title: scMNase-seq_EILP_GC0401


title: scMNase-seq_EILP_GC0421

status: Public on Dec 31 2020

type: SRA

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

country: USA

institute: NHLBI,NIH

library_source: genomic

data_processing:
Basecalling by RTA 1.18.66.3, Illumina instrument run time analysis software
Sequencing reads were aligned to mouse genome (mm9) using Bowtie2 with default parameters.
Reads from replicates were merged and redundant reads were removed from further analysis.
For ChIC-seq samples, reads from replicates were merged for peak calling. Peak calling were performed using MACS2 with default parameters.
For scMNase-seq samples, reads with length between 140 and 180 bp were selected as nucleosome reads while reads with length less than 80 bp were selected as subnucleosomal reads.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIC-seq and DNase-seq samples, .wig files contain normalized tag density, which can be uploaded to UCSC genome browser for visulization. For scMNase-seq samples, bed files provide genomic positions on chromosomes for nucleosomes (140-180 bp) and subnucleosomes (<80 bp).

molecule: genomic DNA

organism: Mus musculus

source_name: EILP

growth_protocol: Samples were isolated by cell sorting from bone marrow single cell suspensions

extract_protocol:
For scMNase-Seq, single live cells for EILP, EILPTcf7-/-, ILCP were sorted by flow cytometer and deposited directly into 96 well plate, which containing 32 μl of cell lysis buffer  (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 2 mM CaCl2, 0.1% Triton X-100). 32 μl of cell lysis buffer. 8 μl diluted MNase (1:3000 in lysis buffer) was added to the sorted cells and incubated at 37 °C for 5 minutes. The reaction was stopped by addition of 80 μl of stop buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 0.15% SDS, 10mM EGTA), and 1 μl of 20 mg/ml Proteinase K. Following incubation at 65°C for 2 hours, DNA was purified by Phenol-chloroform extraction and precipitation with ethanol in the presence of glycogen.
For MNase-seq libraries, DNA were end-repaired in 50 μl of reaction volume at RT for 45 minutes using End-It DNA-Repair kit (Epicenter, Cat#ER81050) according to the manufacturer’s instructions. Next, DNA were purified by enzyme reaction clean kit (Qiagen). The blunted DNA fragments were subject to adding 3 end A base using the Klenow fragment (3′ → 5′ exo-) (NEB). The DNA was then ligated with the ‘‘Y’’-shaped Illumina adaptor and amplified for 16 cycles using indexing primers with the PCR condition: 98°C,10”; 67°C, 30”; 72°C, 30”. PCR products between 150-250 bp were isolated on 2% E-gel for sequencing on Illumina Hiseq-3000.

tag: strain

tag: genotype/variation

tag: tissue

value: bone marrow

tag: sorting profile

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1-


title: scMNase-seq_EILP_GC0395


title: scMNase-seq_EILP_GC0394


title: scMNase-seq_EILP_GC0392


title: scMNase-seq_EILP_GC0997


title: scMNase-seq_EILP_GC0393


title: scMNase-seq_EILP_GC0389


title: scMNase-seq_EILP_GC0386


title: scMNase-seq_EILP_GC0388


title: scMNase-seq_EILP_GC0384


title: scMNase-seq_EILP_GC0387


title: scMNase-seq_EILP_GC0385


title: scMNase-seq_EILP_GC0383


title: scMNase-seq_EILP_GC0382


title: scMNase-seq_EILP_GC0408


title: scMNase-seq_EILP_GC0381


title: scMNase-seq_EILP_GC0372


title: scMNase-seq_EILP_GC0371


title: scMNase-seq_EILP_GC0403


title: scMNase-seq_EILP_GC0374


title: scMNase-seq_EILP_GC0370


title: scMNase-seq_EILP_GC0367


title: scMNase-seq_EILP_GC0366


title: scMNase-seq_EILP_GC0368


title: scMNase-seq_EILP_GC0364


title: scMNase-seq_EILP_GC0369


title: scMNase-seq_EILP_GC0365


title: scMNase-seq_EILP_GC0391


title: scMNase-seq_EILP_GC0390


title: scMNase-seq_EILP_GC0357


title: scMNase-seq_EILP_GC0355


title: scMNase-seq_EILP_GC0358


title: scMNase-seq_EILP_GC0347


title: scMNase-seq_EILP_GC0348


title: scMNase-seq_EILP_GC0362


title: scMNase-seq_EILP_GC0363


title: scMNase-seq_EILP_GC0346


title: scMNase-seq_EILP_GC0378


title: scMNase-seq_EILP_GC0340


title: scMNase-seq_EILP_GC0341


title: scMNase-seq_EILP_GC0338


title: scMNase-seq_EILP_GC0345


title: scMNase-seq_EILP_GC0339


title: scMNase-seq_EILP_GC0344


title: scMNase-seq_EILP_GC0332


title: scMNase-seq_EILP_GC0336


title: scMNase-seq_EILP_GC0337


title: scMNase-seq_EILP_GC0335


title: scMNase-seq_EILP_GC0334


title: scMNase-seq_EILP_GC0324


title: scMNase-seq_EILP_GC0323


title: scMNase-seq_EILP_GC0322


title: scMNase-seq_EILP_GC0315


title: scMNase-seq_EILP_GC0320


title: scMNase-seq_EILP_GC0316


title: scMNase-seq_EILP_GC0317


title: scMNase-seq_EILP_GC0318


title: scMNase-seq_EILP_GC0314


title: scMNase-seq_EILP_GC0313


title: scMNase-seq_EILP_GC0312


title: scMNase-seq_EILP_GC0311


title: scMNase-seq_EILP_GC0310


title: scMNase-seq_EILP_GC0307


title: scMNase-seq_EILP_GC0306


title: scMNase-seq_EILP_GC0343


title: scMNase-seq_EILP_GC0309


title: scMNase-seq_EILP_GC0305


title: scMNase-seq_EILP_GC0296


title: scMNase-seq_EILP_GC0295


title: scMNase-seq_EILP_GC0294


title: scMNase-seq_EILP_GC0293


title: scMNase-seq_EILP_GC0291


title: scMNase-seq_EILP_GC0302


title: scMNase-seq_EILP_GC0299


title: scMNase-seq_EILP_GC0298


title: scMNase-seq_EILP_GC0319


title: scMNase-seq_EILP_GC0290


title: scMNase-seq_EILP_GC0289


title: P6-3

city: Wuxi

first: Lanmei

last: Wang

address: East Shanshui Road 9

country: China

institute: Freshwater Fisheries Research Centre of Chinese Academy of Fishery Sciences

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Refseq C. carpio reference genome using Hisat2 aligner with default parameters.
The mapped reads from each sample were assembled using StringTie v1.3.3b, then assembled transcripts were annotated using gﬀcompare program (v 0.10.1) from the stringTie packageand. The unknown transcripts were used to lncRNA identification using CPAT, NR and Pfam.
Rawcounts of mRNA and lncRNA genes in each sample were quantified using featureCounts program, while RPKM value was used to estimate the relative expression levels among samples.
EdgeR R package was used to identify differentially expressed mRNAs (DE-mRNAs) and differentially expressed lncRNAs (DE-lncRNAs) with rawcounts of genes. The genes with absolute value of |log2 (fold change)| >= 1 and FDR of < 0.05 were considered as significantly differential expressed.
Genome_build: GCF_000951615.1
Supplementary_files_format_and_content: tab-delimited text files include raw count for each Sample

molecule: total RNA

organism: Cyprinus carpio

source_name: embryo

growth_protocol: The common carp used in the experiment is a new fish variety derived from the original parents of Jian carp (C. carpio var. jian), Huanghe carp (C. carpio haematopterus) and Heilongjiang common carp (C. carpio haermatopterus) after five generations combined selection by Freshwater Fisheries Research Center (FFRC), Chinese Academy of Fishery Sciences (CAFS), which is designated as FFRC No.2 strain common carp. Embryos were obtained by natural spawning.

extract_protocol:
Total RNA was isolated using the standard TRIzol (Invitrogen) protocol
Genomic DNA was removed prior to RNA purity and integrity evaluation. An equal amount of total RNA of each stage was pooled separately. The strand-specific cDNA libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) after depletion of rRNA by the Epicentre Ribo-zero rRNA Removal Kit (Epicentre, Madison, WI, USA), according to standard procedures

treatment_protocol: The stages of embryonic development were observed and photographed under an microscope. The test samples consisted of six embryonic stages: cleavage stage(2 hours post-fertilization (hpf) embryos) (P1), blastocyst stage (6 hpf) (P2), gastrulation stage (12 hpf) (P3), organ formation stage (20 hpf) (P4), hatching stage (64 hpf) (P5) and 1 dph larva (P6) (Supplementary fig). All samples were immediately frozen in liquid nitrogen and then stored at −80 °C for further use.

value: embryo

tag: developmental stage

value: 1 dph larva

value: FFRC No.2 strain

tag: genotype

value: WT


title: P6-2


title: P4-3

value: organ formation (20 hpf)


title: P5-3

value: hatching stage (64 hpf)


title: P5-2


title: scMNase-seq_EILP_GC0304


title: P4-2


title: P6-1


title: P3-3

value: gastrulation (12 hpf)


title: P4-1


title: scMNase-seq_EILP_GC0301


title: scMNase-seq_EILP_GC0303


title: P3-2


title: scMNase-seq_EILP_GC0300


title: P2-3

value: blastocyst (6 hpf)


title: P3-1


title: P2-1


title: P1-2

value: cleavage (2 hours post-fertilization hpf)


title: P1-3


title: P2-2


title: Fermentation liquid, S31

city: WUXI

first: YANG

last: SUN

address: LIHU ROAD

institute: JIANGNAN UNIVERSITY

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v2.2.3
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using HTSeq software to analyze the gene expression level of each sample, and the model used was union.
Genome_build: https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP005927.1
Supplementary_files_format_and_content: .txt file reports RPKMs

organism: Serratia marcescens

source_name: Fermentation liquid

growth_protocol: Incubating JNB 5-1 at 30C and 37C in LB medium

extract_protocol:
RNA was extracted using an RNeasy kit (Vazyme, Nanjing, China).
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. For prokaryotic samples, rRNA is removed using a specialized kit that leaves the mRNA. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（ 5X） . First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（ RNaseH-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter,Beverly, USA). Then 3 µl USER Enzyme (NEB， USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: After incubating JNB 5-1 at 30C and 37C for 22 hours, the growth temperature of 2 bottles was interchanged to continue the cultivation, and the remaining 2 bottles continued to be cultured at the original temperature until 36h. Total RNA was sampled at 12h and 24h, at 36h, respectively, and sequenced to analyze the effect of temperature on PG production by S. marcescens. In order to distinguish the samples, we named the samples S11, S12, S13, S14, S21, S22, S23, S24, S31, S32, S33, S34. S11, S12, S13, S14 were sampled at 12h (T12). S21, S22, S23, S24 were sampled at 24h (T24), S21 was converted from 30C to 37C and S24 was converted from 37C to 30C at 22h. S31, S32, S33 and S34 were sampled at 36h (T36), S31 was converted from 30C to 37C and S34 was converted from 37C to 30C at 22h.

value: JNB 5-1

tag: treatment

value: 30C (converted to 37C at 22h)

tag: time of sampling


title: Fermentation liquid, S24

value: 37C (converted to 30C at 22h)


title: Fermentation liquid, S23


title: P5-1


title: Fermentation liquid, S22


title: P1-1


title: Fermentation liquid, S34


title: WS3

city: Stellenbosch

first: Anna-Maria

last: Oberholster

state: Western Cape

address: JC Smuts Building, Van der Bijl Street

department: Genetics

country: South Africa

institute: University of Stellenbosch

data_processing:
Quality check with FastQC
Trimming, using Trimmomatic v0.39, ILLUMINACLIP:./adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:5:30 HEADCROP:20 MINLEN:40
De novo assembly, Trinity v2.8.6
Transcript quantification, Trinity v2.8.6 making use of RSEM
Genome_build: De novo
Supplementary_files_format_and_content: *tab delimited text file with 8 columns; 1:transcript_id, 2:gene_id, 3:length, 4:effective_length, 5:expected_count, 6:TPM, 7:FPKM, 8:IsoPct;  *Fasta file of all de novo assembled transcripts

organism: Withania somnifera

source_name: supplemented with 100mM NaCl

growth_protocol: Plants were maintained at 21 degrees celsius in a growth room with high intensisty LED- and growlux growth lights. Plants were allowed to grow for 70 days and watered with Hoagland’s solution throughout.

extract_protocol:
Qiagen RNeasy kit
TruSeq Stranded Total RNA LT Sample Prep Kit (Plant) with Ribo-Zero using the TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E

treatment_protocol: Plants were maintained at 21 degrees celsius in a growth room with high intensisty LED- and growlux growth lights. After 70 days of growth the experimental plants were exposed to daily 200ml doses of Hoaglands Solution supplemented with 100mM NaCl for 1 week. After the 1 week period the leaves were collected.

value: leaves


title: Fermentation liquid, S32


title: WS2


title: Fermentation liquid, S21


title: Fermentation liquid, S11


title: WC2

source_name: control


title: Fermentation liquid, S14


title: SAM_1

data_processing:
Quality check with FastQC
Trimming, using Trimmomatic v0.39, ILLUMINACLIP:./adapters/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:5:30 HEADCROP:20 MINLEN:40
De novo assembly, Trinity v2.8.6
Transcript quanitification, Trinity v2.8.6 making use of RSEM
Genome_build: De novo
Supplementary_files_format_and_content: tab delimited text file with 8 columns; 1:transcript_id, 2:gene_id, 3:length, 4:effective_length, 5:expected_count, 6:TPM, 7:FPKM, 8:IsoPct

organism: Diuraphis noxia

source_name: Whole organism

growth_protocol: Both biotpes were maintained on preference hosts.

extract_protocol:
Qiagen RNeasy kit
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E protocol

tag: biotype

value: SAM

tag: sample size

value: 100 individuals

value: mixed


title: Fermentation liquid, S12


title: Fermentation liquid, S13


title: SA1_3


title: SA1_1


title: Fermentation liquid, S33


title: WC3


title: SAM_2


title: SA1_2


title: SAM_3


title: WS1


title: S3_RNA

city: Tallahassee

first: Nicholas

middle: James

last: Waddell

state: FL

address: 319 Stadium Dr

department: Biological Sciences

institute: Florida State University

description:
ribo-depleted RNA
tissue punch

data_processing:
Base-calling was performed by RTA3.  Resulting sequencing reads were demultiplexed using bcl2fastq_v1.8.4.
Sequenced reads were trimmed for adapter sequences, low-quality base-calls (< 20;phred 33), and too short reads (< 20 bases), and trimmed 10 base-pairs from the 5’ end of reads; then, the resulting trimmed reads were mapped to the rn6 reference genome using hisat2 using default parameters.
Aligned reads were assigned to gene features using featureCounts v1.5.0-p3 counting on the meta-feature level.  Multi-mapping reads and multi-overlapping reads were ignored.
Differential gene expression was calculated using EdgeR v3.20.9.  Genes passed filtering criteria if at least 3 samples had at minimum .5 counts per million.
Genome_build: rn6
Supplementary_files_format_and_content: The processed data files are unnormalized count files for each sample individually. These files were created using featureCounts and gene-level features were assigned.  The columns are as follows: Ensembl Gene ID, Unnormalized Counts for Sample.

organism: Rattus norvegicus

source_name: Stress Biological Replicate 3

extract_protocol:
Total RNA was isolated using the ZR-Duet DNA/RNA MiniPrep kit (cat. D7001) from Zymo Research Corp.  This kit is suitable for extraction of DNA and RNA molecules from a wide range of sources using trade-marked Clear-Spin column technology.
100 ng of total RNA was applied to the NEBNext® rRNA Depletion Kit (New England Biolabs, Inc., Ipswich, MA) to remove ribosomal RNAs (rRNAs) according to manufacturer’s protocol. The resulting rRNA-depleted samples were then used to generate RNA sequencing libraries by using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, Inc., Ipswich, MA). Briefly, RNA samples were fragmented, and cDNA was synthesized from the first and second strands, consecutively. The ends of the libraries were ligated to universal Illumina adaptors included in the kit. RNA-seq libraries were individually indexed with NEBNext® Multiplex Oligos for Illumina (New England Biolabs, Inc., Ipswich, MA) and amplified through 11 cycles of PCR amplification.

treatment_protocol: prolonged unpredictable stress, two stressors per day including: restraint (4hr), forced swim (15C, 5min), elevated platform (30min), tilted cage with wet bedding on orbital shaking (45o angle, 100 cycle/min. 1hr)

value: Sprague Dawley

tag: Sex

value: male

value: pre-frontal cortex

tag: age

value: 3-5 wks (juvenile adolescent)


title: S4_RNA

description:
ribo-depleted RNA
tissue punch

source_name: Stress Biological Replicate 4


title: S2_RNA

description:
ribo-depleted RNA
tissue punch

source_name: Stress Biological Replicate 2


title: S1_RNA

description:
ribo-depleted RNA
tissue punch

source_name: Stress Biological Replicate 1


title: WC1


title: C3_RNA

description:
ribo-depleted RNA
tissue punch

source_name: Control Biological Replicate 3


title: C2_RNA

description:
ribo-depleted RNA
tissue punch

source_name: Control Biological Replicate 2


title: Normal skin [033_31_HC]

type: RNA

city: Ann Arbor

first: Celine

middle: C

last: Berthier

state: MI

address: 1150 W. Medical Center Dr, MSRB2

institute: University of Michigan

description: Gene expression data from human normal skin biopsy

hyb_protocol: Biotin labeled cDNA was fragmented and hybridized to Affymetrix Human Gene 2.1  ST arrays (Santa Clara, CA) according to the manufacturer protocol.

scan_protocol: GeneChip arrays were scanned by using the Affymetrix GeneTitan system (software version 3.2.4.1515) according to the Affymetrix Expression Analysis Technical Manual.

data_processing: The data were analyzed using R software version 3.6.1 using custom CDF version 23.0.0 and modified Affymetrix_1.58.0 package from BrainArray: RMA method and Human Entrez Gene custom CDF annotation version 23 were used for the normalization.

label: biotin

organism: Homo sapiens

source_name: Skin biopsy from human

label_protocol: Biotinylated cRNA were prepared using the NuGEN Encore Biotin Module (Encore Biotin Module Manual, P/N M01111 v6) following the manufacturer's protocol.

extract_protocol: Total RNA was isolated using the E.N.Z.A. FFPE RNA Kit (Omega Bio-tek) (Norcross, GA) following manufacturer’s instructions.

value: Skin biopsy

tag: disease

value: Normal skin


title: Normal skin [030_28_HC]


title: Normal skin [027_25_HC]


title: Normal skin [031_29_HC]


title: Normal skin [029_27_HC]


title: C1_RNA

description:
ribo-depleted RNA
tissue punch

source_name: Control Biological Replicate 1


title: Normal skin [026_24_HC]


title: cSLE skin lesion [025_23_cSLE]

description: Gene expression data from human childhood-onset lupus lesional skin biopsy

value: cSLE skin lesion


title: cSLE skin lesion [024_22_cSLE]


title: Normal skin [032_30_HC]


title: C4_RNA

description:
ribo-depleted RNA
tissue punch

source_name: Control Biological Replicate 4


title: JM Lesional skin [017_17_JM_L]

description: Gene expression data from human JM lesional skin biopsy

value: JM Lesional skin


title: cSLE skin lesion [021_20B_cSLE]


title: JM Non-lesional skin [015_15_JM_NL]

description: Gene expression data from human JM non-lesional skin biopsy

value: JM Non-lesional skin


title: cSLE skin lesion [018_18_cSLE]


title: JM Non-lesional skin [011_11_JM_NL]


title: Normal skin [028_26_HC]


title: JM Non-lesional skin [012_12_JM_NL]


title: JM Non-lesional skin [013_13_JM_NL]


title: JM Non-lesional skin [016_16_JM_NL]


title: cSLE skin lesion [023_21B_cSLE]


title: JM Non-lesional skin [010_10_JM_NL]


title: cSLE skin lesion [022_21A_cSLE]


title: JM Lesional skin [007_07_JM_L]


title: 3D_skin_+_IL17C_2

city: Fukuoka

first: Emi

last: Sato

state: Fukuoka

address: 7-45-1Jyonan-ku, Nanakuma

department: Faculty of Medicine

country: Japan

institute: Fukuoka University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: in vitro 3D epidermal construction, IL17C treat

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: epidermis

tag: cell strain

value: NHEK (normal adult human epidermal keratimocytes)


title: 3D_skin_+_IL17C_1


title: cSLE skin lesion [020_20A_cSLE]


title: JM Lesional skin [009_09_JM_L]


title: NL31

city: Beograd

first: Dragana

last: Dudić

address: Cara Dušana 62-64

country: Serbia

institute: Union Nikola Tesla University

data_processing:
Illumina MiSeq Basecalling
FastQC (QC>30), Trimmomatic (version 0.32) to filter out low-quality reads, primers and adapter sequences
Reads were mapped onto Zea mays B73 reference genome v3 (available at https://www.maizegdb.org/) using TopHat (insert size 130, standard deviation 50, maximum intron size 100.000).
Reads were assembled using Cufflinks (version 2.2.1) and the final transcriptome assembly was obtained by Cuffmerge as in Trapnell et al. (2012)
Differential expression between Lancaster and Non-Lancaster maize inbred lines was obtained using CuffDiff (treshold of absolute value of log2 fold change greater than 1)
Genome_build: B73 RefGen_v3
Supplementary_files_format_and_content: CuffDiff gene expression output file

organism: Zea mays

source_name: Whole transcriptome

growth_protocol: 46 maize inbred lines were grown in the greenhouse under optimal conditions until reaching V4 stage

extract_protocol:
Gene Jet RNA Purification kit (Thermo Fisher Scientific)
Illumina TruSeq(R) Stranded Total RNA LT with Ribo-Zero Plant was used and rRNA was removed using AMPure XP magnetic beads (Beckman Coulter).
Normalized libraries were pooled together and PE 150bp RNAseq was performed on the Illumina MiSeq platform in the IMGGE using MiSeq Reagent Kit v2 (300cycle) with the standard flow cell.

treatment_protocol: none / lines were compared for differential gene expression between two maize genetic resources, Lancaster and Non-Lancaster

tag: maize genetic resource

value: Non-Lancaster (Iowa dent&BSSS)

value: leaf

value: V4 stage


title: NL30


title: M48B

city: London

first: Michalis

last: Barkoulas

address: SAF Building, South Kensington

country: United Kingdom

institute: Imperial College London

data_processing:
Pseudoalignment was performed using Kallisto (Bray et al., Nat Biotechnol 2016) and the WS235 transcriptome from Wormbase
Analysis of counts was performed using Sleuth using the Wald test for two sample comparison (Pimentel et al., Nat Methods 2017)
Genome_build: WS235
Supplementary_files_format_and_content: abundance.h5 is a HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length.

organism: Caenorhabditis elegans

source_name: Infected with M. humicola_48h post L4

growth_protocol: The strains used in this study were cultured and handled according to standard protocols (Brenner, 1974). Gravid adults were bleached to obtain synchronized L4 stage animals which were then treated with M. humicola extract or infected with the pathogen.

extract_protocol:
The animals were collected by washing with M9 at respective time points and RNA was extracted using TRIzol ® reagent. The quality and quantity of RNA was determined respectively using agarose gel electrophoresis and Qubit fluorometer.
The library preparation was done using PE100 strand-specific library preparation protocol as previously described (Zhu et al., Plant Methods 2018)

treatment_protocol: Extract treatment was carried out at 20 °C on nematode growth medium seeded with 200 ml of OP50 E. coli culture. 300 ml of M. humicola extract was added on bacterial lawn prior to additon of animals. Same amount of water was added to control plates. The experiment was performed in triplicates and consisted of 200 animals on each plate. For infection set up, 50 L4 stage animals were added onto a plate with and without (control) 3 previously infected animals with M. humicola on a small bacterial lawn (100 ml) (Osman et al., Curr Biol 2018)

value: WT

value: L4 stage animal

value: Infected with M. humicola

tag: timepoint

value: 48h post L4


title: NL29


title: JM Lesional skin [006_06_JM_L]


title: NL28


title: JM Lesional skin [005_05_JM_L]


title: M48C


title: Control_sample2

city: Northridge

first: Chhandak

last: Basu

state: CA

address: 18111 Nordhoff Street

department: Biology

institute: California State University

data_processing:
Trinity software (v.2.0.6) with the default settings. potential contamination by BLASTing against the NCBI non-redundant (nr) protein database with the blastx command in DIAMOND(v0.71).
The output from DIAMOND was screened for non-plant hits using the MEGAN6 program
Coding regions were identified using TransDecoder (Haas et al 2015) with min length of 180 base pairs, followed by clustering with CD-HIT
Salmon was used for read quantification
The gene expression analysis was conducted using exactTest from the Bioconductor package, edgeR
Supplementary_files_format_and_content: Tab and comma separated files

organism: Paulownia elongata

source_name: leaves

growth_protocol: These plants were grown for 14 days in Promix-HP Mycorrhizae potting soil

extract_protocol:
Total RNA was extracted from both control and treated P. elongata plants using Trizol reagent (Thermofisher Scientific, USA)
After clean-up, cDNA libraries were synthesized (Fig 2) and barcoded using the TrueSeq RNA Sample Prep Kit
Pair-end 76 bp reads were generated using the MiSeq Reagent Kit (v3; Illumina, U.S.A.) on an Illumina MiSeq instrument

treatment_protocol: The conditions for heat stress are 40°C for 24 hours with a photoperiod of 12 hours of light and 12 hours of dark

value: leaves

value: 3 yrs

tag: growth

value: 14 days


title: control_3D_skin_2

source_name: in vitro 3D epidermal construction


title: C48B

source_name: Control_48h post L4

tag: strain

value: Control


title: M48A

tag: genotype/variation


title: C48C


title: NL27

value: Non-Lancaster (BSSS&unknown source)

tag: tissue


title: control_3D_skin_1


title: JM Lesional skin [004_04_JM_L]

value: Skin biopsy


title: Control_sample1


title: JM Lesional skin [002_02_JM_L]

value: JM Lesional skin


title: JM Lesional skin [001_01_JM_L]


title: 3D_skin_+_IL17A_1

source_name: in vitro 3D epidermal construction, IL17A treat


title: 3D_skin_+_IL17A_2


title: JM Lesional skin [003_03_JM_L]


title: Heat_treated_sample2


title: NL25

value: Non-Lancaster (BSSS)


title: NL20

value: Non-Lancaster (BSSS&Amargo)


title: C48A


title: NL23


title: M24B

source_name: Infected with M. humicola_24h post L4

value: 24h post L4


title: Heat_treated_sample1


title: NL21

value: Non-Lancaster (Iowa dent&BSSS)


title: NL22Z

value: leaf


title: Heat_treated_sample3


title: NL26

value: V4 stage


title: M24A

value: WT


title: NL17


title: NL19

value: Non-Lancaster (unkwnown source)


title: C24B

source_name: Control_24h post L4

value: L4 stage animal


title: M12C

source_name: Infected with M. humicola_12h post L4

value: Infected with M. humicola

value: 12h post L4


title: M12B


title: NL18


title: M24C


title: NL15

value: Non-Lancaster (Iowa dent)


title: M12A


title: C12C

source_name: Control_12h post L4


title: NL14


title: C12B


title: NL13


title: C24C


title: C12A


title: NL10

value: Non-Lancaster (BSSS&Iowa dent)


title: NL12


title: X4A

source_name: Extract Treated_4h post L4

value: Extract Treated

value: 4h post L4


title: NL9


title: X4C


title: Treg_Del-1-Fc-rep2

city: Philadelphia

first: George

last: Hajishengallis

state: PA

address: School of Dental Medicine

institute: University of Pennsylvania

data_processing:
Clean reads were mapped to the mouse genome (Ensembl assembly GRCm38) using STAR with default settings after filtering low-quality, adaptor-polluted and high content of unknown base (N) reads
Subsequently, reads count of each annotated gene was calculated by htseq-count (HTSeq version 0.6.0 with parameters “ -q -t exon -m intersection-nonempty -f bam --stranded=no”).
Differential gene expression was analyzed using DEGseq2 and significantly differentially expressed genes (DEGs) were defined by FDR-adjusted p value < 0.05 in the DEL-1-Fc–treated group relative to their expression in the Fc control group.
Genome_build: mm10
Supplementary_files_format_and_content: txt files, count

molecule: polyA RNA

source_name: Regulatory T Cells_Del-1-Fc

growth_protocol: Naive splenic CD4+ cells isolated from 6-week-old WT mice were differentiated to Tregs for 3 days in RPMI 1640 Complete Medium containing pre-coated anti-CD3 (2υg/ml), anti-CD28 (1ug/ml ), TGFβ1 (5ng/ml), IL-2 (40ng/ml) and DEL-1-Fc or Fc control.

extract_protocol:
Total RNA was extracted by Trizol (Life Technologies) and DNA was removed by using TURBO DNA-free Kit (Invitrogen).
PolyA-selected mRNA libraries were generated following the manufacturer’s protocols (BGI).

tag: strain background

value: 6 weeks

value: wild type

tag: cell type

value: Naive splenic CD4+ cells

tag: cell subtype

value: Regulatory T Cells


title: NL7

value: Non-Lancaster (BSSS&unknown source)


title: C4D

source_name: Control_4h post L4

tag: developmental stage

tag: treatment

value: Control


title: C4B


title: NL6

value: leaf


title: NL16

value: Non-Lancaster (BSSS)

value: V4 stage


title: Treg_Del-1-Fc-rep1


title: Treg_Fc-rep2

source_name: Regulatory T Cells_Fc

value: Fc control


title: Treg_Del-1-Fc-rep3


title: NL8

value: Non-Lancaster (BSSS&Amargo)


title: C4A

value: WT

value: L4 stage animal


title: Treg_Fc-rep3


title: X1C

source_name: Extract Treated_1h post L4

value: 1h post L4


title: NL5


title: X1B


title: NL4


title: X1A


title: NL3


title: Treg_Fc-rep1


title: C1C

source_name: Control_1h post L4


title: X4B


title: NL2

value: Non-Lancaster (Iowa dent)


title: NL11

value: Non-Lancaster (Iowa dent&BSSS)


title: NL1


title: C1B


title: L13Z

value: Non-Lancaster (Iowa dent&Ohio)


title: OBS30_4

city: Nanchang

first: Wenqing

last: Tu

address: Changdong Road No.7777

institute: Jiangxi Academy of Science

data_processing:
Paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software.
The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: GRCz11
Supplementary_files_format_and_content: Tab-delimited text file includes TPM values for each gene in each sample

organism: Danio rerio

source_name: zebrafish larvae

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina).  Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length).

tag: genotype

value: Wild type

value: 30 mg/L OBS treated group

value: 4 dpf (days post fertilization)

value: larvae


title: C1A


title: L15

source_name: Whole transcriptome

value: Lancaster


title: OBS30_3


title: L14


title: L12


title: OBS30_1


title: OBS20_2

value: 20 mg/L OBS treated group


title: L10

value: leaf


title: L9


title: PFOS_4

value: 20 mg/L PFOS treated group


title: OBS20_1


title: L8

value: V4 stage


title: OBS20_3


title: PFOS_3


title: L7


title: L6


title: Con_4

value: untreated group


title: L4


title: Con_3


title: Con_2


title: L3


title: L2


title: PHD1 ΔPHD Schi rep3

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

description:
PHD1 PHD deletion Schizont
0079_wo_PHD_Schi_-3_S58

data_processing:
Quality trimming and adapter sequence was performed using Trimmomatic (v0.36).
Low quality bases were trimmed using a sliding window approach with a minimum average quality of 18 in 4 base pair window.  Reads with length <35 base pairs were removed.
The trimmed data was mapped to reference genome (pf3D7_V3.0.fasta) using hisat2 specifying '--max-intronlen 5000'  to avoid spurious aligments.
Bedtools was used to obtain the coverage  and the mapped data was visualized in IGV.
Unique mapping reads corresponding to each gene were obtained using FeatureCounts. Normalizing the read counts and differential expression analysis was performed with DESeq2.
Genome_build: pf3D7_V3.0.fasta
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Plasmodium falciparum

source_name: Schizont stage

growth_protocol: The P. falciparum strain 3D7, GCN5 ΔBrD and PHD1 ΔPHD clones were cultured at 37°C in a gas mixture of 5% CO2, 3% O2 and 92% N2 with type O+ RBCs at 5% hematocrit in RPMI 1640 medium supplemented with 25 mM NaHCO3, 25 mM HEPES, 50 mg/L hypoxanthine, 0.5% Albumax II and 40 mg/ml gentamicin sulfate (Trager and Jensen, 1976). Synchronization of asexual stages was performed by incubation of schizonts with RBCs for 3 h to obtain highly synchronized ring-stage parasites.

extract_protocol:
Parasites at ring, early trophozoite, late trophozoite and schizont stages were harvested by using the ZYMO RNA purification kit.
RNA libraries were prepared by using the KAPA Stranded mRNA Seq kit for the Illumina sequencing platform according to the manufacturer's protocol

treatment_protocol: Domain deletions were generated by single-crossover recobination.

value: 3D7 PHD1 {delta}PHD

value: Whole cell

value: Schizont stage

value: PHD deletion


title: L11


title: GCN5 ΔBrD Schi rep3

description:
GCN5 BrD deletion Schizont
GCN5_wo_Bro_Schi_-3_S59

value: 3D7 GCN5 {delta}BrD

value: BrD deletion


title: PHD1 ΔPHD Schi rep1

description:
PHD1 PHD deletion Schizont
0079_wo_PHD_Schi_-1_S34


title: L1


title: PHD1 ΔPHD Schi rep2

description:
PHD1 PHD deletion Schizont
0079_wo_PHD_Schi_-2_S46


title: 3D7 WT Schi rep2

value: wild type


title: GCN5 ΔBrD Schi rep1

description:
GCN5 BrD deletion Schizont
GCN5_wo_Bro_Schi_-1_S35


title: PHD1 ΔPHD L-trop rep1

description:
PHD1 PHD deletion Ltrop
0079_wo_PHD_L-trop_-1_S31

source_name: Later trophozoite stage

value: Later trophozoite stage


title: 3D7 WT Schi rep1


title: GCN5 ΔBrD L-trop rep2

description:
GCN5 BrD deletion Ltroph
GCN5_wo_Bro_L-trop_-2_S44


title: 3D7 WT Schi rep3


title: GCN5 ΔBrD L-trop rep1

description:
GCN5 BrD deletion Ltroph
GCN5_wo_Bro_L-trop_-1_S32


title: PFOS_2

value: Wild type


title: GCN5 ΔBrD Schi rep2

description:
GCN5 BrD deletion Schizont
GCN5_wo_Bro_Schi_-2_S47


title: PHD1 ΔPHD L-trop rep3

description:
PHD1 PHD deletion Ltrop
0079_wo_PHD_L-trop_-3_S55


title: L5


title: PHD1 ΔPHD L-trop rep2

description:
PHD1 PHD deletion Ltrop
0079_wo_PHD_L-trop_-2_S43


title: 3D7 WT L-trop rep3


title: 3D7 WT L-trop rep2


title: GCN5 ΔBrD L-trop rep3

description:
GCN5 BrD deletion Ltroph
GCN5_wo_Bro_L-trop_-3_S56


title: 3D7 WT L-trop rep1


title: PHD1 ΔPHD E-trop rep3

description:
PHD1 PHD deletion Etrop
0079_wo_PHD_E-trop_-3_S52

source_name: Early trophozoite stage

value: Early trophozoite stage


title: PHD1 ΔPHD E-trop rep2

description:
PHD1 PHD deletion Etrop
0079_wo_PHD_E-trop_-2_S40


title: Control_sample3

source_name: leaves

value: leaves

value: 3 yrs

value: 14 days


title: PHD1 ΔPHD E-trop rep1

description:
PHD1 PHD deletion Etrop
0079_wo_PHD_E-trop_-1_S28


title: SNU449 shNC

city: Guangzhou

first: Dinghua

last: Yang

address: 1838 North Guangzhou Avenue

institute: Nanfang Hospital

data_processing:
Data Filtering: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads
Reads Mapping performed by Bowtie2 to map clean reads to reference gene and use HISAT to reference genome
Gene quantified by FPKM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: SNU449 cell line

growth_protocol: Human prostate cancer cells SNU449 were cultured in RPMI1640 medium supplemented with 10% FBS and incubated at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA for RNA sequencing (RNA-seq) was isolated from SNU449 cells transfected with shRNA expressing lentivirus for 1 week. After extracting from cells, total RNA was quantified and integrity measured by BioAnalyzer 2100. Oligo (dT) magnetic beads were used to select mRNA with polyA tail and the target RNA was obtained after purification.
Fragmented the target RNA and reversed transcription to double-strand cDNA (dscDNA) by N6 random primer. Then End repair was performed. The dscDNA was ligated with adaptor and amplified by PCR. Denatured the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: SNU449 cells (3×105/well) were seeded in 6-well plates and transfected with shRNA expressing lentivirus for 1 week

tag: cell line

value: liver cancer cell

tag: transfection

value: Perform sequence after transfection with FZD2 shNC for 7 days

tag: gentoype

value: Negative control


title: SNU449 shFZD2

value: Perform sequence after transfection with FZD2 shRNA for 7 days

value: FZD2 deficiency


title: GCN5 ΔBrD E-trop rep2

description:
GCN5 BrD deletion Etroph
GCN5_wo_Bro_E-trop_-2_S41

value: Whole cell

tag: age


title: GCN5 ΔBrD E-trop rep3

description:
GCN5 BrD deletion Etroph
GCN5_wo_Bro_E-trop_-3_S53


title: 3D7 WT E-trop rep2


title: 3D7 WT E-trop rep1


title: 3D7 WT E-trop rep3


title: GCN5 ΔBrD E-trop rep1

description:
GCN5 BrD deletion Etroph
GCN5_wo_Bro_E-trop_-1_S29


title: PHD1 ΔPHD RING rep2

description:
PHD1 PHD deletion Ring
0079_wo_PHD_RING_-2_S37

source_name: Ring stage

value: 3D7 PHD1 {delta}PHD

value: Ring stage


title: PHD1 ΔPHD RING rep3

description:
PHD1 PHD deletion Ring
0079_wo_PHD_RING_-3_S49

value: PHD deletion


title: PHD1 ΔPHD RING rep1

description:
PHD1 PHD deletion Ring
0079_wo_PHD_RING_-1_S25


title: GCN5 ΔBrD RING rep3

description:
GCN5 BrD deletion Ring
GCN5_wo_Bro_RING_-3_S50

value: 3D7 GCN5 {delta}BrD

value: BrD deletion


title: 3D7 WT RING rep3

value: wild type


title: GCN5 ΔBrD RING rep1

description:
GCN5 BrD deletion Ring
GCN5_wo_Bro_RING_-1_S26


title: GCN5 ΔBrD RING rep2

description:
GCN5 BrD deletion Ring
GCN5_wo_Bro_RING_-2_S38


title: 3D7 WT RING rep2


title: 3D7 WT RING rep1


title: GAR2108: Raw264.7_Setd1aDel/+_DexLPS_aH3K4me3_rep4

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

country: Germany

institute: TU München

data_processing:
Reads were aligned to the mouse mm10 (GRCm38.6) or Drosophila melanogaster dm6 (BDGP6 release 78) reference genome using BWA-MEM version 0.7.13 with default parameter settings.
PCR duplicates were removed using Picard Tools version 2.0.1.
Peaks  were  called  using  MACS2 version  2.1.1.20160309 in paired-end mode with a FDR threshold of 0.05.
Blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed from the called peaks.
Peaks were annotated to the closest TSS using the ChiPpeakAnno R package v3.18.2. (doi: 10.1186/1471-2105-11-237)
Genome_build: mm10, dm6
Supplementary_files_format_and_content: The .txt files containing the annotated peak positions called with MACS2. The .bw files contain coverage data for visualization in the genome browser.

growth_protocol: Raw264.7 cells were kept at subconfluent conditions in DMEM (Gibco) supplemented with 10% FBS (heat inactivated, Sigma) and 1% penicillin/streptomycin (Gibco). Cells were cultured at 5% CO2 at 37°C in humified incubators. Medium was changed every other day.

extract_protocol: For ChIP-Seq, 40 mio cells per sample or 20 mio cells in case of H3K4me1/me2/me3 were fixed as mentioned in the sample section either for 30 min in 2 mM DSG (#C1104 ProteoChem) and 10 min 1% MeOH-free formaldehye (#2890, ThermoFisher) or 10 min 1% formaldehyde at room temperature. Remaining formaldehyde was quenched with 150 uM glycin, cells collected and washed 2x in ice-cold D-PBS. Pellets were stored at -80°C until ChIP was performed. For ChIP-Seq nuclei were extracted in Fast-IP buffer (150 mM NaCl, 5 mM EDTA (pH=7.5), 5 mM Tris (pH=7.5), 1% Triton X-100, 0.5% NP40), chromatin sonicated in shearing buffer (1% SDS, 10 uM EDTA (pH=8),50 mM Tris (pH=8)) using the Bioruptor Pico (Diagenode) for 10-15 cycles (30s on/off) at high settings. Sonicated chromatin was diluted 1:10 in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 uM EDTA (pH= 8), 16.7 uM Tris (pH=8), 167 mM NaCl) and the immunoprecipitation against the protein of interest was performed over night at 4°C. Antigen-antibody complexes were captured with protein A/G Dynabeads (Life Techn. #11202D or #11204D), 5x washed in Fast-IP buffer. Reverse crosslink was performed overnight at 65°C and proteins degraded with 100 uM proteinase K. The DNA was puriefied using Quiagen PCR purification kit according to manufacture?s manual (#28006).

treatment_protocol: Raw264.7 cells were either treated with 1 uM dexamethason (Dex, Sigma #D4902) or 0.1% EtOH (=vehicle) for 16 h followed by 3h treatment with 100 ng/ul LPS (Sigma #L2630).

value: Balb/c

tag: Sex

value: male

tag: spike-in

value: Drosophila melanogaster

value: 16h 1uM Dex, 3h 100ng/ul LPS

tag: fixation

value: 10min 1% FA

tag: antibody

value: rabbit monoclonal a-H3K4me3 (05-745R, Millipore)


title: GAR2107: Raw264.7_Setd1aDel/+_DexLPS_aH3K4me3_rep3

tag: strain


title: GAR2105: Raw264.7_Setd1aDel/+_LPS_aH3K4me3_rep3

value: 16h 0.1% EtOH, 3h 100ng/ul LPS


title: GAR2104: Raw264.7_wt_DexLPS_aH3K4me3_rep2

value: wt


title: GAR2101: Raw264.7_wt_LPS_aH3K4me3_rep2


title: GAR1958: Raw264.7_Setd1aDel/+_DexLPS_aH3K4me3_rep2


title: GAR1957: Raw264.7_Setd1aDel/+_DexLPS_aH3K4me3_rep1


title: GAR1954: Raw264.7_Setd1aDel/+_LPS_aH3K4me3_rep1


title: Comfrey Chicken 26

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

institute: FBN Dummerstorf

hyb_protocol: Labelled DNA was hybridized on ChiGene-1_0-st Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor. Raw intensities were normalized using the RMA (Robust Multichip Average) approach

organism: Gallus gallus

source_name: Comfrey supplement_whole blood cells

label_protocol: Total RNA samples were used to generate biotinylated DNA targets using the GeneChip WT PLUS Regent Kit Affymetrix, Santa Clara, CA, USA). Processing of arrays followed manufacturer’s instructions according to the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

extract_protocol: Blood cloths were ground into powder in liquid nitrogen. Approximately 100 mg of each sample was subjected to 600 µl of TRIzol reagent (Invitrogen, Karlsruhe, Germany). After DNaseI treatment the RNA was column-purified using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: Standard control diet vs. standard diet supplemented with Comfrey

tag: breed

value: broiler chicken

value: female

tag: age (month)

tag: treatment/diet

value: Comfrey supplement

tag: tissue/cell type

value: whole blood cells


title: Comfrey Chicken 32


title: Comfrey Chicken 30


title: NL32

tag: maize genetic resource

value: Non-Lancaster (Iowa dent&BSSS)

tag: tissue

value: leaf

value: V4 stage


title: Comfrey Chicken 27

source_name: Control diet_whole blood cells

value: Control diet


title: Comfrey Chicken 29


title: Comfrey Chicken 23


title: Comfrey Chicken 31


title: Comfrey Chicken 20


title: Comfrey Chicken 25


title: GAR1951: Raw264.7_wt_LPS_aH3K4me3_rep1

tag: cell type

tag: treatment


title: GAR2103: Raw264.7_wt_DexLPS_aH3K4me3_rep1

tag: genotype


title: Comfrey Chicken 19


title: MUC9125: Raw264.7_wt_DexLPS_aH3K4me2_rep5

value: rabbit polyclonal a-H3K4me2 (ab7766, Abcam)


title: Comfrey Chicken 24


title: Comfrey Chicken 22


title: C24A

source_name: Control_24h post L4

tag: genotype/variation

value: WT

tag: developmental stage

value: L4 stage animal

value: Control

tag: timepoint

value: 24h post L4


title: Comfrey Chicken 18

tag: Sex


title: Comfrey Chicken 28


title: Comfrey Chicken 17

value: male


title: GAR1955: Raw264.7_Setd1aDel/+_LPS_aH3K4me3_rep2

value: Balb/c

tag: spike-in

value: Drosophila melanogaster

value: 10min 1% FA

value: rabbit monoclonal a-H3K4me3 (05-745R, Millipore)


title: Comfrey Chicken 16

value: broiler chicken

value: female


title: Comfrey Chicken 21

value: Comfrey supplement

value: whole blood cells


title: MUC11273: Raw264.7_Setd1aDel/+_LPS_aH3K4me2_rep3

value: 16h 0.1% EtOH, 3h 100ng/ul LPS

tag: fixation


title: MUC9124: Raw264.7_Setd1aDel/+_DexLPS_aH3K4me2_rep3

value: 16h 1uM Dex, 3h 100ng/ul LPS

tag: antibody


title: Comfrey Chicken 14


title: MUC11271: Raw264.7_wt_LPS_aH3K4me2_rep2

tag: strain

value: wt


title: MUC11272: Raw264.7_Setd1aDel/+_DexLPS_aH3K4me2_rep2

value: rabbit polyclonal a-H3K4me2 (ab7766, Abcam)


title: GAR21492157: Raw264.7_wt_DexLPS_aH3K4me2_rep3


title: Comfrey Chicken 15

tag: breed

value: Control diet


title: MUC11270: Raw264.7_wt_DexLPS_aH3K4me2_rep4


title: GAR1948: Raw264.7_Setd1aDel/+_DexLPS_aH3K4me2_rep1


title: Comfrey Chicken 13

tag: age (month)


title: Comfrey Chicken 11

tag: treatment/diet


title: Comfrey Chicken 9

tag: tissue/cell type


title: Comfrey Chicken 7


title: Comfrey Chicken 6


title: Comfrey Chicken 10


title: GAR1947: Raw264.7_Setd1aDel/+_LPS_aH3K4me2_rep2


title: Comfrey Chicken 4


title: Comfrey Chicken 5


title: #3 Daf- B mem

city: Umeå

first: Johan

last: Henriksson

address: 6K och 6L, Sjukhusområdet

country: Sweden

institute: Molecular Infection Medicine Sweden (MIMS)

hyb_protocol: 5ug of fragmented and biotinylated ss DNA target were hybridized to Affymetrix Human Clariom D arrays in a GeneChip Hybridization Oven 645 (16h-18h at 45C). The arrays were washed and stained in a Gene Chip Fluidics Station 450.

scan_protocol: Arrays were scanned in an Affymetrix Gene Chip Scanner 3000 7g according to standard protocol.

data_processing: Data was loaded in R and analyzed using the affy package. RMA transformation was applied

source_name: DAF-negative memory B cells

label_protocol: Affymetrix WT Pico kit with 9 cycles amplification was used to generate amplified and biotinylated sense-strand DNA targets from approximately 2ng total RNA.

growth_protocol: Human tonsils were homogenized, passed through a 70 µm cell strainer and frozen in FBS with 10% DMSO.

extract_protocol: Cells in RLT buffer were processed with Qiagen RNAeasy Mini Kit with DNAse treatment.

treatment_protocol: Tonsil suspensions were thawed and stained with antibodies, then sorted on a BD FACSAriaIII. GC B cells were gated as viable, CD3-, CD14-, CD19+, CD20+, CD38+, IgD-. Then GC B cells were divided into DAFhi and DAFlo.

tag: patient

value: Daf-

value: Bmem


title: Comfrey Chicken 12


title: #3 Daf+ Bmem

source_name: DAF-positive memory B cells

value: Daf+


title: #2 Daf+ Bmem


title: #3 Daf- GC B cells

source_name: DAF-negative GC B cells


title: Comfrey Chicken 8


title: GAR1946: Raw264.7_Setd1aDel/+_LPS_aH3K4me2_rep1

value: male


title: #2 Daf- B mem


title: GAR1942: Raw264.7_wt_LPS_aH3K4me2_rep1

value: Balb/c


title: GAR1945: Raw264.7_wt_DexLPS_aH3K4me2_rep2

value: Drosophila melanogaster


title: #1 Daf+ Bmem


title: #2 Daf+ GC B cells

source_name: DAF-positive GC B cells


title: GAR1944: Raw264.7_wt_DexLPS_aH3K4me2_rep1

value: 10min 1% FA


title: #3 Daf+ GC B cells


title: GAR2146: Raw264.7_wt_DexLPS_aGR_rep2

value: no

value: 30min 2mM DSG/10min 1% FA

value: rabbit polyclonal a-GR (24050-1-AP, ProteinTech)


title: GAR2148: Raw264.7_wt_DexLPS_aGR_rep3


title: #1 Daf- B mem


title: Comfrey Chicken 1

value: broiler chicken

value: female


title: #1 Daf- GC B cells


title: Comfrey Chicken 2

value: Comfrey supplement

value: whole blood cells


title: Comfrey Chicken 3


title: #1 Daf+ GC B cells


title: RNA of DAS3

first: Wenru

last: Li

address: No.100, Xianliezhong Road

institute: Institute of Microbiology, Guangdong Academy of Sciences

data_processing:
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 Vontaining 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  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008).
Genome_build: Pseudomonas aeruginosa PAO1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Pseudomonas aeruginosa PAO1

source_name: Transcriptome of DAS-treated P. aeruginosa PAO1

growth_protocol: Every 50 mL LB medium was inoculated exponential growth phase of P. aeruginosa PAO1, with the bacterial concentration of 1.0E8 CFU/mL.  All the three triplicate experiment groups were incubated in a water bath shaker at 37C with a shaking rate at 180 rpm for 5 hours.

extract_protocol:
Cells of P. aeruginosa PAO1 were 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 3 ug of total RNA for the Vonstruction of sequencing libraries.
Strand specific library: The construct method of strand specific library is similar to that of NEB library expect that when synthesizing the second strand cDNA, dTTP is replayed by dUTP. After overhangs of the purified double-stranded cDNA are converted into blunt ends, adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization, the second strand cDNA is digested by USER enzyme. The following step is identical with NEB library construction.

treatment_protocol: LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAO1 at a concentration of 1.0E8 CFU/mL. Dially sulfide and diallyl ether were then added at a concentration of either 0 (control) or 0.625 μl/mL, respectively, in triplicate. All nine experiment groups were incubated in a water bath shaker at 37C with a shaking rate of 180 rpm for 5 h.

value: Diallyl sulfide (DAS)

tag: growth phase

value: exponential


title: RNA of DAS1


title: RNA of DAS2


title: Lin-CD34-CD16+CD56- cells - progeny, biol rep 8

city: Rome

first: Andrea

last: Pelosi

state: RM

address: Viale di San Paolo, 15

department: Laboratories

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

hyb_protocol: Hybridization of each fragmented and labeled target was performed using the GeneChip® Hybridization, Wash and Stain Kit (Affymetrix; Thermo Fisher Scientific, Inc).  Targets were diluted in hybridization buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes, incubated at 45 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip® cartridge. A single GeneChip® Human Clariom D was then hybridized with each biotin-labeled sense target.  Hybridizations were performed for 16 h at 45 °C in a rotisserie oven (60 RPM). GeneChip® cartridges were washed and stained with GeneChip® Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0001 standard protocol.

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G using default parameters. Affymetrix GeneChip® Command Console software (AGCC) was used to acquire GeneChip® images and generate .DAT and .CEL files

data_processing: The data were analyzed with Transcriptome Analysis Console v. 4.0 software (Thermo Fisher Scientific) using default Affymetrix configuration settings and gene-level SST-RMA summarization alghorithm.

source_name: Lin-CD34-CD16+CD56- progeny

label_protocol: The total RNA (10 ng) was reverse transcribed using GeneChip® WT Pico Reagent Kit (Affymetrix; Thermo Fisher Scientific, Inc.) following manufacturer’s protocol.  The obtained antisense cRNA was purified using Nucleic Acid Binding Beads (GeneChip® WT Pico Reagent Kit, Affymetrix) and used as a template for reverse transcription to produce single-stranded DNA in the sense orientation. During this step, dUTP was incorporated. The DNA was then fragmented using uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) and labeled with DNA labeling reagent covalently linked to biotin using terminal deoxynucleotidyl transferase (TdT, GeneChip® WT Pico Reagent Kit, Affymetrix)

extract_protocol: Total RNA was extracted using TRIzol reagent and purified with RNeasy Micro kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s protocol

tag: cell type

value: NKG2C+ NK cells

tag: cell subtype

value: Lin-CD34-CD16+CD56- progeny


title: CD34+DNAM-1brCXCR4+ cells - progeny, biol rep 1

source_name: CD34+DNAM-1brCXCR4+ progeny

value: CD34+DNAM-1brCXCR4+ progeny


title: Lin-CD34-CD16+CD56- cells - progeny, biol rep 2


title: Peripheral blood - mature NK cells, biol rep 2

source_name: Mature peripheral blood NK cells

value: Mature peripheral blood NK cells


title: RNA of DAO3

source_name: Transcriptome of DAE-treated P. aeruginosa PAO1

tag: treatment

value: diallyl ether (DAE)


title: RNA of DAO1


title: RNA of control3

source_name: Transcriptome of control of P. aeruginosa PAO1

value: native; control


title: RNA of DAO2


title: Longissimus_Genmascq_Pig_912

city: SAINT GILLES

first: Frederic

last: Herault

address: 16 le Clos

department: Animal Genetic

country: France

institute: INRAE

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers containing 300 ng of cyanine 3-labeled cRNA sample per hybridization. The hybridization reactions were performed at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit. Slides were disassembled and washed for 1 minute at room temperature in SSPE wash solution 1 (6x SSPE + 0.005% Sarcosine) and in SSPE wash solution 2 (0.06x SSPE + 0.005% Sarcosine) for one minute at room temperature. The microarrays were then treated with Agilent Stabilization and Drying Solution at room temperature for 30 seconds.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Raw data from 15198 probes fluorescent hybridization signal intensities were log transformed and centered within sample by subtraction of sample median from all raw values.

organism: Sus scrofa

source_name: Longissimus lumborum muscle

label_protocol: Total RNA (500 ng) from each animal was labeled individually with Cy3 by using the Quick-Amp Labeling Kit following the manufacturer’s instructions.

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

tag: gender

value: F

tag: pig number

tag: ChIP


title: Longissimus_Genmascq_Pig_911


title: Longissimus_Genmascq_Pig_913


title: RNA of control2


title: Lin-CD34-CD16+CD56- cells - progeny, biol rep 5


title: Longissimus_Genmascq_Pig_909


title: Peripheral blood - mature NK cells, biol rep 3


title: Longissimus_Genmascq_Pig_893

value: M


title: Longissimus_Genmascq_Pig_906


title: RNA of control1


title: Lin-CD34-CD16+CD56- cells - progeny, biol rep 4


title: CD34+DNAM-1brCXCR4+ cells - progeny, biol rep 2


title: Lin-CD34-CD16+CD56- cells - progeny, biol rep 7


title: Longissimus_Genmascq_Pig_891


title: Longissimus_Genmascq_Pig_892


title: Longissimus_Genmascq_Pig_883


title: Longissimus_Genmascq_Pig_881


title: Peripheral blood - mature NK cells, biol rep 1


title: Lin-CD34-CD16+CD56- cells - progeny, biol rep 1


title: Longissimus_Genmascq_Pig_889


title: Longissimus_Genmascq_Pig_882


title: Longissimus_Genmascq_Pig_879


title: Longissimus_Genmascq_Pig_886


title: Lin-CD34-CD16+CD56- cells - progeny, biol rep 3


title: Longissimus_Genmascq_Pig_880


title: Longissimus_Genmascq_Pig_781


title: Longissimus_Genmascq_Pig_801


title: Longissimus_Genmascq_Pig_782


title: Longissimus_Genmascq_Pig_804


title: Male TCDD 1000 ng/kg rep5 [Bisulfite-Seq]

city: Toronto

first: Stephenie

last: Prokopec

state: Ontario

address: 661 University Avenue, Suite 510

country: Canada

institute: Ontario Institute for Cancer Research

data_processing:
BS-Seq reads were aligned with Bismark (v0.15.0), using Bowtie2 (v2.2.6); Bismark was run using default settings, using single-end, unidirectional fastq files.
Aligned files were coordinate sorted using samtools (v1.3) and library-level merged with duplicate reads marked using picard tools (v1.141)
Bismark’s methylation extractor tool, with --comprehensive, --merge_non_CpG, --cytosine_report, --CX, --split_by_chromosome, and --bedGraph settings, was used to extract the number of methylated and unmethylated reads at each CpG position in each sample.
The resulting data files for each sample were loaded into the R statistical environment (v3.3.1) and pooled across treatment groups using the DMRcaller package (v1.6.0) on a per-chromosome basis (due to computational intensity).
Genome_build: rn6
Supplementary_files_format_and_content: <SAMPLE>.merged.CX_report_merged.txt.gz: tab separated file containing <chromosome, position, strand, count methylated, count unmethylated, C-context, trinucleotide context>

source_name: liver, male Sprague-Dawley,TCDD treated F0, 1000 ng/kg

growth_protocol: Upon weaning, same-sex littermates were housed in stainless steel, wire-mesh bottom cages with pelleted rat feed (R36, Lactamin, Stockholm, Sweden) and tap water available ad libitum. The housing environment was maintained at 21±0.2°C and relative humidity at 50±3%, with a 12/12h artificial light/dark cycle.

extract_protocol:
Target capture was carried out using the Agilent SureSelect XT Rat Methyl-Seq kit.
Library preparation, quality control, target capture and sequencing was performed at the Biomedicum Functional Genomics Unit (FuGU) at the University of Helsinki.  Sequencing was performed using Illumina NextSeq 500 with the NextSeq 500/550 v2 kit (High Output) to produce single-end directional reads (75bp read length).

treatment_protocol: Pregnant F0 dams were treated by oral gavage with a single bolus of either TCDD (30, 100, 300 or 1000 ng/kg) dissolved in corn oil vehicle or vehicle alone (5mL/kg) on gestational day 11.

value: Sprague-Dawley

tag: Sex

value: male

tag: tissue

value: testes

tag: lineage (f0 dam, f1 male, f2 male, f3)


title: Longissimus_Genmascq_Pig_878


title: Male CornOil rep5 [Bisulfite-Seq]

source_name: liver, male Sprague-Dawley, corn oil treated F0

value: Corn Oil vehicle


title: Male TCDD 1000 ng/kg rep3 [Bisulfite-Seq]


title: Longissimus_Genmascq_Pig_777


title: Longissimus_Genmascq_Pig_739


title: Longissimus_Genmascq_Pig_752


title: Longissimus_Genmascq_Pig_708


title: Longissimus_Genmascq_Pig_773


title: Longissimus_Genmascq_Pig_778


title: Longissimus_Genmascq_Pig_765


title: Longissimus_Genmascq_Pig_715


title: Longissimus_Genmascq_Pig_768


title: Longissimus_Genmascq_Pig_719


title: Longissimus_Genmascq_Pig_707


title: Longissimus_Genmascq_Pig_761


title: Longissimus_Genmascq_Pig_747


title: Longissimus_Genmascq_Pig_746


title: Longissimus_Genmascq_Pig_720


title: Male CornOil rep2 [Bisulfite-Seq]


title: Longissimus_Genmascq_Pig_697


title: Male TCDD 1000 ng/kg rep7 [Bisulfite-Seq]


title: Male CornOil rep1 [Bisulfite-Seq]


title: Male TCDD 1000 ng/kg rep1 [Bisulfite-Seq]


title: Longissimus_Genmascq_Pig_703


title: Longissimus_Genmascq_Pig_726


title: Longissimus_Genmascq_Pig_713


title: Longissimus_Genmascq_Pig_741


title: Male CornOil rep3 [Bisulfite-Seq]


title: Longissimus_Genmascq_Pig_688


title: Longissimus_Genmascq_Pig_677


title: Longissimus_Genmascq_Pig_691


title: BMDM_GR_rep3

data_processing:
Reads were aligned to the mouse mm10 reference genome using BWA-MEM version 0.7.13 with default parameter settings.
PCR duplicates were removed using Picard Tools version 1.119.
Peaks  were  called  using  MACS2 version  2.1.0 in paired-end mode with a FDR threshold of 0.05.
Blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed from the called peaks.
Peaks were annotated to the closest TSS using the ChiPpeakAnno R package v3.16.0. (doi: 10.1186/1471-2105-11-237)
Genome_build: mm10
Supplementary_files_format_and_content: The .txt files containing the annotated peak positions called with MACS2 version 2.1.0. The .bw files contain coverage data for visualization in the genome browser.

source_name: bone marrow-derived macrophages

growth_protocol: Macrophages were differentiated from the bone marrow of wildtype male mice. Shortly femur and tibia were dissected from mice and the bone marrow flushed into Falcon tubes with RPMI (ThermoFisher Scientific). AKC lysis was performed to remove erythrocytes and cells seperated from tissue residues by Ficoll gradient (Ficoll-Paque Premium; GE Healthcare #17-5442-02 ). The isolated bone marrow-derived cells were differentiated in DMEM (4.5 g/l glucose, Sigma) containing 30% of supernatant from L929 cells (producing M-CSF and GM-CSF), 20% heat-inactivated FBS and 1% Pen/Strep for 7 days on non-tissue culture treated plates. The medium was changed after 3 days. After 7 days the differentiated macrophages were dissociated using Versene (ThermoFischer Scientific #15040066) at RT and seeded at 20 mio cells/15-cm plate in serum-free conditions (macrophage-SFM medium (ThermoFisher Scientific #12065074)) for treatment and fixation.

extract_protocol:
For ChIP-Seq, 40 mio cells per sample were fixed as mentioned in the sample section either for 30 min in 2 mM DSG (#C1104 ProteoChem) and 10 min 1% MeOH-free formaldehye (#2890, ThermoFisher) or 10 min/15 min 1% formaldehyde at room temperature. Remaining formaldehyde was quenched with 150 uM glycins, cells collected and washed 2x in ice-cold D-PBS. Pellets were stored at -80°C until ChIP was perormed. For ChIP-Seq nuclei were extracted in Fast-IP buffer (150 mM NaCl, 5 mM EDTA (pH=7.5), 5 mM Tris (pH=7.5), 1% Triton X-100, 0.5% NP40), chromatin sonicated in shearing buffer (1% SDS, 10 uM EDTA (pH=8),50 mM Tris (pH=8)) using the Bioruptor Pico (Diagenode) for 10-15 cycles (30s on/off) at high settings. Sonicated chromatin was diluted 1:10 in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 uM EDTA (pH= 8), 16.7 uM Tris (pH=8), 167 mM NaCl) and the immunoprecipitation against the protein of interest was performed over night at 4°C. Antigen-antibody complexes were captured with protein A/G Dynabeads (Life Techn. #11202D or #11204D), 5x washed in Fast-IP buffer. Reverse crosslink was performed overnight at 65°C and proteins degraded with 100 uM proteinase K. The DNA was puriefied using Quiagen PCR purification kit according to manufacture‘s manual (#28006).
Library preperation was performed from 2 ng of ChIP DNA using the Kapa Hyper Prep Kit with PCR library amplification (#KK8504, KapaBiosystems) according to the manufactur's protocol. Shortly, ChIP DNA was end-repaired and A-tailed before adapter ligation. After adapter ligation, the ChIP DNA was purified with Agencourt AMPure XP beads (#A63880, Beckman Coulter) and size-selected for 360-600 bp using the Pippin Prep System from Saga Science. The size-selected library is amplified by PCR using the Kapa Hyper Prep Kit (#KK8504,KapaBiosystems) and purified terminally with Agencourt AMPure XP beads (#A63880, Beckman Coulter).

treatment_protocol: Macrophages were either treated with 1 uM dexamethason (Dex, Sigma #D4902) or 0.1% EtOH (=vehicle) for 16 h followed by 3h treatment with 100 ng/ul LPS (Sigma #L2630).

tag: spike-in

value: no

value: 16h 1uM Dex, 3h 100ng/ul LPS

tag: fixation

value: 30min 2mM DSG/10min 1% FA

tag: antibody

value: rabbit polyclonal a-GR (24050-1-AP, ProteinTech)


title: Longissimus_Genmascq_Pig_672


title: Longissimus_Genmascq_Pig_674


title: Longissimus_Genmascq_Pig_676


title: Longissimus_Genmascq_Pig_663


title: Longissimus_Genmascq_Pig_661


title: Longissimus_Genmascq_Pig_652


title: Longissimus_Genmascq_Pig_642


title: Longissimus_Genmascq_Pig_646


title: Longissimus_Genmascq_Pig_653


title: Longissimus_Genmascq_Pig_668


title: Longissimus_Genmascq_Pig_680


title: Longissimus_Genmascq_Pig_728


title: Longissimus_Genmascq_Pig_660


title: Longissimus_Genmascq_Pig_671


title: Longissimus_Genmascq_Pig_667


title: Longissimus_Genmascq_Pig_629


title: Lin-CD34-CD16+CD56- cells - progeny, biol rep 6


title: BMDM_DexLPS_Cxxc1_rep1

value: rabbit monoclonal a-CGBP (ab198977, Abcam)

tag: strain


title: Longissimus_Genmascq_Pig_626


title: BMDM_LPS_Cxxc1_rep3

value: 16h 0.1% EtOH, 3h 100ng/ul LPS


title: BMDM_DexLPS_Cxxc1_rep2


title: Longissimus_Genmascq_Pig_630


title: BMDM_LPS_Cxxc1_rep1

value: rabbit polyclonal a-CGBP (ab198977, Abcam)


title: BMDM_LPS_Cxxc1_rep2


title: Longissimus_Genmascq_Pig_622


title: Longissimus_Genmascq_Pig_639


title: BMDM_LPS_Setd1a_rep2

value: 10min 1% FA

value: rabbit polyclonal a-hSet1 (A300-289A, BethylLabs)


title: BMDM_DexLPS_H3K27Ac_rep2

value: rabbit polyclonal a-H3K27Ac (ab4729, Abcam)


title: Longissimus_Genmascq_Pig_616


title: BMDM_DexLPS_Setd1a_rep2


title: Longissimus_Genmascq_Pig_618


title: BMDM_DexLPS_H3K27Ac_rep1


title: Longissimus_Genmascq_Pig_609


title: BMDM_LPS_Setd1a_rep1


title: Longissimus_Genmascq_Pig_619


title: Longissimus_Genmascq_Pig_625


title: Longissimus_Genmascq_Pig_605


title: BMDM_LPS_H3K27Ac_rep1


title: Longissimus_Genmascq_Pig_612


title: BMDM_DexLPS_H3K4me1_rep3

value: Drosophila melanogaster

value: rabbit polyclonal a-H3K4me1 (C15410194, Diagenode)


title: Longissimus_Genmascq_Pig_613

value: M


title: BMDM_DexLPS_H3K4me1_rep2


title: BMDM_DexLPS_Setd1a_rep1


title: Longissimus_Genmascq_Pig_615


title: BMDM_DexLPS_H3K4me1_rep1


title: BMDM_LPS_H3K4me1_rep3


title: BMDM_LPS_H3K27Ac_rep2


title: Longissimus_Genmascq_Pig_620


title: Longissimus_Genmascq_Pig_604


title: BMDM_LPS_H3K4me1_rep2


title: Longissimus_Genmascq_Pig_590


title: Longissimus_Genmascq_Pig_602


title: BMDM_DexLPS_H3K4me3_rep3

value: rabbit monoclonal a-H3K4me3 (05-745R, Millipore)


title: BMDM_DexLPS_H3K4me3_rep2

value: male


title: Longissimus_Genmascq_Pig_593


title: Longissimus_Genmascq_Pig_607


title: BMDM_LPS_H3K4me3_rep1


title: BMDM_LPS_H3K4me3_rep2


title: Longissimus_Genmascq_Pig_587


title: Longissimus_Genmascq_Pig_576


title: BMDM_LPS_H3K4me1_rep1


title: Longissimus_Genmascq_Pig_572


title: Longissimus_Genmascq_Pig_583


title: Longissimus_Genmascq_Pig_573


title: Longissimus_Genmascq_Pig_564

value: F


title: Longissimus_Genmascq_Pig_559


title: BMDM_LPS_H3K4me2_rep3

value: rabbit polyclonal a-H3K4me2 (ab7766, Abcam)


title: Longissimus_Genmascq_Pig_565


title: BMDM_LPS_H3K4me3_rep3


title: BMDM_DexLPS_H3K4me2_rep1

value: no


title: BMDM_DexLPS_H3K4me3_rep1

value: 16h 1uM Dex, 3h 100ng/ul LPS


title: BMDM_LPS_H3K4me2_rep2


title: Longissimus_Genmascq_Pig_556


title: Longissimus_Genmascq_Pig_555


title: BMDM_LPS_H3K4me2_rep1


title: StarParent_2

city: Serdang

first: Gayathri

middle: Thevi

last: Selvarajah

state: Selangor

address: University Putra Malaysia

department: Faculty of Veterinary Medicine

country: Malaysia

institute: University Putra Malaysia

description: CMT-Star cells grown in culture

hyb_protocol: 0.825 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Hi-RPM Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Canine Gene Expression Microarray (V2:021193) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) with 5 μm resolution at wavelengths of 532 nm (Cy3) using the extended dynamic range (10–100 %) setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters with protocol GE1_1200_Jun14 to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Canis lupus familiaris

source_name: Cell line CMT-Star, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were maintained in DMEM with 10% FBS in 5% CO2 at 37 degrees Celcius.

extract_protocol: Total RNA was extracted from CMT-Stylo cells, CMT-Star cells and their respective cancer stem cells using the RNeasy Plus Mini Kit (Qiagen®) according to manufacturer’s instructions. To ensure DNA-free extracted RNA, a two-step genomic DNA removal was employed which included the manufacturer’s recommendation using the gDNA column spin and additional incubation with RNase-free DNase (Qiagen®) to digest genomic DNA. The concentration and purity of the RNA was determined using nano-spectrophotometer. RNA integrity number (RNA) was determined using a Bioanalyzer, and samples with RIN 7 and above were used for one color microarray hybridization using Agilent platform.

treatment_protocol: To develop CMT-Star cells from CMT-Stylo, the cells were exposed to increasing concentration of doxorubicin in complete growth media, until the cells became resistant at the level of 100 nM doxorubicin exposure over several months. To isolate cancer stem cells (CSC) from CMT-Stylo and CMT-Star cell respectively, Phycoerythrin (PE) conjugated CD24 antibody (clone M1/69, BD Pharmingen) and Allophycocyanin (APC) conjugated CD44 antibody (clone IM7, BD Pharmingen) were used.

value: cell line

value: doxorubicin treated


title: StyloParent_2

description: CMT-Stylo cells grown in culture

source_name: Cell line CMT-Stylo, replicate 2

value: non treated


title: BMDM_DexLPS_H3K4me2_rep2


title: StyloParent_1

description: CMT-Stylo cells grown in culture

source_name: Cell line CMT-Stylo, replicate 1


title: StarParent_1

description: CMT-Star cells grown in culture

source_name: Cell line CMT-Star, replicate 1


title: Longissimus_Genmascq_Pig_552


title: StarCSC_2

description: Cancer stem cells (CSC) isolated from CMT-Star cells which are CD44+, CD24-/low and ALDH+.

source_name: Cells sorted from CMT-Star through flow cytometry, replicate 2

value: sorted cells from cell line


title: StarCSC_1

source_name: Cells sorted from CMT-Star through flow cytometry, replicate 1


title: StyloCSC_2

description: Cancer stem cells (CSC) isolated from CMT-Stylo cells which are CD44+, CD24-/low and ALDH+.

source_name: Cells sorted from CMT-Stylo through flow cytometry, replicate 2


title: Longissimus_Genmascq_Pig_551


title: Longissimus_Genmascq_Pig_537


title: Longissimus_Genmascq_Pig_547


title: Longissimus_Genmascq_Pig_539


title: Tet2WT KitD816V-Rep1

city: MARSEILLE

first: erinn

last: soucie

address: 27 Boulevard Lei Roure

institute: CRCM

data_processing:
Sequenced reads were trimmed using Trim Galore v0.4.2 (parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --retain_unpaired --stringency 5).
Reads were aligned to the mouse mm10 genome using BSMAP v2.74 (parameters -v 2 -w 100 -r 1 -x 400 -m 30 -n 1 -D C-CGG).
We extracted methylation percent values as the ratio of the number of Cs over the total number of Cs and Ts with methratio.py from BSMAP v2.74 (parameters -z -u -g).
We then filtered CGs to have a minimum sequencing depth of 8x using custom developped scripts in R v3.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: IGV files containing methylation scores for all CGs with at least 8x sequencing depth.

source_name: Primary murine mast cells derived from bone marrow, Tet2+/+ KitD816V , Rep1

growth_protocol: Primary mast cells were derived from bone marrow of either Tet2+/+ or Tet2-/- C57BL/6J Tet2LacZ

extract_protocol:
Sorted GFP-positive/KitD816V and GFP-negative/control cell fractions were directly lysed and genomic DNA was isolated using the DNAeasy kit (Qiagen) for RRBS.
RRBS libraries were prepared as previously described (Auclair G. et al, Genome Biol. 15, 545, 2014). Briefly, we digested 100 ng of genomic DNA 5 hours with MspI (Thermo Scientific), followed by end-repair and A-tailing (Klenow fragment, Thermo Scientific) and ligation to methylated adapters (T4 DNA ligase, Thermo Scientific) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel with the MinElute kit (Qiagen) and bisulfite-converted with the EpiTect Bisulfite kit (Qiagen) using two consecutive rounds of conversion. Final RRBS libraries were amplified with 14 cycles of PCR.

treatment_protocol: mice, isolated and cultured in OptiMEM/10% FCS (Life Technologies) media supplemented with 10 ng/ml IL3 (Peprotech), 50ug/ml Penicillin/streptomycin, and 1% beta-mercaptoethanol (both Life Technologies) on tissue culture treated plastic, at 37°C, 5% CO2. Non-adherent cells were selected for 15 days under these conditions, at which point cultures were infected with lenti-virus carrying the KitD816V allele and GFP (ires). For infection, we used a single 2h spinoculation in the presence of 6μg/ml polybrene. Infected cells were further expanded for 15 days, for a total of 30 days of in vitro culture, and then GFP-negative and positive fractions (cultures were 40-80% GFP-positive) were FACS sorted on FACSAria using DIVATM (Becton- Dickinson) software for direct lysis and gDNA isolation.

value: C57BL/6J Tet2LacZ

tag: genotype

value: Tet2+/+ KitD816V


title: Longissimus_Genmascq_Pig_517


title: Longissimus_Genmascq_Pig_542


title: Longissimus_Genmascq_Pig_546


title: Longissimus_Genmascq_Pig_550


title: Longissimus_Genmascq_Pig_535


title: Tet2WT KitD816V-Rep2

source_name: Primary murine mast cells derived from bone marrow, Tet2+/+ KitD816V , Rep2


title: Longissimus_Genmascq_Pig_516


title: Longissimus_Genmascq_Pig_531


title: Longissimus_Genmascq_Pig_499


title: Longissimus_Genmascq_Pig_532


title: Longissimus_Genmascq_Pig_493


title: Longissimus_Genmascq_Pig_509


title: Longissimus_Genmascq_Pig_530


title: StyloCSC_1

source_name: Cells sorted from CMT-Stylo through flow cytometry, replicate 1


title: Longissimus_Genmascq_Pig_492


title: Longissimus_Genmascq_Pig_498


title: Longissimus_Genmascq_Pig_534


title: Longissimus_Genmascq_Pig_490


title: Longissimus_Genmascq_Pig_424


title: Tet2WT control-Rep1

source_name: Primary murine mast cells derived from bone marrow, Tet2+/+ , Rep1


title: Tet2WT control-Rep2

source_name: Primary murine mast cells derived from bone marrow, Tet2+/+ , Rep2


title: Longissimus_Genmascq_Pig_420


title: Tet2KO KitD816V-Rep2

source_name: Primary murine mast cells derived from bone marrow, Tet2-/- KitD816V , rep2

value: Tet2-/- KitD816V


title: Tet2KO KitD816V-Rep1

source_name: Primary murine mast cells derived from bone marrow, Tet2-/- KitD816V , Rep1


title: Tet2KO control-Rep1

source_name: Primary murine mast cells derived from bone marrow, Tet2-/- , Rep1


title: Tet2KO control-Rep2

source_name: Primary murine mast cells derived from bone marrow, Tet2-/- , Rep2


title: Longissimus_Genmascq_Pig_422

source_name: Longissimus lumborum muscle


title: Longissimus_Genmascq_Pig_413


title: Longissimus_Genmascq_Pig_417


title: Longissimus_Genmascq_Pig_414


title: Longissimus_Genmascq_Pig_412


title: Longissimus_Genmascq_Pig_415


title: Longissimus_Genmascq_Pig_662


title: Longissimus_Genmascq_Pig_403


title: Longissimus_Genmascq_Pig_410


title: Longissimus_Genmascq_Pig_408


title: VX2012022_PBMC_Day14

city: Beijing

first: Yiming

last: Shao

state: Beijing

address: No. 155 Changbai Road, Changping District

department: National Center for AIDS/STD Control and Prevention

institute: Chinese Center for Disease Control and Prevention

hyb_protocol: After hybridization on Human PrimeView Arrays for 16 h at 45C and 60 rpm in Hybridization Oven 640 (Affymetrix, Santa Clara, CA, USA), slides were washed and stained with a Fluidics Station 450 (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Scanning was performed on a seventh-generation GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA, USA). Affymetrix GCOS software was used to perform image analysis and generate raw intensity data.

data_processing: Initially, data quality was assessed by background level, 3 labeling bias, RNA quality and pair-wise correlation among samples. For the PrimeView chip, the customized CDF (version 22, ENTREZG) downloaded from the BrainArray website was performed in probe set mapping. IQR was applied for raw data filtering using the genefilter package, and the threshold was set to remove probes/genes with IQR less than the 50th percentile of the IQR across all probes/genes. Normalization was performed with RMA algorithm that includes global background adjustment and quantile normalization. The resulting matrix showed genes as rows and samples as columns was log2 transformed and used as input for linear modeling using the limma package. The limma package was performed to identify differentially expressed genes (DEG) at any time point post immunization, compared with baseline (Day 0). Empirical Bayes moderation of the standard error and Benjamini and Hochberg false-discovery rate (FDR) correction for multiple testing were employed, and the criteria for differentially expressed genes (DEG) were threshold fold change more than 1.3 and BH adjusted FDR less than 0.05.

label: Biotin

source_name: human Day14

label_protocol: Total RNA were amplified, labeled and purified by using the GeneChip 3IVT Express Kit (Affymetrix, Santa Clara, CA, USA) followed the manufacturer instructions to obtain biotin labeled cRNA.

extract_protocol: After PMBC isolation, 1 million PBMC cells were lysed in 1 ml of TRIzol (Life technologies, Carlsbad, CA, USA) immediately and stored at -80C. The samples were thawed and RNA extracted following the manufacturer instructions. The quality of the RNA was assessed by using Nanodrop 2000 Spectrometer (Thermo Scientific, MA, USA) as well as by visualization of the integrity of the 28S and 18S band on Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, USA).  Qualified total RNA was further purified by RNeasy micro kit (QIAGEN, GmBH, Germany) and removed genomic contamination by RNase-Free DNase Set (QIAGEN, GmBH, Germany).  The purified RNA was stored at -80C.

value: PBMC

tag: time point

tag: nab respond

value: HighResponder

tag: vaccination interval regimen

tag: subject id


title: VX2012022_PBMC_Day7

source_name: human Day7

tag: cell type


title: VX2012022_PBMC_Day0

source_name: human Day0


title: VX2012019_PBMC_Day28

source_name: human Day28


title: Longissimus_Genmascq_Pig_398


title: VX2012019_PBMC_Day7


title: VX2012019_PBMC_Day14


title: VX2012022_PBMC_Day28


title: VX2012019_PBMC_Day3

source_name: human Day3


title: VX2012018_PBMC_Day28

value: LowResponder


title: Longissimus_Genmascq_Pig_394

value: M


title: Longissimus_Genmascq_Pig_419


title: VX2012019_PBMC_Day0


title: Longissimus_Genmascq_Pig_392


title: Longissimus_Genmascq_Pig_389


title: Longissimus_Genmascq_Pig_390


title: Longissimus_Genmascq_Pig_391


title: VX2012018_PBMC_Day7


title: Longissimus_Genmascq_Pig_406


title: VX2012022_PBMC_Day3


title: VX2012018_PBMC_Day14


title: Longissimus_Genmascq_Pig_388


title: Longissimus_Genmascq_Pig_387


title: VX2012018_PBMC_Day3


title: VX2012017_PBMC_Day28

value: NonResponder


title: Longissimus_Genmascq_Pig_384


title: VX2012018_PBMC_Day0


title: H3K27ac ChIPSeq Tet2+/+ KitD816V,Rep2

description: S001246_Tet2pp_n30_GFPpos_W30p_Chip-11027_R1_001

data_processing:
Sequencing quality control was done with FastQC v0.11.6.
Cleaning up raw sequencing reads were performed with sickle v.0.6.3 (-q 20 , -l 25 parameters).
Cleaned Reads were mapped with the Bowtie2 V2.3.4.1 software to the mm10 (GRCm38), with on average 37 million, 35 million,38 million aligned reads/sample for PU.1, H3K27ac, H3K4me1 respectively.
SAM files where converted to BAM files and indexed using samtools V1.7.
The peak calling was carried out using MACS version 2.1.1.20160309 software (-q 0.01 for PU.1 ChiP, --broad for H3K27ac and H3K4me1 ChIP).
BedGraph control subtracted files were obtained using bdgcmp from same version of MACS.
Finaly BedGraph files were sorted and converted to bigwig files using bedGraphToBigWig V.4 for IGV visualization purpose.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig V.4 for IGV visualization purpose.

source_name: H3K27ac ChIPSeq Tet2+/+ KitD816V

growth_protocol: Primary mast cells were derived from bone marrow of either Tet2+/+ or Tet2-/- C57BL/6J Tet2LacZ  mice, isolated and cultured in OptiMEM/10% FCS (Life Technologies) media supplemented with 10 ng/ml IL3 (Peprotech), 50ug/ml Penicillin/streptomycin, and 1% beta-mercaptoethanol (both Life Technologies) on tissue culture treated plastic, at 37°C, 5% CO2. Non-adherent cells were selected for 15 days under these conditions, at which point cultures were infected with lenti-virus carrying the KitD816V allele and GFP (ires). For infection, we used a single 2h spinoculation in the presence of 6μg/ml polybrene. Infected cells were further expanded for 15 days, for a total of 30 days of in vitro culture, and then GFP-negative and GFP-positive fractions (cultures were 40-80% GFP-positive) were FACS sorted on FACSAria using DIVATM (Becton- Dickinson) software. Sorted cultures were expanded for 1-2 months in growth media. Fresh media was added to all cultures 1 day before fixation for ChIp. Fixed cell pellets were snap frozen in liquid nitrogen and stored at -80 degrees celcius.

extract_protocol:
The nuclei/chromatin suspension was sonicated using a Bioruptor Pico Sonnicator (Diagenode) for 20 cycles at 4°C. Sheared chromatin size was confirmed to be between 100-800 base-pairs on average by agarose gel. Two million cell equivalents were used for each ChIP. The following antibodies were used: H3K4me1 (Abcam, ab8895), H3K27ac (Abcam, ab4729), PU.1 (Santa Cruz Biotechnology, sc-352), Erg-1/2/3 (Santa Cruz Biotechnology, sc-354) and antibodies against total Stat5 (Santa Cruz, sc-835). ChIP samples were quantified using the Qubit Fluorometric quantification System (ThermoFisher) and using a DNA high sensitivity DNA kit on a Bioanalyzer (Agilent).
ChIP-seq libraries were made using the Multiplex Library Preparation Kit (Diagenode). Nine cycles of PCR were used for all libraries. After library DNA was purified, library concentration was measured by Qubit, and size distribution was determined by Bioanalyzer. Each ChIP-seq library was sequenced for single-end reads of Illumina HiSeq 4000 (between 100-800 bp read length). Biological replicates for ChIP-seq were performed on independently derived primary mast cell cultures from 2 different mice for each sample and both sequenced.

treatment_protocol: Primary mast cells cultures were fixed by the addition of 1/10 volume of freshly made cross- linking solution (11% formaldehyde, 100mM NaCl, 1mM EDTA, 0.5 mM EGTA, 50mM Hepes pH 7.8) directly to cell medium and incubation at room temperature (RT) for 10 minutes. Formaldehyde was then quenched for 5 minutes at RT by the addition of 2.5M Glycine solution to a final concentration of 125mM. Fixed cells were washed twice with cold PBS, counted, and transferred in 50ml Falcon tubes. Cells were then pelleted by centrifugation at 700g for 5 minutes at 4°C, snap-frozen in liquid nitrogen and stored at −80°C for storage or shipment on dry-ice. Each batch of 10 million cells was lysed and processed using reagents and according to the protocol provided by the ChIP-IT High Sensitivity® (HS) Kit (Active Motif).

tag: genotype/variation

value: Primary murine mast cells derived from bone marrow

tag: chip antibody

value: H3K27ac(Abcam, ab4729)


title: Longissimus_Genmascq_Pig_378

tag: gender

tag: pig number


title: VX2012017_PBMC_Day14


title: Longissimus_Genmascq_Pig_377

value: F

tag: ChIP


title: Longissimus_Genmascq_Pig_368


title: VX2012016_PBMC_Day28


title: Longissimus_Genmascq_Pig_373


title: Longissimus_Genmascq_Pig_374


title: H3K27ac ChIPSeq Tet2+/+,Rep2

description: S001247_Tet2pp_n31_GFPneg_W31m_Chip-11028_R1_001

source_name: H3K27ac ChIPSeq Tet2+/+


title: VX2012017_PBMC_Day3


title: Longissimus_Genmascq_Pig_386


title: Longissimus_Genmascq_Pig_354


title: VX2012017_PBMC_Day0


title: VX2012016_PBMC_Day3


title: VX2012016_PBMC_Day0


title: Longissimus_Genmascq_Pig_347


title: Longissimus_Genmascq_Pig_365


title: VX2012015_PBMC_Day28


title: VX2012017_PBMC_Day7


title: H3K27ac ChIPSeq Tet2-/- KitD816V,Rep2

description: S001244_Tet2mm_n29_GFPpos_K29p_Chip-11026_R1_001

source_name: H3K27ac ChIPSeq Tet2-/- KitD816V


title: Longissimus_Genmascq_Pig_338


title: VX2012015_PBMC_Day7


title: Longissimus_Genmascq_Pig_336


title: VX2012015_PBMC_Day14


title: Longissimus_Genmascq_Pig_357


title: Longissimus_Genmascq_Pig_341


title: VX2012015_PBMC_Day3


title: Longissimus_Genmascq_Pig_315


title: Longissimus_Genmascq_Pig_313


title: VX2012014_PBMC_Day14


title: VX2012016_PBMC_Day7


title: Longissimus_Genmascq_Pig_314


title: Longissimus_Genmascq_Pig_339


title: H3K27ac ChIPSeq Tet2-/-,Rep2

description: S001243_Tet2mm_n29_GFPneg_K29m_Chip-11025_R1_001

source_name: H3K27ac ChIPSeq Tet2-/-


title: VX2012015_PBMC_Day0


title: VX2012012_PBMC_Day28


title: VX2012014_PBMC_Day3


title: VX2012014_PBMC_Day0


title: VX2012014_PBMC_Day28


title: Longissimus_Genmascq_Pig_309


title: VX2012012_PBMC_Day14


title: Longissimus_Genmascq_Pig_310


title: VX2012016_PBMC_Day14


title: H3K4me1 ChIPSeq Tet2+/+ KitD816V,Rep2

source_name: H3K4me1 ChIPSeq Tet2+/+ KitD816V

value: H3K4me1(Abcam, ab8895)


title: Longissimus_Genmascq_Pig_300


title: Longissimus_Genmascq_Pig_304


title: Longissimus_Genmascq_Pig_302


title: Longissimus_Genmascq_Pig_303


title: H3K4me1 ChIPSeq Tet2+/+,Rep2

source_name: H3K4me1 ChIPSeq Tet2+/+


title: VX2012012_PBMC_Day3


title: VX2012014_PBMC_Day7


title: H3K4me1 ChIPSeq Tet2+/+ KitD816V,Rep1


title: Longissimus_Genmascq_Pig_299


title: VX2012011_PBMC_Day28


title: Longissimus_Genmascq_Pig_297


title: Longissimus_Genmascq_Pig_298


title: H3K4me1 ChIPSeq Tet2+/+,Rep1


title: H3K4me1 ChIPSeq Tet2-/- KitD816V,Rep2

source_name: H3K4me1 ChIPSeq Tet2-/- KitD816V


title: H3K4me1 ChIPSeq Tet2-/- KitD816V,Rep1


title: VX2012011_PBMC_Day14


title: VX2012011_PBMC_Day7


title: VX2012012_PBMC_Day0


title: VX2012011_PBMC_Day0


title: VX2012012_PBMC_Day9

source_name: human Day9


title: Longissimus_Genmascq_Pig_293


title: H3K4me1 ChIPSeq Tet2-/-,Rep2

source_name: H3K4me1 ChIPSeq Tet2-/-


title: Longissimus_Genmascq_Pig_294


title: Longissimus_Genmascq_Pig_296


title: VX2012009_PBMC_Day14


title: VX2012009_PBMC_Day28


title: Longissimus_Genmascq_Pig_291


title: PU.1 ChIPSeq Tet2+/+ KitD816V,Rep2

source_name: PU.1 ChIPSeq Tet2+/+ KitD816V

value: PU.1 (Santa Cruz, SC-352 )


title: H3K4me1 ChIPSeq Tet2-/-,Rep1


title: VX2012011_PBMC_Day3


title: PU.1 ChIPSeq Tet2+/+ KitD816V,Rep1


title: Longissimus_Genmascq_Pig_289


title: PU.1 ChIPSeq Tet2+/+,Rep1

source_name: PU.1 ChIPSeq Tet2+/+


title: PU.1 ChIPSeq Tet2+/+,Rep2


title: VX2012009_PBMC_Day0


title: VX2012009_PBMC_Day7


title: Longissimus_Genmascq_Pig_287

source_name: Longissimus lumborum muscle


title: VX2012007_PBMC_Day28


title: PU.1 ChIPSeq Tet2-/- KitD816V,Rep1

source_name: PU.1 ChIPSeq Tet2-/- KitD816V


title: VX2012007_PBMC_Day14

source_name: human Day14


title: Longissimus_Genmascq_Pig_282


title: PU.1 ChIPSeq Tet2-/-,Rep2

source_name: PU.1 ChIPSeq Tet2-/-


title: VX2012007_PBMC_Day7

source_name: human Day7


title: Longissimus_Genmascq_Pig_284


title: PU.1 ChIPSeq Tet2-/- KitD816V,Rep2


title: PU.1 ChIPSeq Tet2-/-,Rep1


title: VX2012009_PBMC_Day3

source_name: human Day3


title: Longissimus_Genmascq_Pig_288


title: Longissimus_Genmascq_Pig_285


title: VX2012007_PBMC_Day3


title: 6x-HCPro from T-DNA input tissue

city: Madrid

first: Tomas

last: Canto

state: Madrid

address: Ramiro de Maeztu 9

department: Environmental Plant Biology

country: Spain

institute: CSIC

description:
Sample 1
sRNA reads 18-30 nt of total RNA samples

data_processing:
Raw files uploaded as received from FASTERIS SA
Processed files trimmed from adaptors, cleaned from reads with erroneous characters, and analyzed for sRNA abundance
Supplementary files linked to the Series record contain quantitative data from our analysis that was used for making figures of the manuscript.
Genome_build: The genomic sequence of A. tumefaciens used was that of Wood et al., (2001; GenBank accession number AE007869.2).
Genome_build: The genomic sequence of N. benthamiana (version 0.5), obtained from the University of Sydney (http://sydney.edu.au/; Naim et al., 2012).
Genome_build: The genomic sequence of Potato virus X (construct pgR107; GenBank accession number: AY297842.1)
Supplementary_files_format_and_content: sRNAabundance18to30nt

organism: Nicotiana benthamiana

source_name: infiltrated tissue

growth_protocol: Plant leaf tissue was agroinfiltrated with binary vectors expressing HCPro variants or mRFP (samples 1-8) or infected with a PVX vector expressing 6x-HCPro

extract_protocol:
Libraries were constructed by FASTERIS SA
Illumina Version NextSeq HighBase; Calling pipeline: - NextSeq Control Software 2.2.0.4 - RTA 2.4.11

treatment_protocol: At 4 days after infiltration or a 7 days after infection, leaf tissues were collected and total RNAs extracted (input samples 1,3,5,7,9).  Histidine-tagged HCPro variants were purified under non-denaturing conditions and the associated RNAs were then isolated (samples 2,4,6,8,10)

tag: tissue

value: leaf

tag: agroinfiltrated with

value: binary vector expressing 6x-HCPro

tag: viral suppressor activity

value: suppression of silencing active

tag: sample type

value: plant leaf tissue (input)


title: Longissimus_Genmascq_Pig_280


title: Longissimus_Genmascq_Pig_279


title: Longissimus_Genmascq_Pig_278


title: VX2012007_PBMC_Day9


title: VX2012007_PBMC_Day0

source_name: human Day0


title: Longissimus_Genmascq_Pig_276


title: VX2012007_PBMC_Day1

source_name: human Day1


title: VX2012007_PBMC_Hour4

source_name: human Hour4


title: Longissimus_Genmascq_Pig_274


title: VX2012006_PBMC_Day28

source_name: human Day28


title: Longissimus_Genmascq_Pig_272


title: Longissimus_Genmascq_Pig_383


title: VX2012006_PBMC_Day14


title: Longissimus_Genmascq_Pig_275


title: Longissimus_Genmascq_Pig_267


title: Root DMSO Rep3

city: Tokyo

first: Dichao

last: Ma

address: 1-1-1 Yayoi, Bunkyo-ku

department: Graduate School of Agricultural and Life Sciences

institute: The University of Tokyo

hyb_protocol: Hybridization, washing, staining procedures were run on Fluidics Station 450 (Affymetrix) with GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G.

data_processing:
Data procession was performed with Expression Console Version 1.3 (Affymetrix).
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

label: bintin

organism: Arabidopsis thaliana

source_name: roots of estradiol inducible CLE2 overexpressing Arabidopsis that roots were treated with DMSO

label_protocol: Sense-strand DNA target preparation was performed in combination with Ambion WT Expression Kit (Affymetrix) and GeneChip WT Terminal Labeling Kit and Controls Kit (Affymetrix).

growth_protocol: Surface sterilized Arabidopsis seeds were sown on half Murashige and Skoog medium and vertically cultured at 22°C under continuous white light (25–30 μmol m−2 s-−1) for 7 days.

extract_protocol: Total RNAs used in transcriptional analyses were prepared using RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: Roots of 7-day-old estradiol inducible CLE2 overexpressing plants were treated with 5 mM β-estradiol for 24 h. After the 24-h induction, roots and shoots of plants were sampled separately and used for microarray analysis.

tag: age

value: overexpressing estradiol-inducible-CLE2

value: 7-day-old seedlings

tag: treatment

value: DMSO

value: Roots


title: VX2012006_PBMC_Day7

value: PBMC


title: Longissimus_Genmascq_Pig_257


title: VX2012006_PBMC_Day9

value: LowResponder


title: Longissimus_Genmascq_Pig_269


title: VX2012006_PBMC_Day3


title: Shoot DMSO Rep3

source_name: shoots of estradiol inducible CLE2 overexpressing Arabidopsis that roots were treated with DMSO

value: Shoots


title: Longissimus_Genmascq_Pig_259


title: Shoot Est Rep3

source_name: shoots of estradiol inducible CLE2 overexpressing Arabidopsis that roots were treated with estradiol

value: estradiol


title: Longissimus_Genmascq_Pig_263

value: M


title: VX2012006_PBMC_Day1


title: VX2012006_PBMC_Hour4


title: Shoot DMSO Rep2


title: Root Est Rep3

source_name: roots of estradiol inducible CLE2 overexpressing Arabidopsis that roots were treated with estradiol


title: Root DMSO Rep2


title: Longissimus_Genmascq_Pig_256


title: Shoot Est Rep2


title: Shoot DMSO Rep1


title: VX2012005_PBMC_Day28


title: Root Est Rep2


title: Longissimus_Genmascq_Pig_248


title: Root DMSO Rep1


title: VX2012006_PBMC_Day0


title: Longissimus_Genmascq_Pig_247


title: Longissimus_Genmascq_Pig_255


title: Longissimus_Genmascq_Pig_197


title: VX2012005_PBMC_Day14


title: VX2012005_PBMC_Day9

source_name: human Day9


title: VX2012005_PBMC_Day3


title: Longissimus_Genmascq_Pig_182


title: Longissimus_Genmascq_Pig_184


title: VX2012005_PBMC_Day1


title: VX2012005_PBMC_Hour4


title: Shoot Est Rep1


title: Longissimus_Genmascq_Pig_183


title: VX2012005_PBMC_Day7


title: Longissimus_Genmascq_Pig_176


title: Longissimus_Genmascq_Pig_171


title: VX2012004_PBMC_Day28

value: HighResponder


title: Longissimus_Genmascq_Pig_181

value: F


title: Root Est Rep1


title: VX2012004_PBMC_Day14


title: VX2012005_PBMC_Day0