title: INPUT_Ad-D3

status: Public on Feb 23 2019

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description:
Formaldehyde crosslinking, cross-link reversal at 68oC for 6 h, DNA purification (PCI) and Illumina library preparation
lad_Ad-D3-rep1.bed
lad_Ad-D3-rep2.bed
H3K9me3_Ad-D3.bw

data_processing:
ChIP-seq reads were aligned to the hg19 reference genome using bowtie2 version 2.1.0
Hi-C reads were aligned and processed using hiclib
Duplicate reads were removed using picard MarkDuplicates
ChIP and Input experiments were ensured to have equal read depth per chromosome by downsampling the deeper sequenced experiment
Peak calling was done using EDD version 1.1.7
bigWig files generated using deepTools 2.0
Genome_build: hg19
Supplementary_files_format_and_content: bed files with four columns: chromosome, start position, end position, score;bigwig files

source_name: Human primary adipose stem cells

growth_protocol: Human normal adipose tissue-derived mesenchymal stem cells were prepared from subcutaneous liposuction material. Cells were cultured under proliferative conditions in DMEM/F12 containing 10% fetal calf serum, 10 ng/ml epidermal growth factor (Sigma-Aldrich E9644) and 20 ng/ml basic fibroblast growth factor (FGF2; Sigma-Aldrich F5392). Cells at passage 5-7 were used in two independent differentiation experiments, each towards adipose or neuronal lineages.

extract_protocol:
For RNA-seq, total mRNA was isolated from Neu-D1 and Neu-D3 cells using the Qiagen RNeasy kit and processed for Illumina library preparation and sequencing. For ChIP-seq of lamin B1, cells at each differentiation time point were fixed with 1% formaldehyde for 10 min, lysed for 10 min in ChIP lysis buffer (50 mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS, protease inhibitors and 1 mM PMSF) and sonicated 4 times 10 min in a Bioruptor (Diagenode) to generate 200 base-pair DNA fragments. After sedimentation, the supernatant was collected and diluted 10-fold in RIPA (140 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, protease inhibitors, 1 mM PMSF). Chromatin was incubated overnight at 4oC with the anti-lamin B1 antibody coupled to Dynabeads Protein A/G (Invitrogen). ChIP samples were washed 4 times in ice-cold RIPA, crosslinks reversed and DNA eluted for 6 h at 68oC in 50 mM NaCl, 20 mM Tris-HCl pH 7.5, 5 mM EDTA, 1% SDS and 50 ng/µl Proteinase K. DNA was purified using phenol-chloroform isoamylalcohol and dissolved in H2O prior to processing for Illumina library preparation and sequencing. For Hi-C, 25 million cells per time point and differentiation replicate were cross-linked with fresh 1% formaldehyde (Pierce) for 12 min at room temperature on a rocker. Excess formaldehyde was quenched with 0.125 M glycine for 5 min and cells washed 3 times 5 min in ice-cold PBS. Crosslinked cells were lysed in lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630 and protease inhibitors) on ice for 15 min and homogenised by Douncing with a B-pestle (tight) in lysis buffer until nuclei were released, as assessed by microscopy. The lysate was sedimented, the pellet was resuspended in NEBuffer 2 (10 mM Tris-HCl pH 7.9, 50 mM NaCl, 10 mM MgCl2, 1 mM dithiothreitol) containing 0.1% SDS, and incubated at 65oC for 10 min. SDS was quenched on ice with 1% Triton X-100 and the sample digested with HindIII overnight at 37oC. Digested fragments were labelled with biotin-14-dCTP and blunt-end ligated. Crosslinks were reversed at 65oC overnight, the ligated DNA was purified by phenol-chloroform:isoamylalcohol (Ambion), desalted and RNAse-treated. DNA was sheared to ~100-300 base-pairs by Covaris sonication and size-fractionated on AMpure XP magnetic beads (Beckman Coulter). Biotinylated DNA fragments were pulled-down with Streptavidin beads and processed for Illumina adapter ligation and library preparation.
Illumina sequencing libraries were generated as per Illumina protocols.

treatment_protocol: Two days before induction of differentiation, proliferating cells (hereafter, ‘Pro’ stage) were harvested and processed for Hi-C or ChIP. For adipogenic differentiation, harvested ‘Pro’ cells were reseeded in DMEM/F12/10% serum without growth factors. Adipogenesis was induced 48 h later (D0) by addition of 10 µg/ml insulin, 200 µM indomethacin, 0.5 µM 1-methyl-3 isobutylxanthine and 1 µM dexamethasone. Medium was left with the cells for the 3 days of differentiation. Cells were collected on D1 and D3 (Ad-D1 and Ad-D3) and processed for Hi-C or ChIP. Neuronal differentiation was initiated on D0. In brief, medium was removed on D0 and cells were washed twice 4 min in pre-warmed Gibco serum-free DMEM (Thermo Fisher Scientific). Washing medium was removed and differentiation was induced by adding Gibco Neurobasal medium (Thermo Fisher Scientific) supplemented with 1% fetal calf serum, 1x B27 (Thermo Fisher Scientific), 0.5 mM IBMX, 1 µm dexamethasone, 10 µm forskolin, 200 µm 8CTP-cAMP and 10 mM valproic acid. Medium was left with the cells for the 3 days of differentiation. Cells were collected on D1 and D3 (Neu-D1 and Neu-D3) and processed for Hi-C or RNA isolation for RNA-seq.

value: Day 3

tag: cell type

value: ASCs on day 3 after adipogenic induction

value: input

tag: replicate


title: INPUT_D0

type: SRA

description:
Formaldehyde crosslinking, cross-link reversal at 68oC for 6 h, DNA purification (PCI) and Illumina library preparation
lad_D0-rep1.bed
lad_D0-rep2.bed
H3K9me3_D0.bw

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: time point

value: Day 0

value: ASCs on the day of differentiation induction

tag: chip antibody


title: INPUT_Pro

description:
Formaldehyde crosslinking, cross-link reversal at 68oC for 6 h, DNA purification (PCI) and Illumina library preparation
lad_Pro-rep1.bed
lad_Pro-rep2.bed

value: Day -2 (proliferative; "Pro")

value: Proliferating adipose stem cells (ASCs) in growth medium


title: Uhrf1hepKO, PHx, 24hrs rep 1

status: Public on May 31 2019

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

description:
Gene_counts.csv, Gene_FPKMs.csv
24hrs_KO1

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic,trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignments of trimmed reads were performed using tophat2  v2.1.0, with the parameters “–no-novel-junctions” and “–G”
Cufflinks  v2.2.1 was used to derive FPKM values. Read counts were generated using HTseq count
Test of differential expression  was implemented by DESeq2 in Bioconductor
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing reads counts and FPKM

molecule: total RNA

organism: Mus musculus

source_name: mouse liver

growth_protocol: mice were feed with normal diet

extract_protocol:
RNA was extracted using Zymo Duet DNA/RNA dual-extraction kit
RNA-seq libraries were prepared according to Illumina TruSeq RNA sample preparation with polyA
RNA-seq, Illumina Hi-Seq platform, 100bp paired-end reads

treatment_protocol: 8-12 week old mice underwent 2/3 partial hepatectomy surgery between 9am - noon

tag: strain

tag: tissue

value: liver

tag: genotype

tag: treatment

value: PHx

tag: time


title: Morula K27me3 C2 CUT&RUN

status: Public on Mar 01 2019

city: Boston

first: Wenhao

last: Zhang

state: MA

address: Warren Alpert Bldg, Rm 160, 200 Longwood Ave

department: Genetics

country: USA

institute: Harvard Medical School

data_processing:
H3K27me3 CUT&RUN reads were mapped to human reference genome (hg19) using Bowtie2 (version 2.3.4.1) paired-end alignment mode (parameters: -N 1 -L 25 -X 2000 --no-mixed --no-discordant). Multiple-mapped reads were removed and duplicates were further filtered using Picard MarkDuplicate. Then genome was divided into 100bp bins and  the numbers of reads per kilobase of bin per million reads sequenced (RPKM) in each bin was calculated.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited bed files including number of reads in 100bp bin in the genome for each CUT&RUN sample

source_name: human morula embryo

growth_protocol: Human morula embryos were generated by ICSI from patients who have singed consents for providing their otherwise discarded material for research. Briefly, 2PN zygotes were cultured in global® total® medium supplemented with HAS (LifeGlobal, CT, USA) under 5% O2, 6-7% CO2, and 88-89% N2. Then, embryos did not meet the freezing criteria for clinical purpose but developed to the morula like stage were collected and stored at -80 degree centigrade for ChIP-seq and RNA-seq.

extract_protocol:
Briefly, 7 and 8 morula embryos were combined and transferred in a 1.5-ml tube containing 50 ul wash buffer [20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine (Sigma-Aldrich), and 1x protease inhibitor cocktails (Sigma-Aldrich)]. The embryos were then captured with BioMagPlus Concanavalin A (Polysciences), and incubated with a rabbit anti-H3K27me3 antibody (1/100, C15410069, Diagenode) for 16 hours at 4℃ in antibody incubation buffer [20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x protease inhibitor cocktails (EDTA-free tablet, Roche), 2 mM EDTA, and 0.02% Digitonin (Life technologies)]. After unbound antibodies were washed away, protein A-MNase (pA-MN, a gift from Dr. Steven Henikoff) was added at a 1:280 ratio (500 ng/ml) and incubated for 3 hours at 4°C. After washes, CaCl2 was added to a final concentration of 2 mM to activate pA-MN, and the reaction was carried out for 20 min at 4℃ and then stopped by addition of 1/10 volume of 10xSTOP buffer [1,700 mM NaCl, 100 mM EDTA, 20 mM EGTA, 250 μg/mL RNase A (Invitrogen) and 250 μg/mL glycogen (Invitrogen)]. The protein-DNA complexes were released by 10 min incubation at 37℃ followed by centrifugation for 5 min at 16,000g at 4℃. After transferring the supernatant to a new Lo-bound tube, 1/100 volume of 10% SDS and 1/80 volume of 25 mg/ml Proteinase K (Life technologies) were added and incubated at 55℃ for at least 1 hour. DNA was then precipitated by phenol/chloroform/isoamylalcohol followed by ethanol precipitation with glycogen, and then dissolved in water.
Sequencing libraries were prepared using a NEBNext Ultra II DNA library preparation kit for Illumina (New Engliand Biolabs) according to the manufacturer’s instructions with a few modifications. Briefly, end repair was conducted at 20℃ for 30 min followed by dA-tailing at 65℃ for 30 min. After adaptor ligation at 20℃ for 30 min, the DNA fragments were purified by 1.8x volume of SPRIselect beads (Beckman Coulter) followed by 17 cycles of PCR amplification with NEBNext Ultra II Q5 Master Mix (NEB).  The PCR products were cleaned up with 0.9x volume of SPRIselect beads and quantified using Qubit dsDNA HS assay kit (Agilent Technologies). The libraries were sequenced on a Hiseq2500 with paired-end 100bp reads (Illumina).

value: embryo

tag: developmental stage

value: morula

tag: chip-antibody

value: WT


title: LMNB-Ad-D1-rep2

description:
Formaldehyde crosslinking, lamin B1 ChIP, ChIP DNA purification (PCI) and Illumina library preparation
lad_Ad-D1-rep2.bed

value: Day 1

value: ASCs on day 1 after adipogenic induction

value: anti-lamin B1 antibody (Abcam ab16048), at 10 microgram per 10e7 cells


title: LMNB-Pro-rep2

description:
Formaldehyde crosslinking, lamin B1 ChIP, ChIP DNA purification (PCI) and Illumina library preparation
lad_Pro-rep2.bed


title: Morula K27me3 C1 CUT&RUN


title: LMNB-Ad-D3-rep2

description:
Formaldehyde crosslinking, lamin B1 ChIP, ChIP DNA purification (PCI) and Illumina library preparation
lad_Ad-D3-rep2.bed


title: INPUT_Ad-D1

description:
Formaldehyde crosslinking, cross-link reversal at 68oC for 6 h, DNA purification (PCI) and Illumina library preparation
lad_Ad-D1-rep1.bed
lad_Ad-D1-rep2.bed
H3K9me3_Ad-D1.bw


title: LMNB-Ad-D3-rep1

description:
Formaldehyde crosslinking, lamin B1 ChIP, ChIP DNA purification (PCI) and Illumina library preparation
lad_Ad-D3-rep1.bed


title: auto_4

status: Public on Feb 14 2019

city: Philadelphia

first: Ivan

last: Maillard

state: Pennsylvania

address: 421 Curie Blvd

department: Medicine - Hematology/Oncology

institute: University of Pennsylvania

data_processing:
Multiple fastq files for each sample were first concatenated and then aligned to the mouse genome using STAR (version 2.5.2b) using Ensembl GRCm38 (release 87) annotation for splice guide.
Bam alignments were counted using Subread FeatureCounts (version 1.5.1) and Ensembl GRCm38 (release 87) annotation over the sense strand and assigning to genes with the largest overlap. Genes with a sum less than 10 counts across all samples were discarded.
Differential expression was performed using DESeq2 (version 1.16). All samples were normalized together using the genotype as the condition for the model. Regularized log transformed counts were exported for graphing purposes. Differential genes were identified with pairwise contrasts and filtered for adjusted p-value and log2 fold changed.
Genome_build: GRCm38
Supplementary_files_format_and_content: A text file containing raw sample read counts for each gene. Genes are identified by an Ensembl gene identifier. The FPKM value was calculated from the count data and the length of the gene.

source_name: 4C T cells retrieved from syngeneic recipient

extract_protocol:
Pooled secondary lymphoid organs (cutaneous and mesenteric lymph nodes, spleen) were digested with collagenase IV and DNase I and CD4 T cells enriched using StemCell EasySep Mouse T Cell Isolation Kit (Cat 19852). 4C T cells were sorted by FACS (>99% purity) and total RNA isolated using TRIzol (Invitrogen) and RNeasy Micro kit (Qiagen).
Libraries were prepared with Clontech SMARTer kit. HiSeq Flow Cell v3, HiSeq control software version 2.2.38, RTA(Real-Time Analysis) version 1.18.61, bcl2fastq version 1.8.4

value: CD4 T cell

tag: transplant type

value: Autologous

tag: unique sample identifier


title: auto_3

value: Pooled secondary lymphoid organs (cutaneous and mesenteric lymph nodes, spleen)


title: LMNB-D0-rep1

description:
Formaldehyde crosslinking, lamin B1 ChIP, ChIP DNA purification (PCI) and Illumina library preparation
lad_D0-rep1.bed


title: auto_2


title: LMNB-Pro-rep1

description:
Formaldehyde crosslinking, lamin B1 ChIP, ChIP DNA purification (PCI) and Illumina library preparation
lad_Pro-rep1.bed


title: auto_1


title: sibslivr1: 5 dpf Livers non transgenic siblings-1

status: Public on May 08 2019

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic,trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36
Alignments of trimmed reads were performed using tophat2  v2.1.0, with the parameters “–no-novel-junctions” and “–G”
Accepted bam files were used for counting gene read numbers with HTSeq, -a 10 -s no
Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor
Genome_build: GRCz10
Supplementary_files_format_and_content: .txt Reads count of genes

molecule: polyA RNA

organism: Danio rerio

source_name: liver/pooled

extract_protocol:
Tg(fabp10:nAtf6-cherry; cmlc2:GFP)C+/, were outcrossed to WT TAB 14 and the embryos were sorted and segregated basing on the expression of Cmlc2:GFP. The three different clutches of embryos were collected and dissected over three different days. The embryos were collected inbetween 10- 11 AM. The Liver dissection was also performed on the 5dpf larvae before noon. 25 livers from 5dpf embryos were pooled per sample( Transgenic and WT siblings in two different tubes) and RNA extracted with Trizol as per manufacturer's instructions.The RNA was later treated with DNAse to remove any DNA. They RNA concentration was taken on the Q bit, and then analysed on the Bioanalyser for the integrety and quality of RNA. The RIN score for the samples was above 8.5
RNA-seq libraries were prepared according to Illumina TruSeq RNA sample preparation version 2 protocol with Ribo-Zero Gold (Catalog #: RS-122-2501)

value: pooled liver

tag: genotype/variation


title: anti-Dll1/4_4

source_name: Dll1/4 neutralizing antibodies

value: Allogeneic


title: anti-Dll1/4_2


title: anti-Dll1/4_1


title: LMNB-D0-rep2

description:
Formaldehyde crosslinking, lamin B1 ChIP, ChIP DNA purification (PCI) and Illumina library preparation
lad_D0-rep2.bed

value: Day 0


title: GD_2

source_name: isotype control antibodies - GD

value: Isotype control


title: GD_1


title: LMNB-Ad-D1-rep1

description:
Formaldehyde crosslinking, lamin B1 ChIP, ChIP DNA purification (PCI) and Illumina library preparation
lad_Ad-D1-rep1.bed


title: anti-Dll1/4_3


title: DGCR8KO3

status: Public on Jul 25 2018

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 513 Parnassus Avenue, Campus Box #0525

institute: University of California, San Francisco

description: DGCR8KO_3.unique.Aligned.sortedByCoord.out.bam

data_processing:
For all samples, adapters were trimmed with Cutadapt version 1.14 with the following options: -m 20 -a "A{18}" -a "T{18}" -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC. Reads were mapped with STAR version 2.5.3a to the mm10/Gencode M14 genome with the following settings: --outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.05 --seedSearchStartLmax 25 --winAnchorMultimapNmax 100. Reads were counted with featureCounts version 1.5.3
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts

source_name: ESCs_DGCR8 KO

growth_protocol: ESCs were grown in Knockout DMEM (Invitrogen) supplemented with 15% Fetal Bovine Serum, LIF and 2i (PD0325901 and CHIR99021).

extract_protocol:
RNA was isolated using RNeasy Micro kits (Qiagen).
RNA-Seq libraries were generated using the QuantSeq 3’ FWD kit (Lexogen) and sequenced with single-end 50bp reads.

treatment_protocol: KO cells were generated with CRISPR

value: embryonic stem cells

value: DGCR8 KO


title: DGCR8KO1

description: DGCR8KO_1.unique.Aligned.sortedByCoord.out.bam


title: DGCR8KO2

description: DGCR8KO_2.unique.Aligned.sortedByCoord.out.bam


title: DDX6KO_clone2_1

description: DDX6KO_clone2_1.unique.Aligned.sortedByCoord.out.bam

source_name: ESCs_DDX6 KO

value: DDX6 KO


title: WT3

description: WT_3.unique.Aligned.sortedByCoord.out.bam

source_name: ESCs_wild type

value: wild type


title: Uhrf1hepKO, PHx, 24hrs rep 2

description:
Gene_counts.csv, Gene_FPKMs.csv
24hrs_KO2

value: liver

value: PHx


title: DDX6KO_clone1_2

description: DDX6KO_clone1_2.unique.Aligned.sortedByCoord.out.bam


title: GD_3


title: DDX6KO_clone1_1

description: DDX6KO_clone1_1.unique.Aligned.sortedByCoord.out.bam


title: DDX6KO_clone2_2

description: DDX6KO_clone2_2.unique.Aligned.sortedByCoord.out.bam


title: REF-rep2

status: Public on Aug 31 2018

type: RNA

city: Istanbul

first: Halil

middle: ibrahim

last: KISAKESEN

state: Istanbul

address: ITU MOBGAM, SARIYER

department: Molecular Biology, Genetics and Biotechnology

country: Turkey

institute: Istanbul Technical University

description: Gene expression at log-phase in Yeast Minimal Medium

hyb_protocol: 5 ug Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. Subsequently, the samples were immediately hybridized onto  Agilent Yeast Oligo Microarray (V2) 8x15K G4813 in a rotating Agilent hybridization oven at 65 °C for 17 h.

scan_protocol: Immediately after washing, slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%)

data_processing: The scanned images were analyzed using Feature Extraction Software 9.1 (Agilent) with default parameters (protocol GE1-v1_91 and Grid: 016322_D_F_20070321). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Saccharomyces cerevisiae

source_name: Log-phase rep2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by purification using Absolutely RNA Nanoprep Kit (Agilent).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Growth in Yeast Minimal Medium at 30 ºC and 150 rpm until log phase (OD600 ~1.0)

extract_protocol: RNeasy Mini Kit (Qiagen) was used according to the manufacturer’s instructions.  RNA quality based on Integrity Numbers (RIN) was checked with Agilent 2100 Bioanalyzer.  RNA samples with RIN values > 8 were used in the microarray analysis

treatment_protocol: No treatment

value: Reference strain


title: REF-rep1

source_name: Log-phase rep1


title: REF-rep3

source_name: Log-phase rep3


title: WT1

description: WT_1.unique.Aligned.sortedByCoord.out.bam


title: WT2

description: WT_2.unique.Aligned.sortedByCoord.out.bam


title: DGCR8KO_3_low polysome

description: DGCR8KO_low_3.unique.Aligned.sortedByCoord.out.bam

source_name: ESCs_DGCR8 KO_low polysome

growth_protocol: ESCs were grown in Knockout DMEM (Invitrogen) supplemented with 15% Fetal Bovine Serum, LIF and 2i (PD0325901 and CHIR99021). In order to generate EpiLCs, 400,000 ESCs were plated in a 15cm plate; 24 hours later LIF/2i media was removed, cells were washed with PBS, and EpiLCs were collected ~ 56 hours later

extract_protocol:
For each sample, the monosome, low polysome (2-4 ribosomes), and high polysome (4+ ribosomes were collected). RNA was extracted from gradient fractions with TRIzol LS (Invitrogen) and concentrated with the Zymo Clean and Concentrator-5 kit (Zymo)
QuantSeq 3’ FWD kit (Lexogen)

treatment_protocol: Cells were incubated with 100 ug/ml cycloheximide (Sigma) for 2 minutes and then moved to ice. Cells were washed and scraped in PBS with cycloheximide, spun down, and then lysed. Lysate was loaded onto a 10-50% sucrose gradient and centrifuged at 35,000 RPM for 3 hours. Gradients were collected on a gradient station (Biocomp). For each sample, the monosome, low polysome (2-4 ribosomes), and high polysome (4+ ribosomes were collected).

tag: polysome fraction

value: low polysome


title: hiPSC subline_201B7(+12)_rep2

status: Public on Oct 03 2018

city: Tsukuba

first: Yohei

last: Hayashi

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

country: Japan

institute: RIKEN

description:
201B7(+12)_2
Gene expression of undifferentiated hiPSCs.

hyb_protocol: The cRNA was hybridized with SurePrint G3 Human GE microarray 8x60K (Design ID: 39494).

scan_protocol: To scan the microarray image, an Agilent C scanner (Agilent) was used.

data_processing: To quantify the fluorescence intensity, Feature Extraction 10.7.3 software (Agilent) was used.

source_name: hiPSC subline, 201B7-IA, 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 RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop 1000 (Thermo Fisher), Qubit 2.0 Fluorometer (Thermo Fisher), and Bioanalyzer RNA6000 Nano (Agilent, Santa Clara, CA).

growth_protocol: Human ESC line H9 (WA09) was provided by WISC Bank, WiCell Research Institute, Madison, WI, USA (Amit et al., 2000; Thomson et al., 1998) and cultured only in the National Institute of Biomedical Innovation. The human iPSC lines, namely, parental and abnormal 201B7, were provided by Dr. Shinya Yamanaka, Kyoto University (Takahashi et al., 2007). Human ES/iPSCs with normal or abnormal chromosomes were routinely maintained on bovine fibronectin (2 mg/cm2) in serum-free hESF-FX medium. The hESF-FX medium consisted of mESF basal medium (WAKO, Osaka, Japan) supplemented with 3 factors (3F: 10 µM 2-mercaptoethanol (SIGMA, St. Louis, MO), 20 nM sodium selenite (SIGMA), 10 µM 2-aminoethanol (SIGMA)); 1 mg/ml oleic acid (SIGMA)-conjugated recombinant human serum albumin (rHSA, SIGMA); 10 µg/ml human insulin (SIGMA); 5 µg/ml apo-transferrin (SIGMA); 100 µg/ml ascorbic acid (WAKO); 5 ng/ml human recombinant FGF-2 (Katayama Kagaku Kogyo LTD., Osaka, Japan); and 2 ng/ml human Activin A (R&D systems, Minneapolis, MN) for seeding and without Activin A for culture maintenance (Furue et al., 2008; Kinehara et al., 2013; Yanagihara et al., 2016). The cells were passaged with 1 mg/ml dispase (Roche, Mannheim, Germany) in DMEM with high glucose and a plastic scraper (Sumitomo Bakelite Co., LTD Tokyo, Japan). The cells were split at a ratio of 1:5–1:8 every 7 days.

extract_protocol: Total RNA was isolated from hPSCs or hPSC-derived cells using the RNeasy mini or micro kit (Qiagen, Valencia, CA, USA) and treated with DNase I (Qiagen, Valencia, CA, USA) to remove any genomic contamination.

treatment_protocol: Trisomy 12 hPSC lines were cultured in the same conditions with normal hPSC lines.

tag: cell line

value: hiPSCs

value: trisomy 12

tag: gender

value: female


title: hiPSC line_201B7_rep2

description:
201B7_2
Gene expression of undifferentiated hiPSCs.

source_name: hiPSC line, 201B7, replicate 2

tag: cell type

value: parental


title: hESC subline_H9(+12)_rep2

description:
H9(+12)_2
Gene expression of undifferentiated hPSCs.

source_name: hESC subline, H9(+12), replicate 2

value: hESCs


title: hiPSC subline_201B7(+12)_rep3

description:
201B7(+12)_3
Gene expression of undifferentiated hiPSCs.

source_name: hiPSC subline, 201B7-IA, replicate 3


title: hiPSC subline_201B7(+12)_rep1

description:
201B7(+12)_1
Gene expression of undifferentiated hiPSCs.

source_name: hiPSC subline, 201B7-IA, replicate 1


title: hiPSC line_201B7_rep3

description:
201B7_3
Gene expression of undifferentiated hiPSCs.

source_name: hiPSC line, 201B7, replicate 3


title: hESC line_H9_rep2

description:
H9_2
Gene expression of undifferentiated hPSCs.

source_name: hESC line, H9, replicate 2


title: hiPSC line_201B7_rep1

description:
201B7_1
Gene expression of undifferentiated hiPSCs.

source_name: hiPSC line, 201B7, replicate 1


title: DGCR8KO_2_mono polysome

description: DGCR8KO_mono_2.unique.Aligned.sortedByCoord.out.bam

source_name: ESCs_DGCR8 KO_monosome

value: monosome


title: DGCR8KO_3_high polysome

description: DGCR8KO_high_3.unique.Aligned.sortedByCoord.out.bam

source_name: ESCs_DGCR8 KO_high polysome

value: high polysome


title: hESC subline_H9(+12)_rep1

description:
H9(+12)_1
Gene expression of undifferentiated hPSCs.

source_name: hESC subline, H9(+12), replicate 1


title: DGCR8KO_1_low polysome

description: DGCR8KO_low_1.unique.Aligned.sortedByCoord.out.bam


title: hESC line_H9_rep1

description:
H9_1
Gene expression of undifferentiated hPSCs.

source_name: hESC line, H9, replicate 1


title: DGCR8KO_1_mono polysome

description: DGCR8KO_mono_1.unique.Aligned.sortedByCoord.out.bam


title: DGCR8KO_3_mono polysome

description: DGCR8KO_mono_3.unique.Aligned.sortedByCoord.out.bam


title: hESC line_H9_rep3

description:
H9_3
Gene expression of undifferentiated hPSCs.

source_name: hESC line, H9, replicate 3


title: hESC subline_H9(+12)_rep3

description:
H9(+12)_3
Gene expression of undifferentiated hPSCs.

source_name: hESC subline, H9(+12), replicate 3


title: WT_3_low polysome

description: WT_low_3.unique.Aligned.sortedByCoord.out.bam

source_name: ESCs_wild type_low polysome


title: WT_3_mono polysome

description: WT_mono_3.unique.Aligned.sortedByCoord.out.bam

source_name: ESCs_wild type_monosome


title: DGCR8KO_1_high polysome

description: DGCR8KO_high_1.unique.Aligned.sortedByCoord.out.bam


title: WT_3_high polysome

description: WT_high_3.unique.Aligned.sortedByCoord.out.bam

source_name: ESCs_wild type_high polysome


title: WT_1_mono polysome

description: WT_mono_1.unique.Aligned.sortedByCoord.out.bam


title: WT_1_low polysome

description: WT_low_1.unique.Aligned.sortedByCoord.out.bam


title: GD_4

source_name: isotype control antibodies - GD

value: Pooled secondary lymphoid organs (cutaneous and mesenteric lymph nodes, spleen)

value: CD4 T cell

value: Allogeneic


title: WT_1_high polysome

description: WT_high_1.unique.Aligned.sortedByCoord.out.bam

value: embryonic stem cells


title: DGCR8KO_2_low polysome

description: DGCR8KO_low_2.unique.Aligned.sortedByCoord.out.bam

source_name: ESCs_DGCR8 KO_low polysome

value: DGCR8 KO


title: DGCR8KO_2_high polysome

description: DGCR8KO_high_2.unique.Aligned.sortedByCoord.out.bam


title: WT_2_high polysome

description: WT_high_2.unique.Aligned.sortedByCoord.out.bam

value: wild type


title: WT_2_mono polysome

description: WT_mono_2.unique.Aligned.sortedByCoord.out.bam


title: DGCR8KO 3 total RNA

description: DGCR8KO_3_total.unique.Aligned.sortedByCoord.out.bam

extract_protocol:
rRNA was depleted from Total RNA using the Ribo-Zero Gold kit (Illumina). 80 ug of RNA was biotinylated according to the following protocol Radle et al. (Rädle et al. 2013). Biotinylated 4sU RNA was isolated and washed using M-270 Streptavidin Dynabeads (Invitrogen), eluted with 100mM DTT, and cleaned up with RNeasy minelute columns (Qiagen).
Libraries were generated with the KAPA Stranded RNA-Seq or Stranded HyperPrep library prep kit (Kapa) and sequenced with single-end 50bp reads.

treatment_protocol: Samples were labeled with 500uM 4-thiouridine (4sU) (Sigma) for 30 minutes then extracted with TRIzol (Invitrogen) and split into two groups.

tag: type

value: total RNA


title: DGCR8KO 1 total RNA

description: DGCR8KO_1_total.unique.Aligned.sortedByCoord.out.bam


title: DGCR8KO 2 4sU

description: DGCR8KO_2_4su.unique.Aligned.sortedByCoord.out.bam


title: DGCR8KO 3 4sU

description: DGCR8KO_3_4su.unique.Aligned.sortedByCoord.out.bam


title: DGCR8KO 2 total RNA

description: DGCR8KO_2_total.unique.Aligned.sortedByCoord.out.bam


title: WT_3_total RNA

description: WT_3_total.unique.Aligned.sortedByCoord.out.bam

source_name: ESCs_WT total


title: WT_2_total RNA

description: WT_2_total.unique.Aligned.sortedByCoord.out.bam


title: WT_1_total RNA

description: WT_1_total.unique.Aligned.sortedByCoord.out.bam


title: DDX6KO_clone2_2_high

description: DDX6KO_clone2_3_high.unique.Aligned.sortedByCoord.out.bam

source_name: ESCs_DDX6 KO_high polysome

value: DDX6 KO


title: DDX6KO_clone2_2_mono

description: DDX6KO_clone2_3_mono.unique.Aligned.sortedByCoord.out.bam

source_name: ESCs_DDX6 KO_monosome


title: DGCR8KO 1 4sU

description: DGCR8KO_1_4su.unique.Aligned.sortedByCoord.out.bam


title: DDX6KO_clone2_2_low

description: DDX6KO_clone2_3_low.unique.Aligned.sortedByCoord.out.bam

source_name: ESCs_DDX6 KO_low polysome


title: DDX6KO_clone2_1_high

description: DDX6KO_clone2_2_high.unique.Aligned.sortedByCoord.out.bam


title: DDX6KO_clone2_1_low

description: DDX6KO_clone2_2_low.unique.Aligned.sortedByCoord.out.bam


title: WT_1_4sU

description: WT_1_4su.unique.Aligned.sortedByCoord.out.bam

source_name: ESCs_WT 4sU


title: DDX6KO_clone2_1_mono

description: DDX6KO_clone2_2_mono.unique.Aligned.sortedByCoord.out.bam


title: DDX6KO_clone1_high

description: DDX6KO_clone1_1_high.unique.Aligned.sortedByCoord.out.bam


title: WT_2_4sU

description: WT_2_4su.unique.Aligned.sortedByCoord.out.bam


title: DDX6KO_clone1_mono

description: DDX6KO_clone1_1_mono.unique.Aligned.sortedByCoord.out.bam


title: WT_3_high

description: WT_3_high.unique.Aligned.sortedByCoord.out.bam


title: WT_3_low

description: WT_3_low.unique.Aligned.sortedByCoord.out.bam


title: WT_2_low polysome

description: WT_low_2.unique.Aligned.sortedByCoord.out.bam


title: WT_2_mono

description: WT_2_mono.unique.Aligned.sortedByCoord.out.bam


title: WT_2_high

description: WT_2_high.unique.Aligned.sortedByCoord.out.bam


title: WT_2_low

description: WT_2_low.unique.Aligned.sortedByCoord.out.bam


title: WT_1_high

description: WT_1_high.unique.Aligned.sortedByCoord.out.bam


title: WT_3_4sU

description: WT_3_4su.unique.Aligned.sortedByCoord.out.bam


title: WT_1_low

description: WT_1_low.unique.Aligned.sortedByCoord.out.bam


title: WT_1_mono

description: WT_1_mono.unique.Aligned.sortedByCoord.out.bam


title: DDX6KO_clone1_2_total

description:
DDX6KO_clone1_2_total.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_counts.txt


title: DDX6KO_clone2_2_4su

description:
DDX6KO_clone2_2_4su.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_counts.txt


title: DDX6KO_clone2_1_4su_re-sequenced

description:
DDX6KO_clone2_1_4su.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_reseq_counts.txt


title: DDX6KO_clone2_1_total

description:
DDX6KO_clone2_1_total.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_counts.txt


title: WT 2 4sU_re-sequenced

description:
WT_2_4su.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_reseq_counts.txt


title: DDX6KO_clone2_2_total

description:
DDX6KO_clone2_2_total.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_counts.txt


title: DDX6KO_clone1_1_4su_re-sequenced

description:
DDX6KO_clone1_1_4su.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_reseq_counts.txt


title: WT 3 total

description:
WT_3_total.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_counts.txt


title: WT 3 4sU_re-sequenced

description:
WT_3_4su.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_reseq_counts.txt


title: DDX6KO_clone2_1_4su

description:
DDX6KO_clone2_1_4su.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_counts.txt


title: WT 1 total

description:
WT_1_total.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_counts.txt


title: DDX6KO_clone1_2_4su

description:
DDX6KO_clone1_2_4su.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_counts.txt


title: WT 2 4sU

description:
WT_2_4su.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_counts.txt


title: DDX6KO_clone1_2_4su_re-sequenced

description:
DDX6KO_clone1_2_4su.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_reseq_counts.txt


title: DDX6KO_clone1_low

description: DDX6KO_clone1_1_low.unique.Aligned.sortedByCoord.out.bam


title: DDX6KO_clone1_1_4su

description:
DDX6KO_clone1_1_4su.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_counts.txt


title: WT 3 4sU

description:
WT_3_4su.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_counts.txt


title: WT 1 4sU

description:
WT_1_4su.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_counts.txt


title: WT 1 4sU_re-sequenced

description:
WT_1_4su.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_reseq_counts.txt


title: WT 2 total

description:
WT_2_total.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_counts.txt


title: WT_3_mono

description: WT_3_mono.unique.Aligned.sortedByCoord.out.bam


title: EpiLC 3 Ribosome Protected Fragments

description: EpiLC.RPF3.unique.Aligned.sortedByCoord.out.bam

data_processing:
Adapters were trimmed using cutadapt version 1.14 with the following settings: --minimum-length 26 --maximum-length 32 for the ribosome protected fragments or --minimum-length 32 for the total RNA. Adapater sequence used for trimming: AGATCGGAAGAGCACACGTCT. Reads were mapped with STAR version 2.5.3a to the mm10/Gencode M14 genome with the following settings: --outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.05 --seedSearchStartLmax 13 --winAnchorMultimapNmax 200.
Reads were counted over the CDS from gencode M14 removing the first 45 nucleotides using featureCounts version 1.5.3
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts over CDS region excluding first 45 nucleotides.

source_name: EpiLC_Ribosome Protected Fragments

extract_protocol: Ribosome profiling libraries were generated using the TruSeq Ribosome Profiling kit (Illumina)

value: epiblast like cells

tag: molecule subtype

value: Ribosome protected fragments


title: DDX6KO_clone2_2_4su_re-sequenced

description:
DDX6KO_clone2_2_4su.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_reseq_counts.txt


title: EpiLC 2 total RNA

description: EpiLC.mRNA2.unique.Aligned.sortedByCoord.out.bam

source_name: EpiLC_total RNA


title: EpiLC 3 total RNA

description: EpiLC.mRNA3.unique.Aligned.sortedByCoord.out.bam


title: EpiLC 2 Ribosome Protected Fragments

description: EpiLC.RPF2.unique.Aligned.sortedByCoord.out.bam


title: EpiLC 1 total RNA

description: EpiLC.mRNA1.unique.Aligned.sortedByCoord.out.bam


title: EpiLC 1 Ribosome Protected Fragments

description: EpiLC.RPF1.unique.Aligned.sortedByCoord.out.bam


title: DDX6KO_clone1_1_total

description:
DDX6KO_clone1_1_total.unique.Aligned.sortedByCoord.out.bam
processed data file: DDX6KO_4su_counts.txt


title: ESC 3 total RNA

description: ESC.mRNA3.unique.Aligned.sortedByCoord.out.bam

source_name: ESC_total RNA


title: ESC 2 total RNA

description: ESC.mRNA2.unique.Aligned.sortedByCoord.out.bam


title: ESC 1 total RNA

description: ESC.mRNA1.unique.Aligned.sortedByCoord.out.bam


title: ESC 3 Ribosome Protected Fragments

description: ESC.RPF3.unique.Aligned.sortedByCoord.out.bam

source_name: ESC_Ribosome Protected Fragments


title: EpiLC 1 total

source_name: epiblast like cells_total RNA


title: ESC 2 4sU

description: ESC.4su2.unique.Aligned.sortedByCoord.out.bam

source_name: embryonic stem cells_4sU


title: ESC 2 total

source_name: embryonic stem cells_total RNA


title: ESC 2 Ribosome Protected Fragments

description: ESC.RPF2.unique.Aligned.sortedByCoord.out.bam


title: EpiLC 2 4sU

description: EpiLC.4su2.unique.Aligned.sortedByCoord.out.bam

source_name: epiblast like cells_4sU


title: EpiLC 3 total


title: ESC 1 4sU

description: ESC.4su1.unique.Aligned.sortedByCoord.out.bam


title: EpiLC 3 4sU

description: EpiLC.4su3.unique.Aligned.sortedByCoord.out.bam


title: ESC 3 total


title: ESC 3 4sU

description: ESC.4su3.unique.Aligned.sortedByCoord.out.bam


title: ESC 1 Ribosome Protected Fragments

description: ESC.RPF1.unique.Aligned.sortedByCoord.out.bam


title: EpiLC 1 4sU

description: EpiLC.4su1.unique.Aligned.sortedByCoord.out.bam


title: ESC 1 total


title: EPN, MPE, sample 421 [validation set]

status: Public on Jan 18 2018

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

description:
SAMPLE 421
Methylation data from brain tumor sample.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'.

label: biotin/DNP

source_name: brain tumor

label_protocol: Illumina protocol.

extract_protocol: Illumina protocol.

treatment_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride.

value: brain tumor

tag: methylation class

value: EPN, MPE

tag: material


title: EpiLC 2 total

description: EpiLC.mRNA2.unique.Aligned.sortedByCoord.out.bam


title: EPN, MPE, sample 506 [validation set]

description:
SAMPLE 506
Methylation data from brain tumor sample.

tag: tissue


title: EPN, MPE, sample 954 [validation set]

description:
SAMPLE 954
Methylation data from brain tumor sample.


title: C3

status: Public on Nov 12 2017

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequence, -p 4 -e 100 -y -a -m 10 --best --strata
Trimmed read were mapped to GRCz10 whole genome using tophat2 v2.1.0 with parameters --no-novel-juncs -G
Accepted bam files were used for counting read numbers of each gene with HTSeq, -s no -t exon -i gene_id
Test of differential expression of each genes was implemented by DESeq2 in Bioconductor, genes with reads number less than 10 were filtered out
Genome_build: GRCz10 (https://www.ncbi.nlm.nih.gov/grc/zebrafish)
Supplementary_files_format_and_content: .txt file. Reads count of genes

source_name: 5dpf embryos_liver_control

extract_protocol:
10-20 livers from 5dpf embryos were pooled per sample and RNA was extracted using the Zymo Quick-RNA Micro Kit with on-column DNase treatment per manufacturer's instructions.
RNA-seq libraries were prepared according to Illumina TruSeq RNA sample preparation version 2 protocol

value: 5 dpf

tag: exposed to

value: none (control)

value: liver


title: C2


title: C1


title: A2

source_name: 5dpf embryos_liver_arsenic

value: 1 mM inorganic arsenic


title: A1


title: A3


title: Cre_Pos2

status: Public on Dec 31 2017

hyb_protocol: Nugen amplification/standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: R, data was quantile normalized using beadarray package.

label: biotin

source_name: GV oocytes

growth_protocol: 48 hours prior to injection mice were primed with 5 units of PMSG. GV oocytes were collected in MEM medium supplemented with 2uM milrinone to prevent resumption of meiosis.

extract_protocol: PicoPure RNA Isolation Kit (ARCTURUS)

treatment_protocol: Either Zp3-Cre + or Zp3-Cre - GV oocytes were injected. For one set, 2uM miR-15a mimic (Dharmacon) were injected on a Leica DMI3000 B with an Eppendorf FemtoJet. Oocytes were cultured in MEM medium supplemented with 2uM milrinone overnight at 37˚ and 5% CO2

tag: cre

value: pos

tag: mir


title: Cre_Pos1

label_protocol: Nugen amplification/standard Illumina protocol


title: miR15_Cre_Neg2

value: neg


title: miR15_Cre_Pos2


title: miR15_Cre_Pos3


title: Cre_Pos3


title: miR15_Cre_Pos1


title: ESC1

data_processing:
Abundance estimates were calculated in kallisto version 0.43 from raw fastq files
Genome_build: mm10
Supplementary_files_format_and_content: Transcript abundance estimates from kallisto

source_name: Embryonic stem cell

growth_protocol: ESCs were grown in Knockout DMEM (Invitrogen) supplemented with 15% Fetal Bovine Serum, Lif and 2i (PD0325901 and CHIR99021). To generate Epi cells, ESCs were plated at 400,000 cells/15 plate, 24 hours later LIF and 2i were removed and Epi Cells were collected ~56 hours later

extract_protocol:
RNA was extracted using standard TRIzol protocol
Standard Illumina stranded Tru-Seq paired end

value: embryonic stem cell


title: GV2

source_name: GV oocyte

value: oocyte


title: GV1


title: EpiC2

source_name: In vitro Epiblast cell

value: epiblast cell


title: EpiC1


title: MII1

source_name: MII oocyte


title: MII2


title: ESC2


title: Cre_Neg1


title: Cre_Pos4


title: miR15_Cre_Neg3


title: HeLa input_2

status: Public on Jul 27 2017

city: Stanford

first: Karlene

middle: Anne

last: Cimprich

address: 318 Campus Drive

institute: Stanford University

data_processing:
Base calling CASAVA v1.8.2
Reads were aligned to genome with bowtie2 -p 9 --qc-filter --no-unal --no-mixed --no-discordant . The used reference genome was a concatenation of hg19 to the drosophilla genome r5.37 from FlyBase.
Reads mapping exclusively to the drosophilla genome were filtered out - only reads mapping to hg19 were kept for further processing.
Reads processed into bedpe format using bedtools
Reads sorted and filtered to only include those with mappability score >10 using unix shell utilities
Generate bigwig files using bedtools coverageBed and bedGraphToBigWig from UCSC
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: HeLa

growth_protocol: HeLa cells were cultured in DMEM (GIBCO) supplemented with 10% FBS, 2 mM L-glutamine and penicillin/streptomycin in 5% CO2 at 37°C.

extract_protocol:
DRIP was performed as described in Ginno et al., 2012. Briefly, DNA was extracted with phenol/chloroform in phase lock tubes (5Prime), precipitated with EtOH/sodium acetate, washed with 70% EtOH, and resuspended in TE. DNA was digested with EcoRI, XbaI, SspI, BsrgI, and HindIII (NEB) restriction enzymes overnight at 37 °C. For RNase H-treated samples, 4 ug of DNA was treated with RNase H (NEB, M0297S) overnight at 37 °C. DNA was purified by phenol/chloroform, EtOH/sodium acetate precipitation as described above. 4μg of DNA was bound with 10 μg of S9.6 antibody in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4°C. Protein A/G sepharose beads (Pierce) were added for 2 h. Bound beads were washed 3 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, 0.5% SDS, Proteinase K) for 45 min at 55°C. DNA was purified as described. In addition, sheared Drosophila melanogaster chromatin (Active Motif, 53083) and a Drosophila-specific H2Av antibody (Active Motif, 61686) was spiked-in as a minor fraction of the DRIP DNA to allow normalization of read counts according to the manufacturer’s protocol.
Using asynchronously growing HeLa cells, DRIP followed by library preparation, next generation sequencing, and peak calling were performed as described in Stork et al., 2016 with minor modifications. RNase A pre-treatment before DRIP was conducted with 6 μg/ml of enzyme for 45 min at 37ºC in 10 mM Tris-HCl pH 7.5 supplemented with 0.5M NaCl as described in Sanz et al., 2016 . RNase A pre-treatment before DRIP was conducted with 6 μg/ml of enzyme for 45 min at 37ºC in 10 mM Tris-HCl pH 7.5 supplemented with 0.5M NaCl as described in Sanz et al., 2016 . Libraries were pooled and sequenced on an Illumina HiSeq 4000 machine with paired-end 75bp reads at the Stanford Functional Genomics Facility (NIH grant S10OD018220).

treatment_protocol: HeLa cells were transfected with siRNA against luciferase (Fisher scientific D-001400-01-20) at 20 nM for 72 hours using Dharmafect, according to manufacturer protocols

value: HeLa cells

tag: sample type

value: input

tag: exogenous treatment

value: Control siRNA for luciferase


title: miR15_Cre_Neg1


title: Cre_Neg3


title: Cre_Neg4


title: Cre_Neg2


title: S9.6 DRIP Seq_2

value: DRIP


title: EPN, MPE, sample 679 [validation set]

description:
SAMPLE 679
Methylation data from brain tumor sample.


title: HeLa input_1

data_processing:
Base calling CASAVA v1.8.2
Reads were aligned to genome with bowtie2 -p 9 --qc-filter --no-unal --no-mixed --no-discordant . The used reference genome was a concatenation of hg19 to the drosophilla genome r5.37 from FlyBase.
Reads mapping exclusively to the drosophilla genome were filtered out - only reads mapping to hg19 were kept for further processing.
Reads processed into bedpe format using bedtools
Reads sorted and filtered to only include those with mappability score >10 using unix shell utilities
Generate bigwig files using bedtools coverageBed and bedGraphToBigWig from UCSC
Genome_build: hg19


title: ESC H3K27me3 rep1

status: Public on Sep 15 2016

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

country: China

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using bwa mem command, reads that have map quality score less than 30 were removed from downstream analysis.
Peaks were called using masc2(v 2.0.10.20131216) with the parameters "macs2 callpeak –n Sample -g mm -B -q 0.05 --nomodel --broad --shiftsize=73 --SPMR" relative to input samples.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files are generated using macs2 pileup function and normlized to one million reads per sample using --SPMR option. Scores represent normalized tag counts per million reads.

source_name: mouse embryonic stem cells

extract_protocol:
500cells were washed three times in 0.5% BSA-PBS solution. Lysates were clarified from micrococcal nuclease treated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to KAPA Hyper Prep Kit for illumina platform (kk8504)

treatment_protocol: For MII oocyte and cleavage-stage embryos, the zona pellucida of embryos was removed by 0.5% pronase E (Sigma). Then the embryo was incubated in Ca2+ free CZB for 5 min. Polar bodies were removed by gentle pipetting using an inner diameter of 120 μm fire polished glass needle. For ICM and TE isolation, the zona pellucida of blastocysts was removed by 0.5% pronase E (Sigma). They were then incubated for 20 min in Ca2+ free CZB，the tight junctions TE cells and ICM cells were separated by gently pipetting in a pipette with a diameter of 40-60 μm.

tag: development stage

value: mouse embryonic stem cells

tag: chip antibody

value: H3K27me3(Diagnode, pAb-069-050)

tag: overexpression

value: mouse ES cell R1


title: ESC H3K27me3 rep3


title: ESC H3K27me3 rep4


title: ESC H3K27me3 rep2


title: Genomic DNA from human placenta BS 11

status: Public on Jul 01 2016

city: Atlanta

first: Carmen

last: Marsit

state: GA

address: 1518 Clifton Road

department: Environmental Health

institute: Rollins School of Public Health at Emory University

description: normal infant placenta tissue

hyb_protocol: BeadStudio software v3.2

scan_protocol: Average Beta

data_processing: Normalized proportion of loci value for unmethylated (cytosine), methylated, and hydroxymethylated readings. These values were established using the Houseman method (under review, will follow up with citations when available).

label: Cy5 and Cy3

source_name: Human placenta

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

growth_protocol: genomic DNA was extracted and purified from placenta samples using Qiagen DNeasy Kit according to standard instructions

extract_protocol: bisulphite and oxidative bisulfite converted DNA (performed using Cambridge Epigenetix True Methy Seq kit)  was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

treatment_protocol: Standard Illumina Protocol

value: Male

tag: dna type

value: bisulfite


title: Genomic DNA from human placenta BS 15

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 17

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 21

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 16

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 13

description: normal infant placenta tissue

value: Female


title: Genomic DNA from human placenta BS 12

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 8

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 18

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 10

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 22

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 19

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 23

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 20

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 9

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 6

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 5

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 2

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 14

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 1

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 4

description: normal infant placenta tissue


title: S9.6 DRIP Seq_1


title: ESC input


title: Genomic DNA from human placenta ox-BS 22

description: normal infant placenta tissue

value: oxidative bisulfite


title: Genomic DNA from human placenta BS 7

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 20

description: normal infant placenta tissue


title: Genomic DNA from human placenta BS 3

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 4

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 6

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 16

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 11

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 19

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 17

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 9

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 13

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 14

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 15

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 12

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 2

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 1

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 5

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 7

description: normal infant placenta tissue


title: B6-2

status: Public on Jun 13 2016

data_processing:
Trim adapter sequences from 3' end of the sequence reads in the filtered FASTQ files using a software tool that can remove adapter sequences, such as Flexbar 37. The minimum overlap length (-ao) set to 6, the minimum read length to keep after adapter removal (--m) set to 21, the cutoff for the number of allowed mismatches (-at) set to 2, and defaults for all other parameters.
Use Bismark41 to align the filtered, adapter trimmed sequence reads to the bisulfite converted reference mouse genome mm10 (whole genome alignment approach) and determine the methylation context for each cytosine. Typically set the seed length (-l) to the read length for alignment accuracy and use defaults for all other parameters
Sort aligned reads first by chromosome, then start position, and finally strand, after alignment is complete.
Use custom scripts to iterate over the sorted methylation calls output by Bismark to compute the percent methylation scores of bisulfite converted Cytosines and non-converted C’s for each cytosine methylation context (CpG, CHG, CHH), retaining only the cytosines that have at least phred quality score of 20 and have at least 10x coverage.
Generate a BAM file of the aligned reads using Bismark’s bismark2SAM_v5_xm.pl and Samtools
Genome_build: mm10
Supplementary_files_format_and_content: .txt file provided methylation and coverage for each CpG site with at least 10x coverage

extract_protocol:
Genomic DNA was extracted from each sample using the Qiagen DNA isolation kit
50ng of high quality genomic DNA in 50 microliters (μl) of DNase-free water was used as starting material.The whole library preparation includes Mspl digestion of genomic DNA, Phenol:chloroform clean up, End-repair, A-tailing, adapter ligation, size selection, bisulfite conversion, enrichment PCR and quality control. More details can be referred to Garrett-Bakelman et al., 2015

treatment_protocol: Total livers were isolated between 6-8 weeks old and frozen at -80°C for DNA isolation.

tag: strain background

value: male

tag: age

value: 6-8 weeks

value: liver


title: Mixed-1

value: mixed

tag: gender


title: EZH2_Y641F_855D_MEL_JQEZ5_RNAseq

status: Public on May 02 2016

city: St. Louis

first: George

middle: P.

last: Souroullas

state: MO

address: 660 S. Euclid Av

department: Medicine

institute: Washington University School of Medicine

data_processing:
Reads were aligned using Tophat against the mm9 reference genome
Transcript abundance was computed using cufflinks 1.1.0
Differential expression between WT and Y641F samples was computed using the DESeq package
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file, DEseq2 output of differential expression between EZH2_WT vs EZH2_Y641F samples in BCELLS and MELANOMA

extract_protocol:
Cells were isolated from animals' spleen.  Briefly, spleens were made into single cell suspension, stained with CD19-biotin, washed, stained with antibiotin magnetic beads and separated on an Automacs magnetic separator.
Illumina Tru-seq kit v2; paired-end

treatment_protocol: no treatment, comparing wt vs mutant B cells

tag: strain

tag: cell line

tag: genotype/variation

value: EZH2 gain-of-function Y641F mutation

tag: tissue/cell type

value: Melanoma tumor cell line

tag: cell type

value: Melanocyte


title: EZH2_Y641F_480D_MEL_JQEZ5_RNAseq


title: Genomic DNA from human placenta ox-BS 10

description: normal infant placenta tissue


title: B6-1

tag: tissue


title: Ezh2_Y641F_BCELLS_RNAseq4

value: Spleen

value: CD19+ splenic B cells


title: EZH2_Y641F_480D_MEL_RNAseq


title: EZH2_WT_855_MEL_RNAseq

value: wild type


title: Ezh2_Y641F_BCELLS_RNAseq2


title: Ezh2_Y641F_BCELLS_RNAseq1


title: Ezh2_Y641F_BCELLS_RNAseq3


title: EZH2_Y641F_855D_MEL_JQEZ5_H3K27_IP

data_processing:
Reads were aligned to the reference genome using BWA
Samtools to convert SAM to BAM
Sortsam to index BAM files
Peaks were called using MACS2, - add, --broad, filter for 0, read counts in peaks vs total
Make bigWig for visualization using bam2bigWig
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

growth_protocol: Melanoma cell lines 855, 855D, 480, 480D were grown in IMDM media containing 10%FBS

extract_protocol:
B cells were isolated from animals' spleen.  Briefly, spleens were made into single cell suspension, stained with CD19-biotin, washed, stained with antibiotin magnetic beads and separated on an Automacs magnetic separator.
Illumina Truseq ChIPseq kit

treatment_protocol: Melanoma cell lines were grown in IMDM media containing 1uM JQEZ5 for 5 days

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: Ezh2_WT_BCELLS_RNAseq2


title: EZH2_Y641F_480D_MEL_JQEZ5_H3K27_IP


title: EZH2_WT_480_MEL_RNAseq


title: EZH2_Y641F_855D_MEL_H3K27_IP


title: Ezh2_WT_BCELLS_RNAseq3


title: EZH2_WT_855_MEL_JQEZ5_H3K27_IP


title: EZH2_WT_855_MEL_H3K27_IP


title: EZH2_WT_855_MEL_H3K27_input


title: EZH2_WT_480_MEL_JQEZ5_ H3K27_IP

source_name: EZH2_WT_480_MEL_JQEZ5_ H3K27_IP


title: Ezh2_WT_BCELLS_RNAseq1


title: EZH2_WT_480_MEL_H3K27_input


title: EZH2_WT_480_MEL_H3K27_IP


title: EZH2_Y641F_H3K27_BCELLS_3_IP


title: Ezh2_WT_BCELLS_RNAseq4


title: EZH2_Y641F_H3K27_BCELLS_3_Input


title: EZH2_Y641F_H3K27_BCELLS_2_IP


title: EZH2_Y641F_480D_MEL_H3K27_IP


title: EZH2_Y641F_H3K27_BCELLS_2_Input


title: EZH2_WT_H3K27_BCELLS_3_Input


title: EZH2_Y641F_H3K27_BCELLS_1_IP


title: EZH2_WT_H3K27_BCELLS_3_IP


title: EZH2_Y641F_H3K27_BCELLS_1_Input


title: EZH2_WT_H3K27_BCELLS_2_Input


title: EZH2_WT_H3K27_BCELLS_1_IP


title: EZH2_WT_H3K27_BCELLS_2_IP


title: EZH2_WT_H3K27_BCELLS_1_Input


title: B6_H3K4me3_Input_sample_2

status: Public on Feb 24 2014

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome assembly using BWA v1.2.3
Data was filtered to keep only uniquely mapped reads
peaks were called using MACS v1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: Processed data include merged Bedgraph files from both biological replicates generated by MACS and tab-delimited peaks called by MACS with p-value e-5. To find uncommon peaks we ran MACS using p = e-2, removed all reads described by common peaks from the alignment file, then ran MACS again with p = e-2 and again identified common peaks. Genomic regions found in common from the two rounds of peak calling were pooled. MACS was run on the data again using p = e-5 and the common peaks were subtracted. These 'uncommon' peaks were considered putative PRDM9 peaks and analyzed further for common features (i.e. motif analysis etc.)

source_name: spermatocytes

growth_protocol: Crude isolation of germ cells was conducted from male mice at 12 days post-partum (dpp). For detailed protocol see publication

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented by Mnase digestion. After high speed spin soluble chromatin was removed and used for ChIP
Libraries were prepared for sequencing using Bioo Scientific's NEXTflex ChIP-Seq Kit (protocol version V11.11) without size selection. Amplification of the libraries was done with 20 µL ligation product, 16 ul water, 12 µL NEXTflex ChIP PCR master mix, 2 µL NEXTflex ChIP primer mix and 14-18 cycles of PCR.

value: 12 days post-partum

tag: prdm9 allele

tag: ChIP

value: input


title: B6_H3K4me3_Input_sample_1


title: B6_Hemi_H3K4me3_ChIP_sample_2

status: Public on Apr 09 2015

description:
J2_R1_e-5_peaks.txt.gz
BvH_DiffBind.counts.csv.gz

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-Seq reads were aligned to the mm9 genome assembly using BWA v.0.5.10
ChIP-Seq reads were filtered to keep only uniquely mapped reads
ChIP-Seq peaks were called using MACS v1.4.2
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph and peak files were generated from MACS with p-value e-5. BvH_DiffBind.counts.csv.gz contains the normalized read counts and log fold change for all H3K4me3 peaks exported from R package DiffBind

tag: antibody manufacturer

value: Millipore/EMD

tag: antibody catalog number

tag: antibody lot/batch#


title: B6_Hemi_H3K4me3_ChIP_sample_1

description:
I2_R1_e-5_peaks.txt.gz
BvH_DiffBind.counts.csv.gz

tag: strain background


title: Brain tumor 9422493152_R06C01

status: Public on May 21 2015

description:
Methylation data from ependymal tumor sample.
Location: 1: infratentorial; 2: spinal; 3: supratentorial.

data_processing: Data analysis was performed using the open source statistical programming language R (R Core Team, 2014; http://www.R-project.org/). Raw data files generated by the iScan array scanner were read and preprocessed using the capabilities of the Bioconductor (Version 2.9) package minfi (Version 1.12; Aryee et al., 2014 (PMID 24478339)). With the minfi package using function 'preprocessIllumina', the same preprocessing steps, i.e., background subtraction and normalization using control probes, as in Illumina's GenomeStudio software were performed.

source_name: brain tumor, spinal, SP-MPE, WHO grade 2

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride. DNA was isolated from formalin-fixed and paraffin-embedded (FFPE)  tissue using the blackPREP FFPE DNA Kit (Analytik Jena, Jena, Germany) according to the manufacturer's instructions.

value: ependymal tumor

tag: tumor type

value: primary

tag: molecular subtype

value: SP-MPE

tag: material

value: frozen

tag: location

tag: who grade


title: AUTS2_mBrain_ChIPseq

status: Public on Dec 18 2014

city: New york

first: Zhonghua

state: NY

address: 522 1st Avenue, SML 203

department: Biochemistry and Molecular Pharmacology

institute: New York University School of Medicine

data_processing:
ChIP-seq reads were aligned to the mm9 or hg19 genome assembly using Bowtie with -m1 -v2.
Duplicated reads were removed with samtools rdup.
peaks were called using QESEQ.
ChIP-seq read density files were generated using igvtools
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: txt: called peaks

source_name: brain

growth_protocol: 293T-REx stable lines transfected with HA-tagged PRC1 subunits or an empty vector were grown in standard conditions (DMEM 10% FBS) and kept in selection with zeocin

extract_protocol:
For ChIP-seq in mouse brain, the whole brains were homogenized with a glass douncing homogenizer. The cell homogenate was fixed with 1% paraformaldehyde for eight min at room temperature and quenched with 0.125 M glycine for five min at room temperature, followed by centrifugation through a 29% iodixanol cushion. The nuclei pellet was resuspended and sonicated using a Diagenode Bioruptor to an average size of ~250 bp. After pre-clearing with BSA-blocked protein G Sepharose, chromatin was incubated with antibodies at 4°C overnight. The chromatin immunocomplexes were recovered with the same BSA-blocked protein G beads.For ChIP-seq in 393T-REx cells, cells were crosslinked with 1% formaldehyde for eight min at room temperature and the nuclei were then isolated. As described above, following sonication and pre-clearing, chromatin IP was performed to isolate associated DNA.
For ChIP-seq library construction, 5-10 ng of DNA extracted from the chromatin immunocomplexes. Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 350±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).

tag: mouse strain

tag: Stage

tag: antibody

value: AUTS2 (house made)


title: B6_H3K4me3_ChIP_sample_2

description:
H3K4me3_B6_merge_ChIP.bgd
B6_P9uncommonQB6.bed

tag: age


title: B6_H3K4me3_ChIP_sample_1


title: wrky72-2-MOCK-REP2

status: Public on Aug 09 2010

city: Riverside

first: Kishor

middle: Kumar

last: Bhattarai

address: 9000 University Avenue

department: Plant Pathology

institute: University of California

description: Gene expression data in mock treated wrky72 mutant

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 with 7G.

data_processing: Microarray analysis was performed in the R statistical programming environment using Bioconductor packages (http:/www.bioconductor.org). Values were normalized using the robust multichip averaging (RMA) algorithm in Bioconductor. Statistical analysis was performed with the LIMMA package. The p values were adjusted using the Benjamini and Hochberg method for False Discovery Rate (FDR) of 0.05. Significant up- and down-regulated genes were selected based on an adjusted p-value ≤ 0.01 compared to mock treatments.

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis thaliana plants (accessions Col-0 and  homozygous T-DNA insertion lines SALK_145765 and SALK-055293) were grown on soil in a semi-sterile growth chamber under fluorescent lights (14 hours light, 10 hours dark, 21 centi grades, 100 Einstein/m2/s).

extract_protocol: For harvesting, the aerial plant parts were shock-frozen in liquid nitrogen. Total RNA was isolated from seedlings using TRIZOL (Invitrogen) follwing the manufacturer’s instructions.

treatment_protocol: Aerial tissues of 2 week old soil grown Arabidopsis seedlings were sprayed with 3X10^4 spores/ml of HpaNoco2 or mock solution and harvested at 96 h after the treatment. Mock treatments were sprayed with water only. Three independent biological replicates were performed for each treatment.

tag: genotype/variation

value: wrky72-2 mutant

tag: t-dna insertion line

tag: infection

value: mock treated


title: wrky72-2-NOCO2 INFECTED-REP1

description: Gene expression data in Hpa treated wrky72 mutant

source_name: Aerial tissues of 2 week old soil grown Arabidopsis seedlings

value: Hpa treated


title: wrky72-1-MOCK-REP2

value: wrky72-1 mutant


title: wrky72-1-NOCO2 INFECTED-REP1


title: wrky72-2-MOCK-REP3


title: WT-NOCO2 INFECTED-REP1

description: Gene expression data in Hpa treated WT

value: WT


title: wrky72-2-MOCK-REP1


title: wrky72-2-NOCO2 INFECTED-REP3


title: wrky72-1-NOCO2 INFECTED-REP3


title: wrky72-2-NOCO2 INFECTED-REP2


title: wrky72-1-MOCK-REP3


title: wrky72-1-NOCO2 INFECTED-REP2


title: WT-MOCK-REP2

description: Gene expression data in mock treated WT


title: WT-NOCO2 INFECTED-REP3

description: Gene expression data in Hpa treated WT


title: WT-MOCK-REP3

description: Gene expression data in mock treated WT


title: wrky72-1-MOCK-REP1


title: WT-NOCO2 INFECTED-REP2

description: Gene expression data in Hpa treated WT


title: WT-MOCK-REP1

description: Gene expression data in mock treated WT


title: Genomic DNA from human placenta ox-BS 8

description: normal infant placenta tissue

tag: gender

value: Female

tag: dna type

value: oxidative bisulfite


title: Genomic DNA from human placenta ox-BS 23

description: normal infant placenta tissue

value: Male


title: Genomic DNA from human placenta ox-BS 21

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 3

description: normal infant placenta tissue


title: Genomic DNA from human placenta ox-BS 18

description: normal infant placenta tissue


title: EZH2_Y641F_855D_MEL_RNAseq

tag: strain

tag: cell line

value: EZH2 gain-of-function Y641F mutation

tag: tissue/cell type

value: Melanoma tumor cell line

tag: cell type

value: Melanocyte


title: Mixed-2

tag: strain background

value: mixed

value: male

value: 6-8 weeks

tag: tissue

value: liver