title: N_L1


title: genomic DNA from control sample B055

status: Public on May 10 2023

type: genomic

city: Umeå

first: Magnus

last: Hultdin

state: Vasterbotten

address: 6M-building, NUS, 2d floor

department: Department of Medical Biosciences, Pathology

country: Sweden

institute: Umeå University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation EPIC arrays using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Genome Studio software v2011.1 (Illumina) and R statistical software v4.0.4 (R Core Team)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from the TBD cases was extracted by standard protocols at the Department of Clinical Genetics, Umeå University Hospital, Sweden (n=19) or by clinical genetic laboratories outside of Umeå (n=16). Genomic DNA from the controls was extracted using the Gentra Puregene DNA extraction kit (Gentra Puregene DNA extraction kit, Qiagen, Hilden, DE).

tag: relative telomere length (rtl) group

value: control

tag: phenotype

tag: tissue

value: whole blood

tag: cell type

value: leukocyte


title: genomic DNA from Telomere Biology Disorder case 6

value: extremely short RTL

value: hematological TBD


title: genomic DNA from control sample B049


title: Cow number 20 [B20]

type: SRA

city: Saint Genès-Champanelle

first: christine

last: Leroux

address: Route de Theix

country: France

institute: INRAE

library_source: transcriptomic

data_processing:
The vast majority of the data has a Q score greater than 30 (>99.9% correct)
Adapters were trimmed off. After, the read length distribution showed as expected main peak around 18-23 nt. representing microRNAs
Mapping was performed using bta and chi genome and annotation using miRBase 20
Assembly: bta and chi genome and annotation using miRBase 20
Supplementary files format and content: excel

molecule: total RNA

organism: Bos taurus

source_name: Total RNA was extracted from milk EV of cows. There was 2 group of 5 cows and 4 goats

extract_protocol:
Milk-derived EVs were obtained by sucrose gradient ultracentrifugations. Then, total RNAs were isolated from EV samples by mirVana Total RNA Isolation Kit (Life Technologies) using Trizol LS Reagent (Ambion) in the firts step.
Small RNA-Seq librairies were generated from 100 ng of total RNA using NEBNext library generation kit (New England Biolabs INC.). Sequencing was performed using NewSeq 500 sequencing methodology (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, in the first step, RNA adapters were sequentially ligated to each end of the RNA. Small RNA ligated with 3' and 5' adapters were reverse transcribed and PCR amplified by 15 cycles to create cDNA constructs. Amplified cDNA constructs were size fractionated on a LabChip XT (Caliper Life Sciences) and a band representing adaptors and 15-40 bp insert excised using the manufacturer’s instructions. The final cDNA libraries were checked for quality and quantified using capillary electrophoresis. the libraries were pooled in equimolar concentrations. The library pools were finally quantified again with qPCR and optimal concentration of the library pools used to generate the clusters on the surface of a flow cell before sequencing using NexSeq 500 sequencing methodology and reagents, according to the manufacturer instructions (Illumina).

tag: day in milk

value: milk-derived extracellular vesicle


title: Cow number 62 [B62]


title: KD1_input_R1

city: Köln

first: Alicja

last: Pacholewska

address: Weyertal 115b

country: Germany

institute: Uniklinik Köln

description: KD biological replicate 1 technical replicate 1 input

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the GRCm39 genome assembly using bowtie2 version 2.2.9 with the following configurations: --mm --threads  8 -x $REF  -U $SAMPLE
Bowtie2 output was converted into BAM format, sorted by coordinates with samtools v1.6 with the options: samtools view -Su /dev/stdin | samtools sort -@ 8 - -o BAM/${NAME}.bam
BAM files were filtered for the MAPQ > 30 with samtools v1.6 with the fillowing options: samtools view -bh -q 30
Peaks were called for WT and KD with macs2 v. 2.2.6 using all 6 treatment and all 6 input files (3 biological replicates x 2 technical replicates) with the following options: macs2 callpeak --bdg -g mm
Differential and common peaks were called using macs2 v.2.2.6 bdgdiff
For visualization, peak calling for WT and KD was redone using an additional --SPMR option to get normalized values and bdg files were converted to bigwig files using bedGraphToBigWig function of UCSC tools
Genome_build: GRCm39
Supplementary_files_format_and_content: bw files contain the signal per million reads normalized values for WT/KD condition
Supplementary_files_format_and_content: bed files contain common/WT-specific/KD-specific peaks called with macs2

organism: Mus musculus

source_name: CLL leukemic splenocytes

extract_protocol:
Splenocytes were isolated from leukemic mice. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Illumina TruSeq system

value: CLL leukemic splenocytes

tag: treatment

value: KDM1A knockdown

tag: strain

tag: chip antibody

value: No


title: genomic DNA from Telomere Biology Disorder case 3

value: short RTL


title: Cow number 3 [B3]


title: genomic DNA from control sample B033


title: Em2_input_R2

description: WT biological replicate 2 technical replicate 2 input

value: no


title: Cow number 1 [B1]


title: Em2_input_R1

description: WT biological replicate 2 technical replicate 1 input


title: genomic DNA from Telomere Biology Disorder case 5

value: asymptomatic TBD


title: PBS_Replicate 4

city: Uppsala

first: Venkata Sita Rama Raju

middle: Sita Rama Raju

last: Allam

state: Sweden

address: Husargatan 3

department: IMBIM

institute: Biomedical Center Uppsala University

description:
is_164_004
Raw Counts_PBS.xlsx

data_processing:
Generated data had read lengths with an average of 98-110 bp and high mapping (95% of aligned bases).
Normalized expression values generated by the Torrent Suite™ Software (version 5.10.1) were used for downstream differential gene expression analyses.
Assembly: mm10
Supplementary files format and content: Normalized expression values

source_name: Lung

extract_protocol:
RNA was extracted using the Qiagen RNeasy® plus mini kit
cDNA libraries were created and amplified using the Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit (Life Technologies, Carlsbad, CA) following the protocol of the manufacturer

treatment_protocol: Mice were lightly anesthetized with isoflurane and the anesthetized mice were instilled with 10 mg of house dust mite (HDM) extract reconstituted in 30 ml PBS (Dermatophagoides pteronyssinus) intranasally twice a week for three weeks. Control mice received 30 ml PBS via the intranasal route. To investigate the efficacy of nafamostat on asthmatic features, nafamostat (20 mg/kg in 3% acetic acid in PBS) were administered thirty minutes before each PBS and/or HDM instillation via the intraperitoneal route

value: Lung

tag: genotype

value: wildtype

value: PBS


title: PBS_Replicate 3

description:
is_164_003
Raw Counts_PBS.xlsx


title: PBS_Replicate 2

description:
is_164_002
Raw Counts_PBS.xlsx


title: Em2_H3K4me3_R2

description: WT biological replicate 2 technical replicate 2 treatment


title: PBS_Replicate 1

description:
is_164_001
Raw Counts_PBS.xlsx


title: genomic DNA from control sample B034


title: xmoo1_line_ctrl_3_reseq

city: Freiburg

first: Valérie

last: Hilgers

address: Stübeweg 51

institute: MPI of Immunobiology and Epigenetics

description: CIA assemblies

data_processing:
CIA assembly workflow: FLAIR (Tang et al., 2020) was used for transcriptome assembly. Samples were pooled to perform the assembly. For FLAIR collapse, the FANTOM TSS database (Abugessaisa et al., 2020) was provided to retain only reads with a supported TSS at their 5' end, using --max_ends 5 to allow for multiple 5’-3’ end identification. A minimum of three full-length reads were required for an isoform to be collapsed in the assembly.  For 3’end correction: the organoid PAS database was constructed using FLAM-seq data (Rybak-Wolf et al., 2021) obtained from the same RNA samples from which ONT 1D data were generated. The assembly was corrected using PAS database. The following filtering parameters were considered: 1) All isoforms overlapping a 3' end in a window of 100 nt were retained, 2) 3' ends found in the assembly more distal than the 3' ends found in the database were retained only if they were within the reference annotation and contained a AATAAA signal. For 3' end Correction: 1) 3’ UTR bins were created using the PAS database, starting from the end of the open reading frame, between each consecutive PAS, to the most distal PAS. Isoform 3’ ends falling within the last bin of the 3’ UTR (between the two distal-most PASs) were corrected to the most distal bin, provided the isoform covered more than 10% of the last bin.
Assembly: H. sapiens: hg38
Supplementary files format and content: Processed gtf (General Transfer Format) output of FLAIR assembly, each row represents an exon. Columns are: chromosome name, source, feature type, start,end,score,strand, In the 9th column metadata assigned to each exon: gene_id, transcript_id, exon number

source_name: cerebral organoid

growth_protocol: Cerebral organoids were generated according to modified Lancaster protocol (Lancaster et al., 2013, doi: 10.1038/nature12517),

extract_protocol:
Organoids were dissolved in Trizol und RNA was extracted in bulk. Ribosomal RNA was depleted using Rnase H (Epicentre)
For generation of full-length cDNA libraries, polyadenylated RNA molecules were isolated from total RNA preparations using the NEB’s NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490, NEB). Purified polyadenylated RNA molecules were used for nanopore library preparation using the cDNA-PCR Sequencing protocol (SQK-PCS109, Oxford Nanopore was used). The following modifications were made to the procedure. To eliminate short reads from the final data both input polyadenylated RNA molecules and cDNA molecules were cleaned upon further processing using AMPure XP beads (A63881, Beckman&Coulter) using a magnetic bead sample ratio of 0.4. To exclusively retain cDNA fragments > 3kb the BluePippin device and appropriate separation DNA gel cassettes were used (sage science). Finally, the cDNA was amplified using 14 PCR cycles and 12 min extension time at 65°C. Libraries were sequenced on GridION sequencing device from Oxford Nanopore Technologies. Reads were processed using the pipeline described in: git@github.com:LeilyR/nanoporeReads_dataTransfer.git (For cDNA data: guppy-5.0.7 model: dna_r9.4.1_450bps_sup.cfg was used).
cDNA-PCR Sequencing protocol (SQK-PCS109)

treatment_protocol: untreated

value: cerebral organoid

tag: developmental stage

value: adults


title: Em1_H3K4me3_R2

description: WT biological replicate 1 technical replicate 2 treatment


title: Cow number 2 [B2]


title: heads_Isoseq_3

data_processing:
CIA assembly workflow: FLAIR (Tang et al., 2020) was used for transcriptome assembly. Samples were pooled to perform the assembly. For FLAIR collapse, the Eukaryotic Promoter Database EPD (Dreos et al., 2017) was provided to retain only reads with a supported TSS at their 5' end, using --max_ends 5 to allow for multiple 5’-3’ end identification. A minimum of three full-length reads were required for an isoform to be collapsed in the assembly.  Assemblies were filtered for 3' ends that likely originated from internal priming or truncation during library preparation. We used FLAM-seq and RNA Direct data, as both of these methods allow for poly(A) tail detection, to perform poly(A) tail calling. Only reads containing a poly(A) tail were retained, and were trimmed to a single nucleotide preceding the poly(A) tail. Single nucleotide reads were clustered in 20-nt windows; clusters supported by at least two reads were included in the PAS database. The following filtering parameters were considered: 1) All isoforms overlapping a 3' end in a window of 100 nt were retained, 2) 3' ends found in the assembly more distal than the 3' ends found in the database were retained only if they were within the reference annotation and contained a AATAAA signal. For 3' end Correction: 1) 3’ UTR bins were created using the PAS database, starting from the end of the open reading frame, between each consecutive PAS, to the most distal PAS. Isoform 3’ ends falling within the last bin of the 3’ UTR (between the two distal-most PASs) were corrected to the most distal bin, provided the isoform covered more than 10% of the last bin.
Assembly: D. melanogaster Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 96
Supplementary files format and content: Processed gtf (General Transfer Format) output of FLAIR assembly: each row represents an exon. Columns are: chromosome name, source, feature type, start, end, score, strand. In the 9th column metadata assigned to each exon: gene_id, transcript_id, exon number
Library strategy: Iso-seq

organism: Drosophila melanogaster

source_name: heads

growth_protocol: Flies were grown in 25C on standard apple juice based food

extract_protocol:
3-day-old w1118 flies were collected and flash-frozen in liquid nitrogen and heads were used for RNA extraction.
Iso-seq libraries were prepared using 0.5µg total RNA from 3-day-old w1118 fly heads, processed with the Iso-seq express 2.0 workflow (PacBio) with 14 cycles of PCR amplification and size selection with the BluePippin system for transcripts larger than 3kb according to the manufacturer’s protocol. After SMRTbell adapter addition, libraries were sequenced on 3 SMRTcells on a Sequel I PacBio sequencer. The raw data files were processed with SMRT Link v8 software to generate CCS fastq files. Data analysis was performed using the Iso-seq3 pipeline to generate consensus reads.
Iso-seq express 2.0

value: heads

value: wild type (w1118)


title: xmoo1_line_ctrl_2_reseq

description: CIA assemblies


title: Em2_H3K4me3_R1

description: WT biological replicate 2 technical replicate 1 treatment


title: bone, infected mice bio rep 3

city: Porto

first: Ana

middle: Cordeiro

last: Gomes

state: Porto

address: Rua Alfredo Allen, 208

country: Portugal

institute: I3S: Universidade do Porto Instituto de Investigacao e Inovacao em Saude

data_processing:
Ion Torrent platform specific pipeline software Torrent Suite v5.12
Data from the S5 XL run processed using the Ion Torrent platform specific pipeline software Torrent Suite v5.12 to generate sequence reads, trim adapter sequences, filter and remove poor signal reads, and split the reads according to the barcode.
Differentially expressed genes between infected and non-infected mice were identified by the R package DESeq2 v1.24 with default parameters
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: bone

extract_protocol:
Snap frozen bones were crushed in a liquid nitrogen bath and total RNA was isolated using RNA Mini Kit (Invitrogen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared using Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit following manufacturer's protocol.

value: bone

tag: infection

value: M. avium


title: bone, infected mice bio rep 2


title: heads_Isoseq_2


title: xmoo1_line_ctrl_1_reseq

description: CIA assemblies


title: bone, infected mice bio rep 1


title: heads_Isoseq_1


title: Em1_H3K4me3_R1

description: WT biological replicate 1 technical replicate 1 treatment


title: Em1_input_R1

description: WT biological replicate 1 technical replicate 1 input


title: xmoo1_line_ctrl_3

description: CIA assemblies

source_name: Brain organoid

value: Brain organoid


title: genomic DNA from control sample B040

value: control

value: whole blood

value: leukocyte


title: bone, non-infected mice biol rep 3

value: non-infected


title: heads_FLAMseq_3

description: polyA length estimates per gene, FLAIR assemblies

data_processing:
For FLAM-seq datasets, poly(A) tail length estimation was performed using https://github.com/rajewsky-lab/FLAMAnalysis (Legnini et al., 2019).
Processing of w1118_heads_flam-seq_pooled.isoforms.gtf: FLAIR (Tang et al., 2020) was used for transcriptome assembly. For each tissue and method, all sequencing replicates were merged into a FASTQ file before assembly. For each sample, during the FLAIR correct step, splice junction information from the respective RNA-seq datasets (short reads) was used to correct individual transcriptomes. For FLAIR collapse, the Eukaryotic Promoter Database EPD (Dreos et al., 2017) was provided to retain only reads with a supported TSS at their 5' end, using --max_ends 5 to allow for multiple 5?-3? end identification. A minimum of three full-length reads were required for an isoform to be collapsed in the assembly. The assembled transcriptomes were assessed for novel isoforms as well as structural categories using SQANTI3v.1.2 (Tardaguila et al., 2018).
Assembly: D. melanogaster Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 96
Supplementary files format and content: Files *_gene_polyA_length.csv: contains read name, gene to which read is assigned using FeatureCounts, unique molecular identifier sequence, tail length and tail sequence
Supplementary files format and content: Processed gtf (General Transfer Format) output of FLAIR assembly: each row represents an exon. Columns are: chromosome name, source, feature type, start, end, score, strand, in the 9th column: metadata assigned to each exon: gene_id, transcript_id, exon number
Library strategy: FLAM-seq

extract_protocol:
For head transcriptomes, 3-day-old w1118 flies were collected and flash-frozen in liquid nitrogen and heads were used for RNA extraction.
FLAM-seq libraries were prepared as described in (Legnini, I, et al., 2019) (extended protocol available at 10.21203/rs.2.10045/v1) using 4µg total RNA from 3-day-old w1118 fly heads and 14-16h AEL embryos. After SMRTbell adapter addition, libraries were sequenced on 3 SMRTcells on a Sequel I PacBio sequencer. Three replicates were performed for each tissue. Reads were processed using the FLAMAnalysis pipeline described in (Legnini, I, et al., 2019, https://github.com/rajewsky-lab/FLAMAnalysis)


title: bone, non-infected mice biol rep 2


title: heads_FLAMseq_2


title: normal,  scRNAseq

city: Beijing

first: Jian

last: Wu

address: Beijing Tongren Eye Center, Beijing Key Laboratory of Ophthalmology and Visual Sciences, No. 1 Dong Jiao Min Xiang Street, Dongcheng District, Beijing 100730, P.R. China.

country: China

institute: Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
We perform demultiplex and alignment for the sequencing data with the CellRanger software (10X Genomics) and monkey reference genome (Macaca Mulatta-Mmul8, Macaca Fascicularis-MacFas5). Sequenced data was processed using CellRanger software (version 4.0; 10X Genomics). The count pipeline in the CellRanger Software Suite was applied to demultiplex and barcode the sequences. Based on the calculation of the single-cell expression matrix by CellRanger, filtration, normalization, dimensionality reduction, clustering, and differential gene expression analysis were conducted using the Seurat package (version 3.0).
Assembly: Mmul 8.0
Supplementary files format and content: matrix files

organism: Macaca mulatta

source_name: trabecular meshwork (TM)

extract_protocol:
The TM tissues were placed in tissue preservation solution and transported to the laboratory at 4℃. The sample was removed from the tissue preservation solution and transferred to a pre-cooled 5 ml centrifuge tube. Then, the tissues were digested and incubated in 5 mg collagenase. A dissolved in human albumin at 37 °C on a shaker and gently mechanically dissociated with a pipette for 20 min.  Subsequently, dissociated cells were resuspended in 0.04% nonacetylated BSA and filtered through a 70 µm filter to achieve the maximum number of cells. Viability and cell number were assessed via Trypan Blue (ThermoFisher, USA) and an automatic cell counter Countstar, China). They added PBS (with 0.4% BSA) to adjust the cell concentration to barcoding requirements and library construction (around 1.0x10^6 cells/ml).
Following counting, the appropriate volume for each sample was calculated for a target capture of 10000 cells and was loaded onto the 10x Genomics single-cell-A chip. After droplet generation, samples were transferred onto a pre-chilled 8-well tube (Eppendorf, USA), heat-sealed, and reverse transcription was performed using a Veriti 96-well thermal cycler (Thermo Fisher, USA). After the reverse transcription, cDNA was recovered using the Recovery Agent provided by 10x followed by a Silane DynaBead clean-up (Thermo Fisher, USA) as outlined in the user guide. Purified cDNA was amplified for 12 cycles before being cleaned using SPRIselect beads (Beckman, USA). Samples were diluted 4:1 and run on a Bioanalyzer (Agilent Technologies, USA) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell 3′ Reagent Kits v3 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).

value: trabecular meshwork (TM)

value: normal


title: genomic DNA from control sample B028


title: xmoo1_line_ctrl_1

description: CIA assemblies


title: xmoo1_line_ctrl_2

description: CIA assemblies


title: heads_FLAMseq_1


title: genomic DNA from control sample B030


title: genomic DNA from control sample B029


title: glaucoma,scRNAseq

description: 10x Genomics

value: glaucoma


title: bone, non-infected mice biol rep 1


title: genomic DNA from control sample B027


title: Breast_cancer_108

status: Public on May 09 2023

type: RNA

city: Copenhagen Ø

first: Maria

last: Rossing

address: Blegdamsvej 9

department: Center for Genomic Medicine

country: Denmark

institute: Rigshospitalet

description: Gene expression data from human breast cancer

hyb_protocol: Following fragmentation, approx. 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. The arrays were washed and stained with phycoerytrin-conjugated streptavidin using the Affymetrix Fluidics Station 450.

scan_protocol: The Affymetrix GeneArray 3000 7G scanner was used to generate fluorescent images. Probe intensity files (.CEL files) were generated in the GeneChip Command Console Software (AGCC; Affymetrix, Santa Clara, CA, USA). These were anonymized using R v. 4.0.0 and modified functions from the affxparser package.

data_processing: CEL files were loaded into R v. 4.0.0 and quantile normalized together with 30 existing breast cancer samples. Probe summaries were extracted using RMA from the affy package. ComBat from the sva package was used for batch correction with a set of other samples, and CIT256 subtypes were determined using the citbcmst package. For PAM50 subtyping, the genefu package was used.

label: biotin

source_name: Breast cancer biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for 12 ug total RNA.

extract_protocol: RNA was isolated using the AllPrep DNA/RNA purification kit (Qiagen, Hilden, Germany). The integrity of the RNA was measured using the Agilent RNA 6000 Nano Kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA).

treatment_protocol: Pretreatment breast core tumor biopsies of around 100 mg were stored in RNALater (Thermo Fisher Scientific, Waltham, MA, USA).

value: Breast cancer

tag: er status

value: Positive

tag: her2 status

value: Normal

tag: cit256 subtype

value: lumB

tag: pam50 subtype

tag: rcb status

tag: node status pre-nact

value: Pos

tag: node status post-nact

value: Mac


title: Breast_cancer_106

value: normL

value: Normal-like

value: Neg

value: Mic


title: Breast_cancer_102

value: lumC


title: genomic DNA from control sample B026

tag: relative telomere length (rtl) group

value: control

tag: phenotype

value: whole blood


title: genomic DNA from control sample B023

tag: tissue

tag: cell type

value: leukocyte


title: Breast_cancer_101


title: Breast_cancer_107

value: Basal-like


title: Breast_cancer_098


title: Breast_cancer_104


title: Breast_cancer_103

value: lumA


title: genomic DNA from control sample B008


title: Breast_cancer_100


title: Breast_cancer_109


title: Breast_cancer_105

value: ITC


title: Breast_cancer_096

value: Breast cancer


title: genomic DNA from control sample B018


title: Breast_cancer_092

value: Positive


title: Breast_cancer_099

value: Normal


title: Breast_cancer_095


title: Breast_cancer_090


title: Breast_cancer_097


title: Em1_input_R2

description: WT biological replicate 1 technical replicate 2 input

value: CLL leukemic splenocytes

tag: treatment

value: no

value: No


title: Breast_cancer_091

value: basL


title: genomic DNA from control sample B006


title: genomic DNA from control sample B017


title: genomic DNA from control sample B001


title: genomic DNA from control sample B002


title: genomic DNA from control sample B015


title: Breast_cancer_087


title: Breast_cancer_089

value: lumB

value: Mac


title: Breast_cancer_085

value: Neg


title: Breast_cancer_086

value: lumC


title: Breast_cancer_080

value: normL

value: Pos


title: Breast_cancer_082

value: Mic


title: Breast_cancer_083


title: Breast_cancer_084

value: Normal-like


title: Breast_cancer_079


title: Breast_cancer_093

value: lumA


title: Breast_cancer_081


title: Breast_cancer_075


title: Breast_cancer_078


title: Breast_cancer_073


title: Breast_cancer_072


title: Breast_cancer_070


title: Breast_cancer_074

value: Basal-like


title: Breast_cancer_088

value: Breast cancer


title: Breast_cancer_065

value: Positive


title: Breast_cancer_068

value: Normal


title: Breast_cancer_076


title: Breast_cancer_067


title: Breast_cancer_077


title: Breast_cancer_066

value: mApo


title: Breast_cancer_071


title: Breast_cancer_069


title: Breast_cancer_063


title: Breast_cancer_062


title: Breast_cancer_061


title: Breast_cancer_060


title: Breast_cancer_064


title: Breast_cancer_059


title: Breast_cancer_058


title: Breast_cancer_053

value: ITC


title: Breast_cancer_052


title: Breast_cancer_050


title: Breast_cancer_051


title: Breast_cancer_094


title: Breast_cancer_057


title: Breast_cancer_054


title: Breast_cancer_049


title: Breast_cancer_055


title: Breast_cancer_046


title: Breast_cancer_045


title: Breast_cancer_044


title: Breast_cancer_056


title: Breast_cancer_047


title: Breast_cancer_042


title: Breast_cancer_040


title: Breast_cancer_048


title: Breast_cancer_038


title: Breast_cancer_041


title: Breast_cancer_037


title: Breast_cancer_036


title: Breast_cancer_035


title: Breast_cancer_032


title: Breast_cancer_034


title: Breast_cancer_033


title: Breast_cancer_043


title: Breast_cancer_039


title: Breast_cancer_031


title: Breast_cancer_030


title: Breast_cancer_027


title: Breast_cancer_021


title: Breast_cancer_025


title: Breast_cancer_029


title: Breast_cancer_026


title: Breast_cancer_016


title: Breast_cancer_015


title: Breast_cancer_020


title: Breast_cancer_012


title: Breast_cancer_023


title: Breast_cancer_018


title: Breast_cancer_010


title: Breast_cancer_011


title: Breast_cancer_013


title: Breast_cancer_008


title: Breast_cancer_022


title: Breast_cancer_028


title: Breast_cancer_007


title: Breast_cancer_017


title: Breast_cancer_019


title: Breast_cancer_014


title: Breast_cancer_005


title: Breast_cancer_024


title: Breast_cancer_004


title: Breast_cancer_009


title: Breast_cancer_002


title: Breast_cancer_003


title: Breast_cancer_001


title: Breast_cancer_006


title: Testes  (GSM463937)

city: Tokyo

first: Fuyuki

last: Miya

state: Tokyo

address: 35 Shinanomachi, Shinjuku-ku

department: School of Medicine

country: Japan

institute: Keio University

description: Gene expression data of human testes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were digitalized using GeneChip Operating Software (GCOS) v.1.3 (Affymetrix).
Gene expression array data were normalized using MAS5 algorithm (Affymetrix). Then, to correct for bias between chips, quantile normalization (Bolstad, B. M. et al. Bioinformatics 19, 185-193 (2003)) was applied to all array data using R software.

source_name: pooled human testes total RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Rev. 3, 2009, Affymetrix).

growth_protocol:
hESCs and hiPSCs grown on mitomycin treated mouse embryonic fibroblast feeder cells or SNL feeder cells on gelatin-coated (0.1 %) tissue culture dishes were maintained in standard ES cell medium (DMEM/F12 [Sigma D6421], 20 % KSR [Invitrogen], non-essential amino acid, 0.1 mM 2-mercaptoethanol [Sigma], 4 ng/ml FGF-2 [Peprotech]) at 37 °C 3 % CO2.
For embryoid body (EB) formation, hESC and hiPSC colonies were detached from feeder layer en bloc by dissociation solution (0.25 % Trypsin, 100 μg/ml Collagenase IV [Invitrogen], 1 mM CaCl2, 20 % KSR) and incubated on gelatin coated dishes for 2 hours to remove feeder cells, and plated onto bacteriological dishes to form hEBs in hESC medium without FGF-2.
On day 1, the hEBs were settled down for 5 minutes, and the medium was changed to hEB medium (DMEM/F12, 5 % KSR, non-essential amino acid, 0.1 mM 2-mercaptoethanol). hEBs were cultured in suspension at 37 °C 3 % CO2, and the medium was changed every two days.
On day 30, EBs were collected and dissociated into single cells by TrypLETM Select (Invitrogen), and the dissociated cells were cultured in suspension at 1 x 105 cells/ml in neurosphere medium (Media hormone mix [MHM] medium, which contains DMEM/F-12 [1:1] [Invitrogen], 0.6 % glucose, 2 mM glutamine, 3 mM sodium bicarbonate, 5 mM HEPES, 25 μg/ml insulin, 100 μg/ml transferrin, 20 nM progesterone, 30 nM sodium selenate, and 60 μM putrescine [all from Sigma except for DMEM/F-12] with 2% B27, 20 ng/ml FGF-2, and 10 ng/ml recombinant human LIF [Millipore]) for 12 days to form primary (1st) neurospheres.
Medium was changed at day 6 of neurosphere formation and FGF-2 was added every 2 days. For tertiary neuropshere formation, the neurospheres were dissociated by the same manner and cultured at 1 x 105 cells/ml in MHM with 2 % B27 and 20 ng/ml FGF-2, 10 ng/ml recombinant human LIF.
To assay differentiation, neurospheres were dissociated and plated on poly-L-ornithine/fibronectin-coated cover glasses and allowed to differentiate without growth factors for 10 days.

extract_protocol:
Total RNA was extracted from cells with TRIzol regent (Invitrogen). Additionally, total RNA was purified with Rneasy Mini Kit (Qiagen) and treated with RNase-free DNase Set (Qiagen) to remove any contaminating genomic DNA.
Samples of total RNA from human tissues were purchased from several companies (Clontech, Ambion, Stratagene, Cell Applications). Additionally, total RNA was purified with RNeasy Mini Kit (Qiagen) and treated with RNase-free DNase Set (Qiagen) to remove any contaminating genomic DNA.

tag: ethnicity

value: Caucasian

tag: gender

value: male

value: pooled male

tag: culture days


title: Pancreas  (GSM463929)

description: Gene expression data of human pancreas

source_name: pooled human pancreas total RNA

value: male and female

value: pooled


title: SpinalCord  (GSM463934)

description: Gene expression data of human spinal cord

source_name: pooled human spinal cord total RNA


title: Uterus  (GSM463941)

description: Gene expression data of human uterus

source_name: pooled human uterus total RNA

value: female

value: pooled female


title: GDC_36

description: Gene expression data of human glioma-initiating cells GDC36

source_name: glioma-initiating cells, GDC36

value: glioma-initiating cells GDC36

tag: source

value: Cultured glioma-initiating cells from glioblastoma tissues from patient


title: Spleen  (GSM463935)

description: Gene expression data of human spleen

source_name: pooled human spleen total RNA


title: Lung  (GSM463928)

description: Gene expression data of human lung

source_name: pooled human lung total RNA


title: Thymus  (GSM463938)

description: Gene expression data of human thymus

source_name: pooled human thymus total RNA


title: Trachea  (GSM463940)

description: Gene expression data of human trachea

source_name: pooled human trachea total RNA


title: SkeletalMuscle  (GSM463932)

description: Gene expression data of human skeletal muscle

source_name: pooled human skeletal muscle total RNA


title: Thyroid  (GSM463939)

description: Gene expression data of human thyroid

source_name: pooled human thyroid total RNA


title: SmallIntestine  (GSM463933)

description: Gene expression data of human small intestine

source_name: pooled human small intestine total RNA


title: Cerebellum (GSM463921)

description: Gene expression data of human cerebellum

source_name: pooled human cerebellum total RNA


title: Stomach  (GSM463936)

description: Gene expression data of human stomach

source_name: pooled human stomach total RNA


title: FetalBrain  (GSM463924)

description: Gene expression data of human fetal brain

source_name: pooled human fetal brain total RNA


title: Prostate  (GSM463930)

description: Gene expression data of human prostate

source_name: pooled human prostate total RNA


title: SalivaryGland  (GSM463931)

description: Gene expression data of human salivary gland

source_name: pooled human salivary gland total RNA


title: oh-NSC-3-fb_3

description: Gene expression data of human fetal neural stem/progenitor cells  oh-NSC-3-fb_3

source_name: fetal neural stem/progenitor cells, oh-NSC-3-fb_3

value: Cultured neural stem/progenitor cells from forebrain tissues from Japanese human fetuses aged 10 gestational week

value: 227 days


title: Liver  (GSM463927)

description: Gene expression data of human liver

source_name: pooled human liver total RNA


title: oh-NSC-7-fb_1

description: Gene expression data of human fetal neural stem/progenitor cells  oh-NSC-7-fb_1

source_name: fetal neural stem/progenitor cells, oh-NSC-7-fb_1

value: Cultured neural stem/progenitor cells from forebrain tissues from Japanese human fetuses aged 9 gestational week

value: 292 days


title: Cortex (GSM463923)

description: Gene expression data of human cortex

source_name: pooled human cortex total RNA


title: Kidney  (GSM463926)

description: Gene expression data of human kidney

source_name: pooled human kidney total RNA


title: BoneMarrow (GSM463920)

description: Gene expression data of human bone marrow

source_name: pooled human bone marrow total RNA


title: Heart  (GSM463925)

description: Gene expression data of human heart

source_name: pooled human heart total RNA


title: oh-NSC-7-fb_2

description: Gene expression data of human fetal neural stem/progenitor cells  oh-NSC-7-fb_2

source_name: fetal neural stem/progenitor cells, oh-NSC-7-fb_2

value: 304 days


title: GDC_40

description: Gene expression data of human glioma-initiating cells GDC40

source_name: glioma-initiating cells, GDC40

value: glioma-initiating cells GDC40


title: Colon (GSM463922)

description: Gene expression data of human colon

source_name: pooled human colon total RNA


title: oh-NSC-7-fb_3

description: Gene expression data of human fetal neural stem/progenitor cells  oh-NSC-7-fb_3

source_name: fetal neural stem/progenitor cells, oh-NSC-7-fb_3

value: 316 days


title: GDC_21

description: Gene expression data of human glioma-initiating cells GDC21

source_name: glioma-initiating cells, GDC21

value: glioma-initiating cells GDC21


title: oh-NSC-3-fb_2

description: Gene expression data of human fetal neural stem/progenitor cells  oh-NSC-3-fb_2

source_name: fetal neural stem/progenitor cells, oh-NSC-3-fb_2

value: 215 days


title: 414C2_3rdDiffNeuron

description: Gene expression data of human tertiary differentiated neuron 414C2

source_name: tertiary differentiated neuron, 414C2

tag: cell line

value: differentiated from 414C2 iPS

value: 76 days from differentiation


title: 253G1_3rdDiffNeuron

description: Gene expression data of human tertiary differentiated neuron 253G1

source_name: tertiary differentiated neuron, 253G1

value: differentiated from 253G1 iPS


title: oh-NSC-3-fb_1

description: Gene expression data of human fetal neural stem/progenitor cells  oh-NSC-3-fb_1

source_name: fetal neural stem/progenitor cells, oh-NSC-3-fb_1

value: 203 days


title: 409B2_3rdDiffNeuron

description: Gene expression data of human tertiary differentiated neuron 409B2

source_name: tertiary differentiated neuron, 409B2

value: differentiated from 409B2 iPS

value: female


title: 414C2_1stNS

description: Gene expression data of human primary neurospheres 414C2

source_name: primary neurospheres, 414C2

value: 42 days from differentiation


title: 409B2_1stNS

description: Gene expression data of human primary neurospheres 490B2

source_name: primary neurospheres, 409B2


title: 409B2_3rdNS

description: Gene expression data of human tertiary neurospheres 409B7

source_name: tertiary neurospheres, 409B2

value: 66 days from differentiation


title: 253G4_3rdDiffNeuron

description: Gene expression data of human tertiary differentiated neuron 253G4

source_name: tertiary differentiated neuron, 253G4

value: differentiated from 253G4 iPS


title: 201B7_3rdDiffNeuron

description: Gene expression data of human tertiary differentiated neuron 201B7

source_name: tertiary differentiated neuron, 201B7

value: differentiated from 201B7 iPS


title: 201B7_1stDiffNeuron

description: Gene expression data of human primary differentiated neuron 201B7

source_name: primary differentiated neuron, 201B7

value: 40 days from differentiation


title: 414C2_1stDiffNeuron

description: Gene expression data of human primary differentiated neuron 414C2

source_name: primary differentiated neuron, 414C2


title: KhES1_3rdDiffNeuron

description: Gene expression data of human tertiary differentiated neuron KhES1

source_name: tertiary differentiated neuron, KhES1

value: differentiated from KhES1 ES


title: 201B7_3rdNS

description: Gene expression data of human tertiary neurospheres 201B7

source_name: tertiary neurospheres, 201B7


title: KhES1_3rdNS

description: Gene expression data of human tertiary neurospheres KhES1

source_name: tertiary neurospheres, KhES1


title: KhES2_1stDiffNeuron

description: Gene expression data of human primary differentiated neuron KhES2

source_name: primary differentiated neuron, KhES2

value: differentiated from KhES2 ES


title: 414C2_3rdNS

description: Gene expression data of human tertiary neurospheres 414C2

source_name: tertiary neurospheres, 414C2


title: 253G1_1stNS

description: Gene expression data of human primary neurospheres 253G1

source_name: primary neurospheres, 253G1


title: 253G4_1stNS

description: Gene expression data of human primary neurospheres 253G4

source_name: primary neurospheres, 253G4


title: 253G1_1stDiffNeuron

description: Gene expression data of human primary differentiated neuron 253G1

source_name: primary differentiated neuron, 253G1


title: 253G1_3rdNS

description: Gene expression data of human tertiary neurospheres 253G1

source_name: tertiary neurospheres, 253G1


title: KhES1_1stDiffNeuron

description: Gene expression data of human primary differentiated neuron KhES1

source_name: primary differentiated neuron, KhES1


title: KhES2_3rdDiffNeuron

description: Gene expression data of human tertiary differentiated neuron KhES2

source_name: tertiary differentiated neuron, KhES2


title: 253G4_3rdNS

description: Gene expression data of human tertiary neurospheres 253G4

source_name: tertiary neurospheres, 253G4


title: KhES2_1stNS

description: Gene expression data of human primary neurospheres KhES2

source_name: primary neurospheres, KhES2


title: 201B7_1stNS

description: Gene expression data of human primary neurospheres 201B7

source_name: primary neurospheres, 201B7


title: KhES2_3rdNS

description: Gene expression data of human tertiary neurospheres KhES2

source_name: tertiary neurospheres, KhES2


title: 253G4_1stDiffNeuron

description: Gene expression data of human primary differentiated neuron 253G4

source_name: primary differentiated neuron, 253G4


title: KhES1_1stNS

description: Gene expression data of human primary neurospheres KhES1

source_name: primary neurospheres, KhES1


title: Col_H3_Set9

city: Vienna

first: Bhagyshree

middle: Babasaheb

last: Jamge

address: Dr. Bohr Gasse -3

country: Austria

institute: Gregor Mendel Institute

description: ChIP

data_processing:
For alignment and quality check of sequenced samples, bedtools v2.27.1 (PMID: 25199790) was used to convert the raw BAM files to fastq.
FastQC v0.11.8 (Andrews 2010) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to generate quality reports for all sequencing data.
Reads were trimmed using trim_galore v0.6.5 (DOI:10.5281/zenodo.5127898.)
Reads were aligned to the TAIR10 Arabidopsis genome using Bowtie2 (Langmead and Steven L Salzberg 2013) with default settings
Picard v2.22.8 (broadinstitute.github.io/picard/) was used to mark  duplicated reads.
The bamCompare function from Deeptools was used to normalize ChIP samples to Input or H3. log2 ratio (ChIP/ (Input or H3)) bigwig files.
Assembly: TAIR10
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

source_name: 12 day Seedlings

growth_protocol: Col-0 wild type (WT) Arabidopsis thaliana seeds were stratified at 4˚C in the dark for three days. Seeds were grown on ½ MS sterilized plates in the growth chamber under long day (LD) conditions (21˚C; 16 h light/8 h dark). After 10 days seedling tissue was freshly harvested.

extract_protocol:
Freshly harvested tissues (0.3 g of tissue was used for each immunoprecipitation) were fixed with 1% formaldehyde for 15 min and the cross-linking reaction was stopped by the addition of 125 mM glycine. . Crosslinked tissues were frozen and ground with a mortar and pestle in liquid nitrogen to obtain a fine powder. Ground tissues were resuspended in M1 buffer (10 mM sodium phosphate pH 7.0, 100 mM NaCl, 1 M hexylene glycol, 10 mM 2-mercaptoethanol, and protease inhibitor (Roche)), and the suspension was filtered through miracloth. Nuclei were precipitated by centrifugation and washed six times with M2 buffer (10 mM sodium phosphate pH 7.0, 100 mM NaCl, 1 M hexylene glycol, 10 mM MgCl2, 0.5% Triton X-100, 10 mM 2-mercaptoethanol, and protease inhibitor), and then further washed once with M3 buffer (10 mM sodium phosphate pH 7.0, 100 mM NaCl, 10 mM 2-mercaptoethanol, and protease inhibitor). Nuclei pellets were rinsed and resuspended in a sonication buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS, and protease inhibitor) and sonicated with a Covaris E220 High Performance Focused Ultrasonicator for 15 min at 4˚C (Duty factor 5.0; PIP 140.0; Cycles per Burst 200) in 1 ml Covaris milliTUBE. After chromatin shearing, the debris were removed by centrifugation and the solutions containing chromatin fragments were diluted with three times the volume of ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS, and protease inhibitor). After dilution, protein A/G magnetic beads (50 µl for one gram of tissue; Thermo Fisher Scientific) were added to sheared chromatin and incubated at 4˚C for 1 hour with rotation. Pre-cleared samples were collected and incubated with 5 µg of anti-H3 (Abcam, ab1791), anti-H2A.X.3/5, anti-H2A.13, anti-H2A.2, anti-H2A.Z.9, anti-H2A.Z.11, anti-H2A.W.6, anti-H2A.W.7, anti-H1, anti-H3K36me3 (Abcam, ab9050), anti-H3K27me3 (Millipore, 07-449), anti-H3K4me3 (Abcam, ab8580), anti-H3K4me1 (Abcam, ab8895), anti-H3K27me1 (Millipore 17-643), anti-H4K20me1 (Abcam, ab9051), anti-H3K9me1 (Abcam, ab8896) or anti-H3K9me2 (Abcam, ab1220) antibodies at 4˚C overnight with rotation. After incubation, samples were mixed with 30 µl of protein A/G magnetic beads, incubated at 4˚C for 3 hours with rotation, washed twice with low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), once with high salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), once with LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.25 M LiCl, 1% IGEPAL® CA-630, and 0.1% deoxycholic acid), and twice with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). Immunoprecipitated DNA was eluted by adding 500 µl of elution buffer (1% SDS and 0.1 M NaHCO3), incubated at 65˚C for 15 min, and mixed with 51 µl of reverse crosslink buffer (40 mM Tris-HCl pH 8.0, 0.2 M NaCl, 10 mM EDTA, 0.04 mg/ml proteinase K (Thermo Fisher Scientific)). The reaction mixture was then incubated at 45˚C for 3 hours and subsequently at 65˚C for 16 hours. After crosslink reversal, DNA was treated with 10 µg of RNaseA (Thermo Fisher Scientific), incubated at room temperature for 30 min, and purified with a MinElute PCR purification kit (Qiagen).
For ChIP-seq, libraries were prepared either with  Nugen Ovation Ultralow V2 DNA-Seq library prep kit (NuGen) or NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs) following the manufacturer’s instructions. The libraries were sequenced with an Illumina Hiseq 2000 to generate single-end 50 bp reads.

tag: ecotype

value: 12 day Seedlings

tag: chip antibody


title: Col_H2A.13_Set9

description: ChIP


title: Col_H2A.2_Set9

description: ChIP


title: Col_H2A.Z.11_Set8

description: ChIP


title: Col_H2A.Z.11_Set9

description: ChIP


title: Col_H2A.Z.9_Set9

description: ChIP


title: HDF

description: Gene expression data of human dermal fibroblast

source_name: human dermal fibroblast (origin of iPSCs)

value: human dermal fibroblast

value: 36-year-old Caucasian female


title: Col_Input_Set9

description: ChIP

value: Input


title: 414C2_EB

description: Gene expression data of human embryoid body 414C2

source_name: embryoid body, 414C2

value: differentiated from 414C2 iPS

value: 30 days from differentiation


title: 201B7_EB

description: Gene expression data of human embryoid body 201B7

source_name: embryoid body, 201B7


title: 253G4_EB

description: Gene expression data of human embryoid body 253G4

source_name: embryoid body, 253G4


title: 414C2_iPS

description: Gene expression data of human induced pluripotent stem cell 414C2

source_name: induced pluripotent stem cell, 414C2

value: induced from human dermal fibroblast of 36-year-old Caucasian female


title: 409B2_EB

description: Gene expression data of human embryoid body 409B2

source_name: embryoid body, 409B2


title: 201B6_EB

description: Gene expression data of human embryoid body 201B6

source_name: embryoid body, 201B6

value: differentiated from 201B6 iPS


title: Col_H3_Set8

description: ChIP


title: KhES2_EB

description: Gene expression data of human embryoid body KhES2

source_name: embryoid body, KhES2


title: KhES1_ES

description: Gene expression data of human embryonic stem cell KhES1

source_name: embryonic stem cell, KhES1

value: derived from inner cell mass of Japanese blastocysts


title: Col_H2A.13_Set8

description: ChIP


title: 253G1_EB

description: Gene expression data of human embryoid body 253G1

source_name: embryoid body, 253G1

value: differentiated from 253G1 iPS

value: female


title: 253G1_iPS

description: Gene expression data of human induced pluripotent stem cell 253G1

source_name: induced pluripotent stem cell, 253G1


title: KhES1_EB

description: Gene expression data of human embryoid body KhES1

source_name: embryoid body, KhES1


title: 409B2_iPS

description: Gene expression data of human induced pluripotent stem cell 409B2

source_name: induced pluripotent stem cell, 409B2


title: KhES3_EB

description: Gene expression data of human embryoid body KhES3

source_name: embryoid body, KhES3

value: differentiated from KhES3 ES

value: male


title: KhES3_ES

description: Gene expression data of human embryonic stem cell KhES3

source_name: embryonic stem cell, KhES3


title: 253G4_iPS

description: Gene expression data of human induced pluripotent stem cell 253G4

source_name: induced pluripotent stem cell, 253G4


title: Col_H2A.2_Set8

description: ChIP

source_name: 12 day Seedlings


title: 201B6_iPS

description: Gene expression data of human induced pluripotent stem cell 201B6

source_name: induced pluripotent stem cell, 201B6


title: Col_H2A.Z.9_Set8

description: ChIP


title: 201B7_iPS

description: Gene expression data of human induced pluripotent stem cell 201B7

source_name: induced pluripotent stem cell, 201B7


title: Col_H2A.W.7_Set6

description: ChIP

source_name: 10 day Seedlings

value: 10 day Seedlings


title: Col_Input_Set8

description: ChIP


title: KhES2_ES

description: Gene expression data of human embryonic stem cell KhES2

source_name: embryonic stem cell, KhES2


title: Col_H3_Set6

description: ChIP


title: Col_H2A.W.6_Set6

description: ChIP


title: Col_H3K27me3_Set5

description: ChIP


title: Col_H3K27me1_Set5

description: ChIP


title: Col_H3K9me2_Set5

description: ChIP


title: Col_H3K36me3_Set5

description: ChIP


title: Col_Input_Set6

description: ChIP


title: Col_H3_Set5

description: ChIP


title: Col_H3K9me1_Set4

description: ChIP


title: Col_H1_Set3

description: ChIP


title: Col_Input_Set4

description: ChIP


title: Col_H3_Set3

description: ChIP


title: Col_Input_Set3

description: ChIP


title: Col0_H3K4me1_Set2

description: ChIP


title: Col0_H4K20me1_Set2

description: ChIP


title: Col_H3K9me1_Set5

description: ChIP


title: Col0_H3K4me3_Set2

description: ChIP


title: Col0_H2A.W.7_Set2

description: ChIP


title: Col_H3_Set4

description: ChIP


title: Col0_H3K9me1_Set2

description: ChIP


title: Col0_Input_Set2

description: ChIP


title: Col0_H3_Set2

description: ChIP


title: Col0_H3K27me3_Set2

description: ChIP


title: Col_Input_Set5

description: ChIP


title: Leaves, dePs_ETI_6h, Rep3

city: Saint Paul

first: You

last: Lu

state: MN

address: 1500 Gortner Avenue

department: Department of Plant and Microbial Biology

country: USA

institute: University of Minnesota, Twin Cities

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample535

data_processing:
quality filter (during lane de-multiplexing): reads with any undetermined bases (N) in the barcode were removed
barcode trimming: internal barcodes were trimmed off of sequence reads
artifacts filtering: reads that resemble seqeuncing artifacts were removed using the artifacts filter in the fastx toolkit
read mapping: reads were mapped to TAIR10 transcripts using bowtie version bowtie-0.12.8
counting mapped reads: reads mapping to the forward strand of transcript(s) from a single gene were tallied (raw counts)
Genome_build: TAIR10
Supplementary_files_format_and_content: raw counts for reads mapped to TAIR10 genes

source_name: leaves

growth_protocol: Plants were grown under a 12hr photoperiod in a controlled environment at 22°C and 75% relative humidity.

extract_protocol:
Total RNA extraction
Stranded mRNA Tag-Seq libraries were prepared as previously described, Rallapalli et al. BMC Genomics. 2014;15:341. doi: 10.1186/1471-2164-15-341

treatment_protocol: 3 leaves (leaf stages 7-9) of a single plant of each genotype from 31-32 days-old plants were syringe-inoculated with a 50 μM solution of estradiol or water (mock), and harvested at the indicated time after treatment. Leaves of plants from the same genotype and time point sampling in four independent experiments were pooled into a single biological replicate.

tag: genotype

value: 50 μM Ed

tag: timepoint

value: 6 h


title: Col0_H2A.W.6_Set1

description: ChIP


title: Col0_Input_Set1

description: ChIP


title: Col0_H2A.X_Set1

description: ChIP


title: Col0_H3_Set1

description: ChIP


title: Leaves, rr_Ed_6h, Rep3

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample539


title: Leaves, depS_ETI_6h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample534


title: Leaves, GUS_Ed_6h, Rep3

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 6 h, 3rd repeat
sample540


title: Leaves, dEps_ETI_6h, Rep3

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample536


title: Leaves, Deps_ETI_6h, Rep3

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample537


title: Leaves, DePs_ETI_6h, Rep3

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample532


title: Leaves, DEps_ETI_6h, Rep3

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample533


title: Leaves, deps_ETI_6h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample538


title: Leaves, DepS_ETI_6h, Rep3

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample531


title: Leaves, dEpS_ETI_6h, Rep3

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample529


title: Leaves, dEPs_ETI_6h, Rep3

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample530


title: Leaves, dePS_ETI_6h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample528


title: Leaves, DEpS_ETI_6h, Rep3

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample526


title: Leaves, DEPs_ETI_6h, Rep3

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample527


title: Leaves, DePS_ETI_6h, Rep3

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample525


title: Leaves, dEPS_ETI_6h, Rep3

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample524


title: Leaves, DEPS_ETI_6h, Rep3

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 6 h, 3rd repeat
sample523


title: Leaves, deps_ETI_5h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample520

value: 5 h


title: Leaves, rr_Ed_5h, Rep3

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample521


title: Leaves, dEps_ETI_5h, Rep3

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample518


title: Leaves, Deps_ETI_5h, Rep3

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample519


title: Leaves, depS_ETI_5h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample516


title: Leaves, DEps_ETI_5h, Rep3

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample515


title: Leaves, dePs_ETI_5h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample517


title: Leaves, dEPs_ETI_5h, Rep3

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample512


title: Leaves, DEPs_ETI_5h, Rep3

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample509


title: Leaves, dEpS_ETI_5h, Rep3

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample511


title: Leaves, DePS_ETI_5h, Rep3

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample507


title: Leaves, DEPS_ETI_5h, Rep3

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample505


title: Leaves, DEpS_ETI_5h, Rep3

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample508


title: Leaves, DePs_ETI_5h, Rep3

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample514


title: Leaves, DepS_ETI_5h, Rep3

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample513


title: Leaves, rr_Ed_4h, Rep3

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample503

value: 4 h


title: Leaves, dePS_ETI_5h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample510


title: Leaves, dEPS_ETI_5h, Rep3

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample506


title: Leaves, Deps_ETI_4h, Rep3

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample501


title: Leaves, GUS_Ed_4h, Rep3

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 4 h, 3rd repeat
sample504


title: Leaves, GUS_Ed_5h, Rep3

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 5 h, 3rd repeat
sample522


title: Leaves, dePs_ETI_4h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample499


title: Leaves, depS_ETI_4h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample498


title: Leaves, DePs_ETI_4h, Rep3

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample496


title: Leaves, DEps_ETI_4h, Rep3

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample497


title: Leaves, dEPs_ETI_4h, Rep3

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample494


title: Leaves, dePS_ETI_4h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample492


title: Leaves, dEpS_ETI_4h, Rep3

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample493


title: Leaves, DEPs_ETI_4h, Rep3

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample491


title: Leaves, DEpS_ETI_4h, Rep3

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample490


title: Leaves, dEPS_ETI_4h, Rep3

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample488


title: Leaves, DePS_ETI_4h, Rep3

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample489


title: Leaves, DEPS_ETI_4h, Rep3

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample487


title: Leaves, GUS_Ed_3h, Rep3

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 3 h, 3rd repeat
sample486

value: 3 h


title: Leaves, deps_ETI_3h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample484


title: Leaves, dePs_ETI_3h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample481


title: Leaves, Deps_ETI_3h, Rep3

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample483


title: Leaves, deps_ETI_4h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample502


title: Leaves, DEps_ETI_3h, Rep3

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample479


title: Leaves, dEPs_ETI_3h, Rep3

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample476


title: Leaves, DePs_ETI_3h, Rep3

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample478


title: Leaves, DepS_ETI_3h, Rep3

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample477


title: Leaves, dEps_ETI_4h, Rep3

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample500


title: Leaves, dEpS_ETI_3h, Rep3

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample475


title: Leaves, dePS_ETI_3h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample474


title: Leaves, DEPs_ETI_3h, Rep3

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample473


title: Leaves, DEpS_ETI_3h, Rep3

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample472


title: Leaves, dEPS_ETI_3h, Rep3

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample470


title: Leaves, DEPS_ETI_3h, Rep3

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample469


title: Leaves, GUS_Ed_2h, Rep3

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 2 h, 3rd repeat
sample468

value: 2 h


title: Leaves, DepS_ETI_4h, Rep3

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 4 h, 3rd repeat
sample495


title: Leaves, deps_ETI_2h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample466


title: Leaves, Deps_ETI_2h, Rep3

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample465


title: Leaves, rr_Ed_3h, Rep3

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample485


title: Leaves, dEps_ETI_3h, Rep3

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample482


title: Leaves, dEps_ETI_2h, Rep3

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample464


title: Leaves, dePs_ETI_2h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample463


title: Leaves, depS_ETI_3h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample480


title: Leaves, DEps_ETI_2h, Rep3

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample461


title: Leaves, depS_ETI_2h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample462


title: Leaves, dEPs_ETI_2h, Rep3

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample458


title: Leaves, DepS_ETI_2h, Rep3

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample459


title: Leaves, DePs_ETI_2h, Rep3

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample460


title: Leaves, dEpS_ETI_2h, Rep3

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample457


title: Leaves, DEPs_ETI_2h, Rep3

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample455


title: Leaves, dePS_ETI_2h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample456


title: Leaves, DEPS_ETI_2h, Rep3

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample451


title: Leaves, DEpS_ETI_2h, Rep3

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample454


title: Leaves, DePS_ETI_3h, Rep3

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 3 h, 3rd repeat
sample471


title: Leaves, GUS_Ed_1h, Rep3

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 1 h, 3rd repeat
sample450

value: 1 h


title: Leaves, dEPS_ETI_2h, Rep3

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample452


title: Leaves, rr_Ed_1h, Rep3

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample449


title: Leaves, deps_ETI_1h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample448


title: Leaves, Deps_ETI_1h, Rep3

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample447


title: Leaves, dePs_ETI_1h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample445


title: Leaves, dEps_ETI_1h, Rep3

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample446


title: Leaves, depS_ETI_1h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample444


title: Leaves, rr_Ed_2h, Rep3

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample467


title: Leaves, DEps_ETI_1h, Rep3

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample443


title: Leaves, DePs_ETI_1h, Rep3

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample442


title: Leaves, DepS_ETI_1h, Rep3

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample441


title: Leaves, DePS_ETI_1h, Rep3

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample435


title: Leaves, dEpS_ETI_1h, Rep3

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample439


title: Leaves, dEPs_ETI_1h, Rep3

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample440


title: Leaves, dEPS_ETI_1h, Rep3

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample434


title: Leaves, dePS_ETI_1h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample438


title: Leaves, DEPs_ETI_1h, Rep3

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample437


title: Leaves, DEPS_ETI_1h, Rep3

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample433


title: Leaves, DEpS_ETI_1h, Rep3

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 1 h, 3rd repeat
sample436


title: Leaves, rr_Ed_0h, Rep3

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample431

value: 0 h


title: Leaves, DePS_ETI_2h, Rep3

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample453


title: Leaves, GUS_Ed_0h, Rep3

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 0 h, 3rd repeat
sample432


title: Leaves, dEps_ETI_0h, Rep3

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample428


title: Leaves, Deps_ETI_0h, Rep3

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample429


title: Leaves, dePs_ETI_0h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample427


title: Leaves, depS_ETI_0h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample426


title: Leaves, DEps_ETI_0h, Rep3

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample425


title: Leaves, DepS_ETI_0h, Rep3

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample423


title: Leaves, dEpS_ETI_0h, Rep3

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample421


title: Leaves, dEPs_ETI_0h, Rep3

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample422


title: Leaves, DEPs_ETI_0h, Rep3

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample419


title: Leaves, dePS_ETI_0h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample420


title: Leaves, DEpS_ETI_0h, Rep3

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample418


title: Leaves, DePS_ETI_0h, Rep3

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample417


title: Leaves, DEPS_ETI_0h, Rep3

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample415


title: Leaves, deps_mock_5h, Rep3

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample412

value: mock


title: Leaves, Deps_mock_5h, Rep3

description:
Leaves from mock-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample411


title: Leaves, depS_mock_5h, Rep3

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample408


title: Leaves, dePs_mock_5h, Rep3

description:
Leaves from mock-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample409


title: Leaves, DePs_mock_5h, Rep3

description:
Leaves from mock-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample406


title: Leaves, deps_ETI_0h, Rep3

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample430


title: Leaves, DepS_mock_5h, Rep3

description:
Leaves from mock-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample405


title: Leaves, dEPs_mock_5h, Rep3

description:
Leaves from mock-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample404


title: Leaves, DePs_ETI_0h, Rep3

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample424


title: Leaves, DEpS_mock_5h, Rep3

description:
Leaves from mock-treated pad4-1/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample400


title: Leaves, DePS_mock_5h, Rep3

description:
Leaves from mock-treated ein2-1/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample399


title: Leaves, dePS_mock_5h, Rep3

description:
Leaves from mock-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample402


title: Leaves, DEPS_mock_5h, Rep3

description:
Leaves from mock-treated Col-0/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample397


title: Leaves, dEPS_mock_5h, Rep3

description:
Leaves from mock-treated dde2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample398


title: Leaves, rr_mock_2h, Rep3

description:
Leaves from mock-treated rps2/rpm1/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample395


title: Leaves, Deps_mock_2h, Rep3

description:
Leaves from mock-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample393


title: Leaves, dEPS_ETI_0h, Rep3

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample416


title: Leaves, GUS_mock_5h, Rep3

description:
Leaves from mock-treated Col-0/pER-GUS plants at 5 h, 3rd repeat
sample414


title: Leaves, dePs_mock_2h, Rep3

description:
Leaves from mock-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample391


title: Leaves, deps_mock_2h, Rep3

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample394


title: Leaves, dEps_mock_2h, Rep3

description:
Leaves from mock-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample392


title: Leaves, dEps_mock_5h, Rep3

description:
Leaves from mock-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample410


title: Leaves, DEps_mock_5h, Rep3

description:
Leaves from mock-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample407


title: Leaves, DEps_mock_2h, Rep3

description:
Leaves from mock-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample389


title: Leaves, DepS_mock_2h, Rep3

description:
Leaves from mock-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample387


title: Leaves, DePs_mock_2h, Rep3

description:
Leaves from mock-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample388


title: Leaves, dEpS_mock_5h, Rep3

description:
Leaves from mock-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample403


title: Leaves, DEPs_mock_2h, Rep3

description:
Leaves from mock-treated sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample383


title: Leaves, DEpS_mock_2h, Rep3

description:
Leaves from mock-treated pad4-1/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample382


title: Leaves, dePS_mock_2h, Rep3

description:
Leaves from mock-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample384


title: Leaves, dEpS_mock_2h, Rep3

description:
Leaves from mock-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample385


title: Leaves, DEPs_mock_5h, Rep3

description:
Leaves from mock-treated sid2-2/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample401


title: Leaves, DePS_mock_2h, Rep3

description:
Leaves from mock-treated ein2-1/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample381


title: Leaves, DEPS_mock_2h, Rep3

description:
Leaves from mock-treated Col-0/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample379


title: Leaves, rr_mock_0h, Rep3

description:
Leaves from mock-treated rps2/rpm1/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample377


title: Leaves, deps_mock_0h, Rep3

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample376


title: Leaves, GUS_mock_0h, Rep3

description:
Leaves from mock-treated Col-0/pER-GUS plants at 0 h, 3rd repeat
sample378


title: Leaves, GUS_mock_2h, Rep3

description:
Leaves from mock-treated Col-0/pER-GUS plants at 2 h, 3rd repeat
sample396


title: Leaves, dePs_mock_0h, Rep3

description:
Leaves from mock-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample373


title: Leaves, depS_mock_0h, Rep3

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample372


title: Leaves, depS_mock_2h, Rep3

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample390


title: Leaves, DEps_mock_0h, Rep3

description:
Leaves from mock-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample371


title: Leaves, DePs_mock_0h, Rep3

description:
Leaves from mock-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample370


title: Col0_H3K9me2_Set2

description: ChIP


title: Leaves, DepS_mock_0h, Rep3

description:
Leaves from mock-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample369


title: Leaves, rr_mock_5h, Rep3

description:
Leaves from mock-treated rps2/rpm1/pER-AvrRpt2 plants at 5 h, 3rd repeat
sample413


title: Leaves, dEPs_mock_2h, Rep3

description:
Leaves from mock-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample386


title: Leaves, dEPs_mock_0h, Rep3

description:
Leaves from mock-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample368


title: Leaves, dEpS_mock_0h, Rep3

description:
Leaves from mock-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample367


title: Col0_H3K36me3_Set2

description: ChIP


title: Leaves, DEpS_mock_0h, Rep3

description:
Leaves from mock-treated pad4-1/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample364


title: Leaves, DEPs_mock_0h, Rep3

description:
Leaves from mock-treated sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample365


title: Leaves, dePS_mock_0h, Rep3

description:
Leaves from mock-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample366


title: Leaves, DePS_mock_0h, Rep3

description:
Leaves from mock-treated ein2-1/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample363


title: Leaves, DEPS_mock_0h, Rep3

description:
Leaves from mock-treated Col-0/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample361


title: Leaves, rr_Ed_6h, Rep2

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample359


title: Leaves, dEPS_mock_2h, Rep3

description:
Leaves from mock-treated dde2-2/pER-AvrRpt2 plants at 2 h, 3rd repeat
sample380


title: Leaves, dEPS_mock_0h, Rep3

description:
Leaves from mock-treated dde2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample362


title: Leaves, GUS_Ed_6h, Rep2

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 6 h, 2nd repeat
sample360


title: Leaves, deps_ETI_6h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample358


title: Leaves, Deps_ETI_6h, Rep2

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample357


title: Leaves, Deps_mock_0h, Rep3

description:
Leaves from mock-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample375


title: Leaves, dEps_mock_0h, Rep3

description:
Leaves from mock-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 3rd repeat
sample374


title: Leaves, depS_ETI_6h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample354


title: Leaves, DePs_ETI_6h, Rep2

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample352


title: Leaves, DepS_ETI_6h, Rep2

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample351


title: Leaves, dEps_ETI_6h, Rep2

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample356


title: Leaves, dEpS_ETI_6h, Rep2

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample349


title: Leaves, dEPs_ETI_6h, Rep2

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample350


title: Leaves, dePS_ETI_6h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample348


title: Leaves, DEPs_ETI_6h, Rep2

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample347


title: Leaves, DEpS_ETI_6h, Rep2

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample346


title: Leaves, dEPS_ETI_6h, Rep2

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample344


title: Leaves, DEPS_ETI_6h, Rep2

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample343


title: Leaves, rr_Ed_5h, Rep2

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample341


title: Leaves, deps_ETI_5h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample340


title: Leaves, GUS_Ed_5h, Rep2

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 5 h, 2nd repeat
sample342


title: Leaves, Deps_ETI_5h, Rep2

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample339


title: Leaves, dePs_ETI_5h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample337


title: Leaves, dEps_ETI_5h, Rep2

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample338


title: Leaves, DEps_ETI_5h, Rep2

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample335


title: Leaves, DepS_ETI_5h, Rep2

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample333


title: Leaves, dEpS_ETI_5h, Rep2

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample331


title: Leaves, dEPs_ETI_5h, Rep2

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample332


title: Leaves, DEPs_ETI_5h, Rep2

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample329


title: Leaves, dePs_ETI_6h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample355


title: Leaves, DEps_ETI_6h, Rep2

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample353


title: Leaves, DEpS_ETI_5h, Rep2

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample328


title: Leaves, DePS_ETI_5h, Rep2

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample327


title: Leaves, dEPS_ETI_5h, Rep2

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample326


title: Leaves, dePS_ETI_5h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample330


title: Leaves, GUS_Ed_4h, Rep2

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 4 h, 2nd repeat
sample324


title: Leaves, dEps_ETI_4h, Rep2

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample320


title: Leaves, deps_ETI_4h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample322


title: Leaves, DePS_ETI_6h, Rep2

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 6 h, 2nd repeat
sample345


title: Leaves, rr_Ed_4h, Rep2

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample323


title: Leaves, Deps_ETI_4h, Rep2

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample321


title: Leaves, DEps_ETI_4h, Rep2

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample317


title: Leaves, depS_ETI_4h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample318


title: Leaves, DePs_ETI_4h, Rep2

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample316


title: Leaves, DePs_ETI_5h, Rep2

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample334


title: Leaves, DepS_ETI_4h, Rep2

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample315


title: Leaves, DEPs_ETI_4h, Rep2

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample311


title: Leaves, dEpS_ETI_4h, Rep2

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample313


title: Leaves, DEpS_ETI_4h, Rep2

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample310


title: Leaves, dePS_ETI_4h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample312


title: Leaves, GUS_Ed_3h, Rep2

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 3 h, 2nd repeat
sample306


title: Leaves, DePS_ETI_4h, Rep2

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample309


title: Leaves, dEPS_ETI_4h, Rep2

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample308


title: Leaves, rr_Ed_3h, Rep2

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample305


title: Leaves, deps_ETI_3h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample304


title: Leaves, DEPS_ETI_4h, Rep2

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample307


title: Leaves, Deps_ETI_3h, Rep2

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample303


title: Leaves, dePs_ETI_3h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample301


title: Leaves, DEps_ETI_3h, Rep2

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample299


title: Leaves, depS_ETI_5h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample336


title: Leaves, DEPS_ETI_5h, Rep2

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample325


title: Leaves, dEps_ETI_3h, Rep2

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample302


title: Leaves, depS_ETI_3h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample300


title: Leaves, DePs_ETI_3h, Rep2

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample298


title: Leaves, DepS_ETI_3h, Rep2

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample297


title: Leaves, dePs_ETI_4h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample319


title: Leaves, dePS_ETI_3h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample294


title: Leaves, DEPs_ETI_3h, Rep2

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample293


title: Leaves, DEpS_ETI_3h, Rep2

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample292


title: Leaves, dEPs_ETI_4h, Rep2

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 4 h, 2nd repeat
sample314


title: Leaves, DePS_ETI_3h, Rep2

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample291


title: Leaves, dEpS_ETI_3h, Rep2

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample295


title: Leaves, dEPS_ETI_3h, Rep2

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample290


title: Leaves, GUS_Ed_2h, Rep2

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 2 h, 2nd repeat
sample288


title: Leaves, deps_ETI_2h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample286


title: Leaves, rr_Ed_2h, Rep2

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample287


title: Leaves, Deps_ETI_2h, Rep2

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample285


title: Leaves, dEps_ETI_2h, Rep2

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample284


title: Leaves, depS_ETI_2h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample282


title: Leaves, dePs_ETI_2h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample283


title: Leaves, dEPs_ETI_2h, Rep2

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample278


title: Leaves, DEps_ETI_2h, Rep2

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample281


title: Leaves, DepS_ETI_2h, Rep2

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample279


title: Leaves, DePs_ETI_2h, Rep2

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample280


title: Leaves, dEpS_ETI_2h, Rep2

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample277


title: Leaves, DEPs_ETI_2h, Rep2

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample275


title: Leaves, dePS_ETI_2h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample276


title: Leaves, dEPS_ETI_2h, Rep2

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample272


title: Leaves, DEPS_ETI_2h, Rep2

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample271


title: Leaves, dEPs_ETI_3h, Rep2

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample296


title: Leaves, GUS_Ed_1h, Rep2

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 1 h, 2nd repeat
sample270


title: Leaves, DEpS_ETI_2h, Rep2

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample274


title: Leaves, DePS_ETI_2h, Rep2

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample273


title: Leaves, deps_ETI_1h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample268


title: Leaves, rr_Ed_1h, Rep2

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample269


title: Leaves, DePs_ETI_1h, Rep2

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample262


title: Leaves, dEps_ETI_1h, Rep2

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample266


title: Leaves, DEps_ETI_1h, Rep2

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample263


title: Leaves, depS_ETI_1h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample264


title: Leaves, dePs_ETI_1h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample265


title: Leaves, Deps_ETI_1h, Rep2

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample267


title: Leaves, DepS_ETI_1h, Rep2

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample261


title: Leaves, dEPs_ETI_1h, Rep2

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample260


title: Leaves, DEpS_ETI_1h, Rep2

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample256


title: Leaves, DEPs_ETI_1h, Rep2

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample257


title: Leaves, dEpS_ETI_1h, Rep2

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample259


title: Leaves, DePS_ETI_1h, Rep2

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample255


title: Leaves, dEPS_ETI_1h, Rep2

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample254


title: Leaves, deps_ETI_0h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample250


title: Leaves, DEPS_ETI_1h, Rep2

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample253


title: Leaves, rr_Ed_0h, Rep2

description:
Leaves from estradiol-treated rps2/rpm1/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample251


title: Leaves, DEPS_ETI_3h, Rep2

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 3 h, 2nd repeat
sample289


title: Leaves, GUS_Ed_0h, Rep2

description:
Leaves from estradiol-treated Col-0/pER-GUS plants at 0 h, 2nd repeat
sample252


title: Leaves, Deps_ETI_0h, Rep2

description:
Leaves from estradiol-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample249


title: Leaves, dEps_ETI_0h, Rep2

description:
Leaves from estradiol-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample248


title: Leaves, dePs_ETI_0h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample247


title: Leaves, DepS_ETI_0h, Rep2

description:
Leaves from estradiol-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample243


title: Leaves, depS_ETI_0h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample246


title: Leaves, DePs_ETI_0h, Rep2

description:
Leaves from estradiol-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample244


title: Leaves, DEps_ETI_0h, Rep2

description:
Leaves from estradiol-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample245


title: Leaves, DEPs_ETI_0h, Rep2

description:
Leaves from estradiol-treated sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample239


title: Leaves, dEpS_ETI_0h, Rep2

description:
Leaves from estradiol-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample241


title: Leaves, dePS_ETI_0h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample240


title: Leaves, dEPs_ETI_0h, Rep2

description:
Leaves from estradiol-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample242


title: Leaves, DEpS_ETI_0h, Rep2

description:
Leaves from estradiol-treated pad4-1/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample238


title: Leaves, dEPS_ETI_0h, Rep2

description:
Leaves from estradiol-treated dde2-2/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample236


title: Leaves, DePS_ETI_0h, Rep2

description:
Leaves from estradiol-treated ein2-1/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample237


title: Leaves, rr_mock_5h, Rep2

description:
Leaves from mock-treated rps2/rpm1/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample233


title: Leaves, GUS_mock_5h, Rep2

description:
Leaves from mock-treated Col-0/pER-GUS plants at 5 h, 2nd repeat
sample234


title: Leaves, dePS_ETI_1h, Rep2

description:
Leaves from estradiol-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 1 h, 2nd repeat
sample258


title: Leaves, deps_mock_5h, Rep2

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample232


title: Leaves, Deps_mock_5h, Rep2

description:
Leaves from mock-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample231


title: Leaves, DEPS_ETI_0h, Rep2

description:
Leaves from estradiol-treated Col-0/pER-AvrRpt2 plants at 0 h, 2nd repeat
sample235


title: Leaves, dePs_mock_5h, Rep2

description:
Leaves from mock-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample229


title: Leaves, dEps_mock_5h, Rep2

description:
Leaves from mock-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample230


title: Leaves, DepS_mock_5h, Rep2

description:
Leaves from mock-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample225


title: Leaves, DEps_mock_5h, Rep2

description:
Leaves from mock-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample227


title: Leaves, depS_mock_5h, Rep2

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample228


title: Leaves, dEPs_mock_5h, Rep2

description:
Leaves from mock-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample224


title: Leaves, DePs_mock_5h, Rep2

description:
Leaves from mock-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample226


title: Leaves, DEPs_mock_5h, Rep2

description:
Leaves from mock-treated sid2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample221


title: Leaves, dEpS_mock_5h, Rep2

description:
Leaves from mock-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample223


title: Leaves, dePS_mock_5h, Rep2

description:
Leaves from mock-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample222


title: Leaves, DePS_mock_5h, Rep2

description:
Leaves from mock-treated ein2-1/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample219


title: Leaves, dEPS_mock_5h, Rep2

description:
Leaves from mock-treated dde2-2/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample218


title: Leaves, DEpS_mock_5h, Rep2

description:
Leaves from mock-treated pad4-1/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample220


title: Leaves, GUS_mock_2h, Rep2

description:
Leaves from mock-treated Col-0/pER-GUS plants at 2 h, 2nd repeat
sample216


title: Leaves, rr_mock_2h, Rep2

description:
Leaves from mock-treated rps2/rpm1/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample215


title: Leaves, dePs_mock_2h, Rep2

description:
Leaves from mock-treated dde2-2/ein2-1/sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample211


title: Leaves, Deps_mock_2h, Rep2

description:
Leaves from mock-treated ein2-1/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample213


title: Leaves, DEPS_mock_5h, Rep2

description:
Leaves from mock-treated Col-0/pER-AvrRpt2 plants at 5 h, 2nd repeat
sample217


title: Leaves, dEps_mock_2h, Rep2

description:
Leaves from mock-treated dde2-2/pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample212


title: Leaves, DEps_mock_2h, Rep2

description:
Leaves from mock-treated pad4-1/sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample209


title: Leaves, depS_mock_2h, Rep2

description:
Leaves from mock-treated dde2-2/ein2-1/pad4-1/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample210


title: Leaves, DePs_mock_2h, Rep2

description:
Leaves from mock-treated ein2-1/sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample208


title: Leaves, DepS_mock_2h, Rep2

description:
Leaves from mock-treated ein2-1/pad4-1/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample207


title: Leaves, dEPs_mock_2h, Rep2

description:
Leaves from mock-treated dde2-2/sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample206


title: Leaves, dEpS_mock_2h, Rep2

description:
Leaves from mock-treated dde2-2/pad4-1/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample205


title: Leaves, DEPs_mock_2h, Rep2

description:
Leaves from mock-treated sid2-2/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample203


title: Leaves, dePS_mock_2h, Rep2

description:
Leaves from mock-treated dde2-2/ein2-1/pER-AvrRpt2 plants at 2 h, 2nd repeat
sample204