_6h

description: vpe infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group04_set2_pmr4-1_Pst-aR2_6h

description: pmr4-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group04_set2_sag101-2_Pst-aR2_6h

description: sag101-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: Mouse_mammary_tumor_5

status: Public on Jun 04 2016

type: genomic

city: Lausanne

first: Vincent

last: Roh

address: Bugnon 25A

country: Switzerland

institute: SIB

description:
Mammary tumor biological replicate 5
MH286

hyb_protocol: Cy3 and Cy5 labeled DNA were mixed and incubated with mouse Cot-1 DNA, 1x Agilent Blocking Agent and 1x Hi-RPM Buffer.  Samples were heated at 95C for 3 minutes, then 37C for 30 minutes before loading them on a gasket slide. The slide was then loaded into Agilent SureHyp chambers and incubated for 24h at 65C for 24h (with rotation)

scan_protocol: After the washing steps, the slides were scanned on an Agilent Scanner G2505C

data_processing: Agilent Feature Extraction Software (v 10.5.1.1 and v 11.0.1.1) was used for data processing. Partek Genomic Suite was used for segmentation analysis.

source_name: Pik3ca^H1047R mammary tumor

label_protocol: 1 µg of genomic DNA was labeled using the Agilent genomic DNA enzymatic labeling kit according to the manufacturer's instructions (Cy3 and Cy5 at 1mM, thermocycler conditions: 37C for 2h, then 65C for 10 minutes). Labeled DNA was cleaned.using Amicon Ultra 30kDA filters

extract_protocol: Genomic DNA extraction using QIAgen DNEasy blood and tissue kit, according to the manufacturer's instructions

value: Mixed FVBN/Bl6

value: Mammary tumor

source_name: Pik3ca^H1047R liver

value: Liver


title: Mouse_mammary_tumor_11

description:
Mammary tumor biological replicate 11
MFP138


title: Mouse_mammary_tumor_10

description:
Mammary tumor biological replicate 10
MH251


title: Mouse_mammary_tumor_7

description:
Mammary tumor biological replicate 7
HMF498


title: Mouse_mammary_tumor_3

description:
Mammary tumor biological replicate 3
MH232


title: MLL-AF9 (rep1, rep2, rep3)

status: Public on Jul 20 2011

description: Biological replicates 1-3.

hyb_protocol: 60 C for 17hr

scan_protocol: Agilent Technologies Scanner G2505B US22502580

data_processing: R and Bioconductor have been used for data normalization with Loess for within array and aquantile for between array analysis.

source_name: miR-150 MLL-AF9 cells

label_protocol: 1 µg of total RNA were reversed transcribed and labeled with Agilent QuickAmp kit

growth_protocol: Cells were cultured in methylcellulose semisolid culture media with SCF (20ng/ml), IL3 (10ng/ml), IL6 (10ng/ml) and Flt3L (50ng/ml) and 200ug/ml hygromycin for selection

extract_protocol: Total RNAs from mouse tissues or isolated cells were extracted using Trizol (Invitrogen, Carlsbad, CA) followed by column purification with miRNeasy extraction kits (Qiagen, Germany)

treatment_protocol: Cells that are expressing miRNAs were sorted by flowcytometry based on GFP expression

value: miR-150- MLL-AF9

value: MDH MLL-AF9


title: mutant-group04_set2_pen2-1_Pst-aR2_6h

description: pen2-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group04_set2_pad4-1sag101-2_Pst-aR2_6h

description: pad4-1sag101-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group04_set2_Col-0_Pst-aR2_6h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: Mouse_mammary_tumor_8

description:
Mammary tumor biological replicate 8
HMF194


title: Mouse_mammary_tumor_4

description:
Mammary tumor biological replicate 4
MH356


title: Mouse_mammary_tumor_1

description:
Mammary tumor biological replicate 1
MH348


title: mutant-group04_set2_nho1-2_Pst-aR2_6h

description: nho1-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: Mouse_mammary_tumor_9

description:
Mammary tumor biological replicate 9
MH316


title: mutant-group04_set1_sag101-2_Pst-aR2_6h

description: sag101-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: Mouse_mammary_tumor_6

description:
Mammary tumor biological replicate 6
MH248


title: mutant-group04_set1_vpe_Pst-aR2_6h

description: vpe infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group04_set1_pad4-1sag101-2_Pst-aR2_6h

description: pad4-1sag101-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group04_set1_pen2-1_Pst-aR2_6h

description: pen2-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: Mouse_mammary_tumor_2

description:
Mammary tumor biological replicate 2
MH203


title: mutant-group03_set3_npr1-1_Pst-aR2_6h

description: npr1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana npr1-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group04_set1_coi1-1_Pst-aR2_6h

description: coi1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group03_set3_jin1-1_Pst-aR2_6h

description: jin1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana jin1-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group03_set3_mpk6-2_Pst-aR2_6h

description: mpk6-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana mpk6-2, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group03_set3_mpk3_Pst-aR2_6h

description: mpk3 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana mpk3, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group03_set3_jar1-1_Pst-aR2_6h

description: jar1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana jar1-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group04_set1_nho1-2_Pst-aR2_6h

description: nho1-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group04_set1_Col-0_Pst-aR2_6h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group03_set2_jar1-1_Pst-aR2_6h

description: jar1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group03_set2_jin1-1_Pst-aR2_6h

description: jin1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group03_set3_ein3-1_Pst-aR2_6h

description: ein3-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana ein3-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group04_set2_coi1-1_Pst-aR2_6h

description: coi1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group03_set3_Col-0_Pst-aR2_6h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.


title: mutant-group03_set2_mpk6-2_Pst-aR2_6h

description: mpk6-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group03_set1_mpk3_Pst-aR2_6h

description: mpk3 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group03_set2_dde2-2_Pst-aR2_6h

description: dde2-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.

source_name: Arabidopsis thaliana dde2-2, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group03_set1_jin1-1_Pst-aR2_6h

description: jin1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group03_set2_npr1-1_Pst-aR2_6h

description: npr1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group03_set2_mpk3_Pst-aR2_6h

description: mpk3 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group03_set1_ein3-1_Pst-aR2_6h

description: ein3-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group03_set1_npr1-1_Pst-aR2_6h

description: npr1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group03_set1_Col-0_Pst-aR2_6h

value: 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2


title: mutant-group03_set1_mpk6-2_Pst-aR2_6h

description: mpk6-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group03_set3_dde2-2_Pst-aR2_6h

description: dde2-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.


title: mutant-group03_set1_dde2-2_Pst-aR2_6h

description: dde2-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group03_set2_ein3-1_Pst-aR2_6h

description: ein3-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group02_set3_rbohD_Pst-aR2_6h

description: rbohD infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana rbohD, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h

value: rbohD


title: mutant-group02_set3_rbohF_Pst-aR2_6h

description: rbohF infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana rbohF, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h

value: rbohF


title: mutant-group02_set3_rbohDF_Pst-aR2_6h

description: rbohDF infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana rbohDF, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h

value: rbohDF


title: mutant-group02_set3_nia2_Pst-aR2_6h

description: nia2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana nia2, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group02_set3_noa1_Pst-aR2_6h

description: noa1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana noa1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group02_set3_Col-0_Pst-aR2_6h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group03_set2_Col-0_Pst-aR2_6h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group03_set1_jar1-1_Pst-aR2_6h

description: jar1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group02_set2_rbohF_Pst-aR2_6h

description: rbohF infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group02_set2_Col-0_Pst-aR2_6h


title: mutant-group02_set2_rbohDF_Pst-aR2_6h

description: rbohDF infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group02_set1_rbohF_Pst-aR2_6h

description: rbohF infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group02_set2_noa1_Pst-aR2_6h

description: noa1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group02_set1_rbohDF_Pst-aR2_6h

description: rbohDF infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group02_set1_Col-0_Pst-aR2_6h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group02_set1_noa1_Pst-aR2_6h

description: noa1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group01_set3_sid2-2_Pst-aR2_6h

description: sid2-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana sid2-2, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group02_set1_nia2_Pst-aR2_6h

description: nia2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group02_set1_rbohD_Pst-aR2_6h

description: rbohD infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group01_set3_rps2-101C_Pst-aR2_6h

description: rps2-101C infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana rps2-101C, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group01_set3_pad4-1_Pst-aR2_6h

description: pad4-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana pad4-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group01_set3_pbs2-1_Pst-aR2_6h

description: pbs2-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana pbs2-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group01_set3_ndr1-1b_Pst-aR2_6h

description: ndr1-1b infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana ndr1-1b, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group02_set2_rbohD_Pst-aR2_6h

description: rbohD infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group01_set3_Col-0_Pst-aR2_6h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.


title: mutant-group01_set3_ein2-1_Pst-aR2_6h

description: ein2-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana ein2-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group01_set2_pbs2-1_Pst-aR2_6h

description: pbs2-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group01_set2_rps2-101C_Pst-aR2_6h

description: rps2-101C infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group01_set2_ndr1-1b_Pst-aR2_6h

description: ndr1-1b infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group02_set2_nia2_Pst-aR2_6h

description: nia2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group01_set2_pad4-1_Pst-aR2_6h

description: pad4-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group01_set2_sid2-2_Pst-aR2_6h

description: sid2-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group01_set2_ndr1-1_Pst-aR2_6h

description: ndr1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.

source_name: Arabidopsis thaliana ndr1-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group04_set1_pmr4-1_Pst-aR2_6h

description: pmr4-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.

source_name: Arabidopsis thaliana pmr4-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group01_set2_Col-0_Pst-aR2_6h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group01_set1_sid2-2_Pst-aR2_6h

description: sid2-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group01_set1_ndr1-1b_Pst-aR2_6h

description: ndr1-1b infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group01_set3_ndr1-1_Pst-aR2_6h

description: ndr1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set3 experiment.


title: mutant-group01_set1_ein2-1_Pst-aR2_6h

description: ein2-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group01_set1_Col-0_Pst-aR2_6h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group00_set2_ein3-1_Pst-aR2_6h

description: ein3-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group01_set1_rps2-101C_Pst-aR2_6h

description: rps2-101C infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group01_set1_ndr1-1_Pst-aR2_6h

description: ndr1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group01_set1_pbs2-1_Pst-aR2_6h

description: pbs2-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group01_set2_ein2-1_Pst-aR2_6h

description: ein2-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group00_set2_noa1_Pst-aR2_6h

description: noa1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group00_set2_npr1-1_Pst-aR2_6h

description: npr1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.

source_name: Arabidopsis thaliana npr1-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group00_set2_mpk3_Pst-aR2_6h

description: mpk3 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.

source_name: Arabidopsis thaliana mpk3, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: mutant-group00_set2_rbohD_Pst-aR2_6h

description: rbohD infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group00_set1_pad4-1_Pst-aR2_6h

description: pad4-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group00_set1_rbohD_Pst-aR2_6h

description: rbohD infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group00_set1_npr1-1_Pst-aR2_6h

description: npr1-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group01_set1_pad4-1_Pst-aR2_6h


title: mutant-group00_set2_pad4-1_Pst-aR2_6h

description: pad4-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group00_set2_ein2-1_Pst-aR2_6h


title: mutant-group00_set1_noa1_Pst-aR2_6h

description: noa1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group00_set1_mpk3_Pst-aR2_6h

description: mpk3 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group00_set2_Col-0_Pst-aR2_6h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set2 experiment.


title: mutant-group00_set1_Col-0_Pst-aR2_6h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: mutant-group00_set1_ein3-1_Pst-aR2_6h

description: ein3-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.

source_name: Arabidopsis thaliana ein3-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2-infiltrated, 6h


title: set3_Ws-2_Pst-aR2_6h

status: Public on Aug 09 2007

description: Ws-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set3 experiment.

data_processing: The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray. The residual Eij is assumed to be independent and normally distributed. Stable genes-based quantile normalization was applied for slide-to-slide comparisons. set1_Col-0_Pst-aR2_6h, set2_Col-0_Pst-aR2_6h, set3_Col-0_Pst-aR2_6h, set1_Col-0_mock_6h, set2_Col-0_mock_6h, set3_Col-0_mock_6h, set1_Cvi-1_Pst-aR2_6h, set2_Cvi-1_Pst-aR2_6h, set3_Cvi-1_Pst-aR2_6h, set1_Cvi-1_mock_6h, set2_Cvi-1_mock_6h, set3_Cvi-1_mock_6h, set1_Est-1_Pst-aR2_6h, set2_Est-1_Pst-aR2_6h, set3_Est-1_Pst-aR2_6h, set1_Est-1_mock_6h, set2_Est-1_mock_6h, set3_Est-1_mock_6h, set1_Kas-1_Pst-aR2_6h, set2_Kas-1_Pst-aR2_6h, set3_Kas-1_Pst-aR2_6h, set1_Kas-1_mock_6h, set2_Kas-1_mock_6h, set3_Kas-1_mock_6h, set1_Kin-0_Pst-aR2_6h, set2_Kin-0_Pst-aR2_6h, set3_Kin-0_Pst-aR2_6h, set1_Kin-0_mock_6h, set2_Kin-0_mock_6h, set3_Kin-0_mock_6h, set1_Ler-0_Pst-aR2_6h, set2_Ler-0_Pst-aR2_6h, set3_Ler-0_Pst-aR2_6h, set1_Ler-0_mock_6h, set2_Ler-0_mock_6h, set3_Mt-0_mock_6h, set1_Mt-0_Pst-aR2_6h, set2_Mt-0_Pst-aR2_6h, set3_Mt-0_Pst-aR2_6h, set1_Mt-0_mock_6h, set2_Mt-0_mock_6h, set3_Ler-0_mock_6h, set1_Tsu-1_Pst-aR2_6h, set2_Tsu-1_Pst-aR2_6h, set3_Tsu-1_Pst-aR2_6h, set1_Tsu-1_mock_6h, set2_Tsu-1_mock_6h, set3_Tsu-1_mock_6h, set1_Ws-2_Pst-aR2_6h, set2_Ws-2_Pst-aR2_6h, set3_Ws-2_Pst-aR2_6h, set1_Ws-2_mock_6h, set2_Ws-2_mock_6h, and set3_Ws-2_mock_6h were normalized together. Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu). Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.

source_name: Arabidopsis thaliana Ws-2, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2-infiltrated, 6h

growth_protocol: Plants were grown in pots with LG3 germinating mix (Sun Gro Horticulture, Bellevue, USA) at a density of 9 plants per pot and kept at 22 degrees Celsius and 80% humidity with a 10 hour day length.

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2 and harvested 6h later.

tag: Genotype

tag: Tissue

tag: Age

tag: Treatment

tag: Time point


title: set3_Ws-2_mock_6h

description: Ws-2 infiltrated with water, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Ws-2, leaves, water-infiltrated, 6h

treatment_protocol: Individual leaves were infiltrated in the morning using a needle-less syringe with water and harvested 6h later.

value: water


title: set3_Tsu-1_Pst-aR2_6h

description: Tsu-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Tsu-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2-infiltrated, 6h


title: set3_Tsu-1_mock_6h

description: Tsu-1 infiltrated with water, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Tsu-1, leaves, water-infiltrated, 6h


title: set3_Ler-0_mock_6h

description: Ler-0 infiltrated with water, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Ler-0, leaves, water-infiltrated, 6h


title: set3_Mt-0_Pst-aR2_6h

description: Mt-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Mt-0, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2-infiltrated, 6h


title: set3_Mt-0_mock_6h

description: Mt-0 infiltrated with water, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Mt-0, leaves, water-infiltrated, 6h


title: set3_Kin-0_Pst-aR2_6h

description: Kin-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Kin-0, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2-infiltrated, 6h


title: mutant-group00_set1_ein2-1_Pst-aR2_6h

description: ein2-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying AvrRpt2, harvested 6h after infiltration in set1 experiment.


title: set3_Kin-0_mock_6h

description: Kin-0 infiltrated with water, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Kin-0, leaves, water-infiltrated, 6h


title: set3_Est-1_mock_6h

description: Est-1 infiltrated with water, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Est-1, leaves, water-infiltrated, 6h


title: set3_Kas-1_mock_6h

description: Kas-1 infiltrated with water, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Kas-1, leaves, water-infiltrated, 6h


title: set3_Cvi-1_mock_6h

description: Cvi-1 infiltrated with water, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Cvi-1, leaves, water-infiltrated, 6h


title: set3_Cvi-1_Pst-aR2_6h

description: Cvi-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Cvi-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2-infiltrated, 6h


title: set3_Est-1_Pst-aR2_6h

description: Est-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Est-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2-infiltrated, 6h


title: set3_Col-0_Pst-aR2_6h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2-infiltrated, 6h


title: set2_Tsu-1_Pst-aR2_6h

description: Tsu-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set2 experiment.


title: set2_Ws-2_Pst-aR2_6h

description: Ws-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set2 experiment.


title: set2_Ws-2_mock_6h

description: Ws-2 infiltrated with water, harvested 6h after infiltration in set2 experiment.


title: set2_Tsu-1_mock_6h

description: Tsu-1 infiltrated with water, harvested 6h after infiltration in set2 experiment.


title: set3_Ler-0_Pst-aR2_6h

description: Ler-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Ler-0, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2-infiltrated, 6h


title: set2_Ler-0_Pst-aR2_6h

description: Ler-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set2 experiment.


title: set2_Ler-0_mock_6h

description: Ler-0 infiltrated with water, harvested 6h after infiltration in set2 experiment.


title: set2_Mt-0_Pst-aR2_6h

description: Mt-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set2 experiment.


title: set3_Col-0_mock_6h

description: Col-0 infiltrated with water, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Col-0, leaves, water-infiltrated, 6h


title: set3_Kas-1_Pst-aR2_6h

description: Kas-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set3 experiment.

source_name: Arabidopsis thaliana Kas-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2-infiltrated, 6h


title: set2_Col-0_mock_6h

description: Col-0 infiltrated with water, harvested 6h after infiltration in set2 experiment.


title: set2_Cvi-1_mock_6h

description: Cvi-1 infiltrated with water, harvested 6h after infiltration in set2 experiment.


title: set2_Col-0_Pst-aR2_6h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set2 experiment.


title: set2_Est-1_mock_6h

description: Est-1 infiltrated with water, harvested 6h after infiltration in set2 experiment.


title: set2_Cvi-1_Pst-aR2_6h

description: Cvi-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set2 experiment.


title: set2_Est-1_Pst-aR2_6h

description: Est-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set2 experiment.


title: set1_Ws-2_mock_6h

description: Ws-2 infiltrated with water, harvested 6h after infiltration in set1 experiment.

source_name: Arabidopsis thaliana Ws-2, leaves, water-infiltrated, 6h


title: set1_Tsu-1_mock_6h

description: Tsu-1 infiltrated with water, harvested 6h after infiltration in set1 experiment.


title: set1_Ws-2_Pst-aR2_6h

description: Ws-2 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set1 experiment.

source_name: Arabidopsis thaliana Ws-2, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2-infiltrated, 6h


title: set1_Tsu-1_Pst-aR2_6h

description: Tsu-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set1 experiment.

source_name: Arabidopsis thaliana Tsu-1, leaves, 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2-infiltrated, 6h


title: set1_Mt-0_mock_6h

description: Mt-0 infiltrated with water, harvested 6h after infiltration in set1 experiment.


title: set1_Mt-0_Pst-aR2_6h

description: Mt-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set1 experiment.


title: set2_Kin-0_Pst-aR2_6h

description: Kin-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set2 experiment.


title: set2_Kas-1_Pst-aR2_6h

description: Kas-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set2 experiment.


title: set2_Kin-0_mock_6h

description: Kin-0 infiltrated with water, harvested 6h after infiltration in set2 experiment.


title: set1_Ler-0_mock_6h

description: Ler-0 infiltrated with water, harvested 6h after infiltration in set1 experiment.

source_name: Arabidopsis thaliana Ler-0, leaves, water-infiltrated, 6h


title: set1_Ler-0_Pst-aR2_6h

description: Ler-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set1 experiment.


title: set1_Kin-0_Pst-aR2_6h

description: Kin-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set1 experiment.


title: set1_Col-0_Pst-aR2_6h

description: Col-0 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set1 experiment.


title: set1_Cvi-1_Pst-aR2_6h

description: Cvi-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set1 experiment.


title: set1_Est-1_mock_6h

description: Est-1 infiltrated with water, harvested 6h after infiltration in set1 experiment.


title: set1_Kin-0_mock_6h

description: Kin-0 infiltrated with water, harvested 6h after infiltration in set1 experiment.


title: set1_Est-1_Pst-aR2_6h

description: Est-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set1 experiment.


title: set1_Kas-1_mock_6h

description: Kas-1 infiltrated with water, harvested 6h after infiltration in set1 experiment.


title: set1_Kas-1_Pst-aR2_6h

description: Kas-1 infiltrated with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 carrying avrRpt2, harvested 6h after infiltration in set1 experiment.


title: set1_Cvi-1_mock_6h

description: Cvi-1 infiltrated with water, harvested 6h after infiltration in set1 experiment.


title: set1_Col-0_mock_6h

description: Col-0 infiltrated with water, harvested 6h after infiltration in set1 experiment.


title: set2_Mt-0_mock_6h

description: Mt-0 infiltrated with water, harvested 6h after infiltration in set2 experiment.


title: Col-0_Pst-avrRpt2_6h_set2

status: Public on Aug 18 2006

description: Col-0 infected with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 avrRpt2, harvested 6h after injection in set2 experiment, 6h, set2

hyb_protocol: Labeled RNA was suspended in hybridization buffer (50% Formamide, 5xSSC, 0.1% SDS, 10 ug Sheared Salmon Sperm DNA (Eppendorf), 50 pmol calbation oligo, a Cy5-labeled 69mer oligonucleotide)

data_processing: The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray.  The residual Eij is assumed to be independent and normally distributed.  Stable genes-based quantile normalization was applied for slide-to-slide comparisons.  Col-0_Pst-avrRpt2_6h_set1, rps2-101C_Pst-avrRpt2_6h_set1, ndr1-1_Pst-avrRpt2_6h_set1, ndr1-1blind_Pst-avrRpt2_6h_set1, rps2-101C_Pst-avrRpt2_6h_set2, ndr1-1_Pst-avrRpt2_6h_set2, ndr1-1blind_Pst-avrRpt2_6h_set2,  were normalized together.  Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu).  Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.

source_name: Arabidopsis thalia leaves, Pseudomonas syringae pv. tomato DC3000 avrRpt2 injected, 6h

label_protocol: Following procedure was performed with Amino Allyl MessageAmp aRNA Amplification Kit II (Ambion).  First, cDNA was synthesized from 1ug of total RNA.  Next, RNA was in vitro transcribed.  The RNA was then labeled with Alexa555 in coupling reaction.

growth_protocol: Plants were grown in pots with BM-2 soil (Berger Peat Moss Ltd, Quebec, Canada) at a density of 9 plants per pot and kept at 22 degrees Celsius and 75% humidity with a 12 hour day length.

treatment_protocol: Individual leaves were injected in the morning using a needle-less syringe with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 avrRpt2 and harvested 6h later.

value: Col-0, Tissue:leaves, Age:4 weeks post planting


title: ndr1-1blind_Pst-avrRpt2_6h_set2

description: ndr1-1blind infected with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 avrRpt2, harvested 6h after injection in set2 experiment, 6h, set2

data_processing: The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray.  The residual Eij is assumed to be independent and normally distributed.  Stable genes-based quantile normalization was applied for slide-to-slide comparisons.  Col-0_Pst-avrRpt2_6h_set1, rps2-101C_Pst-avrRpt2_6h_set1, ndr1-1_Pst-avrRpt2_6h_set1, ndr1-1blind_Pst-avrRpt2_6h_set1, Col-0_Pst-avrRpt2_6h_set2, rps2-101C_Pst-avrRpt2_6h_set2, ndr1-1_Pst-avrRpt2_6h_set2,  were normalized together.  Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu).  Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.

value: ndr1-1blind, Tissue:leaves, Age:4 weeks post planting


title: rps2-101C_Pst-avrRpt2_6h_set2

description: rps2-101C infected with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 avrRpt2, harvested 6h after injection in set2 experiment, 6h, set2

data_processing: The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray.  The residual Eij is assumed to be independent and normally distributed.  Stable genes-based quantile normalization was applied for slide-to-slide comparisons.  Col-0_Pst-avrRpt2_6h_set1, rps2-101C_Pst-avrRpt2_6h_set1, ndr1-1_Pst-avrRpt2_6h_set1, ndr1-1blind_Pst-avrRpt2_6h_set1, Col-0_Pst-avrRpt2_6h_set2, ndr1-1_Pst-avrRpt2_6h_set2, ndr1-1blind_Pst-avrRpt2_6h_set2,  were normalized together.  Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu).  Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.

value: rps2-101C, Tissue:leaves, Age:4 weeks post planting


title: ndr1-1_Pst-avrRpt2_6h_set2

description: ndr1-1 infected with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 avrRpt2, harvested 6h after injection in set2 experiment, 6h, set2

data_processing: The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray.  The residual Eij is assumed to be independent and normally distributed.  Stable genes-based quantile normalization was applied for slide-to-slide comparisons.  Col-0_Pst-avrRpt2_6h_set1, rps2-101C_Pst-avrRpt2_6h_set1, ndr1-1_Pst-avrRpt2_6h_set1, ndr1-1blind_Pst-avrRpt2_6h_set1, Col-0_Pst-avrRpt2_6h_set2, rps2-101C_Pst-avrRpt2_6h_set2, ndr1-1blind_Pst-avrRpt2_6h_set2,  were normalized together.  Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu).  Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.

value: ndr1-1, Tissue:leaves, Age:4 weeks post planting


title: ndr1-1blind_Pst-avrRpt2_6h_set1

description: ndr1-1blind infected with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 avrRpt2, harvested 6h after injection in set1 experiment, 6h, set1

data_processing: The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray.  The residual Eij is assumed to be independent and normally distributed.  Stable genes-based quantile normalization was applied for slide-to-slide comparisons.  Col-0_Pst-avrRpt2_6h_set1, rps2-101C_Pst-avrRpt2_6h_set1, ndr1-1_Pst-avrRpt2_6h_set1, Col-0_Pst-avrRpt2_6h_set2, rps2-101C_Pst-avrRpt2_6h_set2, ndr1-1_Pst-avrRpt2_6h_set2, ndr1-1blind_Pst-avrRpt2_6h_set2,  were normalized together.  Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu).  Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.


title: ndr1-1_Pst-avrRpt2_6h_set1

description: ndr1-1 infected with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 avrRpt2, harvested 6h after injection in set1 experiment, 6h, set1

data_processing: The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray.  The residual Eij is assumed to be independent and normally distributed.  Stable genes-based quantile normalization was applied for slide-to-slide comparisons.  Col-0_Pst-avrRpt2_6h_set1, rps2-101C_Pst-avrRpt2_6h_set1, ndr1-1blind_Pst-avrRpt2_6h_set1, Col-0_Pst-avrRpt2_6h_set2, rps2-101C_Pst-avrRpt2_6h_set2, ndr1-1_Pst-avrRpt2_6h_set2, ndr1-1blind_Pst-avrRpt2_6h_set2,  were normalized together.  Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu).  Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.


title: rps2-101C_Pst-avrRpt2_6h_set1

description: rps2-101C infected with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 avrRpt2, harvested 6h after injection in set1 experiment, 6h, set1

data_processing: The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray.  The residual Eij is assumed to be independent and normally distributed.  Stable genes-based quantile normalization was applied for slide-to-slide comparisons.  Col-0_Pst-avrRpt2_6h_set1, ndr1-1_Pst-avrRpt2_6h_set1, ndr1-1blind_Pst-avrRpt2_6h_set1, Col-0_Pst-avrRpt2_6h_set2, rps2-101C_Pst-avrRpt2_6h_set2, ndr1-1_Pst-avrRpt2_6h_set2, ndr1-1blind_Pst-avrRpt2_6h_set2,  were normalized together.  Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu).  Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.


title: Col-0_Pst-avrRpt2_6h_set1

description: Col-0 infected with 1x10E8 cfu/ml Pseudomonas syringae pv. tomato DC3000 avrRpt2, harvested 6h after injection in set1 experiment, 6h, set1

data_processing: The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray.  The residual Eij is assumed to be independent and normally distributed.  Stable genes-based quantile normalization was applied for slide-to-slide comparisons.  rps2-101C_Pst-avrRpt2_6h_set1, ndr1-1_Pst-avrRpt2_6h_set1, ndr1-1blind_Pst-avrRpt2_6h_set1, Col-0_Pst-avrRpt2_6h_set2, rps2-101C_Pst-avrRpt2_6h_set2, ndr1-1_Pst-avrRpt2_6h_set2, ndr1-1blind_Pst-avrRpt2_6h_set2,  were normalized together.  Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu).  Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.


title: Col-0_PsmES4326_24hpi_C_miniarray_2

status: Public on Apr 08 2006

description: Pseudomonas syringae ES4326 inoculated, 24hpi, set C

scan_protocol: Slide was scaneed using Genepix4000B with low and high voltages of photomultiplier at 532nm and constant voltage at 635nm.

data_processing: The median of ratios for each spot was processed by the following linear model: Sij = mu + Ai + Bj + Eij where Sij denotes the log2-transformed, median of ratios for the spot, mu denotes a constant, Ai and Bj denote the effects of i-th gene and j-th subarray.  The residual Eij is assumed to be independent and normally distributed.  Stable genes-based quantile normalization was applied when the estimated expression value in different slides was compared.  Col_MgSO4_24h_C_miniarray_1, Col_MgSO4_24h_C_miniarray_2, Col_Psm_24h_C_miniarray_1, and Col_Psm_24h_C_miniarray_2 were normalized together.  Perl scripts for the linear model and the normalization are available for non-commercial research conducted upon request (Fumiaki Katagiri, katagiri@umn.edu).  Spots with bad quality (missing, lints, and high background) were flagged as indicated in Flag in the attached .gpr file for this sample.

source_name: Arabidopsis thalia leaves, PsmES4326 treated, 24hpi

treatment_protocol: Individual leaves were injected in the morning using a needle-less syringe with 10E4 cfu cm-2 PsmES4326 (suspended in 5mM MgSO4) and harvested 24 hours later.

value: Col-0, Tissue:leaves, Age:33 days post planting


title: Col-0_PsmES4326_24hpi_C_miniarray_1


title: Col-0_MgSO4_24hpi_C_miniarray_2

description: Mock inoculated control, 24hpi, set C

source_name: Arabidopsis thalia leaves, MgSO4 treated, 24hpi

treatment_protocol: Individual leaves were injected in the morning using a needle-less syringe with 5mM MgSO4 and harvested 24 hours later.


title: Col-0_MgSO4_24hpi_C_miniarray_1

description: Mock inoculated control, 24hpi, set C


title: set2_Kas-1_mock_6h

description: Kas-1 infiltrated with water, harvested 6h after infiltration in set2 experiment.

value: leaves

value: 4 week-old


title: PID2027_Day28

status: Public on Feb 16 2022

city: Stanford

first: Madeleine

last: Scott

address: 729 Lagunita Dr

institute: Stanford

data_processing:
Illumina ? For basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using kallisto (v0.46.0) quant
quantified raw reads from kallisto count were normalized using DESeq2
Genome_build: Hg38
Supplementary_files_format_and_content: tab-delimited raw gene counts per sample

source_name: blood

extract_protocol:
Blood was taken directly before (Baseline = BL) or after vaccination
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blood

tag: day

tag: Sex

value: Female

value: Included


title: CD8PBL.Pt15

status: Public on Nov 16 2021

data_processing:
The amplified cDNA from each channel of the Chromium System was used to construct an Illumina sequencing library and sequenced on a HiSeq 2500 with 150 cycle sequencing (asymmetric reads per 10x Genomics).
Illumina basecall files (*.bcl) were converted to FASTQs using CellRanger v3.1.0 (10X Genomics), which usesbcl2fastq v2.17.1.14for FASTQ files generation.
FASTQ files were aligned to GRCh38 human reference genome and transcriptome using the CellRanger v3.1.0 software pipeline with default parameters
UMIs were calculated by CellRanger v3.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: Market Exchange Format (MEX) matrices (.mtx) containing the UMI counts for each cell;  TSV files (.tsv) with genes and barcode sequences corresponding to row and column indices of the MEX file, respectively

source_name: CD8 T cells from peripheral blood

extract_protocol:
CD8+ T cells in peripheral blood lymphocytes and  tumor-infiltrating lymphocytes from 2 melanoma patients were isolated using fluorescence activated cell sorting (FACS). Further processing on sorted cells was conducted using  Chromium Single Cell 5' Gene Expression kit (10x Genomics).
Single-cell gel beads in emulsion (GEMs) macrophages were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium Single Cell 5' Gene Expression (10x Genomics) according to manufacturer's protocol.

value: peripheral blood

value: melanoma

value: CD8+ T cells