title: Sham_Mouse_2_Left

city: Charlottesville

first: Hirofumi

last: Watanabe

state: Virginia

address: 409 Lane Rd, Bldg MR4

department: Department of Pediatrics, Child Health Research Center

institute: University of Virginia School of Medicine

data_processing:
We used FastQC to assess the quality of FASTQ file reads.
Prior to alignment, we removed low quality reads and adapter sequences using Trimmomatic0.36.
We aligned FASTQ reads to the GRCm38/ENSEMBL mouse genome using Salmon0.7.2.
Transcript-level estimates of expression were scaled up to gene level estimates using the Tximport 1.2.0 R package, with the “lengthScaledTPM” argument for abundance estimation.
Genome_build: mm10
Supplementary_files_format_and_content: abundance, counts

source_name: Renin cells

extract_protocol:
Renin cells were isolated from the kidney cortex of the Ren1c-YFP mice at 8 to 12 weeks of age after 72 hours of aortic coarctation or sham surgeries using FACS. A kidney cortex was dissected, minced with a razor blade, and transferred into a 15 mL tube with 5 mL of enzymatic solution (0.3% collagenase A [Millipore-Sigma], 0.25% trypsin [Millipore-Sigma], and 0.0021% DNase I [Millipore-Sigma]). The tubes were placed flat inside a shaking incubator (80 RPM) for 15 minutes at 37°C. Then, the solution was pipetted up/down ten times with a sterile transfer pipette and allowed to settle for 2 minutes, and the supernatant was collected in a fresh tube on ice. The enzymatic solution was added to the 15 mL tube containing the remaining undigested cortexes, and the digestion procedure was repeated a total 3 times. The supernatants collected from the 3 digestions were pooled and centrifuged at 1,100 g for 4 minutes at 4°C using a Sorvall RT7 refrigerated centrifuge (Sorvall, Newtown, CT). The cell pellet was resuspended with fresh buffer 1 (130 mM NaCl, 5 mM KCl, 2 mM CaCl2, 10 mM glucose, 20 mM sucrose, 10 mM HEPES, pH 7.4), and the suspension was poured through a sterile 100 μm nylon cell strainer (Corning Inc., Corning, NY) and washed with the buffer 1. The flow-through was poured through a sterile 40 μm nylon cell strainer (Corning Inc.) and washed with buffer 1. The flow-through was centrifuged at 1,100 g for 4 min at 4°C. The cell pellet was resuspended in 1.5 mL of resuspension buffer [PBS, 1% FBS, 1 mM EDTA, DNAase I (Millipore-Sigma)]. The dead cells were labeled with DAPI (Millipore-Sigma). Cells were analyzed and sorted by FACS using Influx Cell Sorter (Becton Dickinson, Franklin Lakes, NJ). The living cells labeled with YFP not staining positive with DAPI were sorted and directly collected into the 1x Reaction buffer of SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Mountain View, CA). One thousand cells from each kidney were used to make the cDNA library of each sample.
Samples were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio USA, Mountain View), according to the user manual. The cDNA was amplified with 13 cycles of PCR. cDNA was isolated using the Agencourt AMPure XP Kit (Beckman Coulter, Brea, CA) and eluted in the Fluidigm dilution reagent (Takara Bio USA). Samples were quantified using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA) and qualified using the High Sensitivity D5000 ScreenTape System (Agilent Technologies, Santa Clara, CA). Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA) was used to make cDNA libraries tagmented and indexed with unique barcodes suitable for Illumina sequencing.

treatment_protocol: The mice received aortic coarctation between the roots of the right and left renal arteries. Sham-treated mice underwent the same procedure, with the exception of exposing aorta and aortic coarctation.

value: Primary kidney


title: PS2-S-2 (Peg_SHAMf1_res)

status: Public on May 26 2021

type: SRA

city: Rehovot

first: Tomer

last: Chen

address: P.O.box 26

department: Plant and Environmental Sciences

country: Israel

institute: Weizmann Institute of Science

description:
MARS-seq
6A

library_source: transcriptomic

data_processing:
Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
MARS-seq analysis was done using the UTAP transcriptome analysis pipeline (Kohen et al., 2019). Reads were trimmed using cutadapt, (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to genome Tair-11 using STAR,  v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Araport annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream):
We used the 3 end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode.
Genome_build: Further analysis is done for genes having minimum 5 read in at least one sample.
Supplementary_files_format_and_content: Normalization of the counts and differential expression analysis was performed using DESeq2 , with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana seedling shoots exposed to 30% PEG + 1mM SHAM for 2h

growth_protocol: Arabidopsis (Arabidopsis thaliana; ecotype Columbia-0) seedlings (7 d old) were grown under white light in a 16-h-light/8-h-dark cycle at 21°C on Murashige and Skoog medium, supplemented with 1% (w/v) Suc and 0.8% (w/v) Phytoagar (Invitrogen).

extract_protocol:
Three replicates of Arabidopsis seedlings (30 to 50 7-d-old seedlings per biological replicate) were used for each treatment. After treatment, the roots and shoots were separated, and RNA was extracted separately from frozen tissues using a standard Trizol extraction method (Sigma-Aldrich).
Libraries were prepared with the MARS-seq protocol (Diego Adhemar Jaitin, 2017) and sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).

treatment_protocol: For osmotic stress treatment, PEG average molecular weight 8,000 powder (Sigma-Aldrich) was used. For PEG solutions, 30% (w/v), PEG was dissolved in double-distilled (dd)H2O and pH was adjusted to 5.8 using HCl and KOH osmotic pressure measured at -2.0 MPa. Solutions were supplemented with His (5 mm) or SHAM (0.1 mm) where indicated in Seedlings were exposed to 30% PEG + 1mM SHAM  for 0, 1, 2, 3 h in aqueous solution.

tag: tissue

value: Shoot

tag: genotype

value: WT

tag: treatment

value: 30% PEG + 1mM SHAM for 2h


title: Sham_Mouse_2_Right

country: USA

organism: Mus musculus

tag: cell type

tag: age

value: Adult

tag: strain


title: Trex1-KO BMDM  + H151 rep2

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

country: China

institute: PICB

description: expressed RNA in BMDM cells of Trex1-ko mice after H151 treatment

data_processing:
Basecalling based on Illumina Casava1.7 software
After RNA sequencing reads quality checking, RNA-seq data were mapped to the mouse genome (mm10) using Hisat2 using default parameters。
The gene expression abundance was estimated by counting number of reads mapped to the cognate gene exons using featurecount
Genome_build: mm10 (mouse)
Supplementary_files_format_and_content: tab-delimited text files include gene ID and expression level in reads count for each sample

source_name: BMDM cell

growth_protocol: Trex1+/- mice were kindly licensed by Dr. Tomas Lindahl and Dr. Deborah Barnes (Cancer Research U.K., London) and provided by Dr. Nan Yan (University of Texas Southwestern Medical Center). Trex1-/- mice were generated by further mating the male and female Trex1+/- mice and were genotyped by standard PCR. 6-8 weeks old WT mice were purchased from the Model Animal Research Center of Nanjing University. BMDMs were obtained from tibial and femoral bones from 6~8 weeks WT and Trex1-/- mice and cultured with 1640 medium containing L929 cell supernatant, 10% FBS, 1% GlutaMAX™ Supplement (Gibco), 50 μM β-Mercaptoethanol for 7 days. These cells were maintained in a humidified 5% CO2 incubator at 37˚C

extract_protocol:
Total RNA of BMDMs were extracted with Trizol reagent (Invitrogen).
A cDNA library was generated from polyA+ RNA according to the Illumina RNAseq protocol. The cDNA library was sequenced on an Illumina Hiseq2500 in a 1x150 bp run.

treatment_protocol: BMDMs were incubated with DMSO,SN-011 (500 nM) and H-151 (500 nM) for 12 hours, respetively

tag: cell line

value: Bone-marrow-derived macrophage


title: Trex1-KO BMDM  + H151 rep1


title: PS2-R-2 (Peg_SHAMf1_res)

description:
MARS-seq
5F

source_name: Arabidopsis thaliana seedling roots exposed to 30% PEG + 1mM SHAM for 2h

value: Root


title: PS2-R-3 (Peg_SHAMf1_res)

description:
MARS-seq
5G


title: PS2-S-3 (Peg_SHAMf1_res)

description:
MARS-seq
6B


title: PH0-R-3 (Peg_SHAMf1_res)

description:
MARS-seq
8A

source_name: Arabidopsis thaliana seedling roots exposed to water for 1h

value: water for 1h


title: Coarctation_Mouse_3_Right


title: Trex1-KO BMDM  + SN-011 rep2

description: expressed RNA in BMDM cells of Trex1-ko mice after SN-011 treatment


title: PS1-S-2 (Peg_SHAMf1_res)

description:
MARS-seq
5C

source_name: Arabidopsis thaliana seedling shoots exposed to 30% PEG + 1mM SHAM for 1h

value: 30% PEG + 1mM SHAM for 1h


title: PS1-S-3 (Peg_SHAMf1_res)

description:
MARS-seq
5D


title: PS2-R-1 (Peg_SHAMf1_res)

description:
MARS-seq
5E


title: PS1-S-1 (Peg_SHAMf1_res)

description:
MARS-seq
5B


title: Trex1-KO BMDM  + SN-011 rep1


title: PS3-R-2 (Peg_SHAMf1_res)

description:
MARS-seq
6D

source_name: Arabidopsis thaliana seedling roots exposed to 30% PEG + 1mM SHAM for 3h

value: 30% PEG + 1mM SHAM for 3h


title: PS1-R-3 (Peg_SHAMf1_res)

description:
MARS-seq
5A

source_name: Arabidopsis thaliana seedling roots exposed to 30% PEG + 1mM SHAM for 1h


title: Trex1-KO BMDM rep2

description: expressed RNA in BMDM cells of Trex1-ko mice


title: Coarctation_Mouse_3_Left


title: Sham_Mouse_1_Right


title: PS1-R-2 (Peg_SHAMf1_res)

description:
MARS-seq
4H


title: 0hrs

city: Boston

first: Kai

middle: W

last: Wucherpfennig

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology and Virology

institute: Dana Farber Cancer Institute

data_processing:
De-multiplexing, alignment to the mm10 mouse genome and UMI counting were performed using Cell Ranger (version 2.0.1, 10X Genomics)
All samples were then aggregated by using the “cellranger aggr” function without depth normalization
After getting the digital cell by gene expression matrix, the cells with poor quality (cells with high percentage of mitochondrial gene reads, cells express less than 200 genes and cells which show high doublet scores determined by DoubletFinder (v2.0.2)) were filted
The Seurat package in R was then used for analyses
Genome_build: mm10
Supplementary_files_format_and_content: Each RNA sequenting sample contains a compressed tab-delimited text files including matrix.mtx (UMI count matrix in a sparse matrix format), genes.tsv (Gene names) and barcodes.tsv (Cell barcodes).

source_name: Spleen and lymph nodes

growth_protocol: Cells were cultured in RPMI-1640 supplemented with 10% FBS, 2mM L-glutamine, 100ug/mL streptomycin, and 100ug/mL penicillin

extract_protocol:
Cells were enriched by FACS and processed for 10X genomics sequencing immediately as per 10X genomics instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment is inclusion or exclusion of MDSCs

value: OT-I CD8+ T cells

tag: time point


title: PS1-R-1 (Peg_SHAMf1_res)

description:
MARS-seq
4G


title: Sham_Mouse_1_Left


title: PS0-S-3 (Peg_SHAMf1_res)

description:
MARS-seq
4F

source_name: Arabidopsis thaliana seedling shoots exposed to water for 1h


title: Trex1-KO BMDM rep1


title: Coarctation_Mouse_2_Right


title: PS0-S-2 (Peg_SHAMf1_res)

description:
MARS-seq
4E


title: Coarctation_Mouse_2_Left


title: WT BMDM + SN-011 rep2

description: expressed RNA in BMDM cells of wild-type mice after SN-011 treatment


title: PS0-S-1 (Peg_SHAMf1_res)

description:
MARS-seq
4D


title: WT BMDM + SN-011 rep1


title: PS0-R-2 (Peg_SHAMf1_res)

description:
MARS-seq
4B


title: PS0-R-3 (Peg_SHAMf1_res)

description:
MARS-seq
4C


title: PS0-R-1 (Peg_SHAMf1_res)

description:
MARS-seq
4A


title: WT BMDM rep2

description: expressed RNA in BMDM cells of wild-type mice


title: S0-S-3 (Peg_SHAMf1_res)

description:
MARS-seq
1F


title: Coractation_Mouse_1_Left


title: Coarctation_Mouse_1_Right


title: S0-S-2 (Peg_SHAMf1_res)

description:
MARS-seq
1E


title: S0-R-3 (Peg_SHAMf1_res)

description:
MARS-seq
1C


title: S0-R-2 (Peg_SHAMf1_res)

description:
MARS-seq
1B


title: MEF cells-RiboSeq_HF2

city: Indianapolis

first: Ronald

middle: C

last: Wek

state: IN

address: 635 N. Barnhill Dr. MS4067

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

data_processing:
Library strategy: Ribosome profiling
Barcodes and sequencing adapters were trimmed using FASTX toolkit
reads mapping to rRNA and tRNA were identified and removed from analysis pipeline using bowtie
reads were aligned to GRCm38 genome using HISAT2
mapped reads were assigned to annotated genomic features of GRCm38 using htseq-count
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text file generated by htseq-count showing the number of reads mapping to each gene

molecule: polyA RNA

source_name: Mouse Embryonic Fibroblasts

growth_protocol: MEF cells grown in high-glucose DMEM supplemented with 10% Fetal Bovine Serum and 1x Penicilin/Streptomycin

extract_protocol:
For Total RNASeq, RNA was extracted with Trizol reagent according to manufacturer's protocol. For RiboSeq, lysate was digested with 100 units of RNase I (Ambion) at 4°C for 1 h with mild agitation. Sample digestion was quenched by adding 200 units of SUPERase·IN (Ambion). Digested samples were then placed on top of 10 –50% sucrose gradients supplemented with SUPERase·IN and subjected to ultracentrifugation in a Beckman SW41Ti rotor at 40,000 rpm for 2 h at 4°C. Following centrifugation, the fractions corresponding to the monosome peak of the digested samples were collected using a Biocomp piston gradient fractionator coupled with a Gilson fraction collector and stored in TRIzol LS reagent. RFPs and total RNA were collected using TRIzol reagent. Total RNA was fragmented by alkaline hydrolysis. RFPs and fragmented RNA were collected by gel extraction from a 15% denaturing TBE-urea gel (Invitrogen).
For total RNA sequencing: total RNA extracted by trizol was fragmented by alkaline hydrolysis and run on 15% denaturing TBE gel then extracted and barcoded sequencing adapters were ligated. For RiboSeq: Protocol from Ingolia Nat Methods .2017 (doi:10.1016/j.ymeth.2017.05.028) was followed with ribosomal RNA depletion performed with Ambion Ribominus kit.

treatment_protocol: Cells treated with 100nM halofuginone for 6Hrs in high-glucose DMEM supplemented with 10% dialyzed Fetal bovine Serum and 1x Penicilin/Streptomycin. Control samples were treated with same dialyzed FBS containing media without halofuginone for 6Hrs

value: Mouse Embryonic Fibroblasts

value: 100nM halofuginone for 6Hrs

tag: rna population

value: RNA (size selected)


title: S0-R-1 (Peg_SHAMf1_res)

description:
MARS-seq
1A


title: MEF cells-RiboSeq_HF3


title: S0-S-1 (Peg_SHAMf1_res)

description:
MARS-seq
1D


title: MEF cells-RiboSeq_HF1


title: H2O2 R 3a (H2O2_RB)

description:
MARS-seq
X11E

source_name: Arabidopsis thaliana seedling roots exposed to 5 mM H2O2 3h

treatment_protocol: Seedlings were exposed to 5 mM H2O2 or 10  µM RB in aqueous solution for 0, 1, 2, 3 h or  5 mM H2O2 or 10  µM in aqueous solution for 2h .

value: 5 mM H2O2 3h


title: H2O2 R 2c (H2O2_RB)

description:
MARS-seq
X11D

source_name: Arabidopsis thaliana seedling roots exposed to 5 mM H2O2 2h

value: 5 mM H2O2 2h


title: MEF cells-RiboSeq_control3

value: untreated


title: H2O2 R 2b (H2O2_RB)

description:
MARS-seq
X11C


title: H2O2 R 3b (H2O2_RB)

description:
MARS-seq
X11F


title: FENDRR_Cro Male

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

data_processing:
The qualified libraries are fed into Illumina sequencers after pooling according to its effective concentration and expected data volume
Paired-end reads were directionally mapped to the genomic loci of mousse genome (GRCm38.p6) by TopHat2.
Cufflinks/Cuffdiff analysis was run to identify the dysregulated RNAs
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Gene expression file generated by cuffdiff analysis

source_name: Lung tissue

extract_protocol:
Total RNA was isolated from  mouse lung tissues by using Tri reagent
Libraries were prepared with the Illumina mRNA Library Preparation kit. mRNA is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

tag: transfection

value: FENDRR

value: asbestos

value: Lung tissue

tag: gender

value: male


title: FENDRR_Cro Female

value: female


title: MEF cells-RiboSeq_control2


title: H2O2 R 2a (H2O2_RB)

description:
MARS-seq
X11B

value: WT


title: H2O2 R 1b (H2O2_RB)

description:
MARS-seq
X10H

source_name: Arabidopsis thaliana seedling roots exposed to 5 mM H2O2 1h

value: Root

value: 5 mM H2O2 1h


title: H2O2 R 1c (H2O2_RB)

description:
MARS-seq
X11A


title: MEF cells-RiboSeq_control1


title: VC_Cro Male

value: VC


title: VC_Cro Female


title: H2O2 R 1a (H2O2_RB)

description:
MARS-seq
X10G


title: WT BMDM rep1

value: Bone-marrow-derived macrophage


title: MEF cells-RNAseq_HF3

data_processing:
Barcodes and sequencing adapters were trimmed using FASTX toolkit
reads mapping to rRNA and tRNA were identified and removed from analysis pipeline using bowtie
reads were aligned to GRCm38 genome using HISAT2
mapped reads were assigned to annotated genomic features of GRCm38 using htseq-count
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text file generated by htseq-count showing the number of reads mapping to each gene

value: Total RNA


title: H2O2 R 0c (H2O2_RB)

description:
MARS-seq
X10F

value: water for 1h


title: MEF cells-RNAseq_HF2

value: Mouse Embryonic Fibroblasts

value: 100nM halofuginone for 6Hrs


title: H2O2 R 0b (H2O2_RB)

description:
MARS-seq
X10E


title: FENDRR_TiO2 Female

value: control


title: VC_TiO2 Female


title: FENDRR_TiO2 Male


title: H2O2 R 0a (H2O2_RB)

description:
MARS-seq
X10D


title: RBH R 2a (H2O2_RB)

description:
MARS-seq
X10A

source_name: Arabidopsis thaliana seedling roots exposed to 5 mM H2O2 and 10  µM MRB for 2h

value: 5 mM H2O2 and 10  µM MRB for 2h


title: MEF cells-RNAseq_HF1


title: H2O2 R 3c (H2O2_RB)

description:
MARS-seq
X11G

value: 5 mM H2O2 3h


title: RB R 3b (1O_H2O2)

description:
MARS-seq
X9G

source_name: Arabidopsis thaliana seedling roots exposed to 10  µM RB for 3h

value: 10  µM RB for 3h


title: RB R 3c (1O_H2O2)

description:
MARS-seq
X9H


title: MEF cells-RNASeq_control3

value: untreated


title: VC_TiO2 Male

value: Lung tissue


title: MEF cells-RNASeq_control2


title: RBH R 2b (H2O2_RB)

description:
MARS-seq
X10B


title: Balb_mut_neutrophils

city: Birmingham

first: David

last: Crossman

state: AL

address: 720 20th Street South

department: Genetics

institute: University of Alabama at Birmingham

description: 4 wk old Ift88Orpk BALB/c Neutrophils

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
Raw sequence reads were aligned to the reference genome using STAR version??? using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from the aligned reads using Cufflinks version 2.2.1 using parameters --library-type fr-firststrand -G -L
Transcript abundances were also calculated from the aligned reads using HTSeq-count version ?? using paramaters -r pos -t exon -i gene_id -a 10 -s no -f bam
Differential expression was calculated using Cufflinks Cuffdiff package using default parameters
Genome_build: Gencode GRCm38.p4.ReleaseM11
Supplementary_files_format_and_content: tab-delimited Excel file containing raw read counts from HTSeq-count for each gene in each sample

source_name: Liver

extract_protocol:
For flow sorting of individual cell populations from whole liver, tissue was harvested and digested in RPMI containing 0.5 mg/ml collagenase with 100U/ml DNase type I for 30 minutes at 37 C with agitation.  Single cell suspensions were obtained and cells were stained as described above. For isolation of cholangiocytes, we used dolichos biflorus agglutinin (DBA) (RL-1032, Vector Laboratories), a well-established, cell surface marker of bile duct cholangiocytes30. Cells were sorted into individual tubes containing buffer RLT (Catalog #:74104 Qiagen, Hilden, Germany) to lyse the cells. Ultrapure RNA was isolated using the RNeasy kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol. The quality of RNA was determined using the Agilent 2100 bioanalyzer and only used if the RNA integrity number was above 7. We combined an equal amount of RNA from 6-8 individual mice per genotype (equal number of males and females) for RNA sequencing studies. Thus, the RNA sequencing data presented is an average of 6-8 biological replicates per group.
The NEBNext mRNA library prep kit for Illumina with ribosome reduction was used to generate the cDNA library, which was subsequently sequenced using Illumina NextSeq500 with paired end 75bp sequencing and aligned to the University of California, Santa Cruz (UCSC) GRCm38/mm10 reference genome using the STAR software package31. For each sample, at least 25 million reads were obtained.  Following alignment, HTSeq-count (version 0.9.1) was used to count the number of reads mapping to each gene32.  Fragments per kilobase of transcript per million mapped reads (FPKM) and pairwise differential expression were calculated using the Cufflinks suite (https://github.com/cole-trapnell-lab/cufflinks) and HTSeq-Count/DESeq2 was used to identify the most highly variable genes between groups.

value: 4 weeks old

value: BALB/c

value: Neutrophils


title: RB R 2b (1O_H2O2)

description:
MARS-seq
X9D

source_name: Arabidopsis thaliana seedling roots exposed to 10  µM RB for 2h

value: Root

value: WT

value: 10  µM RB for 2h


title: RB R 3a (1O_H2O2)

description:
MARS-seq
X9F


title: RB R 2a (1O_H2O2)

description:
MARS-seq
X9C


title: RB R 2c (1O_H2O2)

description:
MARS-seq
X9E


title: Balb_mut_chloang

description: 4 wk old Ift88Orpk BALB/c Cholangiocytes

value: Cholangiocytes


title: MEF cells-RNASeq_control1

value: Total RNA


title: Balb_mut_Ly6clo_mac

description: 4 wk old Ift88Orpk BALB/c Ly6clo infiltrating macrophages

value: Ly6clo infiltrating macrophages


title: RB R 1c (1O_H2O2)

description:
MARS-seq
X9B

source_name: Arabidopsis thaliana seedling roots exposed to 10  µM RB for 1h

value: 10  µM RB for 1h


title: RBH R 2c (H2O2_RB)

description:
MARS-seq
X10C


title: RB R 1a (1O_H2O2)

description:
MARS-seq
X8H


title: RB R 0a (1O_H2O2)

description:
MARS-seq
X8E

value: water for 1h


title: RB R 0c (1O_H2O2)

description:
MARS-seq
X8G


title: FMO5-OE T1_20C

city: Madrid

first: Rafa

last: Catalá

address: C/Ramiro de Maeztu n9

department: Biotechnology

country: Spain

institute: Centro de Investigaciones Biologicas

data_processing:
The original image data produced by the sequencer (Illumina HiSeq2000) was transferred into sequences, which were defined as “raw reads” (or “raw data”) and saved as “.fastq” files.
Raw data was cleaned removing adaptor sequences, reads with a percentage of unknown Ns greater than 5% and low quality reads (reads with >50% bases with quality index <5). Clean reads were saved as ".fastq" files.
Reads were mapped to reference Arabidopsis genome TAIR10 release using SOAP2 software (Li et al, 2009). No more than two mismatches per read were allowed.
The gene expression level was calculated using the RPKM method (Mortazavi et al, 2008) using uniquely mapped reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Text files includes the number of uniquely mapped clean reads, length, coverage  and the corresponding estimation of expression level (RPKM) for each gene model.

source_name: 12-day-old seedlings

growth_protocol: Seedlings were grown during 12 days under long-day photoperiods (photon flux of 90 µmol m-2 s-1) on 0.5X GM medium plates.

extract_protocol:
Seedling were collected, inmediately frozen on liquid nitrogen and stored at -80ºC. For total RNA extraction, frozen tissue was homogenized to a fine powder and total RNA was extracted using TRIzol® Reagent (Life Technologies), treated with DNaseI (Roche) and further cleaned with RNeasy Plant Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: No treatment.

tag: developmental stage

value: seedlings

tag: background ecotype

value: FMO5-OE T1

tag: growth temperature


title: RBH R 2c (1O_H2O2)

description:
MARS-seq
X10C

value: 5 mM H2O2 and 10  µM MRB for 2h


title: RB R 1b (1O_H2O2)

description:
MARS-seq
X9A


title: Col-0_20C


title: WT

city: TianJin

first: Xiao Tong

last: Ma

state: TianJin

address: Blood hospital, 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then use BWA (Li, H. and Durbin, R., 2009) to map clean reads to genome reference and use Bowtie (Langmead B, et al., 2009) to gene reference
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each Sample

source_name: CD45-Ter119- derived stromal cells

extract_protocol:
CD45-Ter119- cells were collected and RNA was harvested using RLT reagent. Qiagen RNeasy Mini Kit (Cat#74104) was used with 1 ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Stromal cells were isolated from bone marow of WT or Twist1 knockout chimeric mice 14 days after tamoxifen treatment

value: stromal cells

value: wild type


title: RBH R 2b (1O_H2O2)

description:
MARS-seq
X10B


title: Twist1-KO


title: Balb_ctrl_ly6clo_mac

description: 4 wk old wild type BALB/c Ly6clo infiltrating macrophages

value: Wild type


title: RBH R 2a (1O_H2O2)

description:
MARS-seq
X10A


title: Balb_ctrl_Ly6chi_mac

description: 4 wk old wild type BALB/c Ly6chi infiltrating macrophages

value: 4 weeks old

value: Ly6chi infiltrating macrophages


title: Balb_mut_Ly6chi_mac

description: 4 wk old Ift88Orpk BALB/c Ly6chi infiltrating macrophages

value: BALB/c


title: Balb_ctrl_Cholang

description: 4 wk old wild type BALB/c Cholangiocytes


title: RB R 0b (1O_H2O2)

description:
MARS-seq
X8F

source_name: Arabidopsis thaliana seedling roots exposed to water for 1h

value: Root


title: H3 - suvh4suvh5suvh6 R1

city: Ottawa

first: Jean-Sebastien

last: Parent

state: Ontario

address: 960 Carling Avenue

country: Canada

institute: Agriculture and Agri-Food Canada

description: Chromatin

library_source: genomic

data_processing:
[WGBS]  Adaptor sequences were removed using Trimmomatic, trimmed reads were then aligned on the Arabidopsis TAIR10 genome using Bismark. Methylation information was extracted from alignment files and methylation rate at every position with coverage above 5 was put in bedGraph format.
[ChIP-seq]  Adaptor sequences were removed using Trimmomatic, trimmed reads were then aligned on the Arabidopsis TAIR10 genome using Bowtie2. Alignment files were converted to bam files using Samtools and duplicates were removed using Picard tools. Genome-wide coverage was obtained with Bedtools and put in bedGraph format.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph

molecule: genomic DNA

source_name: suvh4suvh5suvh6 mature embryos

growth_protocol: Plants were grown under long day conditions at 22 °C. Seeds were sown directly on soil after stratification in distilled water at 4 °C for three days. For embryo isolation, mature fruits were collected from the primary inflorescence after seven to eight weeks of growth.

extract_protocol:
Siliques were cut open with insulin syringe needles, whole seeds were transferred on microscope slide in a drop of PBS and embryos were squeezed out putting pressure with a micro-slide. Embryos were then manually separated from the other tissues and washed three times in PBS before freezing in liquid nitrogen.Fixed chromatin was isolated from approximately 2000 to 3000 mature embryos using a scaled-down version of a protocol found elsewhere. Briefly, embryo pellets kept at -80 °C are thawed on ice in 1 % formaldehyde. Vacuum is applied for 10 min before adding glycine to a final concentration of 0.125 M and vacuum is applied for another 5 min. Embryos are collected at the bottom of the 1.7 mL tube by spinning 1 min at 5000 rpm and washed three times with distilled water. Once last wash is removed, tubes are put in liquid nitrogen and embryos are ground to a fine powder with pre-cooled plastic pestle and 750 uL of extraction buffer I (0.4 M Sucrose, 10 mM Tris-HCl pH 8.0, 10 mM MgCl2, 25 mM β-mercaptoethanol, 1X Halt™ Protease Inhibitors (Thermo Fisher Scientific)  and 0.1 mM PMSF). Slurry is transferred and processed in a 2 mL Dounce homogenizer (MilliporeSigma) and transferred to a 15 mL conical tube on ice. When all samples are processed, tubes are inserted in a mixer slowly rotating at 4 °C form 30 min. The slurries were then filtered through a 40 µm FalconTM cell strainer (Thermo Fisher Scientific)  into a new 50 mL FalconTM tubes and tubes and filters were rinced with 5 mL of buffer I. The new tubes were spun at 4000 rpm for 20 min at 4 °C. Supernatants are poured off and pellets are resuspended in 1.25 mL of extraction buffer II (0.25 M Sucrose, 10 mM Tris-HCl pH 8.0, 10 mM MgCl2, 1% Triton X-100, 5 mM β-mercaptoethanol, 1X Halt™ Protease Inhibitors (Thermo Fisher Scientific)  and 0.1 mM PMSF) and transferred to a new DNA Lobind 1.75 mL tubes (Eppendorf). Tubes are spun at 13,000 rpm for 10 min at 4 °C. Supernatants are discarded and pellets are resuspended in 350 µL of buffer II with repeated pipetting. The solutions are then added to new tubes on top of a 350 µL of buffer III (1.7 M Sucrose, 10 mM Tris-HCl pH 8.0, 2 mM MgCl2, 0.15% Triton X-100, 5 mM β-mercaptoethanol, 1X Halt™ Protease Inhibitors and 0.1 mM PMSF). Tubes are spun at 13,000 rpm for 45 min at 4 °C. Remove supernatants and resuspend pellets in 70 µL of Nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS, 1X Halt™ Protease Inhibitors and 0.1 mM PMSF) with repeated pipetting. Incubate tubes on ice for 30 min. Shear chromatin using a Covaris® S220 ultrasonicator at a frequency of 175 MGh for 6 min. Tubes are spun at 13,000 rpm for 10 min at 4 °C, supernatants (circa 60 µL) are transferred to new tubes.The following procedures are executed in the cold room unless indicated otherwise. 540 µL of ChIP buffer (16.7 mM Tris-HCl pH 8.0, 1.2 mM EDTA, 1.1% Triton X-100, 167 mM NaCl and 1X Halt™ Protease Inhibitors) is added to the sheared chromatin and 20 µL of pre-washed Dynabeads™ Protein A (Thermo Fisher Scientific)  is added for a 1 hour pre-clearing with rotation. Beads are separated with magnet and supernatants are transferred to new tubes. Solutions are split equally between two new tubes. 2.5 µg of antibody is added to each tube, either anti-Histone H3 di-methyl (ab1220 from Abcam) or anti-Histone H3 unmodified  (ab1791). 25 µL of pre-washed beads are added to each tube and they are incubated overnight with rotation. Beads are collected and washed consecutively with 1 mL low salt buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 1% Triton X-100,, 0.1% SDS and 150 mM NaCl), 1 mL high salt buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 1% Triton X-100, 0.1% SDS and 500 mM NaCl), 1 mL LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% Nonidet P-40, 1% sodium deoxycholate and 250 mM LiCl) and 1 mL TE (10 mM Tris-HCl pH 8.0 and 1 mM EDTA) 5min each with rotation. TE wash is repeated then beads are eluted twice with 125 µL of elution buffer (1% SDS and 100mM of NaHCO3) with vortexing and 15 min incubation at 65 °C. After combining the two elutions, 10 µL of 5 M NaCl is added and solutions are incubated at 65 °C overnight to reverse cross-linking. 10 µL of 500 mM EDTA, 20 µL of 1 M Tris-HCl pH 6.5 and 1 µL of 20 mg/mL Proteinase K are added and solutions are incubated at 45 °C for 1 hour. DNA is then purified using Zymo Research ChIP DNA Clean and Concentrator columns eluted twice with 25 µL of 10 mM Tris-HCl pH 8.0.
DNA fragments are made into libraries using the NEBNext Ultra II FS kit (New England Biolabs) according to manufacturer's instructions.

value: kyp-6 suvh5-2 suvh6-1

tag: ecotype

tag: chip antibody

value: H3 from Abcam (ab1791)

value: mature embryos


title: H3 - suvh2suvh9 R2

description: Chromatin

source_name: suvh2suvh9 mature embryos

value: suvh2-1 suvh9-1


title: B6_mut_neutro

description: 4 wk old Ift88Orpk C57BL/6 Neutrophils

value: Neutrophils


title: H3 - drm1drm2 R2

description: Chromatin

source_name: drm1drm2 mature embryos

value: drm1-2 drm2-2


title: Balb_ctrl_neutrophils

description: 4 wk old wild type BALB/c Neutrophils


title: H3 - suvh2suvh9 R1

description: Chromatin


title: H3 - drm1drm2 R1

description: Chromatin


title: H3 - polIV R2

description: Chromatin

source_name: polIV mature embryos


title: H3 - polIV R1

description: Chromatin


title: 4C_LTC4S_donor2_P9

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

description:
LTC4S_LTC4SOld_cis_highinter.bed
LTC4S_LTC4SOld_nearbait_highinter.bed
LTC4S_LTC4SYoung_LTC4SOld_cis_pval0.05_diff.bed
LTC4S_LTC4SOld_nearbait_highinter.bed

data_processing:
Library strategy: 4C-Seq
Quality of the resulting reads was checked by FastQC before reads were aligned to the hg19 genome assembly using bowtie2
Aligned reads were analyzed with the Hidden-Markov-Model-based tool 4Cker.
kth-next-neighbor adaptive window sizes of k = 5 for nearbait (10 MB around the “bait” region of interest) and cis interaction analysis and k = 20 for trans chromosomal interactions were used. We focused particularly on the high-interacting reads that were called in both replicates.
Differential interactions were called with 4Cker, which uses DESeq2 and a FDR corrected p-value < 0.5 to call significant differential interactions between early and late passages.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain high-interacting reads that were called in both replicates by 4Cker.
Supplementary_files_format_and_content: Bed files contain differential interactions called by 4Cker of two replicas between early and late passages.

organism: Homo sapiens

source_name: bone marrow

growth_protocol: Cells were flushed from bone marrow and cultured in Dulbecco’s Modified Eagle Medium (DMEM, 1g/L glucose; PAA, Pasching, Austria) supplemented with 1% penicillin/streptomycin (PAA), 1% L-glutamine, 10% pooled human platelet lysate and 0.1% heparin (5,000 lU/ml, Ratiopharm, Ulm, Germany) at 37° C in an atmosphere with 5% CO2. Cells were harvested by trypsinization when reaching 90% confluency, counted, and re-seeded in a density of 10,000 cells /cm2.

extract_protocol:
Ten million cells from two MSC preparations at early (P2 and 3) and late (P7 and 9) passages were cross-linked with 4% paraformaldehyde (Electron Microscopy Sciences, Hatfield, PA, USA) for 10 min., harvested into ice cold PBS with 0.125 M glycine, and frozen under a protease inhibitor cocktail (Roche, Basel, Suisse). 4C-seq was performed  using ApoI as the primary and DpnII as the secondary restriction enzyme.
Amplicons were sequenced on a HiSeq2500 platform (Illumina).

value: mesenchymal stromal cells

tag: passage

tag: bait region


title: H3 - WT R2

description: Chromatin

source_name: WT mature embryos

tag: genotype

value: WT

tag: tissue


title: H3 - WT R1

description: Chromatin


title: B6_mut_Ly6clo_macro

description: 4 wk old Ift88Orpk C57BL/6 Ly6clo infiltrating macrophages

tag: cell type

value: Ly6clo infiltrating macrophages


title: B6_mut_Ly6chi_macro

description: 4 wk old Ift88Orpk C57BL/6 Ly6chi infiltrating macrophages

tag: age


title: B6_Ctrl_cholang

description: 4 wk old wild type C57BL/6 Cholangiocytes

tag: strain

value: Cholangiocytes


title: 4C_LTC4S_donor1_P7


title: H3K9me2 - suvh4suvh5suvh6 R1

description: Chromatin

value: H3K9me2 from Abcam (ab1220)


title: H3K9me2 - suvh4suvh5suvh6 R2

description: Chromatin


title: B6_Ctrl_Neutro

description: 4 wk old wild type C57BL/6 Neutrophils


title: B6_mut_cholang

description: 4 wk old Ift88Orpk C57BL/6 Cholangiocytes


title: H3K9me2 - suvh2suvh9 R2

description: Chromatin


title: H3K9me2 - suvh2suvh9 R1

description: Chromatin


title: B6_Ctrl_Ly6clo_macro

description: 4 wk old wild type C57BL/6 Ly6clo infiltrating macrophages


title: HepG2_RB7LP_rep3

type: RNA

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

description: gene expression profile three days after 1µg/ml doxycycline treatment.

hyb_protocol: 1.65µg of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/µg cRNA) was fragmented at 60˚C for 30 minutes in a reaction volume of 55µl containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55µl of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to Whole Human Genome microarry 4x44K Ver. 2.0 (G4845A, Agilent Technologies) for 17 hours at 65˚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 37˚C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentHD_GX_1Color and Grid: 026652_D_F_20120130) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered with three filters with GeneSpring software 13 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than 20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was excluded. In the last filter, when the value (log scale) of CV was over 50 percent in both conditions, the probe was excluded. After filtering, control probes were excluded, and log scale values were transformed into normal scale.

source_name: HepG2, RB7LP expressed cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2µg RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HepG2 cells (derived from hepatocyte carcinoma developed in human male; 1886, RIKEN) were cultured in DMEM (04129775, WAKO) containing 10% FBS (AXB30120, Thermo scientific) and 1% penicillin; streptomycin solution (16823291, Wako).

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: HepG2 cells with the tetracycline (Tet)-inducible vector pTRE3G-puro-RB7LP-GFP were treated with or without 1µg/ml doxycycline for 3 days.

tag: cell line

value: liver cancer cell line HepG2

value: RB7LP expression


title: HepG2_CTL_rep3

source_name: HepG2, negative control cell

value: control


title: HepG2_CTL_rep2


title: HepG2_CTL_rep1


title: B6_Ctrl_Ly6chi_macro

description: 4 wk old wild type C57BL/6 Ly6chi infiltrating macrophages

value: 4 weeks old

value: Ly6chi infiltrating macrophages

value: Wild type


title: H3 - ago4ago6ago9 R2

description: Chromatin

source_name: ago4ago6ago9 mature embryos

value: ago4-5 ago6-2 ago9-2


title: H3 - ago4ago6ago9 R1

description: Chromatin

value: H3 from Abcam (ab1791)


title: 4C_KRTAP_donor2_P9

description:
KRTAP_KRTAPOld_cis_highinter.bed
KRTAP_KRTAPOld_nearbait_highinter.bed
KRTAP_KRTAPYoung_KRTAPOld_cis_pval0.05_diff.bed
KRTAP_KRTAPOld_nearbait_highinter.bed


title: 4C_LTC4S_donor1_P2

description:
LTC4S_LTC4SYoung_cis_highinter.bed
LTC4S_LTC4SYoung_nearbait_highinter.bed
LTC4S_LTC4SYoung_LTC4SOld_cis_pval0.05_diff.bed
LTC4S_LTC4SOld_nearbait_highinter.bed


title: HepG2_RB7LP_rep2


title: 4C_KRTAP_donor1_P7


title: H3K9me2 - polIV R2

description: Chromatin

value: mature embryos


title: H3K9me2 - ago4ago6ago9 R2

description: Chromatin


title: H3K9me2 - polIV R1

description: Chromatin


title: H3K9me2 - ago4ago6ago9 R1

description: Chromatin


title: 4C_LTC4S_donor2_P3


title: H3K9me2 - drm1drm2 R2

description: Chromatin


title: H3K9me2 - drm1drm2 R1

description: Chromatin


title: 4C_KRTAP_donor2_P3

description:
KRTAP_KRTAPYoung_cis_highinter.bed
KRTAP_KRTAPYoung_nearbait_highinter.bed
KRTAP_KRTAPYoung_KRTAPOld_cis_pval0.05_diff.bed
KRTAP_KRTAPOld_nearbait_highinter.bed


title: C2C12-m6A_IP1

city: Guangzhou

first: Yu

last: Liang

address: Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital

institute: Sun Yat-sen University

data_processing:
library strategy: MeRIP-seq
Reads were aligned to mm10 using tophat
Peak calling was done with MACS2
Genome_build: mm10
Supplementary_files_format_and_content: txt file showing the peak regions

source_name: mouse myoblast cells

growth_protocol: The C2C12 mouse myoblast cells were cultured in DMEM high glucose (Gibco) supplemented with 15% fetal bovine serum, 100 U/ml of penicillin, and 100 µg/ml of streptomycin in 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from cells and organization using Trizol (Invitrogen) following the manufacturer’s instructions. mRNA was first purified from total RNA using PolyATtract mRNA Isolation System IV (Promega Z5310). 2μg of the puriﬁed mRNA was fragmentized with ZnCl2 buffer at 94°C for 5min. The mRNA fragments were puriﬁed and then subjected to immunoprecipitation with α-m6A antibody (1:100, Synaptic Systems, Cat No: 202003). After extensive wash, the methylated fragments were eluted by competition using free N6-Methyladenosine (Santa Cruz Biotechnology, sc-215524) and then used for library construction with the TruSeq Stranded mRNA Sample Prep Kits (Illumina RS-122-2101). The input and m6A MeRIP libraries were sequenced with Illumina NextSeq 500 with high output kit.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit.

treatment_protocol: The C2C12 cells were maintained in medium and then the cells were differentiated by incubation in DMEM containing 2% horse serum for 3 days. Mice were induced by Tamoxifen (Sigma) for 5 consecutive days and then injected with CTX (Sigma) to establish murine muscle injury model.

value: mouse myoblast cells

value: Knockout

tag: merip antibody

value: m6A (202003 - Synaptic Systems)


title: C2C12-m6A_IP2


title: 4C_KRTAP_donor1_P2

value: mesenchymal stromal cells


title: H3K9me2 - WT R2

description: Chromatin

value: WT


title: D2wt-IP

source_name: muscle

tag: strain background

value: muscle stem cell

value: Normal


title: D2wt-input


title: WGBS - suvh4suvh5suvh6 R1

description: Bisulfite treated DNA

extract_protocol:
Siliques were cut open with insulin syringe needles, whole seeds were transferred on microscope slide in a drop of PBS and embryos were squeezed out putting pressure with a micro-slide. Embryos were then manually separated from the other tissues and washed three times in PBS before freezing in liquid nitrogen. For WGBS, DNA was isolated from approximately 2000 to 3000 mature embryos using the Quick-DNA Microprep Plus Kit (Zymo Research), according to manufacturer instructions. 150 ng of DNA was sheared using a Bioruptor to sizes ranging from 200 bp to 600bp.
The fragments were ligated with methylated adaptors (New England Biolabs) and AMPure bead purified (Beckman Coulter) before being treated with the EZ DNA Methylation-Lightning Kit (Zymo Research), according to manufacturer instructions. Converted DNA was eluted with 20 µL of buffer and 10 µL were used for amplification with Uracyl tolerant polymerase (KAPA Biosystems) with index containing primers (NEB).

value: kyp-6 suvh5-2 suvh6-1


title: 4C_CASR_donor2_P9

description:
CASR_CASROld_cis_highinter.bed
CASR_CASROld_nearbait_highinter.bed
CASR_CASRYoung_CASROld_cis_pval0.05_diff.bed
CASR_CASROld_nearbait_highinter.bed

value: CASR


title: HepG2_RB7LP_rep1

value: liver cancer cell line HepG2

value: RB7LP expression


title: WGBS - suvh2suvh9 R2

description: Bisulfite treated DNA

value: suvh2-1 suvh9-1


title: WGBS - suvh2suvh9 R1

description: Bisulfite treated DNA


title: WGBS - suvh4suvh5suvh6 R2

description: Bisulfite treated DNA


title: H3K9me2 - WT R1

description: Chromatin

value: H3K9me2 from Abcam (ab1220)


title: 4C_CASR_donor1_P7


title: D2mut-IP


title: WGBS - drm1drm2 R1

description: Bisulfite treated DNA

value: drm1-2 drm2-2


title: 4C_CASR_donor2_P3

description:
CASR_CASRYoung_cis_highinter.bed
CASR_CASRYoung_nearbait_highinter.bed
CASR_CASRYoung_CASROld_cis_pval0.05_diff.bed
CASR_CASROld_nearbait_highinter.bed


title: WGBS - ago4ago6ago9 R2

description: Bisulfite treated DNA

value: ago4-5 ago6-2 ago9-2


title: 4C_CASR_donor1_P2


title: D2mut-input


title: C2C12-Input


title: WGBS - ago4ago6ago9 R1

description: Bisulfite treated DNA


title: WGBS - WT R2

description: Bisulfite treated DNA


title: LmnaKO_ATAC_rep1

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files

source_name: Cells of the renin lineage

growth_protocol: Cells were maintained in Dulbecco’s minimal essential medium/Ham’s F12 (DMEM/F12) (Thermo Fisher Scientific, Waltham, MA) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific) at 37˚C.

extract_protocol:
Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay. The cells were thawed in a 37 ˚C water bath, pelleted, and washed with cold PBS. Cell pellets were then resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera DNA Library Prep Kit (Illumina, San Diego, CA).
Tagmented DNA was purified using the MinElute PCR purification kit (QIAGEN, Dusseldorf, Germany), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter, Brea, CA). The resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems, Wilmington, MA) and sequenced with paired-end 42-nt sequencing on the NextSeq 500 sequencer (Illumina).

treatment_protocol: Lmna knockout was performed using CRISPR-Cas9 ribonucleoproteins with Alt-R CRISPR-Cas9 system (Integrated DNA Technologies [IDT], Coralville, IA) and the Amaxa Nucleofector System (Lonza, Basel, Switzerland).

value: Renal afferent arteriolar smooth muscle cell line

value: Lmna KO


title: 4C_Alox12_donor1_P7

description:
Alox12_AloxOld_cis_highinter.bed
Alox12_AloxOld_nearbait_highinter.bed
Alox12_AloxYoung_AloxOld_cis_pval0.05_diff.bed
Alox12_AloxOld_nearbait_highinter.bed


title: LmnaKO_ATAC_rep2


title: 4C_Alox12_donor2_P9


title: Control_ATAC_rep2

value: control


title: WGBS - WT R1

description: Bisulfite treated DNA

value: mature embryos


title: WGBS - drm1drm2 R2

description: Bisulfite treated DNA


title: cep290ex25MO_rep 2

city: Bar Harbor

first: Iain

middle: A

last: Drummond

state: Maine

address: 159 Old Bar Harbor Road Bar Harbor

department: Davis Center for Regenerative Biology and Aging

institute: Mount Desert Island Biological Laboratory

data_processing:
Base-calling by Illumina's HiSeq software
Quality filtering with FastQC
Genome alignment by STAR program Dobin et al. 2013. Bioinformatics. doi: 10.1093/bioinformatics/bts635.
Gene expression counts were calculated by HTSeq. Simon et al. 2014. Bioinformatics. doi:10.1093/bioinformatics/btu638
Differentially expressed gene (DEG) calls were done by edgeR. Robinson et al. 2009. Bioinformatics. doi.org/10.1093/bioinformatics/btp616
Genome_build: Zv9
Supplementary_files_format_and_content: text file RPKM table was generated using HTseq
Supplementary_files_format_and_content: Excel spreadsheets DEG tables were generated using edgeR

organism: Danio rerio

source_name: embryos

growth_protocol: Embryos were raised in petri dishes with aquarium water at 28.5 ºC (50 larvae per 10 cm petri dish).

extract_protocol:
Total RNA was extracted by Trizol-Chloroform-Isopropanol protocol
PolyA selection + NEBNext Ultra Directional RNA Library Prep Kit for Illumina

value: TUAB

tag: embryo

value: whole embryos

value: cep290 exon 25 morphants


title: cep290ex25MO_rep 3


title: WGBS - polIV R1

description: Bisulfite treated DNA


title: 4C_Alox12_donor1_P2

description:
Alox12_AloxYoung_cis_highinter.bed
Alox12_AloxYoung_nearbait_highinter.bed
Alox12_AloxYoung_AloxOld_cis_pval0.05_diff.bed
Alox12_AloxOld_nearbait_highinter.bed

value: mesenchymal stromal cells


title: WGBS - polIV R2

description: Bisulfite treated DNA


title: Control_ATAC_rep1


title: wildtype_TuAB_rep3

value: wild type


title: MZcep290-/-_rep1

value: cep290 maternal zygotic mutant exon16 deletion10bp


title: wildtype_TuAB_rep2


title: Mouse Thyroid Organoid

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

description: Raw Data Files split into two due to size issues.

data_processing:
The raw sequencing data were then processed with the ‘count’ command of the Cell Ranger software (v.2.1.0) provided by 10x Genomics with the option ‘–expect-cells’ set to 10,000 (all other options were used as per default).
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz - Tab separated file containing Cell barcodes. Cell barcodes correspond to columns of the matrix.
features.tsv.gz - Tab separated file containing gene names. Gene names correspond to rows of the matrix.
matrix.mtx.gz - Sparse martix containing counts obtained from Cell Ranger output.

source_name: in vitro differentiated cells

extract_protocol:
Trypsin based dissociation followed by FACS sorting of alive cells
10x Chromium NextGEM SingleCell 5' Kit v2

value: Thyroid Organoid

value: in vitro differentiated cells

tag: Stage

value: a mixture of four different stages of differentiation protocol


title: wildtype_TuAB_rep1


title: O87 dorsal skin

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

data_processing:
The Mouse reference genome as provided by Ensembl (GRCm38/mm10) was used for mapping of (ox)RRBS sequencing reads. Quality control and filtering of low-quality reads was performed using “Trim Galore!” (Babraham Bioinformatics). Quality control indicated no major problems, so Bismark (v.0.16.3, Babraham Bioinformatics) was used in Bowtie2-mode [28], for mapping. Seed length, mismatches and interval during multiseed alignment were set to the default values.
Genome_build: GRCm38

source_name: dorsal skin

growth_protocol: SKH-1 hairless mice (Charles River, Germany) were bred in our facility with free access to water and food (pelleted RM1 diet from SDS Ltd., Witham, Essex, UK), on a 12-h light/ 12-h dark cycle, 35% humidity. The experimental animals were age-matched and female.

extract_protocol:
The mice were then euthanized, individual tumors, tumor-free dorsal skin, and non-irradiated ventral skin were harvested, immediately frozen in liquid N2, and stored at –80 °C. Laser-capture microdissection (on Zeiss Palm Microbeam microscope, Zeiss, UK) was used to enrich for tumor cell populations and prevent contamination by infiltrating inflammatory cells. Genomic DNA was extracted from tumor cells and from matched normal skin samples.
Mouse skin tumors were harvested and snap frozen in liquid N2. Tumor tissue was enriched using laser capture microdissection and genomic DNA was isolated using the QIAmp DNA micro kit (Qiagen) according to the manufacturer‘s protocol. Genomic DNA was then used for oxRRBS library preparation.
Library preparation and sequencing were performed by NXTGNT (Ghent, Belgium). Upon arrival, the samples were subjected by Quant-iT™ PicoGreen™ dsDNA Assay Kit (P7589, ThermoFisher) for quality assessment. No aberrations were detected, and 1 µg DNA was measured for MSP1 digestion. Digestion was performed overnight for 16h at 37°C in a volume of 30 µl and stopped with 5 µl of 0.5 M EDTA. Subsequently, the digestion product was purified with the GeneJET PCR Purification Kit (K0701, ThermoFisher), eluted in 50µl elution buffer and quality was checked again on E-Gel™ EX Agarose Gels, 1% (G401001, ThermoFisher). NEBNext Ultra DNA Library Prep Kit for Illumina (E7370, New England Biolabs) and TrueMethyl seq kit (Feb 2015, Cambridge Epigenetix) were used for library preparations, both kits according the manufacturers recommendations. Samples were splitted into two aliquots (each 275 ng) of which one was oxidated for oxRRBS. After bisulfite conversion and subsequent clean-up reaction, polymerase chain reaction (PCR) amplification was performed. Agencourt AMPure XP Bead Clean-up 1:1 (E6260) was performed for cleanup and DNA fragment length selection. Finally, a DNA high sensitivity chip on the Bioanalyzer (Agilent technologies) and measurements of qPCR quantification according to the Illumina protocol (“qPCR quantification protocol guide”) concluded the last quality control steps.
Sequencing was performed on the NextSeq500 using 7 dark cycles on single read fragments with a length of 76 bp. A concentration of 1.8 pM was loaded with a 15% PhiX spike-in.

treatment_protocol: Starting at 8 weeks of age, the mice were exposed twice a week for 15 weeks on Tuesdays and Fridays to solar-simulated UV radiation (comprised of 2 J/cm2 UVA and 90 mJ/cm2 UVB) delivered from UVA340 lamps (Q-Lab, Germany) in clear bedding-free cages. The radiant dose was confirmed with an external radiometer (X-96 Irradiance Meter; Daavlin, Bryan, OH) before and after each irradiation session. Excessive heating was prevented by use of an electrical fan. After the end of the irradiation schedule, the animals were monitored for a further 20 weeks, and tumors (defined as lesions >1 mm in diameter) and body weights were recorded weekly.

value: skin

tag: tumor stage


title: 1012605

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

data_processing:
Sequencing reads were mapped to SmaI sites in the human genome (hg19) and signatures corresponding to methylated (starting with CCGGG) and unmethylated (starting with GGG) CpG were enumerated for each SmaI/XmaI site.
At each SmaI/XmaI site, let sm be the number of tags corresponding to methylated CpG (i.e., tags starting with CCGGG) and u be the number of tags corresponding to unmethylated CpG (i.e., tags starting with GGG), the methylation value was calculated as 100%*(c*sm/(c*sm+u)), where c is the correction factor based on observed vs expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated plain text files

source_name: mammary epithelila cells

growth_protocol: The primary human mammary epithelial cells were derived from adjacent normal mammary tissue of breast cancer patients using an established commercial protocol of EpiCult®-B human mammary epithelial cell culture (Stemcell Technologies, BC, Canada)16. Established primary HMEC lines were maintained in culture for 4 passages in medium containing 1:1 DMEM/F12 (Life Technologies, Carlsbad, CA), 2.438 g/L sodium bicarbonate, 5% chelated horse serum, 20 ng/ml EGF (BD Biosciences, San Jose, CA), 100 ng/ml cholera toxin (Sigma-Aldrich, St. Louis, MO), 10 mg/L insulin (SigmaAldrich, St. Louis, MO), 0.5 mg/L hydrocortisone (Sigma-Aldrich, St. Louis, MO), Antibiotic-Antimycotic (Life Technologies, Carsbad, CA), and 0.04 mM calcium chloride (Sigma-Aldrich, St. Louis, MO). Genomic DNA was isolated from HMEC lines by phenol-chloroform extraction.

extract_protocol:
Genomic DNA was extracted by phenol/chloroform.
Two micrograms of genomic DNA spiked with 20 ng of methylation standards with defined methylation levels of 0, 25, 50, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was supplemented withdCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Filled in dA-tailed fragments were cleaned using AMPure 2.0X beades and ligated to NEBNext sequencing adaptors.  Hairpin loops at NEB adaptors were cleaved by the USER enzyme.  Fragments of 300-700 bp were size selected by SPRI beads. Size-selected DNA was amplified with NEBNext PCR primers using Kapa high-fidelity DNA polymerase and 12 PCR cycles. Resulting sequencing libraries were purified with SPRI beads.
Restriction enzyme-based DNA methylation profiling.

tag: gender

value: Female


title: 4C_Alox12_donor2_P3


title: MZcep290-/-_rep3


title: O851 dorsal skin

value: tumor


title: cep290ex25MO_rep 1


title: 1012418


title: MDA-MB-231-IV2-control

city: New Taipei

first: Kuo-Wang

last: Tsai

address: No. 289 Jianguo Road, Xindian District, New Taipei City

country: Taiwan

institute: Taipei Tzu Chi Hospital

data_processing:
CAP-miRNA was used for pre-processing and process analytical pipeline for fastq files.
Analytical pipeline: read quality (FastQC), trims adapter sequences (Cutadapt), aligns reads for IGV viewing and detection of mature, precursor, novel miRNAs (miRDeep2).
Raw Count data were normalized into TPM (transcript per million) values
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Breast cancer cell line

growth_protocol: MDA-MB-231 cells and IV2-1 cells were culturein in Dulbecco’s modified Eagle’s medium supplemented with 10% inactivated FBS

extract_protocol:
Total RNA of breast cancer cells was prepared using TRIZOL (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols with MiSeq Reagent Kit v3 (MS-102-3001).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: After transfection with N.C and siLOC550643 for 48hr, RNA was extracted from two samples, MDA-MB-231-IV2-1 with LOC550643 knockdown and control cells

tag: treatment

value: siRNA control transfection for 48hr


title: MDA-MB-231-IV2-LOC550643 knockdown

value: siLOC550643 pool RNA transfection for 48hr


title: 1013014


title: O85 dorsal skin


title: O874 dorsal skin


title: O77 dorsal skin


title: O562_TR dorsal skin


title: 1012115


title: 1011503


title: O562 dorsal skin


title: 1012816


title: 1012129


title: O56_TR dorsal skin


title: 1011258


title: G245_G09_21_NEMO_3L: Liver, NEMOΔhepa mouse, replicate 3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.52.1).

label: biotin

source_name: Liver, obtained from a hepatocyte-specific NEMO knockout mouse (NEMOΔhepa), aged 8 wks

label_protocol: Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Hepatocyte-specific knockout mice for NEMO and KEAP1 were obtained by crossing Alfp-Cre transgenic mice (DOI: https://doi.org/10.1002/(sici)1526-968x(200002)26:2%3C151::aid-gene17%3E3.0.co;2-e; PMID: 10686615) with NEMO-floxed (NEMOf/f) mice (DOI: https://dx.doi.org/10.1084%2Fjem.20082152; PMID: 19635861) or KEAP1-floxed (KEAP1f/f) mice (DOI: https://doi.org/10.1016/j.bbrc.2005.10.185; PMID: 16293230), respectively. Hepatocyte-specific NEMO knock-out mice (NEMOΔhepa) were crossed with hepatocyte-specific KEAP1 knockout mice (KEAP1Δhepa) to generate NEMOΔhepa/KEAP1Δhepa double knockout mice. Animals were housed under specific pathogen-free conditions in the animal facility of University Hospital Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen. All experiments were carried out according to the criteria of the authority for environment conversation and consumer protection of the state North Rhine-Westphalia (LANUV, Germany, protocol #84.02.04.2013.A240).

extract_protocol: RNA was isolated using Qiagen RNeasy Mini Kit (Qiagen), quantified using NanoDrop, and quality was checked with the Agilent 2100 bioanalyzer (Agilent Technologies). Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.

treatment_protocol: Livers or primary hepatocytes of 8 week old male mice of all four genotypes were used for gene expression profiling. Primary hepatocytes were isolated from mouse livers as previously described (DOI: https://doi.org/10.1016/j.jhep.2016.12.011; PMID: 28011329). In short, after cannulation of the inferior vena cava, the portal vein was cut and the liver was perfused first with Ca2+ and Mg2+ free Earle's balanced salt solution (EBSS), second  with EBSS containing Ca2+ (1.8 mM) and Mg2+ (0.813 mM) and HEPES (10 mM) and third with EBSS containing Ca2+, Mg2+ and HEPES and additionally collagenase and an inhibitor of trypsin. The liver was excised and the cells were dispersed in high glucose DMEM supplemented with serum (10% FCS) and antibiotics (Penicillin, Streptomycin) (DMEM complete). Mouse primary hepatocytes were cultured in DMEM complete in a humidified atmosphere containing 5% CO2 at 37°C. The cells were grown in 100 mm dishes or 6-well plates. The cells were allowed to settle down and adhere to culture dishes until the next day and then the medium was replaced with fresh one.

value: Liver

tag: age (wks)


title: 1011652


title: G245_G07_20_NEMO_2L: Liver, NEMOΔhepa mouse, replicate 2

value: hepatocyte-specific NEMO knockout mouse (NEMOΔhepa)


title: MZcep290-/-_rep2


title: G245_H05_22_2KO_1L: Liver, NEMOΔhepa/KEAP1Δhepa mouse, replicate 1

source_name: Liver, obtained from a hepatocyte-specific NEMO/KEAP1 double knockout mouse (NEMOΔhepa/KEAP1Δhepa), aged 8 wks


title: G245_F07_17_KEAP1_2L: Liver, KEAP1Δhepa mouse, replicate 2

source_name: Liver, obtained from a hepatocyte-specific KEAP1 knockout mouse (KEAP1Δhepa), aged 8 wks


title: G245_F05_16_KEAP1_1L: Liver, KEAP1Δhepa mouse, replicate 1

value: hepatocyte-specific KEAP1 knockout mouse (KEAP1Δhepa)


title: G245_H07_23_2KO_2L: Liver, NEMOΔhepa/KEAP1Δhepa mouse, replicate 2

value: hepatocyte-specific NEMO/KEAP1 double knockout mouse (NEMOΔhepa/KEAP1Δhepa)


title: 1011408


title: O56 dorsal skin

value: control


title: G245_H09_24_2KO_3L: Liver, NEMOΔhepa/KEAP1Δhepa mouse, replicate 3


title: O545 dorsal skin


title: O54 dorsal skin


title: 1012840


title: G245_G05_19_NEMO_1L: Liver, NEMOΔhepa mouse, replicate 1


title: G245_F09_18_KEAP1_3L: Liver, KEAP1Δhepa mouse, replicate 3


title: G245_E07_14_WT_2L: Liver, NEMOf/f mouse, replicate 2

source_name: Liver, obtained from a control mouse (NEMOf/f), aged 8 wks

value: control (NEMOf/f)


title: G245_E09_15_WT_3L: Liver, NEMOf/f mouse, replicate 3


title: G245_E05_13_WT_1L_2: Liver, NEMOf/f mouse, replicate 1


title: G245_D09_12_2KO_3PH: Primary hepatocytes, NEMOΔhepa/KEAP1Δhepa mouse, replicate 3

source_name: Primary hepatocytes, obtained from a hepatocyte-specific NEMO/KEAP1 double knockout mouse (NEMOΔhepa/KEAP1Δhepa), aged 8 wks

value: Primary hepatocytes


title: G245_D07_11_2KO_2PH_2: Primary hepatocytes, NEMOΔhepa/KEAP1Δhepa mouse, replicate 2


title: 1012671


title: G245_C09_09_NEMO_3PH: Primary hepatocytes, NEMOΔhepa mouse, replicate 3

source_name: Primary hepatocytes, obtained from a hepatocyte-specific NEMO knockout mouse (NEMOΔhepa), aged 8 wks


title: G245_D05_10_2KO_1PH_2: Primary hepatocytes, NEMOΔhepa/KEAP1Δhepa mouse, replicate 1


title: O45 dorsal skin


title: O444 dorsal skin


title: 1012632


title: G245_C07_08_NEMO_2PH: Primary hepatocytes, NEMOΔhepa mouse, replicate 2


title: G245_C05_07_NEMO_1PH_3: Primary hepatocytes, NEMOΔhepa mouse, replicate 1


title: O44 dorsal skin


title: 1011510


title: 1012336


title: 1011744


title: KO-LPS2h

city: Taipei

first: Li-Chung

last: Hsu

address: No.7, ChungShan S. Rd., ZhongZheng Dist.

department: Graduate institute of Molecular Medicine

institute: National Taiwan University

data_processing:
Library strategy: TAIL-Seq
Basecalls performed using Illumina Hiseq 2000 PE 2*150
Total of 0.5-1.47 million reads were obtained from each sample and uploaded to Galaxy (https://usegalaxy.org/) online tool for further analysis
raw reads were firstly mapped by HISAT2 using RefSeq mm10
trimmed illumina adapter sequences
filter sequences by TTTAAATGAAAAAGGTTGACAAAATAAA (for Zc3h12a), TGTTTAGACTGTCTTCAAACAAATAAA(for Il6), and CTGTAGGCACCATCAAT (linker-1)
Genome_build: mm10
Supplementary_files_format_and_content: readcounts of specific gene includes 702-502_+Ctrl, 702-503_+LPS2h,702-504_+LPS4h, 702-505_-Ctrl, 702-506_-LPS2h, and 702-507_-LPS4h; other files were further filtered out by the specific sequences mentioned below

source_name: Bone marrow

growth_protocol: Bone marrow-derived macrophages (BMDMs) were prepared from femurs and tibia bones of 7-week old mice and bone marrow was flushed out with DMEM medium using a 25-gauge syringe. The bone marrow progenitor cells were harvested, and differentiated in high-glucose DMEM medium containing 20% L929 cell-conditioned medium for 7 days. Adherent BMDMs were collected and cultured in DMEM containing 10 ng/ml M-CSF overnight for further experiments.

extract_protocol:
Total RNAs of BMDMs were harvested using NucleoZol reagent.
cDNA libraries were prepared for sequencing using modified TAIL-Seq protocols

treatment_protocol: LPS stimulation for 2 or 4 hour

tag: Sex

value: female

tag: agent

value: LPS

tag: time point


title: O352 dorsal skin


title: KO-Ctrl

tag: genotype


title: KO-LPS4h


title: G245_B05_04_KEAP1_1PH: Primary hepatocytes, KEAP1Δhepa mouse, replicate 1

source_name: Primary hepatocytes, obtained from a hepatocyte-specific KEAP1 knockout mouse (KEAP1Δhepa), aged 8 wks

tag: tissue


title: G245_B09_06_KEAP1_3PH: Primary hepatocytes, KEAP1Δhepa mouse, replicate 3


title: G245_A07_02_WT_2PH: Primary hepatocytes, NEMOf/f mouse, replicate 2

source_name: Primary hepatocytes, obtained from a control mouse (NEMOf/f), aged 8 wks


title: H3 - suvh4suvh5suvh6 R2

description: Chromatin

source_name: suvh4suvh5suvh6 mature embryos

value: kyp-6 suvh5-2 suvh6-1

tag: ecotype

tag: chip antibody

value: H3 from Abcam (ab1791)

value: mature embryos


title: G245_A09_03_WT_3PH: Primary hepatocytes, NEMOf/f mouse, replicate 3


title: WT-LPS2h

tag: strain

tag: age

value: wild type


title: 1011388

value: Female


title: WT-Ctrl


title: 1011225


title: G245_B07_05_KEAP1_2PH: Primary hepatocytes, KEAP1Δhepa mouse, replicate 2


title: G245_A05_01_WT_1PH: Primary hepatocytes, NEMOf/f mouse, replicate 1


title: O16 dorsal skin

value: skin


title: 1013140


title: B874 dorsal skin

value: tumor


title: Neurog2, Ascl1 double negative rep 4

city: Lethbridge

first: Yaroslav

last: Ilnytskyy

state: AB

address: 4401, University Drive W

department: Biology

institute: University of Lethbridge

description:
Q3-4
processed data file: Q3.merged.bam.Q3_high_conf.bed.WellingtonFootprints.FDR.0.01.bed.gz
processed data file: Q3_knownResults.txt.gz

data_processing:
Library strategy: ATAC-seq
Basecalling and demultiplexing: CASAVA1.9
Initial quality controls: FastQC
Mappping reads to the genome with BWA: bwa -t 11 -M
Creating coverage files in bigwig format: converted bam to bedgraph using bedtools genomeCoverageBed, resulting bedgraphs were converted to bigwig with bedgraphToBigwig from UCSC utilities
Predicted areas of open chromatin using Hotspot software with default settings (http://www.uwencode.org/proj/hotspot/)
Selected hotspots with FDR less then 0.01. Hotspots which were present in all 3 biological replicates were considered to be “high confidence”
Bam files for all 3 biological replicates that belonged to the same genotype were merged together
Merged bam files and high confidence hotspots were used to predict transcriptional factor footprints within hotspot intervals using Wellington algorithm (http://pythonhosted.org/pyDNase/scripts.html)
Detected enriched transcriptional factor motifs using Homer software suite (http://homer.salk.edu/homer/)
Genome_build: mm10
Supplementary_files_format_and_content: [.bigwig] coverage files
Supplementary_files_format_and_content: [.hot.bed] hotspots
Supplementary_files_format_and_content: [.WellingtonFootprints.FDR.0.01.bed] Wellington output
Supplementary_files_format_and_content: [.txt] Homer output. Tab delimited: col1. Motif name; col2. Consensus sequence; col3. P-value; col4. Log p-value; col5. Q-value (Benjamini); col6. Number of target sequences with motif; col7. % of target sequences with motif; col8. Number of background sequences with motif; col9. % background sequences with motif

source_name: dorsal telencephalic

extract_protocol: ATAC-seq was performed as previously described, using 50,000 cells as input material for the transposase reaction (Buenrostro et al., 2015)

tag: genotype/variation

tag: cell type

value: cortical progenitors


title: Neurog2 positive rep 2

description:
Q4-2
processed data file: Q4.merged.bam.Q4_high_conf.bed.WellingtonFootprints.FDR.0.01.bed.gz
processed data file: Q4_knownResults.txt.gz


title: B87 dorsal skin


title: O35 dorsal skin


title: B851 dorsal skin


title: WT-LPS4h


title: Neurog2, Ascl1 double negative rep 3

description:
Q3-3
processed data file: Q3.merged.bam.Q3_high_conf.bed.WellingtonFootprints.FDR.0.01.bed.gz
processed data file: Q3_knownResults.txt.gz


title: Neurog2 positive rep 4

description:
Q4-4
processed data file: Q4.merged.bam.Q4_high_conf.bed.WellingtonFootprints.FDR.0.01.bed.gz
processed data file: Q4_knownResults.txt.gz


title: 1012833


title: Neurog2, Ascl1 double negative rep 2

description:
Q3-2
processed data file: Q3.merged.bam.Q3_high_conf.bed.WellingtonFootprints.FDR.0.01.bed.gz
processed data file: Q3_knownResults.txt.gz


title: Neurog2, Ascl1 positive rep 4

description:
Q2-4
processed data file: Q2.merged.bam.Q2_high_conf.bed.WellingtonFootprints.FDR.0.01.bed.gz
processed data file: Q2_knownResults.txt.gz


title: Neurog2, Ascl1 positive rep 3

description:
Q2-3
processed data file: Q2.merged.bam.Q2_high_conf.bed.WellingtonFootprints.FDR.0.01.bed.gz
processed data file: Q2_knownResults.txt.gz


title: Neurog2 positive rep 3

description:
Q4-3
processed data file: Q4.merged.bam.Q4_high_conf.bed.WellingtonFootprints.FDR.0.01.bed.gz
processed data file: Q4_knownResults.txt.gz


title: B85 dorsal skin


title: Neurog2, Ascl1 positive rep 2

description:
Q2-2
processed data file: Q2.merged.bam.Q2_high_conf.bed.WellingtonFootprints.FDR.0.01.bed.gz
processed data file: Q2_knownResults.txt.gz


title: B77 dorsal skin


title: Ascl1 positive rep 3

description:
Q1-3
processed data file: Q1.merged.bam.Q1_high_conf.bed.WellingtonFootprints.FDR.0.01.bed.gz
processed data file: Q1_knownResults.txt.gz


title: 1012187


title: Ascl1 positive rep 2

description:
Q1-2
processed data file: Q1.merged.bam.Q1_high_conf.bed.WellingtonFootprints.FDR.0.01.bed.gz
processed data file: Q1_knownResults.txt.gz


title: B562_TR dorsal skin


title: 1012846


title: 1012023


title: 277 19.0 Wks M

city: Rochester

first: Soumyaroop

last: Bhattacharya

state: NY

address: 601 Elmwood Ave Box 703

department: Pediatrics

institute: University of Rochester

data_processing:
Sequences were aligned against the human genome version of hg38 using the Splice Transcript Alignment to a Reference (STAR) algorithm
counts were summerized with HTSeq
deSeq2 was used to normalized for total counts (counts per million, CPM)
Genome_build: Hg 38
Supplementary_files_format_and_content: CPM Normalized data

source_name: Lung tissues

extract_protocol:
RNA was extracted from pieces of fetal human lung (T21 and non-T21) using a hand-held homogenizer and following the instructions of the iNtRon Biotechnology, Inc. Easy-SpinTM Total RNA Extraction Kit. Samples were treated with DNAse (Qiagen).
cDNA libraries were generated using 100 ng of RNA isolated from lungs of DS samples (n=19) and age matched controls (n=19). Library construction was performed using the TruSeq Stranded mRNA library kit (Illumina, San Diego, CA).

tag: gestational age (in weeks)

value: M

tag: disease

value: Normal


title: H27931 134d N M


title: B562 dorsal skin

tag: tumor stage


title: H27729 137d N M


title: 1012482

tag: gender


title: O168 dorsal skin


title: 1465 19 Wks N M


title: 1011721


title: H27750 132d N M


title: 1011545


title: 1011381


title: B56_TR dorsal skin


title: B56 dorsal skin


title: B545 dorsal skin


title: wt_M1_2_1

city: nan jing

first: liu

last: lu

state: jiang su

address: Chunhua

department: immunology

institute: nanjing medical university

data_processing:
Basecalls performed using BGISEQ-500
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.p6 whole genome using bowtie v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Data were filtered using SOAPnuke version v1.5.2 with parameters -l 15 -q 0.2 -n 0.05
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: BMDM

growth_protocol: BMDM isolated from colons of WT and drd5-/- mice.

extract_protocol:
RNA isolation
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

treatment_protocol: For RNA sequencing, BMDMs from WT or DRD5-/- mice were untreated or treated DA and stimulated with LPS (100ng/ml), IFN-γ(50ng/ml) or IL-4 (10ng /ml), IL-13 (10ng/ml) for 12 hours. Then perform RNA extraction. RNA samples were constructed and sequenced on a BGISEQ-500 (Beijing Genomic Institution). The filtered data were mapped to the mouse genome through HISAT2, the gene expression was analyzed, the matched readings was calculated, and then all the data was normalized to FPKM.

value: bone

tag: treatment

value: no DA

value: M1 macrophages

value: wt

value: 10 weeks


title: 1011136


title: WT_M1_3_1


title: 2464 18.0 Wks N F

value: F


title: B54 dorsal skin

value: control


title: B45 dorsal skin


title: 2692 17.6 Wks F


title: wt_M1_1_1


title: H27913 125d N M


title: wt_M1DA_3_1

value: DA


title: B444 dorsal skin


title: 1011759


title: 2805 17.1 Wks N F


title: wt_M1DA_2_1


title: 2810 18.1 Wks N M


title: wt_M1DA_1_1


title: B44 dorsal skin


title: B352 dorsal skin


title: 2352 16.3 Wks N F


title: WT_4_DA_3_1

value: M2 macrophages


title: 2559 17.0 Wks N F


title: Ascl1 positive rep 4

description:
Q1-4
processed data file: Q1.merged.bam.Q1_high_conf.bed.WellingtonFootprints.FDR.0.01.bed.gz
processed data file: Q1_knownResults.txt.gz


title: B168 dorsal skin


title: WT_4_DA_2_1


title: H27058 115d N F


title: WT_4_DA_1_1


title: B16 dorsal skin


title: 2306 16.2 Wks N M


title: WT_4_3_1


title: 2244 15.4 Wks N M


title: MOCK_BR3

city: Frankfurt am Main

first: Lukas

last: Jost

address: Altenhöferallee 3

institute: GenXPro GmbH

description: Tn5-tagged chromatin

data_processing:
Illumina bcl2fastq software used for basecalling.
Cleaned reads were mapped onto GRCh38 genome using bowtie2 and raw counts were obtained using HTSeq
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count values for each group
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HEK293T cells

growth_protocol: stably transfected HEK293T cells were expanded in DMEM/FCS

extract_protocol:
genomic DNAChromatin was extracted according to the GenXPro protocol
ATAC-Seq libraries were produced using Nextera Transposase from freshly isolated nuclei, as described by Buenrostro et al 2005 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374986/

treatment_protocol: transgene induction was carried out with 1µg/ml doxyxcycline

tag: transfection

value: empty vector (pSBTet-GP)

value: HEK293T kidney cells

value: transgene was induced for 48h by 1 ug/ml Doxycycline


title: MOCK_BR2

description: Tn5-tagged chromatin


title: Ctrl_PBS_serum_MWCNT_2

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: US11263921_257480912714_S01_GE2_1200_Jun14_2_1.txt

hyb_protocol: Labeled samples were randomly hybridized to Agilent SurePrint G3Human GE 8x60K DNA microarrays, according to the manufacturer’s protocol (Agilent).

scan_protocol: Hybridized slides were scanned using the Agilent microarray scanner (Model G2505C) and raw data were extracted using Agilent feature extraction software (version 12.0.1.1).

data_processing: mRNA expression raw intensity values were quality checked and exported from Agilent Feature Extraction software. The raw intensities were analysed with Bioconductor package Limma. Experiment was two-colour, but the data were analysed as a single-channel arrays.

label_protocol: RNA samples were labeled with Cy3 or Cy5 (Quick Amp Gene Expression Labelling kit, Agilent).

growth_protocol: Female C57BL/6 mice (7−8 weeks old) were purchased from Scanbur A/S (Karslunde, Denmark). They were housed in stainless steel cages with aspen chip bedding, in groups of four. The housing conditions were carefully controlled with temperature (20−21 °C) and humidity (40−45%) and 12 h dark/light cycles. Mice received food and water ad libitum.

extract_protocol: After sacrificing the lungs were removed, cut and transferred to RNALater stabilizing solution (Ambion, Life Technologies, CA, USA), and stored at −80 °C. Total RNA (totRNA) from the RNAlater-stabilized lung samples was isolated and purified by phenol/chloroform isolation method according to the instructions by Bioline Reagents.

treatment_protocol: Mice were exposed by oropharyngeal aspiration under isoflurane anesthesia to 10 μg of ENM per day in (50 μL) PBS for 4 consecutive days, mimicking a 1-week exposure scenario. Control mice received a corresponding vehicle, either plain  PBS or PBS supplemented with polyvinylpyrroline (Nanodiamnods NH control) or albumin (MWCNT control). BAL and tissue samples were collected 24 hours after the final exposure.

value: lung

value: 8 w/o

value: female

tag: exposure time

value: 4 days + 24 hours

tag: slide #

tag: functionalization

tag: nanomaterial

value: CTRL


title: CuO_PEG_1

description: US11263921_257480912714_S01_GE2_1200_Jun14_2_4.txt

tag: tissue

value: PEG

value: CuO


title: H27640  98d N F

tag: Sex

value: Normal


title: B35 dorsal skin

source_name: dorsal skin

value: skin


title: Ag_COOH_1

description: US11263921_257480912714_S01_GE2_1200_Jun14_2_3.txt

value: COOH

value: Ag


title: Ctrl_PBS_Au_5_2

description: US11263921_257480912714_S01_GE2_1200_Jun14_2_2.txt


title: MOCK_BR1

description: Tn5-tagged chromatin


title: H27810  94d N F

value: F


title: MLL_minus_AF6_BR3

description: Tn5-tagged chromatin


title: Ctrl_PBS_TiO-rod_3

description: US11263921_257480912714_S01_GE2_1200_Jun14_1_2.txt


title: KO_4_DA_3_1

value: bone

value: DA

tag: genotype

value: DRD5 KO

value: 10 weeks


title: H27632 89d N F


title: H27636  80d N M

value: M


title: MLL_minus_AF6_BR2

description: Tn5-tagged chromatin

value: HEK293T kidney cells

value: transgene was induced for 48h by 1 ug/ml Doxycycline


title: WT_4_1_1

tag: strain

value: no DA

value: M2 macrophages

value: wt


title: KO_4_DA_2_1

tag: age


title: CuO_PEG_3

description: US11263921_257480912704_S01_GE2_1200_Jun14_2_4.txt

value: lung

value: 8 w/o

value: female

value: 4 days + 24 hours

value: PEG


title: CuO_NH3_3

description: US11263921_257480912704_S01_GE2_1200_Jun14_2_3.txt

value: NH

value: CuO


title: WT_4_2_1

value: bone


title: Ctrl_PBS_CuO_3

description: US11263921_257480912704_S01_GE2_1200_Jun14_2_2.txt

value: CTRL


title: KO_4_DA_1_1

value: DA

value: DRD5 KO


title: H27482  136d T21 M

value: M


title: exMLL_minus_AF6_BR2

description: Tn5-tagged chromatin

value: HEK293T kidney cells


title: exMLL_minus_AF6_BR3

description: Tn5-tagged chromatin

value: transgene was induced for 48h by 1 ug/ml Doxycycline


title: KO_4_3_1

value: no DA

value: 10 weeks


title: Ag_PEG_3

description: US11263921_257480912714_S01_GE2_1200_Jun14_1_3.txt

value: Ag


title: H27914 137d T21 M


title: ABR 5747 19 Wks T21 M


title: Ctrl_PBS_TiO-rod_1

description: US11263921_257480912704_S01_GE2_1200_Jun14_2_1.txt

value: lung


title: KO_4_1_1

value: M2 macrophages


title: exMLL_minus_AF6_BR1

description: Tn5-tagged chromatin


title: ABR 5566 19 Wks T21 M


title: MLL_minus_AF6_BR1

description: Tn5-tagged chromatin


title: H27766  132d T21 M


title: D5_M1_3_1

value: M1 macrophages


title: KO_4_2_1


title: Au_5_COOH_1

description: US11263921_257480912704_S01_GE2_1200_Jun14_1_3.txt

value: 8 w/o

value: female

value: 4 days + 24 hours

value: COOH


title: Co2_BR3

description: Tn5-tagged chromatin

value: exMLL-AF6 & AF6-shMLL


title: TiO_COOH_prtcl_3

description: US11263921_257480912704_S01_GE2_1200_Jun14_1_1.txt

value: TiO


title: ND_COOH_2

description: US11263921_257480912704_S01_GE2_1200_Jun14_1_4.txt

value: ND


title: D5_M1_2_1

value: bone

value: DRD5 KO


title: Co2_BR2

description: Tn5-tagged chromatin

value: HEK293T kidney cells


title: 1033 18.1 Wks T21 M

value: M


title: Co2_BR1

description: Tn5-tagged chromatin

value: transgene was induced for 48h by 1 ug/ml Doxycycline


title: 185 18.0 Wks T21 F

value: F


title: TiO_PEG_prtcl_2

description: US11263921_257480912704_S01_GE2_1200_Jun14_1_2.txt

value: PEG


title: D5_M1DA_3_1

value: DA

value: 10 weeks


title: Au_5_PEG_3

description: US11263921_257480912703_S01_GE2_1200_Jun14_2_4.txt

value: lung


title: 3237 17.6 Wks T21 F


title: Co1_BR2

description: Tn5-tagged chromatin

value: MLL-AF6 & AF6-MLL


title: Ag_COOH_3

description: US11263921_257480912714_S01_GE2_1200_Jun14_1_1.txt

value: 8 w/o

value: female

value: Ag


title: Co1_BR1

description: Tn5-tagged chromatin


title: 1865 17.1 Wks T21 F


title: AF6_minus_shMLL_BR3

description: Tn5-tagged chromatin


title: 2246 17.0 Wks T21 F


title: TiO_COOH_rod_2

description: US11263921_257480912703_S01_GE2_1200_Jun14_2_2.txt

value: 4 days + 24 hours

value: COOH


title: DK13-2: DLD1 KMT2A KO-2 rep2 RNAseq

city: Clayton

first: Ron

last: Firestein

state: VIC

address: 21 Wright street

department: CCR

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Basecalling using BGI
Alignment using STAR 2.5.2
Using Featurecounts function (Subread 1.6.3) to generate counts file based on Gencode v90 annotation
Genome_build: hg38
Supplementary_files_format_and_content: Gene level counts

source_name: Colon carcinoma

growth_protocol: Cells were cultured as adherent monolayers in Dulbecco’s Modified Eagle’s Medium (DMEM) (Sigma-Aldrich #D5796) supplemented with 10% (v/v) fetal bovine serum (Bovogen #SFBS-AU), 2mM L-glutamine (Life technologies #25030081), 100 units/mL penicillin and 0.1% (w/v) streptomycin (Life technologies #15140122) (complete DMEM, C-DMEM). Cells were grown at 37°C in a 5% CO2 humidified incubator, and passaged every 2-3 days (30-80% confluency).

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen,#74106) following manufacturer’s instructions.
100bp Paired end

tag: cell line

value: DLD1 colorectal cancer cell line

tag: crispr knockout

value: KMT2A knockout

tag: sgrna sequence

value: TCAGAGTGCGAAGTCCCACA


title: Ctrl_PBS_Au_20_2

description: US11263921_257480912703_S01_GE2_1200_Jun14_2_3.txt

value: CTRL


title: D5_M1_1_1

value: bone

value: no DA

tag: cell type

value: M1 macrophages

value: DRD5 KO


title: MWCNT_COOH_3

description: US11263921_257480912703_S01_GE2_1200_Jun14_2_1.txt

value: CdTE


title: AF6_minus_shMLL_BR2

description: Tn5-tagged chromatin

value: HEK293T kidney cells

value: transgene was induced for 48h by 1 ug/ml Doxycycline


title: 3076 16.3 WKs T21 F

tag: gestational age (in weeks)

value: F

tag: disease


title: TiO_PEG_rod_2

description: US11263921_257480912703_S01_GE2_1200_Jun14_1_1.txt

value: lung

value: 8 w/o

tag: gender

value: PEG

value: TiO


title: Ctrl_PBS_PVP_ND_3

description: US11263921_257480912703_S01_GE2_1200_Jun14_1_2.txt

value: female

value: 4 days + 24 hours


title: Co1_BR3

description: Tn5-tagged chromatin

tag: transfection

value: MLL-AF6 & AF6-MLL

tag: treatment


title: H26056 115d T21 F


title: AF6_minus_shMLL_BR1

description: Tn5-tagged chromatin


title: AF6_minus_MLL_BR3

description: Tn5-tagged chromatin


title: D5_M1DA_1_1

value: DA

value: 10 weeks


title: DK13-1: DLD1 KMT2A KO-2 rep1 RNAseq

value: DLD1 colorectal cancer cell line

value: KMT2A knockout

value: TCAGAGTGCGAAGTCCCACA


title: DK1-3: DLD1 KMT2A KO-1 rep3 RNAseq

value: TACCTGCAGAAGCAAGCTAA


title: Ctrl_PBS_TiO-prtcl_2

description: US11263921_257480912714_S01_GE2_1200_Jun14_1_4.txt

tag: exposure time

tag: slide #

value: CTRL


title: H27836 125d T21 M

value: M


title: DK1-2: DLD1 KMT2A KO-1 rep2 RNAseq


title: AF6_minus_MLL_BR2

description: Tn5-tagged chromatin

value: HEK293T kidney cells

value: transgene was induced for 48h by 1 ug/ml Doxycycline


title: TiO_NH_rod_1

description: US11263921_257480912647_S01_GE2_1200_Jun14_2_3.txt

value: lung

tag: functionalization

value: NH

tag: nanomaterial


title: DK1-1: DLD1 KMT2A KO-1 rep1 RNAseq


title: H27892 98d T21 F

tag: Sex

value: F


title: AF6_minus_MLL_BR1

description: Tn5-tagged chromatin


title: MWCNT_prist_3

description: US11263921_257480912647_S01_GE2_1200_Jun14_2_2.txt

tag: tissue

value: 8 w/o

value: core

value: MWCNT


title: TiO_COOH_prtcl_1

description: US11263921_257480912647_S01_GE2_1200_Jun14_2_1.txt

value: female

tag: strain

value: 4 days + 24 hours

value: COOH

value: TiO


title: TiO_NH_prtcl_2

description: US11263921_257480912647_S01_GE2_1200_Jun14_2_4.txt

tag: age


title: DN-3: DLD1 NTC rep3 RNAseq

tag: cell line

value: DLD1 colorectal cancer cell line

value: control

value: ACAACTTTACCGACCGCGCC


title: DK13-3: DLD1 KMT2A KO-2 rep3 RNAseq

tag: crispr knockout

value: KMT2A knockout

value: TCAGAGTGCGAAGTCCCACA


title: 1560 15.4 Wks T21 M

value: M


title: H26146 97d T21 F


title: 1924 16.2 Wks T21 M


title: H26073  89d T21 F


title: D5_M1DA_2_1

value: bone

value: DA

value: M1 macrophages

tag: genotype

value: DRD5 KO

value: 10 weeks


title: MF+AC_6

city: Frankfurt

first: Tobias

last: Schmid

address: Theodor-Stern-Kai 7

department: Institute of Biochemistry I

institute: Goethe University Frankfurt

data_processing:
raw data were processed using the blue-bee pipeline (https://lexogen.bluebee.com/quantseq/)
[Trimming]  bbduk v35.92
[Alignment]  STAR Aligner with modified ENCODE settings
[Gene Read Counting]  HTSeq-count with kit-specic options (FWD)
[Differential Analysis]  DESeq2 Pipeline
Genome_build: Homo sapiens (GRCh38)
Supplementary_files_format_and_content: text files containing the normalized read counts for MF and MF+AC

source_name: peripheral blood

growth_protocol: CD14+ monocytes isolated from human buffy coats and differentiated into macrophages in macrophage serum-free medium supplemented with 100 U/mL penicillin, 100 μg/mL streptomycin, and 50 ng/mL of macrophage colony-stimulating factor (M-CSF)  for 7 days followed by culture in RPMI 1640 medium supplemented with 10% heat-inactivated FCS, 100 U/mL penicillin, and 100 μg/mL streptomycin

extract_protocol:
Total RNA of non-treated and efferocytotic macrophages was isolated using RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol
Libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD from Illumina (Lexogen)

treatment_protocol: Human macrophages were stimulated with apoptotic Jurkat cells at a 1:3 ratio in 6-well plates for 3 hours. Upon efferocytosis, non-phagocytosed cells were removed and macrophages were washed 3x with PBS, followed by incubation with RPMI 1640 supplemented with 10% heat-inactivated FCS, 100 U/mL penicillin, and 100 μg/mL streptomycin for 3 hours.

tag: cell type

value: macrophages derived from CD14+ monocytes

value: co-cultured with apoptotic Jurkat T cells


title: DN-2: DLD1 NTC rep2 RNAseq

tag: sgrna sequence


title: MF+AC_5


title: DN-1: DLD1 NTC rep1 RNAseq


title: MF+AC_4


title: MF+AC_3


title: H27759 80d T21 M

tag: gestational age (in weeks)

tag: disease


title: MF+AC_2


title: MF+AC_1


title: MF_6

value: untreated


title: Ctrl_PBS_Ag_1

description: US11263921_257480912647_S01_GE2_1200_Jun14_1_2.txt

value: lung

value: 8 w/o

tag: gender

value: female

value: 4 days + 24 hours

value: CTRL


title: Ctrl_PBS_CdTe_3

description: US11263921_257480912647_S01_GE2_1200_Jun14_1_4.txt


title: Au_5_COOH_3

description: US11263921_257480912647_S01_GE2_1200_Jun14_1_1.txt

value: COOH


title: CuO_core_2

description: US11263921_257480912647_S01_GE2_1200_Jun14_1_3.txt

value: core

value: CuO


title: U2OS Control Replicate 1

city: Menlo Park

first: Stephen

last: Shang

state: California

address: 297 Jane Stanford Way

institute: Stanford University

description: H3K9me3 ChIPseq

data_processing:
Library strategy: CRISPR-EChO
Alignment: Bowtie2
Duplicate Removal: samtools
Bigwig Generation: bedtools, bamCoverage
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files *.bw contain indexed binary files

source_name: U2OS Cells with CRISPR-ECHO

growth_protocol: Cells were grown with DMEM and split at 90% confluency.

extract_protocol:
Cell Lysis was performed as per standard ChIP protocol.  DNA was extracted via bead elution with Dynabeads Protein A.
Libraries were constructed as per standard ChIPseq library kit preparation with Novogene.

treatment_protocol: Cells were treated 1 day after splitting with ABA or DMSO in fresh DMSO media and, after reaching 80% confluency, subject to a standard ChIP protocol of 1% crosslinking followed by lysis, sonication, and pulldown with H3K9me3 antibodies.  Full protocol: Roughly 4 × 107 cells per sample were washed with PBS before addition of 1% formaldehyde in fresh media for crosslinking. After 15 minutes, the samples were quenched with glycine to a final concentration of 0.125 mol/L glycine. Cells were then lifted with a cell scraper, spun down, and resuspended in SDS lysis buffer (1% SDS, 10 mmol/L EDTA, 50 mmol/L Tris-HCl, pH 8.1) at a ratio of 1 mL per 2 × 107 cells and frozen at -80 before lysis at room temperature for 1h immediately before sonication. Pulse sonications were performed for 7 minutes at 40% amplitude with 1s on/1 s off on a Qsonica Q500 in 1mL aliquots in 1.5mL Eppendorf tubes with a total of 2 mL with maximum 50% SDS Lysis Buffer solution diluted with ChIP Dilution Buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mmol/L EDTA, 16.7 mmol/L Tris-HCl, pH 8.1, 167 mmol/L NaCl). ChIPs were performed with antibodies for H3K9me3 (Abcam, ab8898). Pulldowns were performed with Dynabeads Protein A (10001D, Lot 00531421). DNA quantities were measured by Qubit 2.0 (Invitrogen Qubit dsDNA HS Assay Kit, Q32854) and Bioanalyzer before sequencing with Novogene targeting 20M reads / sample.

value: Tumor Cell Line

tag: treatment

value: DMSO-treated

tag: chip antibody


title: U2OS ABA treated Replicate 3

description: H3K9me3 ChIPseq

value: ABA-treated


title: U2OS Control Replicate 3

description: H3K9me3 ChIPseq


title: U2OS Control Replicate 2

description: H3K9me3 ChIPseq


title: TiO_core_prtcl_3

description: US11263921_257480912646_S01_GE2_1200_Jun14_2_2.txt

tag: exposure time

tag: slide #

value: TiO


title: MF_5


title: MF_4


title: MF_3


title: U2OS ABA treated Replicate 1

description: H3K9me3 ChIPseq


title: MF_2


title: H1650 9291_rep 3

city: Aurora

first: Natalia

middle: J

last: Gurule

state: CO

department: Craniofacial Biology

institute: University of Colorado Anschutz Medical Campus

description:
PC9 and H1650 cells were suspended in 50% Matrigel/phosphate-buffered saline at 10 million cells per mL and 1 million cells were injected subcutaneously in both flanks of female nu/nu mice. When at least one of the tumors reached a volume of 100 mm3, the mice were randomized into treatment groups of diluent control (1% Polysorbate 80), AZD9291 (5 mg/kg). Drugs were delivered daily by oral gavage.
invivoH1650_ PC9 _AZD9291 _genes.fpkm_table.xlsx
H1650 in vivo

data_processing:
raw fastq files were processed with HISAT2
 Reads were mapped UCSC reference annotation GRCh37(hg19)
Transcripts were assembled against ensemble reference using Cufflinks.
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel file containing FPKMs

source_name: flank xenograft

extract_protocol:
total RNA was purified from cells using Quick-RNA MiniPrep kits (Zymo Research)
Illumina directional mRNA prep
per Novogene protocol for PE150 Illumina NGS

value: lung cancer cell line

value: osimertinib


title: CuO_NH3_1

description: US11263921_257480912646_S01_GE2_1200_Jun14_2_4.txt

tag: functionalization

value: NH

tag: nanomaterial


title: H1650 9291_rep 1

tag: tissue


title: Au_5_PEG_1

description: US11263921_257480912646_S01_GE2_1200_Jun14_1_4.txt

tag: strain

value: PEG


title: MF_1

value: macrophages derived from CD14+ monocytes

value: untreated


title: TiO_NH_rod_3

description: US11263921_257480912646_S01_GE2_1200_Jun14_1_2.txt

value: lung

tag: age

value: 8 w/o