title: Patient5 LIC AR-42

city: Columbus

first: Pu

last: Zhang

address: 1258 Bunkerhill Blvd, AptB

institute: Ohio State University

data_processing:
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterREmoval v2.2.0 to remove sequencing adapters
Reads were aligned against the human decotaminome using HISAT2 v2/0/6 using default parameters
Unaligned deconaminome reads were aligned against the human genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts using GENCODE release M25
Transcript counts were DESeq2 size normalized
Genome_build: GRCh38
Supplementary_files_format_and_content: counts.rep-LIC.xlsx (DESeq2 normalized) generated using Subread FeatureCounts

source_name: Bone marrow

growth_protocol: Patient bone marrow cells were defrosted and cultured in the presence of IL-3, FLT3, GM-CSF and SCF on collagen plates in the presence of RPMI1640+10%FBS.

extract_protocol:
The Clontech SMARTer v4 kit (Takara Bio USA, Inc., Mountain View, CA) was used for extracting and preamplifying samples.
Library construction with the Nextera XT DNA Library Prep Kit (Illumina, Inc., San Diego, CA).

treatment_protocol: Cells were treated with 1) DMSO 2) 0.8uM AR-42 3) 0.1uM KPT-9274 or 4) AR-42+KPT-9274

tag: individual

value: acute myeloid leukemia (AML)

value: Bone marrow

value: FACS-sorted leukemia initiating cells (CD34+CD38-)


title: Neural progenitor cells - cKO_Day9_rep1

status: Public on Feb 10 2021

type: SRA

city: Dresden

first: Tomohisa

last: Toda

address: Tazberg 41

country: Germany

institute: German Center for Neurodegenerative Diseases

description:
LmnB1_gene_count_D9.txt
LmnB1_gene_tpm_D9.txt

library_source: transcriptomic

data_processing:
RNA-sequencing reads were trimmed for low base-quality using SolexaQA++ dynamic trim, v.3.1.3 and aligned to mm10 using RSEM rsem-calculate-expression ( v.1.2.18) with bowtie2 version 4.8.4 expected counts (counts) and normalized transcripts per million (TPM) were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: The counts file is the raw RNA-seq file, and the tpm file is the normalized RNA-seq data.

molecule: polyA RNA

organism: Mus musculus

source_name: Neural progenitor cells

growth_protocol: Mouse NPC cells were cultured in DMEM/F12 supplemented with modified N2/B27 and 10 ng/ml of both EGF and FGF-2.

extract_protocol: EYFP+ cells were sorted by FACS and RNA is isolated using Trizol with Dnase Turbo treatment

tag: cell type

value: LaminB1fl/fl; Ai3 derived neural progenitor cells

tag: strain

tag: treatment

value: Lentivirus:pSox2-Cre 9 days


title: teloHAEC_CRISPRa_E-SELECTIN_Bottom_r1

city: Montreal

first: Florian

last: Wuennemann

address: 5000 Rue Bélanger

country: Canada

institute: Montreal Heart Institute

description: PCR amplified sgRNA sequences

library_source: genomic

data_processing:
Library strategy: DNA-seq
Raw sequencing data from Illumina sequencers was processed from the BCL to the FASTQ format using bcl2fastq.
sgRNA abundances were quantified using MAGECK count (v.0.5.9) against a list of sgRNA sequences in the library.
Supplementary_files_format_and_content: teloHAEC_Endoscreen_sgRNA_counts.tsv.gz

molecule: genomic DNA

organism: Homo sapiens

source_name: teloHAEC

growth_protocol: TeloHAEC stably expressing either Cas9, dCas9-KRAB or dCas9-VP64 (CRISPRa) were cultured in vascular cell basal medium (ATCC PCS-100-030).

extract_protocol:
Genomic DNA from both top and bottom 10% cell fractions separately (around 5M cells in each fraction) using the QIAGEN DNeasy Blood and Tissue kit (Cat No. 69504) according to manufacturer’s instructions.
SgRNA sequences were amplified from genomic DNA via PCR, followed by a cleanup step using the QIAGEN QIAquick PCR purification kit (Cat-#: 28104) according to the manufacturer's instructions. Sequencing libraries were created using Illumina TruSeq adapters according to the manufacturer’s protocols.

treatment_protocol: TeloHAEC cell lines (Cas9, dCas9-KRAB, dCas9-VP64) were infected with lentiviruses at a multiplicity of infection of 0.3. Following viral infection, we cells were selected using zeocin (teloHAEC-dCas9-VP64) or G418 (Cas9/dCas9-KRAB) for five (dCas9-VP64) or seven days (Cas9/-dCas9-KRAB) in vascular cell basal medium (ATCC PCS-100-030) to remove any cells that did not incorporate a vector. After selection, cells expressing Cas9 or dCas9-KRAB were stimulated using TNFɑ (10ng/μl) for four hours to induce a pro-inflammatory response. Following stimulation or culture, cells were immunostained for one of three adhesion molecules (E-SELECTIN, ICAM1, VCAM1) or incubated with fluorescent dye-based reagents for endothelial signaling markers (NO,ROS,Ca2+). Stained cells were sorted by flow cytometry to collect the top and bottom 10% of fluorescently labeled cells (Top, Bottom).

tag: cell line

value: teloHAEC

value: CRISPRa

value: E-SELECTIN

value: Bottom

tag: replicate


title: m25dwt_BM_MEP

city: Bar Harbor

first: Joel

middle: H

last: Graber

state: ME

address: 159 Old Bar Harbor Rd

department: Bioinformatics Core

country: USA

institute: MDI Biological Laboratory

data_processing:
Single-end sequencing was performed on the HiSeq2500 System using TruSeq SBS Kit v4 reagents (Illumina).
Sequence reads were aligned and quantified with the Jackson Laboratory Computational Sciences Civet Single-end RNA-seq Analysis Pipeline (https://github.com/TheJacksonLaboratory/civet/).
Briefly, sequences were preprocessed with an in-house python script that filtered sequences with less than seventy percent of the bases passing a quality threshold of 30, trimmed end bases with quality score less than 30, and filtered sequences where the remaining length was less than seventy percent of the starting length.
The resulting reads were mapped to mouse transcriptome (ENSEMBL version GRCm38.84) using bowtie v2.2.0 (default parameters) and subsequent expression estimates were obtained using rsem-calculate-expression v1.2.19 (default parameters) and counts were third-quartile normalized with an in-house script.
Count matrix normalization (rlog transformation) and differential expression analysis was performed with DESeq2.
Genome_build: GRCm38.84 Genome Reference Consortium Mus musculus Build 38
Supplementary_files_format_and_content: Tab-delimited text file includes third-quantile normalized log2counts for each sample

molecule: total RNA

source_name: Whole mouse

growth_protocol: All mice were maintained in climate- and light cycle-controlled animal facilities at The Jackson Laboratory. Acidified water and 5K52 chow (PMI LabDiet) were provided ad libitum. All experiments were performed in accordance with National Institutes of Health Laboratory Animal Care Guidelines and were approved by the Animal Care and Use Committee (ACUC) of The Jackson Laboratory. All mouse strains used in this study are given in Supplemental Table S1.

extract_protocol:
Stem and myeloid (SMP) progenitor cells (Lin-Sca-Kit+CD34+, CD16_32lo) cells from spleen and bone marrow were sorted as described by Bumm et al., Cancer research 66, 11156-11165, 2006. Megakaryocyte-erythroid progenitors (MEP) were isolated as described in Challen et al., Cytometry A 75, 14-24, 2009. Total RNA was prepared using the PureLink RNA Mini Kit (Invitrogen). Libraries were checked for quality and concentration using the D5000 ScreenTape assay (Agilent Technologies) and quantitative PCR (KAPA Biosystems), according to the manufacturer’s instructions
RNA-seq libraries prepared using the KAPA mRNA HyperPrep Kit (KAPA Biosystems) according to the manufacturer’s instructions.

value: CbyJ.Cby-Rasa3(scat)/Llp +/+

tag: tissue

value: bone marrow

value: MEP

tag: genotype

value: wt

tag: disease state

tag: Stage

value: I

tag: age in days


title: Patient5 LIC Combination

value: Combination


title: HepG2.pCHiC

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

address: Neulaniementie 2

country: Finland

institute: A.I.Virtanen Institute for Molecular Sciences

data_processing:
library strategy: promoter Capture Hi-C (PCHiC)
pCHiC: Sequencing reads were processed with the Hi-C User Pipeline (HiCUP) software v 0.5.8, aligning reads to the human reference genome (GRCh37/hg19) and using all HiCUP default parameters; Significant chromosomal interactions were called with the Capture Hi-C Analysis of Genome Organization (CHiCAGO) software v 1.2.0, using default parameters, including the threshold of 5 for calling significant interactions.
Genome_build: hg19
Supplementary_files_format_and_content: pCHiC: Text file lists the baited (promoter-containing) HindIII fragment and the interacting (other end) HindIII fragment as well as the interaction score from the CHiCAGO software

growth_protocol: HepG2 cells (ATCC, HB-8065) were cultured in Dulbecco’s modified Eagle medium (DMEM; 4.5 g/L glucose, 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin; LONZA) supplemented with 10% fetal bovine serum (FBS; GIBCO). We maintained the cells at 37 °C in a humidified atmosphere at 5% CO2.

extract_protocol:
pCHiC: For the promoter Capture Hi-C in HepG2, 7-10M adherent cells were rinsed with serum-free media prior to trypsinization. We trypsinized and fixed the cells with 2% formaldehyde (EMD Millipore 344198) in serum-free media. We incubated cells in fixation medium with rocking at room temperature for 10 minutes, and then quenched with 1 M ice-cold glycine for a final concentration of 125 mM. After 5 minutes of rocking incubation at room temperature, we rinsed fixed cells twice with ice-cold PBS. Then we incubated the cells with rocking on ice with ice-cold permeabilization buffer (10 mM TrisHCl pH 8, 10 mM NaCl, 0.2 % Igepal CA-630, Complete EDTA-free protease inhibitor cocktail [Roche])36 for 30 minutes. We scraped cells from the culture plate and centrifuged at 2500 x g for 5 minutes at 4C to pellet nuclei. The supernatant was discarded and nuclei were flash frozen in liquid nitrogen and put at -80C.
pCHiC: The Hi-C library was prepared as described in (Rao et al., Cell, 2014) with modifications. We processed 10M nuclei in 5M cell aliquots, closely following Rao et al. protocol I.a.1 except we digested chromatin with 400U of HindIII (New England Biolabs R3104) at 37C overnight with shaking (950 rpm). After digestion, we pelleted nuclei with centrifugation at 2500 x g for 5 minutes at 4C. We performed end-filling and marked with biotin using biotin-14-dCTP (Invitrogen 19518-018), performed in-nucleus ligation, degraded protein using Proteinase K, and performed ethanol precipitation and purification. We sheared 5ug of DNA to 250-550 bp using the Covaris M220 instrument. We performed double size-selection to retain fragments from 250-550 bp using Agencourt AMPure XP beads (Beckman Coulter A63881). We immobilized the fragments containing biotin using DYNAL MyOne Dynabead Streptavidin T1 (Invitrogen 65601) beads. After end-repair and attachment of dATP, we ligated Illumina paired-end adaptors to the bead-bound library following the SureSelectXT user manual for Illumina Paired-End Multiplexed Sequencing (Agilent Technologies). After washing, we resuspended the Hi-C library in 20ul of 1x Tris buffer and subsequently removed the Streptavidin beads from the DNA by heating at 98C for 10 minutes. We then amplified the adaptor-ligated library using 8 PCR cycles and purified using Agencourt AMPure XP beads, following the SureSelectXT user manual. The RNA baits for promoter capture were designed in (Mifsud et al., Nature Genetics, 2015) for capturing HindIII fragments containing gene promoters (Dr. Cameron Osborne kindly shared the exact design). A total of 750 ng of the Hi-C library was hybridized to the biotinylated RNA baits, captured with DYNAL MyOne Dynabead Streptavidin T1 beads, and amplified in a post-capture PCR to add indexes, using 6 PCR cycles. The library was sequenced on the Illumina HiSeq 4000 platform.


title: Patient5 LIC vehicle

value: Vehicle


title: m25dwt_SP_MEP

value: spleen


title: Patient4 LIC AR-42

value: acute myeloid leukemia (AML)


title: 32dscat_SP_MEP

value: CbyJ.Cby-Rasa3(scat)/Llp scat/scat

value: mut

value: II


title: 32dscat_BM_Whole

value: Whole tissue


title: 32dscat_BM_SMP

value: SMP


title: Patient4 LIC vehicle

value: Bone marrow

value: FACS-sorted leukemia initiating cells (CD34+CD38-)


title: 2976_SP_SMP


title: Patient3 LIC Combination


title: Patient4 LIC KPT-9274


title: Patient5 LIC KPT-9274


title: Patient3 LIC KPT-9274


title: 32dscat_SP_Whole


title: 2976_BM_SMP


title: Patient3 LIC vehicle


title: 2976_SP_MEP


title: 2976_BM_Whole


title: Patient2 LIC AR-42


title: 2976_BM_MEP


title: 32dscat_BM_MEP


title: Patient3 LIC AR-42


title: 2953_SP_SMP

value: critical


title: 2955_BM_Whole

value: CbyJ.Cby-Rasa3(scat)/Llp +/+


title: Patient2 LIC KPT-9274


title: Patient2 LIC Combination


title: Patient2 LIC vehicle


title: Patient1 LIC Combination


title: 2953_SP_MEP


title: 2953_BM_Whole

value: bone marrow


title: Patient4 LIC Combination


title: 2953_BM_SMP


title: 2976_SP_Whole


title: 2953_SP_Whole


title: 2868_SP_SMP


title: Patient1 LIC AR-42


title: Patient1 LIC vehicle


title: metastasis_28

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

data_processing:
Raw reads in fastq sequencing files were cleaned to remove Illumina adapters and low quality reads with Trimmomatic (v.0.36).
Trimmed reads were then aligned against the human reference genome (GRCh38.p10, annotation release 89, 2017-05-31) using the STAR aligner (v.2.5.3a).
Alignment files were sorted using Samtools (v.1.5). Reads per gene locus were counted using featureCounts in the Rsubread package  (v.1.28.0) for R (v.3.4.2).
Genome_build: human, GRCh38.p10, annotation release 89, 2017-05-31
Supplementary_files_format_and_content: comma-separated values text file containing counts per gene, as summarized by featureCounts. Gene Ensembl Ids are in the first column. Genes are in rows and samples are in columns. The origin of each sample is indicated in its name (GBM, metastasis or control)

source_name: human brain adenocarcinoma metastasis

extract_protocol:
AllPrep DNA/RNA/protein Kit (Qiagen)
rRNA depletion, SMARTer Stranded Total RNA-seq Pico Input Mammalian Kit (Clontech Laboratories)

treatment_protocol: Mechanical (scissors) and ezymatical (0.08WU/mL Liberase DH, 100U/mL Dnase I) dissociation of tumor tissue followed by endothelial cell enrichment with antibody coupeled magnetic beads (negative selection CD15, CD45; positive selection CD31, Invitrogen).

value: endothelial cell enriched sample

tag: tissue source

value: adenocarcinoma metastasis resection

tag: Sex

value: M


title: metastasis_22


title: 2866_SP_SMP


title: 2822_SP_SMP

value: wt


title: metastasis_21

value: missing


title: 2953_BM_MEP

value: MEP

value: I


title: 2808_SP_SMP

value: spleen


title: metastasis_23

value: F


title: 2810_SP_SMP


title: control_26

source_name: human brain control

value: epilepsy surgery


title: 2761_SP_Whole

value: Whole tissue

value: II


title: control_14

value: autopsy


title: 2761_SP_MEP


title: metastasis_16


title: 2805_SP_SMP

value: SMP


title: 2761_BM_Whole


title: control_12


title: control_11


title: Patient1 LIC KPT-9274

value: acute myeloid leukemia (AML)

value: Bone marrow

value: FACS-sorted leukemia initiating cells (CD34+CD38-)


title: metastasis_30

value: endothelial cell enriched sample


title: 2761_BM_MEP

value: CbyJ.Cby-Rasa3(scat)/Llp +/+

value: bone marrow


title: 2726_SP_Whole

value: CbyJ.Cby-Rasa3(scat)/Llp scat/scat

value: mut


title: 2761_BM_SMP

value: wt


title: control_6

value: M


title: GBM_27

source_name: human glioblastoma multiforme

value: GBM IDH1 wt resection


title: GBM_29


title: 2726_BM_Whole


title: 27265_SP_Whole

value: spleen


title: 2726_BM_SMP


title: 2726_BM_MEP

value: MEP


title: GBM_8


title: GBM_3


title: 27265_BM_Whole

value: Whole tissue


title: 27265_SP_MEP

value: II


title: Serous Ovarian Cancer Patient90

city: Iowa City

first: Jesus

last: Gonzalez Bosquet

state: IA

address: 200 Hawkins Dr

institute: University of Iowa

data_processing:
Whole cell RNAs were purified using the mirVana RNA isolation kit. Yield and purity were assessed with an Agilent Model 2100 DNA Analyzer and a Trinean DropSense 16 spectrophotometer
Genomic DNA (gDNA) was purified using the DNeasy kit. Yield and purity were determined using a NanoDrop 2000 spectrophotometer and horizontal gel electrophoresis (1% agarose in 1X TBE)
Transcription profiling was performed starting with 500 ng of total cellular RNA, which was fragmented, converted to cDNA and ligated to sequencing adaptors containing indexes using the Illumina TruSeq stranded total RNA library preparation kit. Sequencing was performed using Illumina HiSeq 4000 genome sequencer using a 150 bp paired-end SBS chemistry.
RNAseq output BAM files were aligned against Build 38 (GRCh38) of the human genome. Genomic variation was annotated with ANNOVAR software. DNA base calling differences between each cell line and the reference genome was then tabulated for each of the cell lines.
Genome_build: hg38
Supplementary_files_format_and_content: TXT format. Annotated genomic variation

source_name: Human high-grade serous ovarian cancer

growth_protocol: Optimal growth media for each cell line

extract_protocol:
mirVana RNA kit; QIAGEN gDNA kit
Illumina TruSeq stranded total RNA; Illumina Library Quantifiction Kit
150bp paired end SBS chemistry on a HiSeq 4000 platform

tag: subect status

value: Serous Ovarian Cancer Patient

tag: subect id

tag: response to chemotherapy

value: Responders


title: control_15

value: autopsy


title: Serous Ovarian Cancer Patient86

value: Non-responders


title: 27265_BM_SMP

value: SMP


title: 27265_BM_MEP


title: Serous Ovarian Cancer Patient84


title: 2685_SP_Whole

value: I


title: Serous Ovarian Cancer Patient105


title: 2685_SP_MEP

value: CbyJ.Cby-Rasa3(scat)/Llp +/+


title: GBM_9

value: endothelial cell enriched sample


title: 2685_BM_MEP

value: bone marrow


title: 2658_SP_MEP


title: Serous Ovarian Cancer Patient85


title: 2685_BM_Whole


title: 2658_BM_MEP


title: Serous Ovarian Cancer Patient61


title: Serous Ovarian Cancer Patient23


title: 2629_SP_Whole

value: CbyJ.Cby-Rasa3(scat)/Llp scat/scat

value: mut

value: critical


title: 2685_BM_SMP

value: wt


title: Serous Ovarian Cancer Patient100


title: Serous Ovarian Cancer Patient8


title: Serous Ovarian Cancer Patient21


title: Serous Ovarian Cancer Patient87


title: Serous Ovarian Cancer Patient83


title: Serous Ovarian Cancer Patient95


title: 2608_SP_Whole

value: spleen


title: 2658_SP_Whole


title: 2658_BM_Whole


title: 2658_BM_SMP


title: Serous Ovarian Cancer Patient15


title: 2629_SP_SMP


title: 2608_BM_Whole

value: whole tissue


title: Serous Ovarian Cancer Patient69


title: 2629_SP_MEP

value: MEP


title: Serous Ovarian Cancer Patient102


title: Serous Ovarian Cancer Patient18


title: Serous Ovarian Cancer Patient53


title: Serous Ovarian Cancer Patient82


title: Serous Ovarian Cancer Patient72


title: 2629_BM_SMP


title: Serous Ovarian Cancer Patient63


title: 2629_BM_MEP


title: Serous Ovarian Cancer Patient79


title: 2608_SP_SMP


title: Serous Ovarian Cancer Patient64


title: Serous Ovarian Cancer Patient54


title: Serous Ovarian Cancer Patient22


title: Serous Ovarian Cancer Patient68


title: 2608_SP_MEP


title: Serous Ovarian Cancer Patient65


title: Serous Ovarian Cancer Patient3


title: 27_Normal human Astrocytes

city: Bogota

first: Cynthia

last: Martin Jiménez

state: Colombia

address: pontificia universidad javeriana

department: Computational biology

country: Colombia

institute: Pontificia Universidad Javeriana

data_processing:
QC: RNA-seq quality control was assessed via QUARS (QUAlity control for RNA-Seq; github.com/TainVelasco-Luquez/QUARS), a quality control pipeline built on the bioinformatics workflow manager Nextflow (v18.10.1). QUARS integrates FastQC (v0.11.7), to assess sequencing quality, with Fastp [24] (v0.20.0), for automatic adaptor trimming and low-base-quality filtering.
Mapping: Reads were then mapped to Gencode (release 29) reference transcripts and quantified at the gene level using Salmon (v0.13.1), via the nextflow pipeline nf-core (github.com/nf-core/rnaseq). The gene-level count matrix from Salmon was derived using tximport (v1.12), and NOISeq (v2.28) was used to assess sequencing quality through saturation plots.
Creating counts matrix: The gene-level count matrix from Salmon was derived using tximport (v1.12), and NOISeq (v2.28) was used to assess sequencing quality through saturation plots
Low read filtering: Genes were discarded if, after aggregating read counts across the 3 × 2 biological and technical replicates for each treatment, the gene had less than 10 total reads for any of the 3 treatments; this filtering step left a total of 24,893 genes, including non-coding genes.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: There are 3 processed data files, all in csv format. salmon_merged_gene_counts.csv contains the Salmon-produced counts per gene. salmon_merged_transcript_counts.csv contains the Salmon-produced counts per transcript.count_matrix_DESeq2_normalised.csv contains the DESeq2-normalized counts per gene.

source_name: Fetal astrocyte

growth_protocol: Normal Human Astrocyte (NHA) primary cells (Lonza, Basel, Switzerland, Catalog CC-2565) from three different donors (1 male, 2 female) were cultured in Astrocyte Basal Medium (ABM by Lonza, Basel, Switzerland) supplemented with SingleQuots supplements (Lonza, Basel, Switzerland) in a humidified incubator at 37 ºC and 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen, USA), following manufacturer’s instructions. RNase-free DNase I was used to eliminate potential genomic DNA contamination. Samples were shipped at -80C in a nuclease-free buffer solution to the GeneWiz Plainfield (NJ, USA) sequencing facility. After shipment, RNA integrity and concentration were assessed via an Agilent Tapestation Bioanalyzer 2100 (RIN > 7) and Qubit 2.0 fluorometer, respectively.
Strand-specific RNA library preparation with poly(A)+ selection was performed using the TruSeq Stranded mRNA library prep kit following the manufacturer’s protocol (Illumina, San Diego, CA, USA, Catalog # RS-122-2101).  Subsequently, the RNA was sequenced in an Illumina HiSeq machine with a 2x150bp paired-end configuration, yielding a sequencing depth of ~75M reads per sample.

treatment_protocol: Palmitic acid treatment: NHA cells were seeded in 48-well plates at 5,000 cells/cm2 for 12 days, then washed with PBS and starved in free serum DMEM without L-Glutamine, phenol red and supplements (Lonza) for 6 h. Cells were then treated with free-serum DMEM containing palmitic acid (Sigma, St Louis, MO, USA), 1.35% bovine serum albumin (BSA; SigmaSigma, St Louis, MO, USA, lot A2153) as a carrier protein, and 2mM carnitine (Sigma, St Louis, MO, USA) as a transporter into the mitochondrial matrix. Cells were treated with 2 mM of palmitic acid for 24 h. Vehicle condition: received free-serum DMEM with the same concentrations of BSA and carnitine, but no palmitic acid. Tibolone pre-treatment: A third population of cells were pre-treated with 10 nM of tibolone for 24 h before the addition of palmitic acid. Tibolone (Lot T0827, Sigma, St Louis, MO, USA) was dissolved in 100% DMSO as a stock solution at 40 mM, and further dilutions were made with free serum DMEM. DMEM condition: free-serum DMEM.

value: astrocyte

value: Normal Human Astrocyte 3 Batch #612742

value: female

value: PalmiticAcid

tag: rin

tag: dv 200 (rna)


title: 28_Normal human Astrocytes

tag: cell type

value: Normal Human Astrocyte 3 Batch #612743


title: 25_Normal human Astrocytes

value: Normal Human Astrocyte 3 Batch #612740

value: Tibolone+PalmiticAcid


title: 26_Normal human Astrocytes

value: Normal Human Astrocyte 3 Batch #612741


title: 2608_BM_SMP

tag: strain

value: SMP

value: I


title: 2629_BM_Whole

value: CbyJ.Cby-Rasa3(scat)/Llp scat/scat

value: bone marrow

value: Whole tissue


title: Serous Ovarian Cancer Patient14

value: Serous Ovarian Cancer Patient

value: Responders


title: 24_Normal human Astrocytes

value: Normal Human Astrocyte 3 Batch #612739

tag: treatment

value: DMEM


title: 2608_BM_MEP

value: MEP

value: mut

value: critical


title: Serous Ovarian Cancer Patient7


title: Serous Ovarian Cancer Patient39

value: Non-responders


title: Serous Ovarian Cancer Patient20


title: Serous Ovarian Cancer Patient81


title: 30_Normal human Astrocytes

value: astrocyte

value: Normal Human Astrocyte 3 Batch #612745

value: female

value: Vehicle


title: 21_Normal human Astrocytes

value: Normal Human Astrocyte 3 Batch #612736

value: Tibolone


title: Serous Ovarian Cancer Patient78


title: 29_Normal human Astrocytes

value: Normal Human Astrocyte 3 Batch #612744


title: 19_Normal human Astrocytes

value: Normal Human Astrocyte 2 Batch #565620


title: Serous Ovarian Cancer Patient19


title: Serous Ovarian Cancer Patient41


title: Serous Ovarian Cancer Patient36


title: Serous Ovarian Cancer Patient34


title: 20_Normal human Astrocytes

value: Normal Human Astrocyte 2 Batch #565621


title: 23_Normal human Astrocytes

value: Normal Human Astrocyte 3 Batch #612738


title: Serous Ovarian Cancer Patient67

value: Serous Ovarian Cancer Patient


title: Serous Ovarian Cancer Patient76


title: Serous Ovarian Cancer Patient40

value: Responders


title: 22_Normal human Astrocytes

value: Normal Human Astrocyte 3 Batch #612737


title: Serous Ovarian Cancer Patient44


title: 18_Normal human Astrocytes

value: Normal Human Astrocyte 2 Batch #565619

value: PalmiticAcid


title: 15_Normal human Astrocytes

value: Normal Human Astrocyte 2 Batch #565616

value: Tibolone+PalmiticAcid


title: Serous Ovarian Cancer Patient59


title: 16_Normal human Astrocytes

value: astrocyte

value: Normal Human Astrocyte 2 Batch #565617


title: Serous Ovarian Cancer Patient49


title: Giardia lamblia WB: 5'5npac control vs pPMBF1

type: RNA

city: Taipei

first: Chin-Hung

last: Sun

address: Department of Parasitology, College of Medicine, National Taiwan University

department: Department of Parasitology

country: Taiwan

description: stable cell lines

hyb_protocol: Correspondingly fragmented labeled cRNA was then pooled and hybridized to a G. lamblia oligonucleotide microarray (Agilent Technologies, USA) at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5.

data_processing: Scanned images were analyzed by Feature Extraction version 9.1 software (Agilent Technologies, USA), and image analysis and normalization software was used to quantify signal and background intensity for each feature; data were substantially normalized by the rank consistency filtering LOWESS method.

organism: Giardia duodenalis

source_name: Giardia lamblia WB

label_protocol: 0.5 mg of total RNA was amplified by a Low RNA Input Fluor Linear Amp kit (Agilent Technologies) and labeled with Cy3 or Cy5 (CyDye, PerkinElmer Life Sciences) during the in vitro transcription process. 0.825 mg of Cy-labeled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 minutes.

growth_protocol: PCR amplification and standard cloning techniques were used to insert Top3b gene from genomic DNA and then cloned into the pPop2NHA vector, resulting in plasmid pPTop3bI.

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

treatment_protocol: Giardia  cells were transfected with the pPTop3b or 5'5npac plasmid containing the pac gene were selected and maintained with 54 ug/ml puromycin.

value: 5'5npac cells

value: pPMBF1 cells


title: Serous Ovarian Cancer Patient27


title: 14_Normal human Astrocytes

value: Normal Human Astrocyte 2 Batch #565615

value: female

value: DMEM


title: 12_Normal human Astrocytes

value: Normal Human Astrocyte 2 Batch #565613

value: Tibolone


title: Serous Ovarian Cancer Patient9

value: Non-responders


title: 17_Normal human Astrocytes

value: Normal Human Astrocyte 2 Batch #565618


title: 11_Normal human Astrocytes

value: Normal Human Astrocyte 2 Batch #565612


title: 10_Normal human Astrocytes

value: Normal Human Astrocyte 1 Batch #0000514426

value: male

value: Vehicle


title: Serous Ovarian Cancer Patient114

value: Serous Ovarian Cancer Patient

value: Responders


title: 8_Normal human Astrocytes

value: astrocyte

value: Normal Human Astrocyte 1 Batch #0000514424

value: PalmiticAcid


title: 9_Normal human Astrocytes

value: Normal Human Astrocyte 1 Batch #0000514425


title: Serous Ovarian Cancer Patient51


title: Serous Ovarian Cancer Patient47


title: 7_Normal human Astrocytes

value: Normal Human Astrocyte 1 Batch #0000514423


title: Serous Ovarian Cancer Patient13


title: 13_Normal human Astrocytes

value: Normal Human Astrocyte 2 Batch #565614

value: female


title: Serous Ovarian Cancer Patient12


title: Serous Ovarian Cancer Patient115


title: 3_Normal human Astrocytes

value: Normal Human Astrocyte 1 Batch #0000514419

value: DMEM


title: Serous Ovarian Cancer Patient1

value: Non-responders


title: 2_Normal human Astrocytes

value: Normal Human Astrocyte 1 Batch #0000514418

value: Tibolone


title: 1_Normal human Astrocytes

value: Normal Human Astrocyte 1 Batch #0000514417


title: 6_Normal human Astrocytes

value: Normal Human Astrocyte 1 Batch #0000514422

value: male

value: Tibolone+PalmiticAcid


title: Serous Ovarian Cancer Patient31

value: Serous Ovarian Cancer Patient


title: 4_Normal human Astrocytes

value: astrocyte

value: Normal Human Astrocyte 1 Batch #0000514420


title: Serous Ovarian Cancer Patient28

value: Responders


title: mInput_KO

city: Los Angeles

first: Cunyu

last: Wang

state: CA

address: 10833 Le Conte Ave

department: School of Dentistry

institute: university of California, Los Angeles

data_processing:
The reads were aligned to the hg19/mm9 build of the mouse genome using bowtie.
The sam files were converted into bam files, and then sorted using samtools.
Peak calling was perfromed using MACS2 following the instructions.
Genome_build: hg19/mm9
Supplementary_files_format_and_content: peaks

source_name: bone marrow-derived MSCs

growth_protocol: Both human MSCs and mBMSCs were maintained in DMEM supplemented with 15% FBS and 1% penicillin/streptomycin, repsectively.

extract_protocol:
ChIP assays were performed using a ChIP assay kit (Upstate Biotechnology, Cat No: 17-295) per the manufacturer's instructions. Briefly, cells were double crosslinked with 10 mM DTBP for 10 min at room temperature, followed by incubation in 1% formaldehyde for 15 min in a 37 °C water bath. Nuclei were extracted and sonication was perfromed to generate 200–500 bp genomic DNA fragments. Chromatin complexes were immunoprecipitated with the related antibodies and Dynabeads Protein A/G. The precipitated DNA was purified using DNA clean and concentrator (Zymo Research).
Libraries were prepared using KAPA Hyper Prep Kit (Kapa Biosystems, Cat No:  KK8502)

treatment_protocol: The MSCs were subjected to osteogenic induction (OI) for 4 hours.

value: bone marrow-derived MSCs (mBMSCs)

tag: genotype/variation

value: Prx1Cre; Kdm4bf/f mice (KO)


title: mInput_WT

value: Prx1Cre; Kdm4bw/w mice (WT)


title: Serous Ovarian Cancer Patient29


title: mH3K9me3_KO

tag: chip antibody


title: Serous Ovarian Cancer Patient57


title: mKDM4B_KO

data_processing:
The reads were aligned to the mm9 build of the mouse genome using bowtie.
The sam files were converted into bam files, and then sorted using samtools.
Peak calling was perfromed using MACS14 following the instructions.
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: peak and wig


title: Serous Ovarian Cancer Patient30


title: Serous Ovarian Cancer Patient56


title: S009

city: Rochester

first: xianfeng

last: chen

state: MN

address: 1216 2nd St SW

department: Biochem & Molecular Biology

institute: Mayo Clinic

data_processing:
Raw counts were used to calculate differentially expressed lncRNAs using TruSeq SBS kit version-3 and HCS v2.0.12 data collection software
Transcripts per Million (TPM) scaling was performed using QIAGEN OmicSoft software
TPM values were quantile normalized using preprocessCore package in Bioconductor

source_name: Circulating EVs from MetS patients

extract_protocol:
Using the exoRNeasy Serum/Plasma (Qiagen cat# 77044) assay, circulating EVs were isolated following vendor instructions, and RNA subsequently isolated with the miRNeasy serum/plasma advanced kit (Qiagen cat# 217204). Initially, thrombin was added to the plasma for 5 minutes, and sample centrifuged at 2500×g for 15 min. After being mixed with precipitation buffer and incubated at 4°C for 60 minutes, the supernatant was centrifugated at 13,000×g for 5 min. The pellet was resuspended and lysed, and protein precipitated and removed. Isopropanol was added to the supernatant, which was then loaded onto the column. RNA was eluted following 3 washes and stored at -80°C.
Using TruSeq SBS kit version-3 and HCS v2.0.12 data collection software, the cells were sequenced on an Illumina HiSeq 2000. The generated data was analyzed using the MAPRSeq v.1.2.1 system and the Bioinformatics Core standard tool.
RNA libraries were prepared (TruSeq RNA Sample Prep Kit v2, Illumina, San Diego, USA)

tag: gender

value: female

tag: age

value: 24 years old

value: Circulating extracellular vesicles

value: MetS patient


title: S007

tag: disease state


title: Kdm4b_WT_OI

data_processing:
The reads were aligned to the mm9 build of the mouse genome using Tophat.
Expression of the transcript was determined using Cufflinks with Refseq mRNAs to guide assembly.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file with FPKM

source_name: mMSCs from bone marrow

growth_protocol: Primary mBMSCs cultured in presence or absence of osteogenic induction for 4 days.

extract_protocol:
Total RNA was isolated, and purified with Dynabeads™ mRNA Purification Kit (Invitrogen, Cat No: 61006).
Libaray was prepared using Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems, Cat No:  KK8400)

value: mesenchymal stem cell (MSC)

tag: tissue

value: bone marrow

value: wildtype

tag: condition

value: osteogenic induction


title: mKDM4B_WT


title: Serous Ovarian Cancer Patient71

tag: Stage

value: Non-responders


title: Kdm4b_KO_con

value: KDM4B KO

value: control


title: Kdm4b_WT_con


title: 5_Normal human Astrocytes

value: astrocyte

value: Normal Human Astrocyte 1 Batch #0000514421

tag: Sex

value: male

value: Tibolone+PalmiticAcid


title: Serous Ovarian Cancer Patient75

tag: subect status

value: Serous Ovarian Cancer Patient

value: Responders


title: S013

source_name: Circulating EVs from control subjects

value: female

value: 25 years old


title: Serous Ovarian Cancer Patient98

tag: subect id


title: S004

value: 32 years old

value: Circulating extracellular vesicles


title: mH3K9me3_WT

value: bone marrow-derived MSCs (mBMSCs)

value: Prx1Cre; Kdm4bw/w mice (WT)


title: Serous Ovarian Cancer Patient35

tag: response to chemotherapy


title: S005

value: 29 years old

value: MetS patient


title: S012


title: Serous Ovarian Cancer Patient48


title: S006


title: Serous Ovarian Cancer Patient10

value: Non-responders


title: Kdm4b_KO_OI

value: mesenchymal stem cell (MSC)

value: bone marrow

value: KDM4B KO

value: osteogenic induction


title: S011

value: 23 years old

value: control


title: S010

value: male


title: Serous Ovarian Cancer Patient33

value: Serous Ovarian Cancer Patient

value: Responders


title: Serous Ovarian Cancer Patient16


title: Serous Ovarian Cancer Patient45


title: S015

value: female

value: 21 years old


title: Serous Ovarian Cancer Patient62


title: HEPG2.IL1B.8h.rep2

data_processing:
ChIP-Seq: Data was mapped using bowtie allowing up to two mismatches and reporting only one alignment for each read. Poor quality reads were filtered out (minimum 97% of bp over quality cutoff 10)
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq: BigWig files were generated using makeBigWig.pl and peak files were generated using findPeaks

extract_protocol:
ChIP-Seq: Formaldehyde (10′) fixed lysates were clarified from sonicated nuclei and protein–DNA complexes were isolated with H3K27ac antibody (ab4729, Abcam)
ChIP-Seq: DNA was end-repaired using a combination of T4 DNA polymerase, Escherichia coli DNA Pol I large fragment (Klenow polymerase; New England Biolabs) and PNK (Enzymatics Inc., Beverly, MA, USA). The blunt, phosphorylated ends were treated with Klenow fragment (minus exo; New England Biolabs) and dATP to yield a protruding 3- ‘A’ base for ligation of Illumina's adapters that have a single ‘T’ base overhang at the 3′ end. After adapter ligation, ChIP DNA was polymerase chain reaction (PCR) amplified with Illumina genomic adaptors or with NEXTflex DNA barcode adaptors (Bioo Scientific Corporation, Austin, TX, USA) and library fragments were size-selected (150–250 bp) from a 2% agarose gel. All libraries were sequenced on Illumina HiSeq 2000 according to the manufacturer's instructions.

treatment_protocol: ChIP-Seq: HepG2 cells were stimulated with 10ng/mL of IL1B (PHC0814, Gibco™) at 2h, 8h and 23h timepoints. 2 replicates were performed per treatment.

tag: timepoint

value: H3K27ac (ab4729, Abcam).

value: Treated with Il1B for 8h


title: HEPG2.IL1B.23h.rep1

value: Treated with Il1B for 23h


title: HEPG2.input


title: HEPG2.IL1B.23h.rep2


title: Myoblast_T2D_119a prolif.a1.lbe1

city: Malmö

first: Charlotte

last: Ling

address: Jan Waldenströms gata 35, CRC 91:12

department: Clinical Sciences

country: Sweden

institute: Lund University

hyb_protocol: According to the manufacturer's recommendations. Myoblasts and myotubes from one subject were always analyzed on the same chip and the samples from controls and individuals with type 2 diabetes were evenly distributed on the chips to reduce batch effects.

scan_protocol: According to the manufacturer’s recommendations.

data_processing: Probes with a mean detection p-value >0.01 for more than 60% of the samples were filtered out. Data were background-corrected, log2-transformed, and quantile-normalized.

label: biotin

source_name: Myoblast, T2D

growth_protocol: Muscle stem cells were isolated from human vastus lateralis muscle biopsies. Isolated myoblasts were cultured in growth medium (HAM’s/F10 supplemented with 20% fetal bovine serum (FBS), 1% penicillin/streptomycin and 1% Amphotericin B) until 70% confluent. To induce differentiation, cells were incubated in differentiation medium 1 (DMEM with 1.0 g/l L glucose supplemented with 10% FBS and 1% penicillin/streptomycin) for 2 days, followed by differentiation medium 2 (DMEM with 4.5 g/l L glucose supplemented with 2% horse serum and 1% penicillin/streptomycin) until cells were fully differentiated, as determined by visual confirmation of myotube formation (>3 nuclei per myotube in approximately 70% of cells) on day 7. Cells were harvested both as proliferating myoblasts (<50% confluent) and as differentiated myotubes.

extract_protocol: RNA was extracted by Trizol (Invitrogen, ThermoFisher Scientific, Waltham, MA, USA), followed by RNeasy MinElute Cleanup kit (Qiagen #74204). Quantity and purity of RNA were determined using a NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). RNA integrity was determined using the Bioanalyzer system (Agilent, Santa Clara, CA, USA).

tag: diabetes status

value: Type 2 diabetes (T2D)


title: Myoblast_T2D_129a prolif.a1.lbe1

label_protocol: According to the manufacturer’s recommendations.


title: Myotube_T2D_119a diff.a1.lbe1

source_name: Myotube, T2D


title: Myotube_NGT_21a diff.a1.lbe1

source_name: Myotube, NGT

value: Normal glucose tolerance (NGT)


title: Myotube_T2D_29H diff.a1.lbe1


title: Myotube_T2D_20a diff.a1.lbe1


title: Myotube_NGT_105a diff.a1.lbe1


title: Serous Ovarian Cancer Patient58


title: Myoblast_NGT_112a prolif.a1.lbe1

source_name: Myoblast, NGT


title: Serous Ovarian Cancer Patient25


title: Myoblast_T2D_29H prolif.a1.lbe1


title: Myotube_T2D_129a diff.a1.lbe1


title: Myoblast_NGT_105a prolif.a1.lbe1


title: Myotube_NGT_24a diff.a1.lbe1


title: Myotube_NGT_32a diff.a1.lbe1


title: Myoblast_NGT_24a prolif.a1.lbe1


title: Myoblast_NGT_21a prolif.a1.lbe1


title: Myoblast_NGT_32a prolif.a1.lbe1


title: Myoblast_T2D_109a prolif.a1.lbe1


title: Myotube_T2D_109a diff.a1.lbe1


title: Myoblast_T2D_20a prolif.a1.lbe1


title: HEPG2.IL1B.8h.rep1


title: Myotube_NGT_112a diff.a1.lbe1


title: Serous Ovarian Cancer Patient2

value: Non-responders


title: Serous Ovarian Cancer Patient5


title: HEPG2.IL1B.2h.rep1

value: Treated with Il1B for 2h


title: Serous Ovarian Cancer Patient46


title: Myotube_T2D_45 diff.a1.lbe1


title: HEPG2.IL1B.0h.rep2

value: Untreated


title: Serous Ovarian Cancer Patient91


title: HEPG2.IL1B.0h.rep1


title: HEPG2.IL1B.2h.rep2


title: Serous Ovarian Cancer Patient26


title: Serous Ovarian Cancer Patient42


title: Serous Ovarian Cancer Patient60


title: Serous Ovarian Cancer Patient6


title: Myoblast_T2D_45 prolif.a1.lbe1


title: siDAZAP2_DMSO_R2

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

institute: German Center for Cancer Research

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming and quality filtering: Trimmomatic 0.39
Transcriptome mapping: Tophat 2.0.6
computation of count data: htseq.py
Genome_build: hg19
Supplementary_files_format_and_content: count table containing the count values for all genes in all samples

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% (v/v) FCS, 100 U/ml Penicillin, 100 µg/ml Streptomycin, 10 mM HEPES buffer and 2 mM L-Glutamine at 37 °C and 5% CO2.

extract_protocol:
RNA was isolated using TRIzol (Invitrogen) following the manufacturer’s instructions. Total RNA was then purified with the RNA Clean & Concentrator-5 kit (Zymo Research) and reverse-transcribed using SuperScript III reverse transcriptase (Invitrogen), again following the manufacturer’s instructions.
Sequencing libraries were prepared using 1µg of DNAse-treated total RNA in the first step of the TruSeq RNA Sample Preparation v2 protocol (Illumina, Part# 15026495 Rev. A) as recommended by the manufacturer.

treatment_protocol: After siRNA transfection, cells were treated with 50 µM 5-Fluorouracil or the same amount of solvent (DMSO) for 24 h.

tag: cell type

value: human cancer cell line

tag: disease status

value: cancerous


title: siDAZAP2_5-FU_R1


title: siDAZAP2_5-FU_R2


title: siDAZAP2_DMSO_R3


title: siDAZAP2_5-FU_R3


title: Serous Ovarian Cancer Patient17


title: Serous Ovarian Cancer Patient11


title: siDAZAP2_DMSO_R1


title: Myotube_NGT_35a diff.a1.lbe1


title: Serous Ovarian Cancer Patient77


title: Myotube_T2D_127a diff.a1.lbe1


title: Myoblast_NGT_35a prolif.a1.lbe1


title: Myoblast_NGT_55a prolif.a1.lbe1


title: Myoblast_T2D_128a prolif.a1.lbe1


title: Myotube_NGT_55a diff.a1.lbe1


title: Myoblast_T2D_46a prolif.a1.lbe1


title: Myoblast_T2D_127a prolif.a1.lbe1


title: siCTRL_5-FU_R2


title: Serous Ovarian Cancer Patient97


title: Myotube_NGT_40a diff.a1.lbe1


title: siCTRL_5-FU_R3


title: Myotube_T2D_128a diff.a1.lbe1


title: Myoblast_NGT_40a prolif.a1.lbe1


title: Myotube_T2D_46a diff.a1.lbe1


title: Serous Ovarian Cancer Patient94


title: Myoblast_T2D_117a prolif.a1.lbe1


title: Myotube_T2D_117a diff.a1.lbe1


title: Myoblast_T2D_8a prolif.a1.lbe1


title: Myoblast_NGT_14a prolif.a1.lbe1


title: Myotube_NGT_115a diff.a1.lbe1


title: Myotube_T2D_8a diff.a1.lbe1


title: Myotube_NGT_14a diff.a1.lbe1


title: Myotube_NGT_18a diff.a1.lbe1


title: Myoblast_NGT_115a prolif.a1.lbe1


title: siCTRL_5-FU_R1


title: Serous Ovarian Cancer Patient92


title: siCTRL_DMSO_R3


title: Serous Ovarian Cancer Patient113


title: siCTRL_DMSO_R2


title: Serous Ovarian Cancer Patient37


title: siCTRL_DMSO_R1


title: Myoblast_T2D_63a prolif.a1.lbe1


title: Serous Ovarian Cancer Patient24


title: ddm1_2ndgen Rep2

city: Vienna

first: Bhagyshree

middle: Babasaheb

last: Jamge

address: Dr. Bohr Gasse -3

country: Austria

institute: Gregor Mendel Institute

description:
4-5 week old Leaves
ribo Zero depletion

data_processing:
For alignment and visualization, reads were mapped to the TAIR10 Arabidopsis genome using the STAR aligner and bigwig files were generated using the bamCoverage function in DeepTools.
Kallisto v0.46.0 was used to estimate transcript abundance and read counts for all transcripts in TAIR10.
The resulting values per transcript were mapped to gene level using R v3.6.1 (https://www.R-project.org/) and packages tximport v1.12.3 and TxDb.Athaliana.BioMart.plantsmart28 v3.2.2 (https://bioconductor.org/packages/release/data/annotation/html/TxDb.Athaliana.BioMart.plantsmart28.html). Statistical analysis was performed with R v3.5.1 (https://www.R-project.org/) using the DESeq2 v1.22.2 package.
The pairwise comparison between WT Col-0 and ddm1 was performed with default DESeq2 settings. In addition, the shrunken log2 fold changes were calculated using default settings. Genes with False Discovery Rate (FDR) adjusted p-value < 0.05 and an absolute shrunken log2 fold change > 2 were classified as differentially expressed.
Genome_build: TAIR10
Supplementary_files_format_and_content: Kallisto tsv files show the counts and TPMs for each sample.

organism: Arabidopsis thaliana

source_name: Leaves

extract_protocol:
Total RNA was extracted with Spectrum plant total RNA kit (Sigma Aldrich) from 4-5 week old leaves of WT Col-0, F1 DDM1/ddm1 (Col-0Xddm1) and ddm1 2nd generation. Contaminating DNA was removed with a DNA-free DNA removal kit (Thermo Fisher Scientific).
For RNA-seq analyses, rRNA was removed by Ribo-Zero rRNA Removal kit (Illumina). After depletion of rRNA, RNA-seq libraries were generated with NEBNext UltraII directional RNA library prep kit for Illumina (New England Biolabs) following the manufacturer’s instructions. The libraries were sequenced with Illumina Hiseq 2500 to generate single-end 50 bp reads. Samples were prepared from three independent biological replicates.

tag: genotype

value: ddm1(-/-) 2nd generation

value: 4-5 weeks

value: Leaves


title: Myotube_T2D_63a diff.a1.lbe1


title: zr2252_8_RRHP siTET2 rep 2

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

data_processing:
Library strategy: Reduced Representation Hydroxymethylation Profiling
Methyl Midi-Seq: Sequence reads from bisulfite-treated EpiQuest libraries were identified using standard Illumina basecalling software and analysed using a Zymo Research proprietary analysis pipeline, which is written in Python and uses Bismark to perform the alignment (Krueger et al 2011).
Methyl Midi-Seq: Index files were constructed using the bismark_genome_preparation command and the entire reference genome. The --non_directional parameter was applied while running Bismark. All other parameters were set to default. Filled-in nucleotides were trimmed off when doing methylation calling.
Methyl Midi-Seq: The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The genome was partitioned into non-overlapping tiles of length 1 kb and 5mC was profiled within these tiles. Regions with low read coverage (less than 4 reads in any sample) were discarded from the analysis.
Methyl Midi-Seq: The differential 5mC analysis was carried out by methylKit using Fisher Exact test (Akalin et al 2012).
RRHP: Sequence reads from RRHP libraries were first processed to trim off the low quality bases and the P7CG adapter at the 3’ end of the reads. Reads were then aligned to the reference genome using bowtie (Langmead & Salzberg 2012) default parameters and the ‘–best’ setting. Aligned reads with the MspI tag (CCGG) were counted.
RRHP: The correlation analysis between different RRHP libraries was performed by comparing the presence of the tagged reads at each profiled MspI site, and Pearson’s coefficient was calculated accordingly.
RRHP: The genome was partitioned into non-overlapping tiles of length 1 kb and 5hmC was profiled within these tiles. Regions with low read coverage (those with less than 10 reads in any sample) were discarded from the analysis.
RRHP: The differential 5hmC analysis was carried out using DESeq2 (Love et al 2014).
Genome_build: GRCh37

growth_protocol: MCF7 cells were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine, 50 U/ml penicillin, 50 ug/ml streptomycin.

extract_protocol:
DNA was extracted using a DNeasy Blood and Tissue Kit (Qiagen) according to manufacturer’s instructions. DNA was RNase (Sigma) treated on-column (20 µl of 20 mg/mL) for 15 minutes at room temperature. Purified DNA was quantified using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific).
For Methyl Midi-Seq, library preparation, sequencing and initial data processing for genomic analysis of 5mC was undertaken using the Methyl Midi-seq (MMS) service provided externally by Zymo Research (Irvine, California). Cells were harvested and DNA isolated. Subsequently, libraries were prepared from 500 ng of genomic DNA sequentially digested with 60 U of TaqαI and 30 U of MspI (NEB) and then extracted with a DNA Clean & Concentrator kit (Zymo Research). Fragments were ligated to pre-annealed adapters containing 5’-methylcytosine instead of cytosine according to Illumina’s specified guidelines (http://www.illumina.com). Adapter-ligated fragments of 150–250 bp and 250–350 bp were recovered from a 2.5% NuSieve 1:1 agarose gel using a Zymoclean Gel DNA Recovery Kit (Zymo Research). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning Kit (Zymo Research). Preparative-scale PCR was performed and the resulting products were purified using a DNA Clean & Concentrator kit (Zymo Research) for sequencing on an Illumina HiSeq. For RRHP, library preparation, sequencing and initial data processing for genomic analysis of 5hmC was undertaken using the Reduced Representation Hydroxymethylation Profiling (RRHP) service provided externally by Zymo Research (Irvine, California), as described in Petterson et al. (2014). Cells were harvested and DNA isolated as described previously. Subsequently, genomic DNA was fragmented overnight at 37°C with a hydroxymethyl-insensitive enzyme, MspI, and purified using the DNA Clean & Concentrator kit (Zymo Research). Modified Illumina TruSeq P5 and P7 adapters containing 5’-CG overhangs were ligated onto the digested DNA using T4 DNA ligase (2 hours at 16°C). Libraries were then strand extended at 72°C with Taq DNA Polymerase. The adapters were designed to regenerate the 5’-CCGG site at the P5 junction while the P7 adapter generates a 5’-TCGG junction, making it insensitive to MspI digestion. Adapterised libraries were treated with β-glucosyltransferase to label 5-hmC modifications and purified using a DNA Clean & Concentrator kit (Zymo Research). The glucosylated libraries were then subjected to an overnight MspI digestion at 37°C, cutting any fragments not containing a glucosyl-5hmC site at the P5 CCGG junction. After incubation, the libraries were size-selected from 100 bp to 500 bp and purified using a Zymoclean Gel DNA Recovery Kit (Zymo Research). The fragments were amplified using OneTaq 2X Master Mix (NEB), with PCR conditions including an initial denaturation of 94°C for 30 seconds followed by 12 cycles of 94°C for 30 seconds, 58°C for 30 seconds, and 68°C for 1 minute. Fragments containing 5hmC were positively selected during PCR amplification with adapter-specific indexing primers whereas fragments lacking glucosylated-5hmC at the P5 junction were cleaved and, therefore, not amplified by PCR. Amplified libraries were purified using the DNA Clean and Concentrator kit, and multiplexed using equal volumes of the libraries. All adapters and primers used were synthesized by Integrated DNA Technologies.

treatment_protocol: Cells were transfected with ON-TARGETplus SMARTPools (Dharmacon) targeting TET2, or non-targeting siRNA pool as control.

tag: cell line

value: Breast cancer

tag: treatment


title: ddm1_2ndgen Rep3

description:
4-5 week old Leaves
ribo Zero depletion


title: ddm1_2ndgen Rep1

description:
4-5 week old Leaves
ribo Zero depletion


title: Col-0 X ddm1 Rep3

description:
4-5 week old Leaves
ribo Zero depletion

value: Col-0 X ddm1 (F1)


title: zr2252_7_RRHP siNT rep 2

value: siNT


title: Col-0 X ddm1 Rep2

description:
4-5 week old Leaves
ribo Zero depletion


title: Myotube_NGT_23a diff.a1.lbe1


title: Myoblast_NGT_23a prolif.a1.lbe1


title: Myoblast_NGT_18a prolif.a1.lbe1


title: Myoblast_T2D_7a prolif.a1.lbe1


title: zr2252_5_RRHP siNT rep 1


title: zr2252_6_RRHP siTET2 rep 1


title: Myotube_T2D_7a diff.a1.lbe1


title: zr2252_4_MMS siTET2 rep 2

data_processing:
Library strategy: Methyl Midi-Seq
Methyl Midi-Seq: Sequence reads from bisulfite-treated EpiQuest libraries were identified using standard Illumina basecalling software and analysed using a Zymo Research proprietary analysis pipeline, which is written in Python and uses Bismark to perform the alignment (Krueger et al 2011).
Methyl Midi-Seq: Index files were constructed using the bismark_genome_preparation command and the entire reference genome. The --non_directional parameter was applied while running Bismark. All other parameters were set to default. Filled-in nucleotides were trimmed off when doing methylation calling.
Methyl Midi-Seq: The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T. The genome was partitioned into non-overlapping tiles of length 1 kb and 5mC was profiled within these tiles. Regions with low read coverage (less than 4 reads in any sample) were discarded from the analysis.
Methyl Midi-Seq: The differential 5mC analysis was carried out by methylKit using Fisher Exact test (Akalin et al 2012).
RRHP: Sequence reads from RRHP libraries were first processed to trim off the low quality bases and the P7CG adapter at the 3’ end of the reads. Reads were then aligned to the reference genome using bowtie (Langmead & Salzberg 2012) default parameters and the ‘–best’ setting. Aligned reads with the MspI tag (CCGG) were counted.
RRHP: The correlation analysis between different RRHP libraries was performed by comparing the presence of the tagged reads at each profiled MspI site, and Pearson’s coefficient was calculated accordingly.
RRHP: The genome was partitioned into non-overlapping tiles of length 1 kb and 5hmC was profiled within these tiles. Regions with low read coverage (those with less than 10 reads in any sample) were discarded from the analysis.
RRHP: The differential 5hmC analysis was carried out using DESeq2 (Love et al 2014).
Genome_build: GRCh37


title: Myoblast_NGT_92a prolif.a1.lbe1


title: Myotube_NGT_92a diff.a1.lbe1


title: Myotube_NGT_112a

hyb_protocol: According to the manufacturer’s recommendations.

data_processing: Probes with a mean detection p-value >0.01 for more than 60% of the samples were filtered out. Data were background-corrected, log2-transformed, quantile-normalized, and batch-corrected using COMBAT.

value: myotube


title: Myotube_NGT_105a


title: Myoblast_NGT_112a

value: myoblast


title: Myoblast_T2D_119a


title: Myotube_T2D_129a


title: Myotube_T2D_119a


title: Myoblast_T2D_129a


title: Myoblast_NGT_105a


title: Myotube_NGT_21a


title: Myotube_T2D_29H


title: Myotube_T2D_20a


title: Col-0 Rep3

description:
4-5 week old Leaves
ribo Zero depletion

tag: ecotype

value: WT Col-0


title: zr2252_3_MMS siNT rep 2


title: Myoblast_NGT_21a


title: Myoblast_T2D_29H


title: Col-0 Rep2

description:
4-5 week old Leaves
ribo Zero depletion

tag: age


title: zr2252_2_MMS siTET2 rep 1


title: Col-0 X ddm1 Rep1

description:
4-5 week old Leaves
ribo Zero depletion


title: zr2252_1_MMS siNT rep 1


title: Col-0 Rep1

description:
4-5 week old Leaves
ribo Zero depletion


title: jc6295 Input 3h veh MCF7

description: Input 3h veh MCF7

data_processing:
Reads were mapped to hg38 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.1.1.2016 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
The peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences.
For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: GRCh38
Supplementary_files_format_and_content: bed/text

source_name: Input 3h veh MCF7

growth_protocol: MCF7 cells were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine, 50 U/ml penicillin, 50 ug/ml streptomycin. ZR75-1 cells were grown in RPMI supplemented with 10% FBS, 2mM L-glutamine and 50 U/ml penicillin and 50 ug/ml streptomycin.

extract_protocol:
Cells were crosslinked with 2mM DSG for 20 min followed by crosslinking in 1% formaldehyde for 10 min and then quenched in 100mM glycine. Nuclear enrichment was performed followed by sonication for 15 minutes (Bioruptor plus, Diagenode). Chromatin was immunoprecipitated over night using specific antibodies. Beads were washed six times in RIPA buffer and eluted from beads using SDS buffer. After RNase and proteinase K treatment, DNA was purified by phenol/chloroform extraction.
Libraries were prepared using the Thruplex kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: For the siRNA-mediated knockdown, cells were transfected with ON-TARGETplus SMARTPools (Dharmacon) targeting ER or TET2. A non-targeting siRNA pool was used as a control. For fulvestrant (ICI 182 780, "ICI") treatment, cells were treated with 100nM compound or vehicle for 3 hours.

value: Control 3hr

tag: chip antibody

value: input


title: jc6296 Input 3h 100nM ICI MCF7

description: Input 3h 100nM ICI MCF7

source_name: Input 3h 100nM ICI MCF7

value: 100nM Fulvestrant 3hr


title: ddm1_Input_set2_Rep2

description: 4-5 week old Leaves

data_processing:
For alignment and quality check of sequenced samples, bedtools v2.27.1 was used to convert the raw BAM files to fastq. FastQC v0.11.8 was used to generate quality reports for all sequencing data. Reads were filtered and then aligned to the TAIR10 Arabidopsis genome using Bowtie2 with default settings.
Deeptools v3.1.2 was used to examine correlations between the ChIP samples.
The bamCompare function from Deeptools was used to normalize ChIP samples to Input or H3.
Bedtools map was used to calculate average Log2(ChIP/H3) enrichment over TEs in both ddm1 and WT Col-0.
Genome_build: TAIR10
Supplementary_files_format_and_content: Log2(ChIP/H3 or ChIP/Input) normalized bigWig files show the ChIP enrichment for each ChIP sample. These files were generated using Deeptools.

extract_protocol:
Nuclei isolation was performed using 4-5 week old leaves from WT Col-0 and 1st generation ddm1 as described previously. Freshly harvested tissues (0.3 g of tissue was used for each immunoprecipitation) were fixed with 1% formaldehyde for 15 min and the cross-linking reaction was stopped by the addition of 125 mM glycine. Crosslinked tissues were frozen and ground with a mortar and pestle in liquid nitrogen to obtain a fine powder. Ground tissues were resuspended in M1 buffer (10 mM sodium phosphate pH 7.0, 100 mM NaCl, 1 M hexylene glycol, 10 mM 2-mercaptoethanol, and protease inhibitor (Roche)), and the suspension was filtered through miracloth. Nuclei were precipitated by centrifugation and washed six times with M2 buffer (10 mM sodium phosphate pH 7.0, 100 mM NaCl, 1 M hexylene glycol, 10 mM MgCl2, 0.5% Triton X-100, 10 mM 2-mercaptoethanol, and protease inhibitor), and then further washed once with M3 buffer (10 mM sodium phosphate pH 7.0, 100 mM NaCl, 10 mM 2-mercaptoethanol, and protease inhibitor). Nuclei pellets were rinsed and resuspended in sonication buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS, and protease inhibitor). Nuclei were sonicated with a Covaris E220 High Performance Focused Ultrasonicator for 15 min at 4˚C (Duty factor 5.0; PIP 140.0; Cycles per Burst 200) in 1 ml Covaris milliTUBE. After chromatin shearing, the debris was removed by centrifugation and the solutions containing chromatin fragments were diluted with three times the volume of ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS, and protease inhibitor). After dilution, protein A/G magnetic beads (50 µl for one gram of tissue; Thermo Fisher Scientific) were added to sheared chromatin and incubated at 4˚C for 1 hour. Pre-cleared samples were collected and incubated with anti-H3, anti-H2A.X.3/5, anti-H2A.W.6, anti-H1.1/1.2, or anti-H3K9me2 antibodies at 4˚C overnight with rotation. After incubation, samples were mixed with 30 µl of protein A/G magnetic beads, incubated at 4˚C for 3 hours with rotation, washed twice with low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), once with high salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), once with LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.25 M LiCl, 1% IGEPAL® CA-630, and 0.1% deoxycholic acid), and twice with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). Immunoprecipitated DNA was eluted by adding 500 µl of elution buffer (1% SDS and 0.1 M NaHCO3), incubated at 65˚C for 15 min, and mixed with 51 µl of reverse crosslink buffer (40 mM Tris-HCl pH 8.0, 0.2 M NaCl, 10 mM EDTA, 0.04 mg/ml proteinase K). The reaction mixture was then incubated at 45˚C for 3 hours and subsequently at 65˚C for 16 hours. After crosslink reversal, DNA was treated with 10 µg of RNaseA (Thermo Fisher Scientific), incubated at room temperature for 30 min, and purified with a MinElute PCR purification kit (Qiagen).
For ChIP coupled with deep sequencing (ChIP-seq), sequencing libraries were prepared with an NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs) following the manufacturer’s instructions. The libraries were sequenced with an Illumina Hiseq 2500 to generate single-end 50 bp reads. Samples were prepared from two independent biological replicates.

value: ddm1(-/-) 1st generation

tag: tissue


title: ddm1_H1_set2_Rep2

description: 4-5 week old Leaves


title: jc6293 Input 3h veh MCF7

description: Input 3h veh MCF7


title: jc6294 Input 3h 100nM ICI MCF7

description: Input 3h 100nM ICI MCF7


title: jc6291 TET2 3h veh MCF7

description:
TET2 3h veh MCF7
mcf7_tet2_3h_veh.bed.gz bed

source_name: TET2 3h veh MCF7

value: ab94580 (Abcam)


title: Myotube_NGT_24a

value: Normal glucose tolerance (NGT)


title: Myoblast_NGT_24a


title: Col_H1_set2_Rep2

description: 4-5 week old Leaves

value: WT


title: Myotube_NGT_32a


title: jc6292 TET2 3h 100nM ICI MCF7

description:
TET2 3h 100nM ICI MCF7
mcf7_tet2_3h_100nm_ici.bed.gz

source_name: TET2 3h 100nM ICI MCF7


title: Myoblast_T2D_109a

value: Type 2 diabetes (T2D)


title: Col_Input_set2_Rep2

description: 4-5 week old Leaves


title: Myoblast_T2D_20a


title: Myotube_T2D_109a


title: Col_H1_set2_Rep1

description: 4-5 week old Leaves


title: Myotube_T2D_117a


title: Myotube_NGT_35a


title: Myoblast_NGT_32a


title: Myoblast_NGT_40a


title: Myotube_NGT_40a


title: Myoblast_NGT_35a


title: ddm1_H1_set2_Rep1

description: 4-5 week old Leaves


title: jc6289 TET2 3h veh MCF7


title: Myotube_NGT_55a


title: Myoblast_T2D_45


title: Myotube_T2D_45


title: Myoblast_T2D_127a


title: ddm1_Input_set2_Rep1

description: 4-5 week old Leaves


title: jc6290 TET2 3h 100nM ICI MCF7


title: jc6285 TET2 3h veh MCF7


title: jc6288 TET2 3h 100nM ICI MCF7


title: Col_Input_set2_Rep1

description: 4-5 week old Leaves


title: Myoblast_T2D_117a


title: jc6287 TET2 3h veh MCF7


title: ddm1_H2AW6_Rep2

description: 4-5 week old Leaves


title: ddm1_H3K9me2_Rep2

description: 4-5 week old Leaves


title: jc5646 Input siTET2 72h MCF7

description: Input siTET2 72h MCF7

source_name: Input siTET2 72h MCF7

value: No treatment


title: jc5645 Input siNT 72h MCF7

description: Input siNT 72h MCF7

source_name: Input siNT 72h MCF7

value: Control siRNA 72hr


title: jc5642 Input siTET2 72h MCF7

description: Input siTET2 72h MCF7


title: ddm1_H2AX_Rep2

description: 4-5 week old Leaves

value: 4-5 weeks

value: Leaves


title: ddm1_Input_Rep2

description: 4-5 week old Leaves


title: ddm1_H3_Rep2

description: 4-5 week old Leaves


title: Myoblast_T2D_128a


title: Myoblast_NGT_55a


title: Myotube_T2D_128a


title: jc5641 Input siNT 72h MCF7

description: Input siNT 72h MCF7

value: Breast cancer


title: Myoblast_T2D_46a


title: Col_H2AW6_Rep2

description: 4-5 week old Leaves


title: Myoblast_NGT_14a


title: Myotube_NGT_115a


title: Myoblast_NGT_115a


title: Myotube_NGT_18a


title: Myotube_T2D_46a


title: Myotube_T2D_63a


title: Myotube_NGT_14a


title: Myotube_T2D_8a


title: Myoblast_T2D_63a


title: Myotube_NGT_23a


title: Myoblast_T2D_8a


title: Myoblast_NGT_18a


title: Col_H2AX_Rep2

description: 4-5 week old Leaves


title: Myoblast_NGT_23a


title: jc5639 Input siNT 72h MCF7

description: Input siNT 72h MCF7


title: Col_H3K9me2_Rep2

description: 4-5 week old Leaves


title: Col_H3_Rep2

description: 4-5 week old Leaves


title: jc5638 Input siTET2 48h MCF7

description: Input siTET2 48h MCF7

source_name: Input siTET2 48h MCF7


title: Col_Input_Rep2

description: 4-5 week old Leaves


title: HepG2-siMBD2 ctrl [Bisulfite-Seq]

city: BeiJing

first: Wang

last: Yan

address: 16# LinCui Road

country: China

institute: Institute of Psychology

data_processing:
Reads from input were aligned to UCSC Homo sapiens hg19 genome using Burrows-Wheeler Alignment Tool (BWA) (0.7.10), The CHIP bisulfite sequencing reads were aligned to the UCSC Homo sapiens hg19 genome using the Bismark aligner (v0.7.2;)
Preliminary peak detection was performed using Model-based Analysis of ChIP-Seq (MACS v 1.0.1), Peaks were filtered against these over sequenced regions, as they represent suspicious false positive regions. Nonspecific peaks of control and SAM analyses were removed if overlapped with that of input with bedtools
Briefly, the FASTQ reads were trimmed using Trimmomatic 0.30 and aligned with Bismark aligner (v0.7.2;) to the human reference sequence (hg19, Feb. 2009). After removal of duplicated reads, methylation ratios were extracted and methylation differences were calculated using methylKit  according to the user guide (coverage count >5). The differentially methylated CpGs threshold was set at a q-value <0.1 and delta methylation >10%. The differentially methylated sites were annotated with CHIPseeker package.
Fastqc was used for quality control (QC). RNAseq data, paired end reads were aligned to the human reference sequence (hg19, Feb. 2009) with TopHat 2.0.9 with default setting. Aligned bam files were assessed using cufflinks v.2.2.1 to estimate expression levels (FPKM). Differentially expressed genes (DEGs) were delineated by applying the threshold false discovery rate (FDR) <0.05. Reads counts were obtained using HTSeq-count (1.0). Extreme low expressed genes < 2 count-per-million (CPM) were filtered using EdgeR package[44].
Genome_build: hg19
Supplementary_files_format_and_content: peak text files

source_name: HepG2-siMBD2 ctrl

growth_protocol: Human HCC cell lines HepG2, adenocarcinoma SKHep1 cells were purchased from ATCC (HB8065, HTB52, respectively), human untransformed primary hepatocytes (normal hepatocytes, NorHep) were obtained from Celprogen (33003-02). HepG2 and SkHep1 cells were maintained in MEM medium (Gibco), supplemented with 2 mmol/L glutamine (Sigma-Aldrich), 10% fetal bovine serum (FBS; Gibco), 1 U/mL penicillin, and 1 μg/mL streptomycin (Gibco). Untransformed human liver primary cells (NorHep) were maintained in human hepatocyte cell culture complete medium (Celprogen). Cells were grown in a humidified atmosphere of 5% carbon dioxide at 370C.

extract_protocol:
ChIP (Chromatin immunoprecipitation) was performed using ChIP-IT Express Kit (Active motif) according to the manufacturer protocol. Chromatin was sheared to an average size ranging from 200–500bp using Covaris (Covaris, Inc) sonicator. Cells (2million) were fixed using 37% formaldehyde (CalBiochem) at a final concentration of 1% for 10min at room temperature. Incubation of 1/7 volume of 1M glycine for 5min terminated the fixation process. After sonification the samples were centrifuged for 10min at 40C at maximal speed. The supernatant (chromatin) was then immunoprecipitated with the indicated antibodies. DNA and RNA were extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s protocol.
CHIP bisulfite sequencing libraries from the different samples (control and SAM treatment cells) were prepared following the Illumina ChIP-Seq library protocol. Bisulfite conversion of the immunoprecipitated DNA was performed after addition of methylated adaptors and before amplification. EZ DNA Methylation-Gold Kit (Zymo) was used for bisulfite conversion according to the manufacturer’s protocol.  CHIP sequencing libraries were prepared following the Illumina ChIP-Seq library protocol without bisulfite conversion. RNA (4 µg) of control and Mbd2 knock down cells was prepared for sequencing using the TruSeq RNA Sample Prep Kit (Illumina, San Diego, USA) following the manufacturer’s protocol and sequenced in duplicate using Illumina HiSEQ2K platform (Illumina, San Diego, USA)(50bp pair-end reads); Target DNA fragments were captured using capture array we designed covering promoters in human genome. Sequencing was performed on the Illumina HiSEQ2K platform using a standard 50 cycle paired-end read sequencing protocol according to the manufacturer's recommendations.

treatment_protocol: S-adenosylmethionine chloride (SAM) (Life Science Laboratories, Lakewood, NJ) was prepared in buffer containing 0.005M sulphuric acid and 10% ethanol. 200μm SAM or equivalent volume of solution buffer (control) were added to regular culture medium. Media were refreshed daily over a period of 5 days. For Mbd2 depletion we used lentivirus-mediated human pGIPZ shRNA plasmids and control pGIPZ-scrambled shRNA (Open Biosystems). Lentiviral particles were assembled using the following vectors: GFP expression pGIPZ transfer vector which includes the insert (Open Biosystems); pMD2.G (VSV-G envelope expressing plasmid); PAX (packaging plasmid). One day before transfection, 106 HepG2 and Skhep1 cells were plated in a 10 cm dish (20–30% confluence). The next day, 5 μg of each vector were transfected using FuGene HD transfection reagent (Roche) according to the manufacturer’s protocol. Cells were incubated for 48 h.

value: liver


title: Skhep1-siMBD2 ctrl [Bisulfite-Seq]

source_name: Skhep1-siMBD2 ctrl


title: Skhep1-siMBD2 [Bisulfite-Seq]


title: HepG2-siMBD2 [Bisulfite-Seq]


title: Myoblast_NGT_92a


title: Myoblast_T2D_7a


title: Skhep1-siMBD2 [RNA-seq]


title: jc5634 Input siTET2 48h MCF7

description: Input siTET2 48h MCF7


title: Skhep1-siMBD2 ctrl [RNA-seq]


title: HepG2-siMBD2 [RNA-seq]


title: Myotube_NGT_92a

value: myotube


title: jc5632 Input siTET2 48h MCF7

description: Input siTET2 48h MCF7

value: siRNA control


title: Norhep SAM treated cells-input [CHIP-seq]

source_name: Norhep SAM treated cells-input

value: NorHep


title: jc5637 Input siNT 48h MCF7

description: Input siNT 48h MCF7

source_name: Input siNT 48h MCF7

value: Control siRNA 48hr


title: HepG2-siMBD2 ctrl [RNA-seq]


title: Skhep1 SAM treated cells-input [CHIP-seq]

source_name: Skhep1 SAM treated cells-input


title: Myotube_T2D_7a


title: ddm1_H2AW6_Rep1

description: 4-5 week old Leaves


title: Myotube_T2D_127a


title: ddm1_H2AX_Rep1

description: 4-5 week old Leaves


title: ddm1_H3_Rep1

description: 4-5 week old Leaves


title: jc5640 Input siTET2 72h MCF7

description: Input siTET2 72h MCF7

value: input


title: jc5633 Input siNT 48h MCF7

description: Input siNT 48h MCF7


title: jc5631 Input siNT 48h MCF7

description: Input siNT 48h MCF7


title: Norhep cells-input [CHIP-seq]

source_name: Norhep cells-input


title: ddm1_Input_Rep1

description: 4-5 week old Leaves


title: Skhep1 cells-input [CHIP-seq]

source_name: Skhep1 cells-input


title: HepG2 cells-input [CHIP-seq]

source_name: HepG2 cells-input


title: SAM treated NorHep cells-MBD2 [CHIP-seq]

source_name: SAM treated NorHep cells-MBD2


title: jc5622 TET2 siTET2 48h MCF7

description:
TET2 siTET2 48h MCF7
mcf7_tet2_sitet2_48h.bed.gz

source_name: TET2 siTET2 48h MCF7

value: TET2 siRNA 48hr


title: ddm1_H3K9me2_Rep1

description: 4-5 week old Leaves

source_name: Leaves

value: ddm1(-/-) 1st generation


title: NorHep cells-MBD2 [CHIP-seq]

source_name: NorHep cells-MBD2


title: Skhep1 cells-MBD2 [CHIP-seq]

source_name: Skhep1 cells-MBD2


title: Col_H3K9me2_Rep1

description: 4-5 week old Leaves


title: SAM treated HepG2 cells-MBD2 [CHIP-seq]

source_name: SAM treated HepG2 cells-MBD2


title: SAM treated Skhep1 cells-MBD2 [CHIP-seq]

source_name: SAM treated Skhep1 cells-MBD2


title: jc5621 TET2 siNT 48h MCF7

description:
TET2 siNT 48h MCF7
mcf7_tet2_sint_48h.bed.gz

source_name: TET2 siNT 48h MCF7

value: ab94580 (Abcam)


title: Col_H2AX_Rep1

description: 4-5 week old Leaves


title: jc5616 TET2 siTET2 48h MCF7


title: MS2_in_vivo_rep2

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

institute: University of Wuerzburg

description:
MS2-affinity-purified RNA
MS2 only control

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11 (SPI-2 and in vivo, SPI-1 unknown)
FASTQ conversion with bcl2fastq v2.20.0.422 (SPI-2 and in vivo, SPI-1 unknown)
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011). SPI-1: version 1.10/1.12 with parameters -q 20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; SPI-2/in vivo: version 1.16/2.5 with parameters --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
SPI-1/2: read alignment to Salmonella Typhimurium SL1344 genome and MS2-PinT, MS2 and PinT constructs using segemehl version 0.2.0  (parameters for reademption align: -l 12 -P -a 95) (READemption 0.4.3, Förstner et al., 2014); in vivo: read alignment to Salmonella Typhimurium SL1344 and mouse genome as well as MS2-PinT, MS2 and PinT constructs using segemehl version 0.2.0  (parameters for reademption align: -r -l 20 -P -a 90 -S) (READemption 0.4.5, Förstner et al., 2014)
Read quantification via reademption gene_quanti using Salmonella annotations (parameters: -o 1 -t "5UTR,CDS,3UTR,rRNA,tRNA,sRNA,transcript" -a) (READemption 0.4.3/0.4.5, Förstner et al., 2014)
Size factor calculation based on rRNA read counts only via DESeq2 (Love et al., 2014)
Coverage calculation via reademption coverage based on all aligned reads (full-length) (READemption 0.4.5, Förstner et al., 2014)
Extraction of Salmonella raw coverage values (in vivo only) and coverage normalization by rRNA-based size factors
Genome_build: Salmonella Typhimurium SL1344 (GCF_000210855.2) and mouse (GRCm38.p6)
Supplementary_files_format_and_content: wiggle files containing positional read coverage values

organism:
Mus musculus
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Salmonella Typhimurium SL1344 + iBMDM_C5BL6/J_mouse#9456 cells

growth_protocol: Salmonella Thyphimurium strain SL1344 was grown from single colonies in SPI-1, SPI-2 conditions. For SPI-1 cells were grown to OD600nm of 2.0, overexpression of the different constructs was induced by the addition of 0.1% arabinose. After two minutes, a volume of 60OD of cell was harvested and chilled on ice for 5 minutes. To grow Salmonella under SPI-2-inducing conditions, 1 ml of Salmonella grown in LB to OD600nm2 was washed 2x in PBS and 1x in synthetic SPI-2 medium (Löber et al., 2006). The resulting pellet was resuspended in 1 mL of SPI-2 medium and diluted 1:50 in fresh, pre-warmed SPI-2 medium (10 mL total culture volume) in 100 mL Erlenmeyer flasks. The culture was grown at 37°C, 220 rpm until it reached an OD600nm of 0.3 (takes approximately 3 h).

extract_protocol:
Eluted RNA was extracted with phenol-chloroform (V/V) and precipitated by the addition of ethanol (2 vol) and ~15μg of glycogen (1μl of Glycoblue 15mg/ml). RNA samples were treated with DNase I (Fermentas) for 45 min at 37°C. DNase I was then removed using phenol- chloroform extraction and RNA was again precipitated.
The RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at 4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase (11 cycles). The TruSeq barcode sequences which are part of the 5' TruSeq sequencing adapter are included in Table 2. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. The cDNA pool in the size range of 200-550 bp was eluted from a preparative agarose gel. The cDNA pool was paired- end sequenced on an Illumina NextSeq 500 system using 2x50 bp read length.
library strategy: MAPS

treatment_protocol: Cells were centrifuged at 10000 g for 10 minutes and the pellets frozen in liquid nitrogen. After thawing on ice, the pellets were resuspended in 600 μl of chilled Buffer A (20 mM Tris pH8.0, 150 mM KCL, 1 mM of MgCl2, 1 mM DTT). A volume of 750 μl of glass beads was added to the cells and lysed using Retsch (10 min, 30 Hz) (adaptors were pre-chilled at -20°C). Next, lysate was cleared by centrifugation 10 min at 16000g at 4°C and the clear lysate was collected into a new tube. The in-vitro infections of iBMMs (M.O.I 50) was carried out following a previously published protocol (Westermann et al., 2016) with slight modifications. Briefly, two days before infection 2 × 105 iBMMs /mL were seeded in 10 ml complete DMEM (T75 flask). A total of 4 flaks of each cell type were infected with each Salmonella strain. Overnight cultures of Salmonella carrying either PinT (pYC55), MS2-PinT (pSS31) or MS2 (pSS32), were diluted 1:100 in fresh LB medium and grown aerobically to an OD600nm of 2. Bacterial cells were harvested by centrifugation (2 min at 12,000 r.p.m., room temperature) and resuspended in DMEM. In iBMMs infection, bacterial cells were opsonized with 10% mouse serum for 20 min, prior to addition to the cells. After 4h of infection, the mammalian cells where washed with ice cold PBS and lysed with a solution of PBS 0.1% Triton. The bacterial cells where separated from the host cells debris by centrifugation at 500g for 5 min. After, the supernatant containing the bacteria was centrifuged again at 10 000 g for 5 min, washed with PBS and frozen. After elution, the purified RNA was sequenced and mapped to the either the Mouse genome and to the Salmonella genome.  While the lysate is being prepared, affinity purification columns were prepared at the 4°C room. ~70 μl of amylose (New England Biolabs #E8021S) were added to 2mL Bio-Spin disposable chromatography columns (BioRad #732-6008). Amylose beads were washed three times with 2ml of Buffer A. 1ml of Buffer A with 250 pmol of MS2-MBP coat protein was added to the closed column followed incubation with rotation. After 5 minutes, the column was open and the MS2-coat protein was to run through the column and collected in a tube. This incubation step was repeated one more time until the lysate was ready. At this point, the solution was allowed to run and the column was washed once with 1ml of Buffer A.  The clear lysate was subjected to affinity chromatography (all the following steps were performed at 4 °C). Lysate was added to the closed column and incubated for 5 minutes with rotation. After the incubation, the lysate run was collected and the incubation step was repeated. Next, the column is washed 8 times with 2ml of Buffer A. Bound RNA was eluted using 300μl of Elution Buffer (Buffer A + 15 mM maltose). This step was repeated one more time.

tag: condition

value: in vivo

tag: salmonella genetic background

value: Salmonella Typhimurium SL1344 {delta}pinT pMS2

tag: ms2/pint expression

value: MS2 expressed from a constitutive promotor in a plasmid


title: HepG2 SAM treated cells-input [CHIP-seq]

source_name: HepG2 SAM treated cells-input


title: jc5617 TET2 siNT 48h MCF7


title: Col_H3_Rep1

description: 4-5 week old Leaves

value: WT


title: MS2_in_vivo_rep1


title: PinT_in_vivo_rep2

description:
MS2-affinity-purified RNA
PinT only control

value: Salmonella Typhimurium SL1344 {delta}pinT pPinT

value: PinT expressed from a constitutive promotor in a plasmid


title: ddm1_1stgen Rep3

description:
4-5 week old Leaves
ribo Zero depletion

data_processing:
For alignment and visualization, reads were mapped to the TAIR10 Arabidopsis genome using the STAR aligner and bigwig files were generated using the bamCoverage function in DeepTools.
Kallisto v0.46.0 was used to estimate transcript abundance and read counts for all transcripts in TAIR10.
The resulting values per transcript were mapped to gene level using R v3.6.1 (https://www.R-project.org/) and packages tximport v1.12.3 and TxDb.Athaliana.BioMart.plantsmart28 v3.2.2 (https://bioconductor.org/packages/release/data/annotation/html/TxDb.Athaliana.BioMart.plantsmart28.html). Statistical analysis was performed with R v3.5.1 (https://www.R-project.org/) using the DESeq2 v1.22.2 package.
The pairwise comparison between WT Col-0 and ddm1 was performed with default DESeq2 settings. In addition, the shrunken log2 fold changes were calculated using default settings. Genes with False Discovery Rate (FDR) adjusted p-value < 0.05 and an absolute shrunken log2 fold change > 2 were classified as differentially expressed.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files show the read coverage for each sample.

extract_protocol:
Total RNA was extracted with Spectrum plant total RNA kit (Sigma Aldrich) from 4-5 week old leaves of WT Col-0, ddm1 1st generation. Contaminating DNA was removed with a DNA-free DNA removal kit (Thermo Fisher Scientific).
For RNA-seq analyses, rRNA was removed by Ribo-Zero rRNA Removal kit (Illumina). After depletion of rRNA, RNA-seq libraries were generated with NEBNext UltraII directional RNA library prep kit for Illumina (New England Biolabs) following the manufacturer’s instructions. The libraries were sequenced with Illumina Hiseq 2500 to generate single-end 50 bp reads. Samples were prepared from three independent biological replicates.

value: 4-5 weeks

value: Leaves


title: jc5615 TET2 siNT 48h MCF7

value: Breast cancer


title: Col_Input_Rep1

description: 4-5 week old Leaves


title: MS2-PinT_in_vivo_rep2

description:
MS2-affinity-purified RNA
signal sample

value: Salmonella Typhimurium SL1344 {delta}pinT pMS2-PinT

value: MS2-PinT expressed from a constitutive promotor in a plasmid


title: PinT_in_vivo_rep1


title: MS2-PinT_in_vivo_rep1

description:
MS2-affinity-purified RNA
signal sample


title: ddm1_1stgen Rep2

description:
4-5 week old Leaves
ribo Zero depletion


title: HepG2 cells-MBD2 [CHIP-seq]

source_name: HepG2 cells-MBD2

value: liver


title: Col_H2AW6_Rep1

description: 4-5 week old Leaves


title: jc5618 TET2 siTET2 48h MCF7


title: jc5614 ER siTET2 72h MCF7

description:
ER siTET2 72h MCF7
mcf7_er_sitet2_72h.bed.gz

source_name: ER siTET2 72h MCF7

value: TET2 siRNA 72hr

value: ab3575 (Abcam)


title: ddm1_1stgen Rep1

description:
4-5 week old Leaves
ribo Zero depletion


title: jc5610 ER siTET2 72h MCF7


title: jc5609 ER siNT 72h MCF7

description:
ER siNT 72h MCF7
mcf7_er_sint_72h.bed.gz

source_name: ER siNT 72h MCF7

value: Control siRNA 72hr


title: fMSC_D6

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

country: Netherlands

institute: ErasmusMC

data_processing:
The unprocessed fastq files were generated using the Illumina casava 1.8.3 software allowing
for one mismatch in the barcode. Subsequently alignment of the reads was performed using novoalign
with the inclusion of the adapter trimming option (standard illumina adapter) Special settings that
allow for the alignment of short reads were used. Quantification of counts was done using
feature counts against the human small RNA database. Finally differential expression analysis clustering and
principal component analysis was done in the R enviroment using the DESeq2 package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Fetal MSC

growth_protocol: Adult human bone marrow aspirates (40-70 years old) were obtained from the sternum of patients undergoing cardiac surgery after given informed consent and approval of the medical ethics review board. Collection of fetal tissues for research purposes was approved by the medical ethical review board of the Academic Medical Centre (AMC). The fetal human bone marrow samples were obtained from the HIS facility of the AMC, Amsterdam. All material has been collected from donors from whom a written informed consent for the use of the material for research purposes. Low-density mononuclear cells (MNC) were separated by Ficoll gradient centrifugation and cultured in Dulbecco’s modified Eagle’s medium, GlutaMAXtm and low glucose (Thermo Fisher Scientific, USA) supplemented with 10% fetal bovine serum (FBS, Bodinco, The Netherlands) and 1% penicillin-streptomycin (Sigma Aldrich, Germany), referred in this article as BMSC medium. Non adherent cells were removed by replacing the medium after 48 hours of incubation. Cells were either frozen or expanded up to passage 5, in order to harvest sufficient amounts of EVs. Adult and Fetal BMSC-derived EVs were isolated from BMSCs supernatant, after confluent layers of cells cultured in T175 flasks were exposed for 24 hours to serum-free BMSC medium.

extract_protocol:
Total EV-RNA was isolated using the TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions.
Sequencing of miRNAs was performed by Illumina MiSeq with samples prepared with the NEBNext Small RNA library preparation kit (NEB), according to the manufacturer’s instructions.

treatment_protocol: EVs were isolated from 20 mL conditioned medium by low speed centrifugation (1500 rpm, 5 minutes; 4500 rpm, 10 minutes) followed by ultracentrifugation (20,000g, 30 minutes; 100,000g, 1 hour at 4°C) of the supernatant using the SW32Ti rotor (Beckman Coulter, Fullerton, CA, USA).

tag: developmental stage

value: Fetal

value: MSC

tag: sample type

value: Fetal MSC


title: fMSC_D5


title: fMSC_EV_D5

source_name: Extracellular vesicles from Fetal MSC

value: Fetal MSC EV


title: aMSC_EV_D2

source_name: Extracellular vesicles from Adult MSC

value: Adult

value: Adult MSC EV


title: fMSC_D4


title: fMSC_EV_D4


title: jc5608 ER siTET2 72h MCF7


title: aMSC_EV_D3


title: Col-0 WT Rep2

description:
4-5 week old Leaves
ribo Zero depletion

value: WT


title: Col-0 WT Rep1

description:
4-5 week old Leaves
ribo Zero depletion


title: jc5607 ER siNT 72h MCF7


title: fMSC_EV_D6


title: aMSC_D2

source_name: Adult MSC

value: Adult MSC


title: jc5613 ER siNT 72h MCF7


title: aMSC_D1


title: jc5542 TET2 Untreated AB555

description:
TET2 Untreated AB555
tet2_chip_ab555.bed.gz

source_name: TET2 Untreated AB555

value: No treatment

value: ab94580 (Abcam)


title: XVE_12h_Rep3

city: Uppsala

first: Minerva

middle: Susana

last: Trejo Arellano

state: Uppsala

address: Almas Allé 5

department: Plant Biology

institute: SLU

description:
processed data file:
DESeq_NPP1_vs_XVE_genes.txt
DESeq_NPP1_vs_XVE_TEs.txt
DESeq_RPT2_vs_XVE_genes.txt
DESeq_RPT2_vs_XVE_TEs.txt

data_processing:
Quality control was done with an in-house R script
Adapter trimmng was done with reaper (EMBL-EBI)
Clean reads from independent biological replicates were mapped to the TAIR10 genome using Bowtie v.2 (-v 2 -m 1) (Langmead et al., 2009), first replicate wise to evaluate their similarity and after pooled together.
Delineation of significant ChIP-enriched regions and differential analysis between the PCD-inducible and the mock samples were done with SICER (Zang et al., 2009) using the input as the control library with a redundancy threshold of 1, a window size of 200 bp, a gap size of 600 bp, and FDR = 0.01.
For the RNA-seq analyses, untrimmed reads were mapped to the Arabidopsis reference genome TAIR10 using STAR (v2.5.3.a, Dobin et al., 2013). Expression counts were generated using the R function summarizeOverlaps from the package HTSeq in union mode on exons from the reference transcriptome AtRTD2 (Zhang et al., 2017). Differential expression analyses were performed using the R package DESeq2 (v1.20.0, Love et al., 2014). Genes with absolute log2FoldChange >= 1 and FDR <= 0.05 were considered as differentially expressed.
Subsequent analysis were performed in R. The gene and transposable element models used were from TAIR10 gff annotation file
Genome_build: TAIR10
Supplementary_files_format_and_content: For the ChIP-seq, bed files with the enriched peaks are presented
Supplementary_files_format_and_content: For the RNA-seq, tables with the values of the differential expression analysis for genes and TEs are presented in text files

source_name: XVE_12h_mature leaf

growth_protocol: All seeds were surface-sterilized using 70% and 90% ethanol, stratified for 2 days at 4°C, germinated in soil and grown under short day conditions (8 hours light, 16 hours dark) for 6 weeks.

extract_protocol:
RNA was extracted from samples 12 hours after induction from three independent biological replicates using TRIzol reagent (Invitrogen), treated with Turbo DNAse (Thermo Fisher Scientific). For chromatin immunoprecipitation, leaf material at 12 hours after induction was collected in PBS (137 mM NaCl, 2.7 mM KCl, 4.3 mM Na2HPO4, 1.4 mM KH2PO4) supplemented with 0.1% Tween and cross‐linked using 1% formaldehyde for 10 min under vacuum. Cross-linking was stopped by glycine at final concentration 125 mM for 5 min under vacuum. Leaves were rinsed with water, blotted dry and frozen in liquid nitrogen. About 200 mg of liquid nitrogen-frozen leaves were used for crude nuclei extraction according to (Mozgová et al., 2015). ChIP experiments were performed were done as previously described (Mozgová et al., 2015) from three independent biological replicates.
RNA sequencing libraries were prepared using TruSeq RNA Library Preparation Kit v2 (Illumina) and 18 samples were pooled for sequencing in one lane of the Illumina HiSeq2000 platform. ChIP-seq libraries were prepared with Microplex Library Preparation kit v2 (Diagenode) with 2 ng of eluted DNA as starting material and 12 samples were pooled for sequencing in one lane of Ilumina HiSeq 2500 platform with Single reads of 50 bp length.

treatment_protocol: After 6 weeks, plants were vacuum infiltrated with 2µM 17β-estradiol or mock (ddH2O) to induce the expression of transgenes (Brand et al., 2006) and incubated for additional 12 hours under continuous light.

tag: ecotype background

value: Columbia

tag: genotype/variation

value: 6 week old leaves

tag: biological replicate

tag: demultiplexbarcode


title: XVE_12h_Rep2


title: XVE_12h_Rep1


title: Col-0 WT Rep3

description:
4-5 week old Leaves
ribo Zero depletion

source_name: Leaves

value: 4-5 weeks

value: Leaves


title: jc5536 ER Untreated AB555

description:
ER Untreated AB555
er_chip_ab555.bed.gz

source_name: ER Untreated AB555

tag: cell type

value: Breast cancer

value: ab3575 (Abcam)/06-935 (Millipore)


title: jc5541 TET2 Untreated STG195

description:
TET2 Untreated STG195
tet2_chip_stg195.bed.gz

source_name: TET2 Untreated STG195


title: aMSC_EV_D1


title: jc5535 ER Untreated STG195

description:
ER Untreated STG195
er_chip_stg195.bed.gz

source_name: ER Untreated STG195


title: jc5531 Input Untreated AB555

description: Input Untreated AB555

source_name: Input Untreated AB555

value: input


title: RPT2_12h_Rep3

description:
processed data file:
DESeq_RPT2_vs_XVE_genes.txt
DESeq_RPT2_vs_XVE_TEs.txt
DESeq_RPT2_vs_NPP1_genes.txt
DESeq_RPT2_vs_NPP1_TEs.txt

source_name: RPT2_12h_mature leaf


title: RPT2_12h_Rep1


title: HD-f

city: GUANG ZHOU

first: FANG

last: YANG

state: CHINA

address: 74#，ZHONG SHAN 2nd Road

institute: SYSU

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) 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), then dried immediately by brief centrifugation.

scan_protocol: The hybrid chip will then be extensively washed using gene expression wash buffer and scanned using microarray scanner (Agilent p/n G2565BA) to examine fluorescent intensity and determine expression profiles of lncRNA of human PBMC.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Data tables only contain data for the lncRNA features of the array.

source_name: Peripheral Blood, healthy donor, replicate 6

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.

extract_protocol: Total RNA of PBMCS derived from six individuals with active TB disease and healthy controls, respectively, were isolated with TRIzol (Ambion)

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, PBMCs were obtained by density centrifugation of diluted blood (1 part blood to 1 part PBS) over Ficoll-Paque.

value: PBMCs

tag: disease state

value: healthy


title: HD-b

source_name: Peripheral Blood, healthy donor, replicate 2


title: TB-d

source_name: Peripheral Blood, active TB, replicate 4

value: active TB


title: RPT2_12h_Rep2


title: HD-e

source_name: Peripheral Blood, healthy donor, replicate 5


title: jc5529 Input Untreated STG195

description: Input Untreated STG195

source_name: Input Untreated STG195

tag: cell line


title: TB-e

source_name: Peripheral Blood, active TB, replicate 5


title: HD-c

source_name: Peripheral Blood, healthy donor, replicate 3


title: TB-b

source_name: Peripheral Blood, active TB, replicate 2


title: NPP1_12h_Rep3

description:
processed data file:
DESeq_NPP1_vs_XVE_genes.txt
DESeq_NPP1_vs_XVE_TEs.txt
DESeq_RPT2_vs_NPP1_genes.txt
DESeq_RPT2_vs_NPP1_TEs.txt

source_name: NPP1_12h_mature leaf


title: CD138-selected myeloma cells_96

type: genomic

city: Little rock

first: CAN

last: LI

state: AR

address: 4301 W MARKHAM ST

institute: University of Arkansas for Medical Sciences

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics station 450, and scanned using the Gene Chip Scanner 3000.

data_processing:
Hybridization-based genomic profiling arrays were performed according to the manufacturer’s protocols. CEL files obtained by the CytoScan HD array platform were analyzed using the Chromosome Analysis Suite software package (Affymetrix), and the Nexus copy number software (Biodiscovery Inc., Hawthorne, CA, USA) using annotations of genome version GRCh37 (hg19). Only those achieving the manufacturer’s quality cut-off measures were included in the analysis.
Arrays from CD138-selected samples from newly diagnosed multiple myeloma patients' bone marrows.

label: Biotin

source_name: Primary myeloma cells

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from CD138+ cells isolated from MM patients’ bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Qubit fluorometer and agarose gel electrophoresis.

value: Bone marrow


title: CD138-selected myeloma cells_98


title: CD138-selected myeloma cells_94


title: CD138-selected myeloma cells_97


title: jc5410 TET2 Untreated ZR75-1

description:
TET2 Untreated ZR75-1
zr75_1_tet2_untreated.bed.gz

source_name: TET2 Untreated ZR75-1

tag: treatment


title: CD138-selected myeloma cells_93


title: jc5407 TET2 Untreated ZR75-1


title: NPP1_12h_Rep2


title: TB-a

source_name: Peripheral Blood, active TB, replicate 1


title: CD138-selected myeloma cells_92


title: CD138-selected myeloma cells_95


title: jc5405 ER Untreated ZR75-1

description:
ER Untreated ZR75-1
zr75_1_er_untreated.bed.gz

source_name: ER Untreated ZR75-1


title: jc5408 ER Untreated ZR75-1


title: HD-d

source_name: Peripheral Blood, healthy donor, replicate 4


title: TB-c

source_name: Peripheral Blood, active TB, replicate 3


title: input_RPT2_12h_Rep2

source_name: input_RPT2_12h_mature leaf

tag: chip anitbody

value: none (input)


title: NPP1_12h_Rep1


title: jc5404 TET2 Untreated ZR75-1


title: HD-a

source_name: Peripheral Blood, healthy donor, replicate 1


title: input_RPT2_12h_Rep1


title: TB-4

source_name: Peripheral Blood, active TB, replicate 6