title: H3K27me3 TSA_2

city: Basel

first: Primo

last: Schaer

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
ChIP-seq rads were aligned to hg19 using SMALT (v 0.6.2)
High quality alignments were extracted using samtools filter-mapQuality ">30"
domains were defined based on increased densities of center positions of ChIPped fragments using chipseq (http://ccg.vital-it.ch/chipseq/  )
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using bedGraphToBigWig

source_name: T cell leukaemia

growth_protocol: Jurkat cells (acute T cell leukaemia) were cultured in RPMI-1640 medium supplemented with 2 mM L-glutamine, 1 mM Na-pyruvate, 10% FCS and 0.6x penicillin/streptomycin (Sigma-Aldrich) at 37°C in a humidified atmosphere with 5% CO2. Fresh medium was supplied every 48 h.

extract_protocol:
Whole cell lysates of crosslinked cells were sonicated, clarified and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols for  HiSeq platform

treatment_protocol: For ELF-MF exposure experiments, cells were seeded at a density of 10e5 cells/mL and grown for the indicated time without addition of fresh medium. The leukaemic cell line was sinusoidal ELF-MF (50 Hz, 1 mT, 5’ on/10’ off) or sham exposed (50 Hz, 7 µT, 5’ on/10’ off) for approximately 3.5 cell cycles (72 h). As positive control, cells were treated with 10 nM trichostatin A (TSA).

value: Jurkat

value: Trichostatin A (10 nM)

tag: time of treatment

value: 72 hrs

tag: chip antibody


title: H3K27me3 TSA_1

status: Public on Mar 01 2017

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: treatment


title: KDM6A Mut rep 1

city: Singapore

first: Xiaoran

last: Chai

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

library_source: transcriptomic

data_processing:
Illumina Casava1.9 software was used for basecalling
Sequenced reads were trimmed for adaptor sequence,, then mapped to hg19 whole genome using STAR-2.3.0e with parameters --outSAMstrandField intronMotif
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks-2.1.1 with parameters -b -u --max-bundle-frags 100000000
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample

molecule: total RNA

source_name: KDM6A Mut

growth_protocol: Urothelial bladder carcinoma cell lines were maintained under 10% FBS contained culture medium

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Urothelial bladder carcinoma cel lnese were treated with GSK343 (1 uM) for 14 days prior RNA extraction

tag: tissue

value: Urothelial Bladder Carcinoma

tag: genotype

value: Mutant


title: KDM6A WT rep 10

source_name: KDM6A WT

value: wildtype


title: H3K27me3 sham_1

value: sham (50Hz sinus, 0,007 mT, 5' on/10' off)


title: H3K27me3 ELF-MF_2

value: ELF-MF (50Hz sinus, 1 mT, 5' on/10' off)


title: H3K27me3 ELF-MF_1


title: H3K27me3 t0_2

value: 0 hrs


title: H3K27me3 t0_1


title: KDM6A WT rep 8


title: H3K4me2 TSA_2


title: H3K4me2 TSA_1


title: H3K4me2 sham_2


title: H3K4me2 ELF-MF_2


title: H3K4me2 ELF-MF_1


title: H3K4me2 t0_1


title: H3K4me2 t0_2


title: H3K4me2 sham_1


title: H3K27me3 sham_2


title: pOka-WT_36.1

city: Stanford

first: Stefan

last: Oliver

state: California

address: 300 Pasteur Drive, Grant Rm S366

department: Pediatrics

country: USA

institute: Stanford University School of Medicine

data_processing:
Quality control checks of FastQ files was performed using FastQC v0.11.4 Babraham Bioinformatics
Reads were aligned and BAM files generated using STAR v2.5
BAM files containing the aligned reads were used to generate RPKM values, which were calculated using the RNA-seq pipeline in Partek Genomics Suite 6.6
Genome_build: hg19

source_name: pOka ininfected MeWo cells; 36hpi

growth_protocol: MeWo cells were were propagated in culture medium [MEM supplemented with 10% fetal bovine serum (Life Technologies, Grand Island, NY), non-essential amino acids (100μM; Cellgro, Manassas, VA), penicillin-G/streptomycin (100 units/ml; Life Technologies, Grand Island, NY), amphotericin (0.5 mg/ml; Cellgro, Manassas, VA)

extract_protocol:
Total RNA was extracted from melanoma cells using an RNeasy Plus Mini Kit (Qiagen)
Libraries were prepared from HOW MUCH RNA using a TruSeq RNA Preparation Kit

treatment_protocol: Infection with varicella-zoster virus

value: MeWo

tag: virus phenotype

value: Not Applicable

tag: time post infection


title: pOka-WT_12.1

source_name: pOka infected MeWo cells; 12hpi

value: Wild Type


title: None_12.1

source_name: Uninfected MeWo cells; 12hpi


title: None_24.2

source_name: Uninfected MeWo cells; 24hpi


title: pOka-WT_24.2

source_name: pOka ininfected MeWo cells; 24hpi

value: Wild type


title: CAM_1077762

city: Houston

first: Chi Lam

last: Au Yeung

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

data_processing:
Raw sequences obtained from the Illumina platform in FASTQ format were analyzed using publicly available tools.
Quality reads were analyzed using FastQC. Due to the high quality of reads there was no need to trim of filter them.
The sequences were mapped to the GRCh38.p2 human reference genome sequence using a series of programs, including Bowtie2 for short-read mapping, and TopHat for defining exon–intron junctions.
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: The expression level of each transcript was expressed as the fragments per transcript kilobase per million fragments mapped (FPKM) value, which was calculated based on the number of mapped reads using Cufflinks.

source_name: Ascitic fluid-isolated mesothelial cells

extract_protocol:
Samples were lysed in TRI Reagent (Ambion) to obtain total RNA. The RNA integrity was checked using the Agilent Bioanalyzer 2100® (Agilent Technologies, Santa Clara, CA, USA). Samples were depleted of rRNA, then RNA was sheared into smaller fragments with Covaris S220 (Covaris, Woburn, MA, USA).
The cDNA library was prepared using the Beckman SPRIworks system (Beckman Coulter Inc., Fullerton, CA, USA). Library fragments hybridize to complementary oligonucleotides, and clusters of clones are generated in the Illumina cBOT instrument (Illumina).

tag: cell type


title: CAM_1073542

value: Ascitic fluid-isolated mesothelial cells


title: MESO_normal_3

source_name: Human peritoneal mesothelial cells

value: Human peritoneal mesothelial cells


title: MESO_normal_1


title: CAM_1071097


title: ER ChIP-seq DMSO 1

city: Pittsburgh

first: Hatice

middle: Ulku

last: Osmanbeyoglu

state: PA

address: 5117 Centre Ave

institute: University of Pittsburgh

data_processing:
Reads were first processed with Trimmomatic to remove the adaptor sequences and bases with quality scores below 20, and reads with less than 30 remaining bases were discarded.
Trimmed reads were then aligned to hg19 human genome with the bowtie aligner.
ER and FOXA1 peaks were called using MACS2.
Differentially accessible peaks from this atlas were identified with DESeq by counting all read ends overlapping peaks in each condition. DESeq was run with a log2-fold-change threshold of 1, and FDR < 0.1.
The distribution of the peaks around the TSS was calculated using the ChIPpeakAnno package.
Genome_build: hg19 human genome
Supplementary_files_format_and_content: bw files were generated using deeptools.

source_name: Breast Cancer Cell

growth_protocol: T47D cells were maintained in RPMI 1640 with 10% FBS, 1% L-glutamine and 1% penicillin-streptomycin.

extract_protocol:
Cells were lysed and sonicated leading to a DNA average size of 200bp. Protein G dynabeads were pre-incubated with 5μg of ER alpha (sc-543) or FOXA1 (ab5089) with pre cleared chromatin. The complexes were reverse cross-linked and DNA was purified.
ChIP-seq libraries were prepared using 10 ng of DNA and Illumina's TruSeq ChIP sample prep.Libraries were validated using the Agient Technologies 2100 Bioanalyzer and Qubit high sensitivity assay.

treatment_protocol: 10 milion T47D cells were treated with DMSO or BYL719 1μM for 24hr.

tag: passages

tag: chip-antibody

value: ER alpha (sc543) Santa Cruz


title: FOXA1 ChIP-seq BYL719 1

value: FOXA1 (ab5089) Abcam


title: ER ChIP-seq DMSO 2


title: FOXA1 ChIP-seq BYL719 2


title: Input BYL719


title: FOXA1 ChIP-seq DMSO 1


title: Input DMSO


title: ER ChIP-seq BYL719 2


title: FOXA1 ChIP-seq DMSO 2


title: ER ChIP-seq BYL719 1


title: T47D BYL719 2

data_processing:
Library strategy: ATAC-seq
Starting from fastq files containing ATAC-seq paired-end reads, sequencing adaptors were removed using Trimmomatic.
Trimmed reads were mapped to the hg19 human genome using Bowtie2 allowing at most 1 seed mismatch and keeping only uniquely aligned reads.
Duplicates were removed using Picard.
For peak-calling the read start sites were adjusted (reads aligning to the +/- strand were offset by +4bp/-5bp, respectively) to represent the center of the transposon binding-event.
Peak calling was performed on each condition individually by pooling reads from biological replicates, and using MACS2 with a permissive P-value threshold (-p 1e-2).
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using deeptools.

extract_protocol:
50,000 T47D cells were dissociated with acutase treatment and lysed with double the concentration of IGEPAL (0.2%) for successful library preparation.
ATAC-seq libraries were prepared using Illumina's TruSeq ChIP sample prep.Libraries were validated using the Agient Technologies 2100 Bioanalyzer and Qubit high sensitivity assay.

treatment_protocol: 50,000 T47D cells were treated with DMSO or BYL719 1μM for 24hr.

value: breast


title: T47D BYL719 1


title: T47D DMSO 2


title: None_36.1

source_name: Uninfected MeWo cells; 36hpi


title: T47D DMSO 1


title: MESO_normal_2


title: ChIP-Seq GATA3 plus E2

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

data_processing:
Basecalls performed using CASAVA version 1.4
reads were aligned to the mm9 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.

source_name: breast cancer

growth_protocol: MCF7 obtained from ATCC were cultured in DMEM media supplemented with 10% FBS in a 5% CO2 humidified incubator at 37°C.

extract_protocol:
For ChIP-seq, some samples were fixed for 10 minutes with 1% formaldehyde. Fixation was stopped by adding Glycine (0.125M). Chromatin DNA was sheared to 200–500 bp average in size by sonication. Soluble sheared chromatin was immunoprecipitated with specific antibodies or streptavidin beads overnight at 4°C. After washing and elution, the protein–DNA complex was decross-linked by heating at 65°C overnight. Immunoprecipitated DNA was purified by using iPure Diagenode kit.
the libraries were constructed following Illumina’s Chip-Seq Sample prep kit.

treatment_protocol: Before experiment, the MCF7 cells were hormone-stripped in phenol red free DMEM medium plus 5% charcoal-treated FBS for 3-4 days, followed by treatment of 100 nM ICI for 3h, or 100nM 17β-estradiol (E2) ,100nM dexamethasone (Dex) or combine together for 1hr. To perform Biotin-ChIP experiments through Biotin-streptavidin pull-down, we used some BLRP-tagged MCF7 Tet-On inducible stable lines that can in vivo biotinylate BLRP-tagged proteins. To induce BLRP-tagged protein expression, 2μg/ml doxycycline was added into culture media for about 24 hours before hormone treatment and collection.

tag: chip antibody used for chip or oligonucleotides used for chirp (chromatin isolation by rna purification)

value: streptavidin beads


title: ChIP-Seq GR pBox mutant plus E2


title: ChIP-Seq GR pBox mutant plus E2 and Dex


title: ChIP-Seq GATA3 plus E2 and Dex


title: Gro-Seq plus ICI

description:
Nascent RNA sequencing
Gro-seq in MCF7 cells treated with ICI

data_processing:
Library strategy: Gro-seq
Basecalls performed using CASAVA version 1.4
Gro-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.

extract_protocol:
10-20 millions of MCF7 cells treated with E2 or DEX for 1 hr were washed 3 times with cold PBS and then sequentially swelled in swelling  buffer (10mM Tris-HCl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5 min on ice, harvested, and lysed in lysis buffer (swelling buffer plus 0.5% NP-40, 20 units of SUPERase-In, and 10% glycerol). The resultant nuclei were washed two more times with 10ml lysis buffer.
For the run-on assay, resuspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-HCl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of SUPERase-In, 1% sarkosyl, 500 mM ATP, GTP, and Br-UTP, 2 mM CTP) and incubated for 5 min at 30 C. The resultant nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol LS reagent following manufacturer’s instructions. NRO-RNA was fragmented to 300-500nt by alkaline base hydrolysis on ice for 30 min and followed by treatment with DNase I and antarctic phosphatase. At this step, only a small portion of all the RNA species are BrU-labeled. To purify the Br-UTP labeled nascent RNA, the fragmented NRO-RNA was immunoprecipitated with anti-BrdU argarose beads in binding buffer (0.5XSSPE, 1mM EDTA, 0.05% tween) for 1-3 hr at 4 C with rotation. Subsequently, T4 PNK was used to repair the ends of the immunoprecipitated Br-UTP labeled nascent RNA at 37 C for 1 hr. The RNA was extracted and precipitated using acidic phenol-chloroform. cDNA synthesis was performed as per a published method with few modifications. The RNA fragments were subjected to poly-A tailing reaction by poly-A polymerase for 30 min at 37 C. Subsequently, reverse transcription was performed using oNTI223 primer and superscript III RT kit. The cDNA products were separated on a 10% polyacrylamide TBE-urea gel and only those fragments migrating between 100-500bp were excised and recovered by gel extraction. Next, the first-strand cDNA was circularized by CircLigase and relinearized by APE1. Relinearized single strand cDNA (sscDNA) was separated on a 10% polyacrylamide TBE gel and the appropriately sized product (120-320bp) was excised and gel-extracted. Finally, sscDNA template was amplified by PCR using the Phusion High-Fidelity enzyme according to the manufacturer’s instructions. The oligonucleotide primers oNTI200 and oNTI201 were used to generate DNA for deep sequencing.  .

treatment_protocol: Before experiment, the MCF7 cells were hormone-stripped in phenol red free DMEM medium plus 5% charcoal-treated FBS for 3-4 days, followed by treatment of 100 nM ICI for 3h, or 100nM 17β-estradiol (E2) ,100nM dexamethasone (Dex) or combine together for 1hr.


title: Gro-Seq plus ICI and Dex

description:
Nascent RNA sequencing
Gro-seq in MCF7 cells treated with ICI plus Dex


title: ChIP-Seq Input


title: Gro-Seq plus E2

description:
Nascent RNA sequencing
Gro-seq in MCF7 cells treated with E2


title: ChIP-Seq GATA3 plus ICI


title: Gro-Seq plus E2 and Dex

description:
Nascent RNA sequencing
Gro-seq in MCF7 cells treated with E2 plus Dex


title: ChIP-Seq GR pBox mutant plus ICI and Dex


title: ChIP-Seq GR wild type plus ICI and Dex


title: ChIP-Seq ERα plus E2 and Dex

value: Santa Cruz Biotechnologies ERα (HC-20) sc-543


title: ChIP-Seq ERα plus ICI


title: ChIP-Seq ERα plus E2


title: ChIP-Seq GR wild type plus ICI


title: ChIP-Seq ERα plus ICI and Dex


title: ChIP-Seq GR wild type plus E2


title: SLIRP siRNA (Vehicle) Replicate 2

city: Chapel Hill

first: Young

middle: E.

last: Whang

state: NC

address: 22-016 Lineberger Cancer Ctr

department: UNC School of Medicine, Clinical Research, Urologic Oncology Program

institute: University of North Carolina at Chapel Hill

data_processing:
Basecalls by Casava
Alignment by MapSplice2
Genome to transcriptome coordiantes by UBU (https://github.com/mozack/ubu/wiki)
Gene expression estimates by RSEM using Sept 2011 UCSC knownGene transcript definitions
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited matrix of gene level count estimates

source_name: LNCaP prostate cancer cell line

extract_protocol: none supplied by submitter

treatment_protocol: Vehicle vs 1nM DHT

value: LNCaP


title: SLIRP siRNA (Vehicle) Replicate 3


title: SLIRP siRNA (1nM DHT) Replicate 4


title: SLIRP siRNA (Vehicle) Replicate 4


title: SLIRP siRNA (Vehicle) Replicate 1


title: SLIRP siRNA (1nM DHT) Replicate 3


title: SLIRP siRNA (1nM DHT) Replicate 2


title: ChIP-Seq GR wild type plus E2 and Dex


title: Control siRNA (1nM DHT) Replicate 1


title: Control siRNA (Vehicle) Replicate 2


title: Control siRNA (Vehicle) Replicate 4


title: Control siRNA (Vehicle) Replicate 3


title: Control siRNA (Vehicle) Replicate 1


title: SLIRP siRNA (1nM DHT) Replicate 1


title: Control siRNA (1nM DHT) Replicate 4


title: Control siRNA (1nM DHT) Replicate 2


title: ChIP-Seq GR pBox mutant plus ICI


title: Control siRNA (1nM DHT) Replicate 3


title: RRBS_H2O2_HEK293T

city: Chong Qing

first: Xianfeng

last: Li

address: Da ping

department: Department of Gastroenterology, Daping Hospital

country: China

institute: Army Medical University (Third Military Medical University)

data_processing:
Basecalls performed using CASAVA version 1.8
The low quality reads and adapter sequences were firstly removed from the raw reads. The quality of resulted clean reads was checked by FastQC
RRBS reads were aligned to the hg19 genome assembly using SOAP2 with two mismatches allowed in the seed (40 bp)
Unique mapped reads were used for DNA methylation information extraction with software RRBS-Analyser
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Tab-delimited text files include methylation information of each chromosone for each Sample.Scores represent chromosone,position,strand,Cpattern,Csequence,copy number,methylC reads number,unmethylC reads number,binomial expection

source_name: Human Embryonic Kidney 293T cells_with_H2O2

extract_protocol:
Total DNA of HEK293T cell line with or without H2O2 treatment was extracted by proteinase K/phenol.
For each library, 500 ng of genomic DNA was digested overnight with MspI (20 units). After purification, the digested products were blunt-ended. Then dA was added, followed by methylated-adapter (Illumina, CA, USA) ligation. To obtain DNA fractions in 40-120 bp and 120-220 bp range of MspI-digested products, two ranges (160-240 bp and 240-340 bp) of adapter-ligated fractions were excised from 2% agarose gel. The size-selected DNA was bisulfite-treated for two rounds using EpiTect Bisulfite Kit (Qiagen, Venlo, Netherlands) following the manufacturer’s standard protocol. Finally, libraries were generated by amplification with HiFi HotStart Uracil+ ReadyMix (KAPA, MA，USA) and Illumina Multiplexing PCR Primers. Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA) and RT-PCR were used to guarantee the quality and quantity of RRBS library. After RRBS library construction, Illumina HiSeq 2000 was used to sequence those libraries according to the manufacturer’s protocol.

value: Human Embryonic Kidney cells


title: RRBS_Control_HEK293T

source_name: Human Embryonic Kidney 293T cells_without_H2O2


title: Embryoid body with ATRA 0day

city: Gwanju

first: Lee

last: Sung-gwon

address: Yong-bong ro 77

country: South Korea

institute: Chonnam national university

data_processing:
Raw reads of all libraries were trimmed the artificial adaptor sequences which were generated during sequencing run inevitably, and low quality sequences using Trimmomatic.
Then reads were aligned with the mouse genome using Tophat. Mapped reads were assembled with the transcripts and estimated the fragment per kilobase of exon per million fragments mapped (FPKM) which was represented expression level, using by Cufflinks.
Transcripts which were not annotated to gene, were ignored in this study. 167 differentially expressed genes were selected under 5% false discovery rate (FDR) which was calculated Benjamini-Hochberg correction for multiple testing.
Genome_build: mm10(UCSC genome browser)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: mESC was provided from the American Type Culture Collection (ES-E14TG2a; Manassas, VA) and cultured in DMEM-high glucose (GIBCO-BRL, Gaithersburg, MD) with 1% penicillin and streptomycin, 1.7 mM L-glutamine, 0.1 mM β-mercaptoethanol, 5 μg/ml mouse leukemia inhibitory factor (LIF) and 15% Fetal bovine serum (FBS) in an incubator with 37°C and  5% CO2.

extract_protocol:
Total RNA was prepared from cultured EBs using TRI Reagent (Molecular Research Center, Inc., Cincinnati, OH) and cDNAs were synthesized with 3 ug of total RNA using a RT system kit with oligo deoxythymidine (dT) 18 primers (Bioneer, Daejeon, Korea).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Embryoid bodies (EBs) in EB-medium (DMEM with 1% penicillin and streptomycin, 1.7 mM L-glutamine, 0.1 mM β-mercaptoethanol, and 10% FBS) were cultured in suspension and neural differentiation was induced with 5 uM of all- trans retinoic acid (ATRA, Sigma-Aldrich, MO, USA) in EB-media, adding at the 4th and 6th day of EB culture. After 8 days of culturing EB, EBs were cultured in the coated dishes with poly-DL-ornithine (200 ug /ml, Sigma-Aldrich, MO, USA) and mouse laminin (3 μg/ml, Gibco).

tag: protocol

value: ATRA 0day


title: Embryoid body with ATRA 10days

value: ATRA 10days


title: Embryoid body with ATRA 6days

value: ATRA 6days


title: Male_sham_6

city: Daejeon

first: Byungkuk

last: Min

address: 125 Gwahak-ro, Yuseong-gu

department: Development and Differentiation Research Center

institute: KRIBB

description: trimmed fastq file

data_processing:
Raw reads were trimmed using 'trim_galore', and the trimmed reads were aligned on the Bos taurus UMD3.1 (NCBI) with TopHat.
Estimation of gene expression levels and differential expressions were performed using the Cufflinks suit (cufflinks, cuffmerge, cuffdiff).
Genome_build: UMD3.1
Supplementary_files_format_and_content: csv file containing normalized (FPKM) gene expression data

organism: Bos taurus

source_name: bovine blastocysts

growth_protocol: To generate SCNT blastocysts, single donor cell was injected into enucleated oocyte by a micromanipulator with an inverted microscope (Leitz), and each donor-oocyte complex was fused by an Electro Cell Manipulator 2001 (BTX). The fused eggs were activated 4 hours after. Blastocysts were generated 6-8 days post-NT. The quality of each blastocyst was assessed by Hoechst staining, and only high quality embryos with 60-80 blastomeres were chosen for transcriptomic analysis.  For generation of sham SCNT blastocysts, 18-22 hours post-IVF, the zygote with two parental pronuclei was chosen for manipulation. To exactly mimic the physical damage of enucleation, zona pellucida was partially ripped and the polar body and a part of the underlying ooplasm were removed using a micropipette without touching either male or female pronucleus. After 2 hours of incubation, the reconstructed oocytes were activated using 5 µM ionomycin (Sigma) for 5 min, followed by treatment with 2.5 mM 6-dimethyl-aminopurine (DMAP, Sigma) in CR1aa culture media supplemented with 0.3% BSA for 3.5 hours. The oocytes were then in vitro cultured to the blastocyst stage.

extract_protocol:
mRNAs from each blastocyst were extracted using Dynabeads mRNA DIRECT kit (Invitrogen) according to the manufacturer's instruction and converted to cDNA by the pico-profiling method.
Illumina NGS libraries were prepared using the TruSeq DNA Sample Prep kit (Illumina) according to the manufacture's instruction.

tag: Sex

value: male

tag: source

value: sham


title: RT4 control rep 1_14days

source_name: RT4 control

value: Urothelial Bladder Carcinoma Cell line

value: wildtype


title: Male_sham_5

description: trimmed fastq file


title: Male_sham_2

description: trimmed fastq file


title: Male_SCNT_6

description: trimmed fastq file

value: SCNT


title: Male_sham_3

description: trimmed fastq file


title: Male_sham_1

description: trimmed fastq file


title: Embryoid body

value: control


title: Male_SCNT_4

description: trimmed fastq file


title: Male_SCNT_5

description: trimmed fastq file


title: Ku1919 parental GSK343

source_name: Ku1919 parental GSK343

value: Mutant


title: Male_SCNT_3

description: trimmed fastq file


title: Male_SCNT_2

description: trimmed fastq file


title: Male_SCNT_1

description: trimmed fastq file


title: Male_sham_4

description: trimmed fastq file


title: Male_IVF_4

description: trimmed fastq file

value: IVF


title: Male_IVF_6

description: trimmed fastq file


title: Female_Sham_4

description: trimmed fastq file

value: female


title: Female_Sham_5

description: trimmed fastq file


title: Female_Sham_3

description: trimmed fastq file


title: Male_IVF_5

description: trimmed fastq file


title: Male_IVF_3

description: trimmed fastq file


title: Female_Sham_2

description: trimmed fastq file


title: Female_IVF_1

description: trimmed fastq file


title: Female_SCNT_6

description: trimmed fastq file


title: Female_SCNT_4

description: trimmed fastq file


title: Female_SCNT_3

description: trimmed fastq file


title: Male_Donor_Cells

description: trimmed fastq file

value: donor


title: Female_IVF_2

description: trimmed fastq file


title: Female_Donor_Cells

description: trimmed fastq file


title: Female_SCNT_2

description: trimmed fastq file


title: Female_IVF_4

description: trimmed fastq file


title: Female_IVF_3

description: trimmed fastq file


title: Female_IVF_6

description: trimmed fastq file


title: Female_SCNT_5

description: trimmed fastq file


title: Male_IVF_2

description: trimmed fastq file


title: Female_IVF_5

description: trimmed fastq file


title: Male_IVF_1

description: trimmed fastq file


title: o SP

city: Illkirch

first: Frederic

last: Coin

address: 1, rue laurent fries

department: Functional Genomics and Cancer

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

molecule: polyA RNA

source_name: RNA extracts from transformed human fibroblast cellsl treated with SP

extract_protocol:
none provided by the sumbitter
none provided by the sumbitter

value: SP


title: o TPL

source_name: RNA extracts from transformed human fibroblast cells treated with TPL

value: TPL


title: A TPL

source_name: RNA extracts from transformed human fibroblast cells treated with TPL and retinoic acid for 6hrs

value: TPL and retinoic acid for 6hrs


title: A SP

source_name: RNA extracts from transformed human fibroblast cells treated with either SP and retinoic acid for 6hrs

value: either SP and retinoic acid for 6hrs


title: o DMSO

source_name: RNA extracts from transformed human fibroblast cells treated with DMSO

value: DMSO


title: Female_Sham_1

description: trimmed fastq file


title: Hct116_Lena_repl3

city: Boston

first: Eric

middle: S

last: Fischer

state: Massachusetts

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Reads were aligned to the GRCh37/hg19 reference genome using the QuasR Bioconductor package (PMID: 25417205, version 1.12.0) by the qAlign function with parameters maxHits=1 (reporting only uniqely mapped reads) and splicedAlignment=TRUE (spiced alignment using SpliceMap PMID: 20371516).
For each gene, alignments overlapping any of its exons (obtained from UCSC known gene annotation for hg19, as available in the TxDb.Hsapiens.UCSC.hg19.knownGene Bioconductor package) were counted using the QuasR qCount function with default parameters.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Comma-seperated text file with gene annotation (Entrez gene identifier, gene description, gene symbol, number of exonic bases) and raw alignment counts for each gene and sample.
Supplementary_files_format_and_content: matrix table with raw alignment counts per gene for all samples

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and L-glutamine

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following manufacturers instructions
Libraries were prepared using ScriptSeq v2 total RNA library preparation kit following manufacturers instructions

treatment_protocol: Cells were grown as monolayer adherent culture, passaged at ~ 80% confluency. Cells were treated with either 30 µM Lenalidomide or an equivalent amount of DMSO as control. Compound and DMSO were diluted in prewarmed DMEM before addition to the medium.

value: Lenalidomide


title: Hct116_DMSO_repl4


title: Female_SCNT_1

description: trimmed fastq file


title: Hct116_Lena_repl4


title: Hct116_Lena_repl1


title: Hct116_Lena_repl2


title: Hct116_DMSO_repl3


title: Hct116_DMSO_repl2


title: Hct116_DMSO_repl1


title: IMR90 senescent 2

city: Rotterdam

first: Peter

last: de Keizer

address: Wytemaweg 80

department: Molecular Genetics

country: Netherlands

institute: Erasmus University Medical Center

data_processing:
Raw reads were aligned to the human hg19 reference genome using the NARWHAL automation software (Brouwer et al., 2012).
The analysis of the aligned sequencing dataset was performed with TRAP(Derks et al., 2015)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

source_name: Lung

growth_protocol: IMR90 cells were cultured in high glucose Dulbecco’s Modified Eagle’s Medium (Lonza), supplemented with 10% Fetal Calf Serum, penicillin/streptomycin and 0.05% glutamine and were kept at 5% CO2, 3% O2.

extract_protocol:
Total RNA was isolated using Qiazol Lysis Reagent (Qiagen) and purified with the miRNeasy kit (Qiagen).  IlluminaTruSeq mRNA sample preparation kit was used for total RNA enrichment for sequencing poly(A) RNAs .
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were exposed to 10 Gy Gamma rays to induce senescence

value: Fibroblasts

tag: population doublings


title: IMR90 senescent 3


title: IMR90 3


title: IMR90 2


title: IMR90 1


title: IMR90 senescent 1


title: H3K27me3 t5 no-exposure

source_name: neutrophil progenitor cells

growth_protocol: CD34-positive cells isolated from human cord blood of mixed donors were obtained from AllCells (Alabama, United States). Culturing of cells was routinely performed at 37°C in a humidified atmosphere with 5% CO2. CD34+ cells were propagated in Stemline II medium expansion medium (Stemcell technology) supplemented with 100 ng/mL thrombopoietin, 100 ng/mL stem cell factor, 10 ng/mL Flt3-ligand (Peprotech), 5000 U/mL Penicillin and 5 mg/mL Streptomycin (Sigma-Aldrich) for four days. For the neutrophilic differentiation, expanded CD34+ cord blood cells were seeded at a cell density of 10e5 cells/mL in Stemline II medium supplemented with 100 ng/mL stem cell factor, 10 ng/mL Flt3-ligand, 100 ng/mL G-CSF (Peprotech), 5000 U/mL Penicillin and 5 mg/mL Streptomycin (Sigma-Aldrich) and cultured for 5 days. Every second day, fresh cell culture medium was added (1:2 dilution).

treatment_protocol: During neutrophilic differentiation, cells were exposed to a powerline-simulating ELF-MF (50 Hz, 1 mT, 5’ on/10’ off) or to the sham control (50 Hz, 7 µT, 5’ on/10’ off). Control differentiations were done in parallel, either in a µ-metal shielded compartment inside the exposure incubator or in different incubator.

value: human cord blood CD34+ cell-derived neutrophil progenitor cells

tag: exposure conditions

value: no exposure

tag: time of differentiation and exposure

value: 5 days

tag: differentiation

value: 100 ng/ml G-CSF


title: H3K27me3 t5 sham_2

value: ELF-MF (50Hz powerline, 0.007 mT, 5' on/10' off)

tag: chip antibody


title: H3K27me3 t5 ELF-MF_2

value: ELF-MF (50Hz powerline, 1 mT, 5' on/10' off)


title: H3K27me3 t5 sham_1


title: A DMSO

source_name: RNA extracts from transformed human fibroblast cells treated with DMSO and retinoic acid for 6hrs

tag: treatment

value: DMSO and retinoic acid for 6hrs


title: Input t5

value: equal pool of ELF-MF, sham and no exposure


title: H3K27me3 t5 ELF-MF_1


title: H3K4me2 t5 sham_1

value: human cord blood CD34+ cells-derived neutrophil progenitor cells


title: H3K4me2 t5 sham_2


title: H3K27me3 CD34+_2

source_name: human cord blood CD34+ cells

value: expanded human cord blood CD34+ cells

value: 0 days

value: no


title: H3K4me2 t5 no-exposure


title: Input CD34+ cells


title: H3K4me2 t5 ELF-MF_2


title: H3K4me2 CD34+_1


title: S1-NS1mTAD2 Dox 5-3_RNA-seq

city: Kansas City

first: Jianming

last: Qiu

state: KS

address: 3901 rainbow blvd

department: Microbiology

institute: University of Kansas Medical Center

description: l

data_processing:
Illumina Casava1.7 software used for basecalling.
Mapping of RNA-seq reads, transcript assembly, and abundance estimation were conducted using Tuxedo Suite pipeline (TopHat v2.0.9/Cufflinks v2.2.1) and reported with Fragments Per Kilobase of exon per Million fragments mapped (FPKM)
Cuffdiff was used to calculate statistical significance changes to gene expression between NS1-S1 and NS1mTAD2-S1 cell lines with or without Dox induction
Genome_build: GRCh38.83
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: UT7/Epo-S1 cells

growth_protocol: UT7/Epo-S1 cells stably expressing NS1 (NS1-S1) and NS1mTAD2 (NS1mTAD2-S1) were cultured in DMEM medium containing 10% fetal bovine serum (FBS) and 2 units per ml of erythropoietin (Amgen, Thousand Oaks, CA) under normoxia and 5% CO2 at 37 oC.

extract_protocol:
after two days Dox treatment, treated and un-treated cell lines were pelleted and total RNA was extracted using Trizol reagent. NEBNext Ultra RNA library Prep Kit (NEB, catalog# E7530L)  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the cell lines were treated with 5 mg/ml doxycycline (Dox) for inducing the expression of NS1 and NS1mTAD2 proteins, with un-treated cell as control

tag: expressed protein

value: express B19 NS1mTAD2


title: H3K27me3 CD34+_1


title: S1-NS1mTAD2 Dox 5-1_RNA-seq

description: j


title: S1-NS1mTAD2 Dox 0-3_RNA-seq

description: i

value: do not express B19 NS1mTAD2


title: S1-NS1mTAD2 Dox 5-2_RNA-seq

description: k


title: KDM6A WT rep 3

source_name: KDM6A WT

tag: tissue

value: Urothelial Bladder Carcinoma

tag: genotype

value: wildtype


title: S1-NS1mTAD2 Dox 0-1_RNA-seq

description: g


title: S1-NS1mTAD2 Dox 0-2_RNA-seq

description: h


title: S1-NS1 Dox 5-3_RNA-seq

description: f

value: express B19 NS1


title: S1-NS1 Dox 0-3_RNA-seq

description: c

value: do not express B19 NS1


title: S1-NS1 Dox 0-1_RNA-seq

description: a


title: S1-NS1 Dox 5-1_RNA-seq

description: d


title: S1-NS1 Dox 0-2_RNA-seq

description: b


title: CantonS 25 Rep 2

city: boston

first: Edward

last: Kravitz

state: ma

address: 220 longwood avenue

department: neurobiology

institute: Harvard medical school

description: Processed data file: RPKM_gene_level.txt

data_processing:
Sequencing was performed on Illumina HiSeq 2000.
Sequencing reads were mapped to Drosophila transcriptome (dm3 RefSeq annotation) using TopHat v2.0.4.
Gene expression counts were calculated using GenomicFeatures v1.18.7.
Calculation of expression values and differential expression analysis were performed using EdgeR package v3.8.6.
Genome_build: dm3 (BDGP Release 5)
Supplementary_files_format_and_content: RPKM_gene_level.txt: Tab-delimited text file includes RPKMs.

organism: Drosophila melanogaster

source_name: whole head, Canton-S, 25C

growth_protocol: Canton-S or Bully were raised at 19C or 25C.

extract_protocol:
Flies were frozen in liquid nitrogen. ~90 whole heads were collected for each sample and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: Canton-S (CS)

tag: developmental temperature

tag: age

value: 6 days

tag: Stage

value: socially naive adult

value: whole head


title: H3K4me2 t5 ELF-MF_1

data_processing:
ChIP-seq rads were aligned to hg19 using SMALT (v 0.6.2)
High quality alignments were extracted using samtools filter-mapQuality ">30"
domains were defined based on increased densities of center positions of ChIPped fragments using chipseq (http://ccg.vital-it.ch/chipseq/  )
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using bedGraphToBigWig

extract_protocol:
Whole cell lysates of crosslinked cells were sonicated, clarified and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols for  HiSeq platform

tag: cell type

value: ELF-MF (50Hz powerline, 1 mT, 5' on/10' off)

value: 5 days

value: 100 ng/ml G-CSF


title: Bully 25 Rep 1

source_name: whole head, Bully, 25C

value: Hyper-aggressive CS line (Bully)


title: Bully 19 Rep 2

source_name: whole head, Bully, 19C


title: CantonS 25 Rep 1


title: H3K4me2 CD34+_2

value: expanded human cord blood CD34+ cells

value: no exposure


title: Bully 25 Rep 2


title: Bully 19 Rep 1


title: nrpd1a no UV_rep2

city: Strasbourg

first: Jean

last: Molinier

address: 12 rue du General Zimmer

institute: IBMP-CNRS

description: small RNA seq

data_processing:
basecalling performed by FASTERIS company (HiSeq Control Software 2.2.38 - RTA 1.18.61.0 - CASAVA 1.8.2)
3' adapter removal performed by FASTERIS company
mapping performed on Arabidopsis genome (TAIR10) with bowtie (parameters -t -q -y -e 50 -n 0 -a --best --strata)
suppress reads overlapping miR coordinates (with bedtools intersectbed -f 0.9)
filtering reads of 21, 22-23, 24-25, 26-30, 31-40 nt with awk script
Genome_build: TAIR10
Supplementary_files_format_and_content: gff files contain the number of reads. Header names for the gff files : 1. Chromosome, 2. Source, 3. Region, 4. Start, 5. End, 6. Number of reads, 7. Strand, 8. Frame, 9. Annotation

organism: Arabidopsis thaliana

source_name: nrpd1a no UV

growth_protocol: 16/8 photoperiod (light/dark)

extract_protocol:
Total RNA were prepared using Trizol (Sigma)
According to FASTERIS company

treatment_protocol: UV-C treatment (3000 J/m2). Harvest 30 min after UV-C exposure

tag: developmental stage

value: 3 week-old plants

tag: growth condition

value: soil

value: no UV

value: seedlings


title: nrpd1a UV_rep2

description: small RNA seq

source_name: nrpd1a UV

value: UV


title: WT UV_rep3

description: small RNA seq

source_name: WT UV

value: WT Col-0


title: nrpd1a no UV_rep1

description: small RNA seq


title: CantonS 19 Rep 1

source_name: whole head, Canton-S, 19C


title: WT UV_rep4

description: small RNA seq


title: CantonS 19 Rep 2


title: nrpd1a UV_rep1

description: small RNA seq


title: WT UV_rep1

description: small RNA seq


title: WT no UV_rep2

description: small RNA seq

source_name: WT no UV


title: WT UV_rep2

description: small RNA seq


title: S1-NS1 Dox 5-2_RNA-seq

description: e

value: express B19 NS1


title: WT UV rep4

data_processing:
basecalling performed by FASTERIS company (HiSeq Control Software 2.2.38 - RTA 1.18.61.0 - CASAVA 1.8.2)
3' adapter removal performed by FASTERIS company
mapping performed on Arabidopsis genome (TAIR10) with bowtie (parameters -t -q -y -e 50 -n 0 -a --best --strata)
macs2 callpeak -t -c -n -g
Genome_build: TAIR10
Supplementary_files_format_and_content: gff files contain the number of reads for the enriched genomic regions after immunoprecipitation.  Header names for the gff files : 1. Chromosome, 2. Source, 3. IP vs input, 4. Start, 5. End, 6. Enrichment, 7. Strand, 8. Frame, 9. Group

extract_protocol:
Genomic DNA was prepared using the Macherey Nagel plant DNA extraction kit
According to FASTERIS company
DNA was immunoprecipitated using anti-CPD (Cyclobutane Pyrimidine Dimers, CAC-NM-DND-001, CosmoBio, USA)

treatment_protocol: UV-C treatment (3000 J/m2)

tag: ip antibody


title: WT UV rep3

value: anti-CPD (Cyclobutane Pyrimidine Dimers, CAC-NM-DND-001, CosmoBio, USA)


title: WT UV rep2


title: WT no UV rep2


title: WT input

source_name: WT input

value: none (input)


title: WT no UV rep1


title: Th17_Input

city: New York

first: Martin

middle: J.

last: Walsh

state: NY

address: One Gustave L. Levy Pl.

department: Structural and Chemical Biology

institute: Mount Sinai School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.4
read sequences were done QC filtering by FASTX ( -q 20 -p 90 )
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2
peaks were called using MACS version 1.4 using Input as control with the following setting: pvalue cutoff (1.00e-05), model fold (10, 30).
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using MACS.

source_name: primary T cells

growth_protocol: CD4+ T cells were purified from spleen. Naïve T cells were activated with plate bound anti-CD3 and anti-CD28 plus IL6(20ng/mL), TGFb(2.5ng/mL) . The cells were cultured for 48h to 72h before harvesting for further analysis.

extract_protocol:
Whole cell lysates were sonicated and protein-DNA complexes were isolated with antibodies.
ChIP-DNA was end repaired with T4 DNA polymerase and polynucleotide kinase. An A-base was added to the end-repaired DNA fragments. Solexa adaptors were ligated to the ChIP DNA fragments and 200-300bp size fractions were excised from 2% agarose gel stained with GelStar. Adaptor-modified fragments were enriched by 16 cycles of PCR amplification. The DNA library prep was validated in Bioanalyzer for quantity and size.

tag: strain

value: primary T cells

tag: chip-antibody


title: Th17_Smc1_ChIP-seq_group2

value: Smc1 (Bethyl; A300-055A)


title: Th17_Nipbl_ChIP-seq_group2

value: Nipbl (Bethyl; A301-779A)


title: Th17_Smc3_ChIP-seq_group2

value: Smc3 (Abcam; ab9263)


title: Th17_Input_group1

data_processing:
Basecalls performed using CASAVA version 1.4
read sequences were done QC filtering by FASTX ( -q 20 -p 90 )
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2
peaks were called using MACS version 1.4 using Input as control with the following setting: pvalue cutoff (1.00e-05), model fold (10, 30).
Genome_build: mm9
Supplementary_files_format_and_content: bed/peak files were generated using MACS.


title: Th17_WT_Brd4_ChIP-seq_group2

value: Brd4 (Bethyl; IHC-00396)


title: Tdrd6-/- 2

city: Dresden

first: Rolf

last: Jessberger

address: Fiedlerstraße 42

department: Institut für Physiologische Chemie, MTZ

country: Germany

institute: Medizinische Fakultät der TU Dresden

data_processing:
Basecalling: bcl2fastq 1.8.4
Alignment: Alignment of paired-end data against mm10 with gsnap version v2014-12-17; splice sites were supported by using Ensembl version 75 (gsnap -d mm10 --gunzip --use-sarray=1 -B 4 -t 16 -N 1 -s EnsemblGene-75.ss.mm10.iit -n 1 -A sam).
Intron counting: A flattened annotation file was created with DEXSeq (v1.16.10) and dexseq_count.py; bins were counted with dexseq_prepare_annotation.py
Splice site and exon counting: A collapsed annotation file was created with QoRTs (v1.0.1) and bins were counted with the package as well.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *intron.counts.txt: Tab-delimited text file includes intron counts.
Supplementary_files_format_and_content: *spliceJunction_Exon.counts.txt: Tab-delimited text file includes splice junction and exon counts.

source_name: testis, Tdrd6-/-

extract_protocol:
Testes from mice 20dpp were removed, hCD4+ cells were isolated via MACS and RNA was harvested from these cells using Trizol (Invitrogen) reagent according to manufacturer's instructions.
As a first step of library preparation, genomic DNA was removed from the total RNA with DNase I, followed by rRNA depletion using the Ribo-Zero™ Magnetic Gold Kit from Epicentre (an Illumina company). Afterwards, libraries were prepared by following the protocol for NEBNext® Ultra Directional RNA Library Prep Kit.

tag: genotype/variation

value: testis

value: hCD4+ cells


title: Th17_Brd4_ChIP-seq_group1


title: Tdrd6-/- 1


title: Tdrd6+/- 2

source_name: testis, Tdrd6+/-


title: Th17_Input_group2


title: IFNabRKO mesenteric lymph node, Sham 48h, replicate 3

city: Cambridge

first: Mukund

last: Varma

state: MA

address: 415 Main Street

institute: Broad Institute

data_processing:
Alignment with TopHat(v2.0.10)+Bowtie(0.12.9)
Sorting of aligned files using samtools (0.1.19)
Counting of transcripts using htseq
QC of RNASeq using RSeqC
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated file - counts matrix with gene symbols as rows and sample names as columns

source_name: mesenteric lymph node

extract_protocol:
RNA was extracted with with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared using the TruSeq® Stranded Total RNA with Ribo-ZeroTM Gold kit (Illumina) and sequenced using 50-base pair single-end reading on a HiSeq 2500 instrument (Illumina).

value: IFNabRKO

tag: stimulation

value: Sham

tag: stimulation time point

tag: replicate

tag: barcode

value: AGTTCC


title: WT mesenteric lymph node, Sham 48h, replicate 3

value: WT

value: AGTCAA


title: WT mesenteric lymph node, T1L virus 48h, replicate 3

value: T1L virus (10^8 PFU)

value: ATGTCA


title: Tdrd6+/- 1

tag: tissue


title: IFNabRKO mesenteric lymph node, T3D-RV virus 48h, replicate 3

tag: genotype

value: T3D-RV virus (10^8 PFU)

value: GTGAAA


title: IFNabRKO mesenteric lymph node, T3D-RV virus 48h, replicate 2

value: CTTGTA


title: WT UV rep1

value: 3 week-old plants

value: WT Col-0

tag: treatment

value: UV

value: anti-CPD (Cyclobutane Pyrimidine Dimers, CAC-NM-DND-001, CosmoBio, USA)

value: seedlings


title: WT mesenteric lymph node, T3D-RV virus 48h, replicate 2

value: GGCTAC


title: WT mesenteric lymph node, Sham 48h, replicate 2

value: CAGATC


title: IFNabRKO mesenteric lymph node, T3D-RV virus 48h, replicate 1

value: IFNabRKO

value: GCCAAT


title: WT mesenteric lymph node, T3D-RV virus 48h, replicate 1

value: ACAGTG


title: Th17_Stat3KO_Brd4_ChIP-seq_group2

value: Brd4 (Bethyl; IHC-00396)

value: primary T cells


title: IFNabRKO mesenteric lymph node, Sham 48h, replicate 1

value: Sham

value: CGATGT


title: WT mesenteric lymph node, T1L virus 48h, replicate 2

value: WT

value: T1L virus (10^8 PFU)

value: GATCAG


title: WT mesenteric lymph node, Sham 48h, replicate 1

value: ATCACG


title: Thy1.1+YFP+

city: Beijing

first: xuyu

last: zhou

address: 1st West Beichen, Chaoyang

institute: Institute of Microbiology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of  the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were  aligned to the reference genome using TopHat  v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time.(Trapnell, Cole, et al., Nat. Biotechnol 2010)
Genome_build: mm9
Supplementary_files_format_and_content: excel files include FPKM values for each sample

source_name: lymph node and spleen

extract_protocol:
Lymphocytes were isolated from spleens and lymph nodes of Foxp3 ΔCNS1-Cre-Rosa26-YFP mice and furthur enriched for CD4+ T cells using magnetic beads.  Thy1.1-YFP+ and Thy1.1+YFP+ Treg cells were sorted with purity of typically >97% and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: stain

value: lymph node and spleen

value: 6 to 8 weeks

value: Foxp3 dCNS1-Cre-R26-YFP


title: WT mesenteric lymph node, T3D-RV virus 48h, replicate 3

value: T3D-RV virus (10^8 PFU)

value: GTCCGC


title: IFNabRKO mesenteric lymph node, T1L virus 48h, replicate 1

value: TGACCA


title: Th17_Brd2_ChIP-seq_group1

value: Brd2 (Bethyl; IHC-00612)


title: WT mesenteric lymph node, T1L virus 48h, replicate 1

value: TTAGGC


title: IFNabRKO mesenteric lymph node, Sham 48h, replicate 2

value: IFNabRKO

value: ACTTGA


title: ChIP-seq Rpc4 , ZT14, rep2, Maf1 KO

city: Lausanne

first: Francois

last: Mange

state: VAUD

address: Genopode building

department: Center for Integrative Genomic

institute: University of Lausanne

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of Maf1 mice collected at ZT14

data_processing:
Alignment : Tags from both Mouse and human DNA with perfect matches were directly extracted from the eland_extended mode of ELAND (v2e in the Illumina CASSAVA pipeline version 1.82) output, as previously described (Bonhoure et al, 2014).
Alignment : Tags with multiple matches were mapped onto the Mouse genome build Mm9 using the fetchGWI software and allowing 500 repeats on the genome. The tags mapping more than once onto the genome were then attributed a weight corresponding to the number of times the tag was sequenced divided by the number of genomic matches.
Pol III scores were calculated for bins including the annotated gene body ±150bp as the mean log2 (IPtag count/INPUTtag count) of two replicates per condition.
Genome_build: UCSC Mm9 and Hg19
Supplementary_files_format_and_content: bedgraph

source_name: Liver

extract_protocol:
ChiP-seq was performed as described (Bonhoure et al., 2014)
Libraries were prepared with 12 ng of ChIP DNA (ChIP-seq) or genomic DNA (INPUT) according to manufacturer's's instruction with the ChIP-seq DNA Sample prep kit” (Illumina, 1003473)

value: liver

tag: circadian clock

value: Maf1 KO

tag: age

value: 12-14 weeks


title: INPUT, ZT06, rep2, Maf1 KO

description:
ChIP-Seq input
Liver homonegenate of Maf1 mice collected at ZT06


title: INPUT, ZT10, rep2, Maf1 KO

description:
ChIP-Seq input
Liver homonegenate of Maf1 mice collected at ZT10


title: Thy1.1-YFP+


title: INPUT, ZT18, rep2, Maf1 KO

description:
ChIP-Seq input
Liver homonegenate of Maf1 mice collected at ZT18


title: INPUT, ZT22, rep2, Maf1 KO

description:
ChIP-Seq input
Liver homonegenate of Maf1 mice collected at ZT22


title: INPUT, ZT22, rep1, Maf1 KO


title: INPUT, ZT14, rep2, Maf1 KO

description:
ChIP-Seq input
Liver homonegenate of Maf1 mice collected at ZT14


title: INPUT, ZT06, rep1, Maf1 KO


title: INPUT, ZT02, rep1, Maf1 KO

description:
ChIP-Seq input
Liver homonegenate of Maf1 mice collected at ZT02


title: ChIP-seq Rpc4 , ZT10, rep2, Maf1 KO

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of Maf1 mice collected at ZT10


title: ChIP-seq Rpc4 , ZT06, rep2, Maf1 KO

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of Maf1 mice collected at ZT06


title: ChIP-seq Rpc4 , ZT18, rep2, Maf1 KO

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of Maf1 mice collected at ZT18


title: INPUT, ZT02, rep2, Maf1 KO


title: ChIP-seq Rpc4 , ZT22, rep2, Maf1 KO

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of Maf1 mice collected at ZT22


title: IFNabRKO mesenteric lymph node, T1L virus 48h, replicate 3

value: CCGTCC


title: ChIP-seq Rpc4 , ZT02, rep2, Maf1 KO

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of Maf1 mice collected at ZT02


title: INPUT, ZT18, rep1, Maf1 KO


title: INPUT, ZT14, rep1, Maf1 KO


title: INPUT, ZT18, rep2, Arntl KO

description:
ChIP-Seq input
Liver homonegenate of Arntl mice collected at ZT18

value: Arntl KO


title: INPUT, ZT14, rep2, Arntl KO

description:
ChIP-Seq input
Liver homonegenate of Arntl mice collected at ZT14


title: INPUT, ZT02, rep2, Arntl KO

description:
ChIP-Seq input
Liver homonegenate of Arntl mice collected at ZT02


title: ChIP-seq Rpc4 , ZT18, rep2, Arntl KO

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of Arntl mice collected at ZT18


title: ChIP-seq Rpc4 , ZT18, rep1, Maf1 KO


title: ChIP-seq Rpc4 , ZT10, rep2, Arntl KO

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of Arntl mice collected at ZT10


title: ChIP-seq Rpc4 , ZT06, rep2, Arntl KO

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of Arntl mice collected at ZT06


title: ChIP-seq Rpc4 , ZT10, rep1, Maf1 KO


title: ChIP-seq Rpc4 , ZT14, rep1, Maf1 KO

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of Maf1 mice collected at ZT14


title: INPUT, ZT10, rep1, Maf1 KO

description:
ChIP-Seq input
Liver homonegenate of Maf1 mice collected at ZT10


title: ChIP-seq Rpc4 , ZT22, rep2, Arntl KO

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of Arntl mice collected at ZT22


title: WT no UV_rep1

description: small RNA seq

value: 3 week-old plants

value: soil

value: WT Col-0

value: no UV

value: seedlings


title: ChIP-seq Rpc4 , ZT06, rep1, Maf1 KO


title: ChIP-seq Rpc4 , ZT14, rep2, Arntl KO

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of Arntl mice collected at ZT14


title: INPUT, ZT06, rep2, Arntl KO

description:
ChIP-Seq input
Liver homonegenate of Arntl mice collected at ZT06


title: ChIP-seq Rpc4 , ZT02, rep2, Arntl KO

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of Arntl mice collected at ZT02


title: ChIP-seq Rpc4 , ZT22, rep1, Maf1 KO


title: INPUT, ZT02, rep1, Arntl KO


title: ChIP-seq Rpc4 , ZT02, rep1, Maf1 KO


title: ChIP-seq Rpc4 , ZT22, rep1, Arntl KO


title: INPUT, ZT22, rep1, Arntl KO

description:
ChIP-Seq input
Liver homonegenate of Arntl mice collected at ZT22


title: INPUT, ZT18, rep1, Arntl KO


title: INPUT, ZT10, rep1, Arntl KO

description:
ChIP-Seq input
Liver homonegenate of Arntl mice collected at ZT10


title: INPUT, ZT14, rep1, Arntl KO


title: ChIP-seq Rpc4 , ZT10, rep1, Arntl KO


title: INPUT, ZT10, rep2, Arntl KO


title: ChIP-seq Rpc4 , ZT06, rep1, Arntl KO


title: INPUT, ZT22, rep2, Arntl KO


title: ChIP-seq Rpc4 , ZT02, rep1, Arntl KO


title: INPUT, ZT22, rep2, CONSTANTLY FED

description:
ChIP-Seq input
Liver homonegenate of constantly fed  mice collected at ZT22

value: wild type


title: INPUT, ZT26, rep2, CONSTANTLY FED

description:
ChIP-Seq input
Liver homonegenate of constantly fed  mice collected at ZT26


title: INPUT, ZT06, rep2, CONSTANTLY FED

description:
ChIP-Seq input
Liver homonegenate of constantly fed  mice collected at ZT06


title: INPUT, ZT10, rep2, CONSTANTLY FED

description:
ChIP-Seq input
Liver homonegenate of constantly fed  mice collected at ZT10


title: INPUT, ZT14, rep1, CONSTANTLY FED

description:
ChIP-Seq input
Liver homonegenate of constantly fed  mice collected at ZT14


title: INPUT, ZT14, rep2, CONSTANTLY FED


title: INPUT, ZT06, rep1, Arntl KO


title: INPUT, ZT26, rep1, CONSTANTLY FED


title: INPUT, ZT22, rep1, CONSTANTLY FED


title: INPUT, ZT06, rep1, CONSTANTLY FED


title: INPUT, ZT02, rep1, CONSTANTLY FED

description:
ChIP-Seq input
Liver homonegenate of constantly fed  mice collected at ZT02


title: INPUT, ZT10, rep1, CONSTANTLY FED


title: ChIP-seq Rpc4 , ZT26, rep2, CONSTANTLY FED

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of constantly fed  mice collected at ZT26


title: ChIP-seq Rpc4 , ZT22, rep2, CONSTANTLY FED

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of constantly fed  mice collected at ZT22


title: ChIP-seq Rpc4 , ZT18, rep1, Arntl KO

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of Arntl mice collected at ZT18


title: ChIP-seq Rpc4 , ZT14, rep1, Arntl KO


title: ChIP-seq Rpc4 , ZT18, rep2, CONSTANTLY FED

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of constantly fed  mice collected at ZT18


title: ChIP-seq Rpc4 , ZT10, rep2, CONSTANTLY FED

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of constantly fed  mice collected at ZT10


title: ChIP-seq Rpc4 , ZT14, rep2, CONSTANTLY FED

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of constantly fed  mice collected at ZT14


title: ChIP-seq Rpc4 , ZT02, rep2, CONSTANTLY FED

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of constantly fed  mice collected at ZT02


title: ChIP-seq Rpc4 , ZT06, rep2, CONSTANTLY FED

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of constantly fed  mice collected at ZT06


title: ChIP-seq Rpc4 , ZT14, rep1, CONSTANTLY FED


title: INPUT, ZT18, rep2, CONSTANTLY FED

description:
ChIP-Seq input
Liver homonegenate of constantly fed  mice collected at ZT18


title: ChIP-seq Rpc4 , ZT26, rep1, CONSTANTLY FED


title: ChIP-seq Rpc4 , ZT22, rep1, CONSTANTLY FED


title: INPUT, ZT02, rep2, CONSTANTLY FED


title: INPUT, ZT18, rep1, CONSTANTLY FED


title: INPUT, ZT22, rep2, CONTROL

description:
ChIP-Seq input
Liver homonegenate of control mice collected at ZT22


title: INPUT, ZT14, rep2, CONTROL

description:
ChIP-Seq input
Liver homonegenate of control mice collected at ZT14


title: INPUT, ZT18, rep2, CONTROL

description:
ChIP-Seq input
Liver homonegenate of control mice collected at ZT18


title: INPUT, ZT10, rep2, CONTROL

description:
ChIP-Seq input
Liver homonegenate of control mice collected at ZT10


title: INPUT, ZT06, rep2, CONTROL

description:
ChIP-Seq input
Liver homonegenate of control mice collected at ZT06


title: INPUT, ZT02, rep2, CONTROL

description:
ChIP-Seq input
Liver homonegenate of control mice collected at ZT02


title: ChIP-seq Rpc4 , ZT02, rep1, CONSTANTLY FED


title: ChIP-seq Rpc4 , ZT14, rep2, CONTROL

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of control mice collected at ZT14


title: ChIP-seq Rpc4 , ZT22, rep2, CONTROL

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of control mice collected at ZT22


title: ChIP-seq Rpc4 , ZT10, rep2, CONTROL

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of control mice collected at ZT10


title: ChIP-seq Rpc4 , ZT02, rep2, CONTROL

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of control mice collected at ZT02


title: ChIP-seq Rpc4 , ZT06, rep2, CONTROL

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of control mice collected at ZT06


title: INPUT, ZT18, rep1, CONTROL


title: INPUT, ZT06, rep1, CONTROL


title: ChIP-seq Rpc4 , ZT18, rep1, CONSTANTLY FED

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of constantly fed  mice collected at ZT18


title: INPUT, ZT14, rep1, CONTROL


title: ChIP-seq Rpc4 , ZT10, rep1, CONSTANTLY FED

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of constantly fed  mice collected at ZT10


title: INPUT, ZT22, rep1, CONTROL


title: INPUT, ZT10, rep1, CONTROL


title: ChIP-seq Rpc4 , ZT06, rep1, CONSTANTLY FED


title: ChIP-seq Rpc4 , ZT18, rep1, CONTROL

description:
ChIP-Seq antibody: anti-Rpc4 (Bonhoure et al, 2014)
Liver homonegenate of control mice collected at ZT18


title: ChIP-seq Rpc4 , ZT10, rep1, CONTROL


title: INPUT, ZT02, rep1, CONTROL


title: ChIP-seq Rpc4 , ZT02, rep1, CONTROL


title: ChIP-seq Rpc4 , ZT06, rep1, CONTROL


title: ERKO oil 3

city: NEW BRUNSWICK

first: Troy

middle: A.

last: Roepke

state: NJ - New Jersey

address: 84 LIPMAN DR

department: Animal Sciences

institute: Rutgers University

data_processing:
Illumina HiSeq2500
The RNA-seq data were mapped to the mouse genome (mm10) using TopHat v2.0 to produce mapped reads using the mouse gene transfer format (gtf file) as a guide.
Differentially expressed genes were identified using Cuffdiff.
Subsequent statistical analyses among WT, KIKO, and ERKO was performed using the Bioconductor package cummeRbund (Bioconductor, Boston, MA, USA).
To determine if there were any outliers in biological replicates, principle components analysis (PCA) and scatter matrices were evaluated.
Genes that were differentially regulated met the following guidelines: p < 0.05; fragments per kilobase of transcript per million mapped reads (FPKM) values > 1. In addition, we filtered out genes that had a FC > 1.5 after data processing included in the spreadsheets.
Genome_build: mm10
Supplementary_files_format_and_content: Plain text files are constructed for each genotyp, so there are a total of 3 files. Each file contains FPKM values. The Sample 1 are oil-treated and 2 are E2-treated.

source_name: Arcuate nucleus

extract_protocol:
The arcuate nucleus was microdissected following sacrifice and placed in RNA later prior to storage at -80 degrees C. RNA was extracted using Ambion RNAqueous® Micro Kits (Life Technologies, Inc., Carlsbad, CA, USA) according to the manufacturer’s protocol. RNA was run on a Nanodrop and a Agilent Bioanalyzer prior to sending out for sequencing.
Sequencing was conducted at JP Sulzberger Genome Center using an Illumina HiSeq2500

treatment_protocol: wild-type. ERalpha KO and ERalpha KIKO females were ovariectomized followed by injections of either oil or 250 ng of estradiol benzoate on day 5 post-ovx and injections on day 6 post ovx of either oil or 1500 ng of estradiol benzoate. All females were decapitated 24 hr after day 6 injection after 1 hr fast.

value: ERKO

value: Arcuate nucleus

value: oil


title: ChIP-seq Rpc4 , ZT14, rep1, CONTROL


title: ChIP-seq Rpc4 , ZT22, rep1, CONTROL


title: ERKO E2 2


title: ERKO E2 3


title: ERKO oil 1


title: ERKO E2 1


title: KIKO E2 2

value: KIKO


title: KIKO oil 3


title: ChIP-seq Rpc4 , ZT18, rep2, CONTROL


title: KIKO oil 1


title: KIKO oil 2


title: WT E2 3

value: WT


title: WT oil 1


title: WT oil 2


title: WT oil 3


title: KIKO E2 1


title: WT E2 2


title: Input DNA from postnatal cortex

city: Helsinki

first: Gulayse

last: Ince Dunn

state: Finland

address: Haartmaninkatu 8

department: Stem Cells and Metabolism Program

country: Finland

institute: University of Helsinki

data_processing:
Fastq Groomer (Galaxy tool version 1.0.4)
Map with Bowtie for Illumina (Galaxy tool version 1.1.2)
Remove duplicates (Galaxy tool version 1.0.0)
BAM-to-SAM (Galaxy tool version 1.0.3)
Filter SAM (Galaxy tool version 1.0.0)
MACS (Galaxy tool version 1.0.1), tag size 50, band width 200, p-value cutoff for peak detection: 10E-05
MACS (Galaxy tool version 1.0.1), MFOLD ratio:20, extend tag: -1, resolution for saving wiggle files: 10, 3 levels of regions around the peak region to calculate the maximum lambda as local lambda: 1000,5000,10000
Genome_build: mm10
Supplementary_files_format_and_content: wig and bed files
Supplementary_files_format_and_content: [.txt] The overlapping sequences from three separate NeuroD2 ChIP-Seq experiments (with three different antibodies) are presented in this file.

source_name: Input DNA from postnatal cortex

growth_protocol: mouse were kept under standard conditions in their homecages.

extract_protocol:
Tissue was cross-linked by 10 min of 1% formaldehyde treatment. After IP, stringent washes, and proteinase K treatment, DNA was extracted by standard phenol-chloroform extraction and ethanol precipitation.
Library was prepared for the single end read Illumina HiSeq 2500 platform by Genewiz, Inc.

treatment_protocol: Mice did not recieve any treatment

value: BALB/c

value: P0 pup

value: postnatal cortex

tag: chip antibody

value: none (input)


title: WT E2 1


title: GFP ChIP-SEQ from postnatal cortex

description:
This dataset was used as the control file during MACS peak identification, therefore a processed version of it does not exist
GFP-P0-ChIP-SEQ-antibody1

source_name: GFP ChIP-SEQ from postnatal cortex

tag: developmental stage

value: GFP antibody (Santa Cruz, sc-8334, H0612)


title: NeuroD2 ChIP-SEQ from postnatal cortex 1

source_name: NeuroD2 ChIP-SEQ from postnatal cortex

value: NeuroD2 antibody (Abcam, ab168932, GR161014-2)


title: IFNabRKO mesenteric lymph node, T1L virus 48h, replicate 2

value: IFNabRKO

value: T1L virus (10^8 PFU)

value: TAGCTT


title: NeuroD2 ChIP-SEQ from postnatal cortex 2

value: NeuroD2 antibody (Abcam, ab104430, GR94291-1)


title: NeuroD2 ChIP-SEQ from postnatal cortex 3

value: NeuroD2 antibody (Abcam, ab109406, YK010204CS)


title: ERKO oil 2


title: SJMMMB044252_X1-WT-GNP-Myc_Gfi1-6835-tumor-rep4

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: WT mouse GNP with Myc and Gfi1 overexpression

data_processing:
Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (curtadapt) and mapped to the mouse mm9 genome by a pipeline that serially  employs STAR and BWA
Mapped reads were counted with HTSEQ
voom TMM normalized and contrasted using the empirical Bayes pipeline limma in R 3.2.3
Genome_build: mm9
Supplementary_files_format_and_content: count files are txt format files that contain raw read counts that map  to  transcripts for each defined gene.

source_name: GNP granule neural precurser

growth_protocol: G3 MB tumorsphere cells were infected with retroviral vectors for 2 days, and FACS was usedto isolate the RFP+/GFP+ fraction. Cells were expanded in culture, harvested and suspended in Matrigel (BD Bioscience) before 5 x 105 cells were transplanted into the cerebral cortices of CD-1 nu/nu recipient

extract_protocol:
RNA was extracted from mouse G3 MB and Ezh2-deleted tumorsphere cells and tumor chunks using Trizol
The total RNA stranded library prepared from the final PCR products of indexed samples was subjected to 300 bp paired-end sequencing

treatment_protocol: Not applicable

tag: expression modification

value: Gfi1 OE


title: SJMMMB044251_X1-WT-GNP-Myc_Gfi1-6834-tumor-rep3


title: SJMMMB044250_X1-WT-GNP-Myc_Gfi1-6833-tumor-rep2


title: SJMMMB044249_X1-WT-GNP-Myc_Gfi1-6832-tumor-rep1


title: SJMMMB042178_X1-19251-Gfi1OE-TP-rep8

description: G3 mouse tumor model with  Gfi1 overexpression

source_name: mouse tumor


title: SJMMMB042177_X1-19251-Gfi1OE-TP-rep8


title: KIKO E2 3


title: SJMMMB042176_X1-19251-Gfi1OE-TP-rep8


title: SJMMMB042175_X1-19251-Gfi1OE-TP-rep8


title: SJMMMB042174_X1-19251-Gfi1OE-TP-rep8


title: SJMMMB042173_X1-19251-Gfi1OE-TP-rep8


title: SJMMMB042167_X1-19251-Control-TP-rep3

description: baseline MYC amplified G3 mouse tumor model

value: control


title: SJMMMB042171_X1-19251-Gfi1OE-TP-rep8


title: SJMMMB042170_X1-19251-Control-TP-rep6


title: SJMMMB018132_X9-19568-Ezh2-KO-Tumor-rep-3

description: G3 mouse tumor model with EzH2 knocked out

value: Ezh2 KO


title: SJMMMB042166_X1-19251-Control-TP-rep2


title: SJMMMB018132_X8-19568-Ezh2-KO-Tumor-rep-2


title: SJMMMB042165_X1-19251-Control-TP-rep1


title: SJMMMB018132_X12-19568-Ezh2-KO-Ezh2-OE-Tumor-rep3

description: G3 mouse tumor model with EzH2 knockout and Ezh2 overexpression rescue

value: Ezh2 KO and Ezh2 OE


title: SJMMMB042169_X1-19251-Control-TP-rep5


title: SJMMMB018132_X5-19568-Cas9-Ezh2-OE-Tumor-rep2

description: G3 mouse tumor model with  Ezh2 overexpression

value: Ezh2 OE


title: SJMMMB018132_X1-19568-Cas9-Tumor-rep1

value: Cas9 control


title: SJMMMB018132_X6-19568-Cas9-Ezh2-OE-Tumor-rep3


title: SJMMMB018132_X3-19568-Cas9-Tumor-rep3


title: SJMMMB018132_X2-19568-Cas9-Tumor-rep2


title: SJMMMB016797_X5-19568-Ezh2-KO-Tumor-rep2


title: SJMMMB018132_X7-19568-Ezh2-KO-Tumor-rep-1


title: SJMMMB018132_X10-19568-Ezh2-KO-Ezh2-OE-Tumor-rep1


title: SJMMMB016797_X1-19568-Cas9-Tumor-rep1


title: SJMMMB016797_X6-19568-Ezh2-KO-Tumor-rep3


title: SJMMMB016796_X6-19554-Ezh2-KO-Tumor-rep3


title: SJMMMB042172_X1-19251-Gfi1OE-TP-rep8


title: SJMMMB016797_X4-19568-Ezh2-KO-Tumor-rep1


title: SJMMMB016797_X3-19568-Cas9-Tumor-rep3


title: SJMMMB016796_X4-19554-Ezh2-KO-Tumor-rep1


title: SJMMMB016796_X5-19554-Ezh2-KO-Tumor-rep2


title: SJMMMB016795_X6-19251-Ezh2-KO-Tumor-rep3


title: SJMMMB018132_X4-19568-Cas9-Ezh2-OE-Tumor-rep1


title: SJMMMB016796_X2-19554-Cas9-Tumor-rep2


title: SJMMMB016796_X3-19554-Cas9-Tumor-rep3


title: SJMMMB016795_X5-19251-Ezh2-KO-Tumor-rep2


title: SJMMMB016796_X1-19554-Cas9-Tumor-rep1


title: SJMMMB016795_X4-19251-Ezh2-KO-Tumor-rep1


title: SJMMMB016795_X1-19251-Cas9-Tumor-rep1


title: NSCas9Gfi1

data_processing:
We used BWA (version 0.5.9-r26-dev, default parameter) to align the reads to the mouse mm9 genome
marked duplicated reads with Picard with only nonduplicated reads kept by samtools
To control the quality of the data and estimate the fragment size, the nonduplicated version of SPP (version 1.11) was used to draw cross-correlation with support of R (version 2.14.0)
peaks were called using Sicer V1.1
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing locations of defined peaks

source_name: mouse neurospheres

extract_protocol:
Briefly, 5-7 x 107 crosslinked  cells were resuspended in 10 ml buffer 1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM  EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x Sigma protease inhibitor) and  incubated on ice for 10 minutes. Samples were pelleted at 1,350xg for 5 minutes, resuspended in  10 ml buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x  Sigma protease inhibitor) and incubated on ice for 10 minutes. Pelleted samples were  resuspended in 2 ml Covaris sonication buffer (10 mM Tris-HCL, pH 8.0, 1 mM EDTA, 0.1%  SDS, 1x Sigma protease inhibitor) and sonicated using a Covaris E220 focused ultrasonicator.  Samples were diluted with 5 volumes of buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1  mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 1% Triton X-100, 1x Sigma protease  inhibitor). Chromatin was subjected to ChIP using rabbit polyclonal antibodies.
Libraries were prepared according to Illumina's instructions

value: Gfi1 Abcam cat #:ab21061


title: NSSuz12F2Gfi1


title: SJMMMB016797_X2-19568-Cas9-Tumor-rep2


title: SJMMMB016795_X2-19251-Cas9-Tumor-rep2


title: Tumor cells Ezh2KO-Input

source_name: mouse tumor cells

value: Input


title: SJMMMB016795_X3-19251-Cas9-Tumor-rep3


title: NSCas9U6_input


title: NSCas9Suz12F1

value: Cas9 Clontech cat #:632607


title: Tumor cells Ezh2KO-H3K4me3

value: H3K4me3 Abcam cat #:Ab8580


title: NSCas9U6


title: Tumor cells Cas9-Input


title: Tumor cells Ezh2KO-H3K27me

value: H3K27me3 Ali Shilatifard’s lab cat #:9733S


title: Sig70 in E. coli, exponential aerobic growth, rifampicin applied for 20 minutes, replicate 2 (run 423)

city: Madison

first: Rene

last: Welch

state: Wisconsin

address: 626 Johnson St.

department: Statistics

institute: University of Wisconsin-Madison

data_processing:
library strategy: ChIP-exo
Samples 931, 933, 935 and 937 were aligned with bowtie (V 1.1.2) with parameters  --wrapper basic-0 -q -m 1 -l 55 -k 1 -5 3 -3 40 --best -S -p 24, and samples 1311, 1314, 1317 and 1320 were aligned with bowtie (V 1.1.2) with paramters --wrapper basic-0 -q -m 1 -v 2 --best -p 24 -S
Genome_build: K12 - MG1655
Supplementary_files_format_and_content: Each wig file contains the alignd reads of each ChIP-exo sample.

organism: Escherichia coli

source_name: Sig70 in E. coli_exponential aerobic growth_rifampicin

extract_protocol:
The samples were sonicated for a total of 16 minutes and 50 uL protein A/G sepharose. All reactions are performed in an Eppendorf ThermalMixerR while being mixed at 1.4k x rpm. After each reaction, the sepharose was washed with 1 mL of each of the following buffers, leaving 50-100 uL buffer above the sepharose in-between each wash : 1x TE : 10mM Tris-HCl, pH 8.0 + 1 mM EDTA ; 1 x High Salt - 1M NaCl (1% Triton X-100, 50 mM HEPES, pH 8.0, 2 mM EDTA, 0.1% sodium deoxycholate and 1M NaCl) ; 1x Wash Buffer 2 (1% Triton X-100, 50 mM HEPES, pH 8.0, 2 mM EDTA, 0.1% sodium deoxycholate and 0.5M NaCl) ;1x Wash Buffer 3 (1% Triton X-100, 50 mM HEPES, pH 8.0, 2 mM EDTA, 1.0% sodium deoxycholate, 0.25 M LiCl, 1% NP-40, and 10 mM Tris-HCl, pH 8.0) ; 1x TE : 10mM Tris-HCl, pH 8.0 + 1mM EDTA.
The ChIP-exo experiments were generated by following the steps presented by Rhee and Pugh, 2011.

tag: growth condition

value: Exponential + O2

tag: treated with

value: Rifampicin for 20 minutes


title: Tumor cells Cas9-H3K27me


title: Sig70 in E. coli, exponential aerobic growth, no rifampicin applied replicate 2 (run 423)

source_name: Sig70 in E. coli_exponential aerobic growth_no rifampicin


title: SJMMMB018132_X11-19568-Ezh2-KO-Ezh2-OE-Tumor-rep2


title: SJMMMB042168_X1-19251-Control-TP-rep4


title: Tumor cells Cas9-H3K4me3


title: Sig70 in E. coli, exponential aerobic growth, rifampicin applied for 20 minutes, replicate 1 (run 423)


title: Tumor cells Cas9-H3K27ac

value: H3K27acetyl Cell Signaling Technology cat #:8173S


title: Sig70 in E. coli, exponential aerobic growth, no rifampicin applied replicate 1 (run 423)


title: Sig70 in E. coli, static aerobic growth, no rifampicin applied replicate 1 (run 299)

source_name: Sig70 in E. coli_static aerobic growth_no rifampicin

value: Static + O2


title: RV26AC-1h-3h-2

city: Bordeaux

first: Mathieu

last: Paoletti

address: 1 rue Camille Saint Saëns

department: IBGC

institute: CNRS

data_processing:
Illumina sequencing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to P. anserina annotated cds
Paired end mapping with bowtie
conversion into per sample BAM files
per sampe transcript abundance with RSEM
Genome_build: ASM22654v1 (GCA_000226545.1)
Supplementary_files_format_and_content: .txt file reports abundance measurments

organism: Podospora anserina

source_name: WT P. anserina Vegetative Incompatibility reaction

growth_protocol: P. anserina is grown for 3 days at 26°C on D0  solid medium. Bacteria were grown separately for 3 days at 26°C on D0 solid medium. The thermosensitive het-Rhet-V strain is cultured in the same conditions at 32°C

extract_protocol:
RNA was extracted using the RNA plant minikit extraction kit from Qiagen, and DNAse treated and polyA RNA purified before library construction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: P. anserina grown on cellophane stripes are transfered for 2h on bacteria free, D0 medium for control. P. anserina is transferred for 2h or 6h onto bacteria seeded plates at 26°C. For incompatibility sample the het-Rhet-V strain is transfered to 26°C.

tag: protocol

value: vegetative incompatibility reaction


title: Sig70 in E. coli, exponential aerobic growth, no rifampicin applied replicate 1 (run 299)


title: NSCas9Suz12F2


title: Sig70 in E. coli, static aerobic growth, no rifampicin applied replicate 2 (run 299)


title: RV26AC-1h-3h-1


title: CsvsDB11-6h-1

source_name: WT P. anserina transferred to Serratia marcescens seeded plates for 6h

value: reaction to S. marcescens

tag: reaction time


title: CsvsDB11-6h-2


title: CsvsDB11-2h-2

source_name: WT P. anserina transferred to Serratia marcescens seeded plates for 2h


title: Csvs118-6h-1

source_name: WT P. anserina transferred to Serratia fonticola seeded plates for 6h

value: reaction to S. fonticola


title: Tumor cells Ezh2KO-H3K27ac


title: CsvsDB11-2h-1


title: Csvs118-6h-2


title: Cs-2h-control-2

source_name: WT P. anserina control

value: control


title: Csvs118-2h-1

source_name: WT P. anserina transferred to Serratia fonticola seeded plates for 2h


title: Long Day Watered_S9

city: Milano

first: Fabio

last: Fornara

address: Via Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

data_processing:
Cleaned raw reads were generated by BGI Tech Solutions (Hong Kong)
Sequenced reads were mapped to rice genome v.7 using bowtie2 and TopHat2 with default parameters
Reads were uniquely mapped and counted by HTSeq with parameters -s no -a 10 -t gene -i ID
Gene-level differential expression analysis was performed using the R software (version 3.1.2) for statistical computing and edgeR package version 3.6.8 from bioconductor
Genome_build: O. sativa Japonica group cultivar Nipponbare genome version 7.0
Supplementary_files_format_and_content: Count files contain the number of reads per feature uniquely mapped by HTSeq python package (Anders et al. 2015). Text files on the series record contain the genes differentially expressed as output of edgeR (Robinson et al. 2010) in different pairwise comparison as described by the file name (LD = long day, SD = short day, ctrl = normal water regime, drg = plants under 13 days drought stress)

organism: Oryza sativa

source_name: Leaves

growth_protocol: Oryza sativa cv. Nipponbare (NB) seeds were grown in Conviron PGR15 chambers set on temperature/relative humidity cycles of 28ºC/80% during the day and 24ºC/90% during the night. Light was provided by fluorescent tubes and metal halide bulbs (intensity of ~450μE/m-2sec-1)

extract_protocol:
The distal part of the last extended leaf of 2-3 plants was collected and total RNA was isolated and quantified according to (Gómez-Ariza et al. 2015)
RNA libraries were prepared at BGI Tech Solutions (Hong Kong)

treatment_protocol: One hundred seeds of NB were planted on soil in 10L square boxes and plants were grown for 4 weeks under LD conditions and a normal water regime. After 4 weeks, half of the pots were moved to SD. Under each photoperiod, half of the pots were watered normally (control), while the remaining half was subjected to drought stress. Soil water content was monitored every hour using moisture sensors (WaterScout SM 100 Soil Moisture Sensor® and WatchDog A-Series Loggers®)

tag: cultivar

value: Nipponbare

value: leaf

tag: water regime

value: Watered

tag: photoperiod

value: Long Day


title: Long Day Drought_S10

value: Drought


title: Short Day Watered_S11

value: Short Day


title: Short Day Drought_S8


title: Sig70 in E. coli, exponential aerobic growth, no rifampicin applied replicate 2 (run 299)

tag: replicate


title: Short Day Drought_S7

tag: tissue


title: Short Day Watered_S6


title: Long Day Drought_S3


title: flg22 18 hrs; fls2; rep3

city: St Paul

first: Fumiaki

last: Katagiri

state: Minnesota

address: 1500 Gortner Ave

department: Dept of Plant and Microbial Biology

institute: Univ of Minnesota

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 357

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)
sample scaling: A scaling percentile normalization was applied to the raw counts of each sample: raw transcript counts at the 90th percentile of sample count values were scaled to match to the largest 90th percentile value, 300 counts, across all samples.
data transformation: The data were transformed to produce approximately homoscedastic data values, using the transformation log2 (scaled counts+79) - log2 (79). These transformed, scaled data with are referred to as normalized data in the following.
data correction: Normalized data were corrected for statistical artifacts using a mixed linear model for each gene individually: normalized data ~ genotype:time+(1|machine/lane)+(1│barcode)+(1|replicate). The normalized and corrected data are called transcript expression levels here.
Genome_build: TAIR10
Supplementary_files_format_and_content: raw counts for reads mapped to TAIR10 genes

source_name: flg22 18 hrs; fls2

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, BMC Genomics. 2014 May 6;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 1 μM solution of flg22, 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/variation

tag: concise genotype name

tag: hrs after flg22 infiltration

value: 18 hrs

tag: barcode

value: TGTGCGAT

tag: gaiix lane

tag: machine location

value: tsl


title: Long Day Watered_S1


title: flg22 18 hrs; ein2-1 pad4-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 355

source_name: flg22 18 hrs; ein2-1 pad4-1 sid2-2

value: ein2-1 pad4-1 sid2-2

value: Jeps

value: TTGCGCT


title: flg22 18 hrs; dde2-2 ein2-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 353

source_name: flg22 18 hrs; dde2-2 ein2-1 sid2-2

value: dde2-2 ein2-1 sid2-2

value: jePs

value: CAGAGT


title: flg22 18 hrs; dde2-2 pad4-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 354

source_name: flg22 18 hrs; dde2-2 pad4-1 sid2-2

value: dde2-2 pad4-1 sid2-2

value: jEps

value: CATACGT


title: flg22 18 hrs; pad4-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 351

source_name: flg22 18 hrs; pad4-1 sid2-2

value: pad4-1 sid2-2

value: JEps

value: leaf

value: CGAGAT


title: flg22 18 hrs; ein2-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 350

source_name: flg22 18 hrs; ein2-1 sid2-2

value: ein2-1 sid2-2

value: JePs

value: TTGGAT


title: flg22 18 hrs; dde2-2 ein2-1 pad4-1; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 352

source_name: flg22 18 hrs; dde2-2 ein2-1 pad4-1

value: dde2-2 ein2-1 pad4-1

value: jepS

value: 18 hrs

value: GACACT

value: tsl


title: Csvs118-2h-2

value: reaction to S. fonticola


title: flg22 18 hrs; ein2-1 pad4-1; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 349

source_name: flg22 18 hrs; ein2-1 pad4-1

value: ein2-1 pad4-1

value: JepS

value: ATCCT


title: flg22 18 hrs; dde2-2 pad4-1; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 347

source_name: flg22 18 hrs; dde2-2 pad4-1

value: dde2-2 pad4-1

value: jEpS

value: GTACT


title: Cs-2h-control-1

value: control


title: flg22 18 hrs; dde2-2 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 348

source_name: flg22 18 hrs; dde2-2 sid2-2

value: dde2-2 sid2-2

value: jEPs

value: leaf

value: ACTGT


title: flg22 18 hrs; dde2-2 ein2-1; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 346

source_name: flg22 18 hrs; dde2-2 ein2-1

value: dde2-2 ein2-1

value: jePS

value: GCTCT


title: Short Day Drought_S12

value: Nipponbare

value: Drought

value: Short Day


title: flg22 18 hrs; pad4-1; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 344

source_name: flg22 18 hrs; pad4-1

value: JEpS

value: 18 hrs

value: CGGT

value: tsl


title: flg22 18 hrs; sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 345

source_name: flg22 18 hrs; sid2-2

value: JEPs

value: GCAT


title: flg22 18 hrs; ein2-1; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 343

source_name: flg22 18 hrs; ein2-1

value: JePS

value: TCGT


title: Short Day Watered_S5

value: Watered


title: flg22 18 hrs; Col-0; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 341

source_name: flg22 18 hrs; Col-0

value: JEPS

value: leaf

value: TGTGCGAT


title: flg22 18 hrs; dde2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 342

source_name: flg22 18 hrs; dde2-2

value: jEPS

value: AGCT


title: flg22 9 hrs; dde2-2 ein2-1 pad4-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 339

value: dde2-2 ein2-1 pad4-1 sid2-2

value: jeps

value: 9 hrs

value: TTGCGCT


title: flg22 9 hrs; dde2-2 pad4-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 337

source_name: flg22 9 hrs; dde2-2 pad4-1 sid2-2

value: dde2-2 pad4-1 sid2-2

value: jEps

value: CAGAGT


title: flg22 9 hrs; fls2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 340

source_name: flg22 9 hrs; fls2

value: AACAGAGT

value: tsl


title: flg22 9 hrs; dde2-2 ein2-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 336

source_name: flg22 9 hrs; dde2-2 ein2-1 sid2-2

value: dde2-2 ein2-1 sid2-2

value: jePs

value: GACACT


title: Long Day Watered_S2

source_name: Leaves

value: Nipponbare

value: Watered

value: Long Day


title: Long Day Drought_S4

value: leaf

value: Drought


title: flg22 18 hrs; dde2-2 ein2-1 pad4-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 356

value: dde2-2 ein2-1 pad4-1 sid2-2

value: 18 hrs


title: flg22 9 hrs; ein2-1 pad4-1; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 332

source_name: flg22 9 hrs; ein2-1 pad4-1

value: ein2-1 pad4-1

value: JepS

value: 9 hrs

value: ACTGT


title: flg22 9 hrs; ein2-1 pad4-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 338

source_name: flg22 9 hrs; ein2-1 pad4-1 sid2-2

value: ein2-1 pad4-1 sid2-2

value: Jeps

value: CATACGT


title: flg22 9 hrs; pad4-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 334

source_name: flg22 9 hrs; pad4-1 sid2-2

value: pad4-1 sid2-2

value: JEps

value: TTGGAT

value: tsl


title: flg22 9 hrs; dde2-2 pad4-1; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 330

source_name: flg22 9 hrs; dde2-2 pad4-1

value: dde2-2 pad4-1

value: jEpS

value: GCTCT


title: flg22 9 hrs; ein2-1; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 326

source_name: flg22 9 hrs; ein2-1

value: JePS

value: leaf

value: AGCT


title: flg22 9 hrs; pad4-1; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 327

source_name: flg22 9 hrs; pad4-1

value: JEpS

value: TCGT


title: flg22 9 hrs; dde2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 325

source_name: flg22 9 hrs; dde2-2

value: jEPS

value: 9 hrs

value: TGTGCGAT


title: flg22 9 hrs; dde2-2 ein2-1; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 329

source_name: flg22 9 hrs; dde2-2 ein2-1

value: dde2-2 ein2-1

value: jePS

value: GCAT


title: flg22 9 hrs; dde2-2 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 331

source_name: flg22 9 hrs; dde2-2 sid2-2

value: dde2-2 sid2-2

value: jEPs

value: GTACT


title: flg22 9 hrs; sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 328

source_name: flg22 9 hrs; sid2-2

value: JEPs

value: CGGT

value: tsl


title: flg22 9 hrs; Col-0; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 324

source_name: flg22 9 hrs; Col-0

value: JEPS

value: AACAGAGT


title: flg22 5 hrs; dde2-2 ein2-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 319

source_name: flg22 5 hrs; dde2-2 ein2-1 sid2-2

value: dde2-2 ein2-1 sid2-2

value: jePs

value: 5 hrs

value: leaf

value: CGAGAT


title: flg22 5 hrs; dde2-2 ein2-1 pad4-1; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 318

source_name: flg22 5 hrs; dde2-2 ein2-1 pad4-1

value: dde2-2 ein2-1 pad4-1

value: jepS

value: TTGGAT


title: flg22 5 hrs; dde2-2 pad4-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 320

source_name: flg22 5 hrs; dde2-2 pad4-1 sid2-2

value: dde2-2 pad4-1 sid2-2

value: jEps

value: GACACT


title: flg22 5 hrs; pad4-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 317

source_name: flg22 5 hrs; pad4-1 sid2-2

value: pad4-1 sid2-2

value: JEps

value: ATCCT


title: flg22 5 hrs; dde2-2 ein2-1 pad4-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 322

value: dde2-2 ein2-1 pad4-1 sid2-2

value: jeps

value: CATACGT

value: tsl


title: flg22 5 hrs; ein2-1 pad4-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 321

source_name: flg22 5 hrs; ein2-1 pad4-1 sid2-2

value: ein2-1 pad4-1 sid2-2

value: Jeps

value: CAGAGT


title: flg22 5 hrs; fls2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 323

source_name: flg22 5 hrs; fls2

value: 5 hrs

value: leaf

value: TTGCGCT


title: flg22 5 hrs; ein2-1 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 316

source_name: flg22 5 hrs; ein2-1 sid2-2

value: ein2-1 sid2-2

value: JePs

value: ACTGT


title: flg22 5 hrs; dde2-2 sid2-2; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 314

source_name: flg22 5 hrs; dde2-2 sid2-2

value: dde2-2 sid2-2

value: jEPs

value: GCTCT


title: flg22 5 hrs; ein2-1 pad4-1; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 315

source_name: flg22 5 hrs; ein2-1 pad4-1

value: ein2-1 pad4-1

value: JepS

value: GTACT


title: flg22 5 hrs; dde2-2 pad4-1; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 313

source_name: flg22 5 hrs; dde2-2 pad4-1

value: dde2-2 pad4-1

value: jEpS

value: GCAT


title: flg22 5 hrs; Col-0; rep3

description:
concise genotype name indicates the presence (uppercase) or absence (lowercase) of the sectors JA, ET, PAD4, and SA. dde2-2, ein2-1, pad4-1, and sid2-2 remove the JA, ET, PAD4, and SA signaling sectors, respectively.
Sample 307

source_name: flg22 5 hrs; Col-0

value: JEPS

value: tsl