title: iPSC-CM Differentiation, Patient, Day 16

city: Irvine

first: Michael

middle: V.

last: Zaragoza

address: 2042 Hewitt Hall

department: Pediatrics and Biological Chemistry

institute: UC Irvine School of Medicine

data_processing:
Illumina paired-end sequencing was conducted for 28 cycles for Read 1 (cell barcode + UMI tag), 8 cycles for sample index, and 100 cycles for Read 2 (cDNA insert). Multiplex sequencing was done using NovaSeq 6000 with the goal of obtaining at least 50,000 raw reads per cell. Using Illumina bcl2fastq2 software, raw data files (BCL) were processed for index reads, demultiplexed data into sample specific FASTQ files for Read 1 (R1), Read 2 (R2), and sample index (I1).
Cell Ranger v3.0.2 (10x Genomics) was used for read processing and mapping, transcript and cell quantification, and generation of summary metrics. Using the ‘cellranger count’ pipeline, we processed FASTQ files of each sample to identify high-quality reads with valid cell barcodes and UMIs and mapped these reads to human reference genome. Using the number of confidently mapped reads to the transcriptome in each cell, we quantified transcripts to generate a gene-barcode matrix defined by matrix.mtx, barcode.tsv, and features.tsv files for each sample. We used both raw unfiltered gene-barcode matrix (raw_feature_bc_matrix) and filtered gene-barcode matrix (filtered_feature_bc_matrix) in our analysis.
Assembly: Cell Ranger GRCh38-3.0.0
Supplementary files format and content: For each sample, processed data files consists of six total Cell Ranger output files = barcodes.tsv, features.tsv, and matrix.mtx files for filtered_feature_bc_matrix and raw_feature_bc_matrix.

source_name: iPSC-CM Differentiation

extract_protocol:
Cell samples were processed immediately after collection at the UCI Genomics High-Throughput Facility. Sample processing used the droplet-based 10x Chromium system and Chromium Next GEM Single Cell 3ʹ Kit v3 (10X Genomics, Pleasanton, CA).
Sample processing used the 10x Chromium Single Cell 3’ Gene Expression reagent kits v3 with i7 sample index.

value: iPSC-CM Differentiation

value: PA1 iPSC

value: PA1 D16 cells for scRNA-seq


title: iPSC-CM Differentiation, Control, Day 19

status: Public on Sep 03 2024

type: SRA

state: CA

country: USA

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

value: CA1-B iPSC

tag: cell type

value: CA1 D19 cells for scRNA-seq


title: iPSC-CM Differentiation, Control, Day 30

value: CA1-A iPSC

value: CA1 D30 cells for scRNA-seq


title: iPSC-CM Differentiation, Patient, Day 9B

value: PA1 D09B cells for scRNA-seq


title: iPSC-CM Differentiation, Patient, Day 0

value: PA1 D00 cells for scRNA-seq


title: iPSC-CM Differentiation, Control, Day 16

value: CA1 D16 cells for scRNA-seq


title: Pol2-NTD.RS8.WT.rep2

city: Shanghai

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

country: China

institute: Institutes of Biomedical Sciences Fudan University

description:
Pol2-NTD.RS8.WT.ext150.bigWig
Pol2-NTD_RS8_WT_peaks.bed

library_source: genomic

data_processing:
Raw ChIP-seq data were firstly preprocessed to eliminate adapter contamination and low-quality sequences using trim_galore (version: 0.6.6). Trimmed reads shorter than 30 bases were discarded.After trimming, the ChIP-seq data was aligned to the mouse genome build mm10 using bowtie2 (version: 2.4.1) with default parameters. The aligned reads were stored in sam files and then converted to bam files using 'samtools sort'. Duplicates were subsequently removed from the bam files using 'samtools rmdup'.
Uniquely mapped reads were extended to 150 bp using awk command, based on the average length of sonicated chromatin DNA fragments.
The uniquely mapped reads with 150bp extension were converted into base-resolution coverage data in bedGraph format using 'bedtools genomecov'. The resulting bedGraph files were then used to normalize the data based on spike-in reads. After normalization, the bedGraph files were converted to bigWig files using a public UCSC script. These bigWig files are suitable for use in downstream analysis and visualization.
These normalized bedGraph files were uploaded to UCSC genome browser for visualization.
Uniquely mapped reads with 150bp extension in bed format were also used to call peaks by comparing to Input using macs14 (version: 1.4.2) or macs2 (version: 2.2.7.1) with default parameters.
Assembly: mm10
Supplementary files format and content: bigWig, genome coverage signals.
Supplementary files format and content: bed, peaks

molecule: genomic DNA

organism: Mus musculus

source_name: Homogenous synchronous spermatogenic cells

growth_protocol: Briefly, 2-dpp mice were pipette fed 100 μg/g body weight WIN 18,446 (MP), suspended in 1% gum tragacanth, for 7 consecutive days. At Day 8 of WIN 18,446 treatments, these animals were received an i.p. injection of RA (Sigma; 30 μg/g body weight) in dimethyl sulfoxide (DMSO), and were then left to recover for sample collections. The undifferentiated spermatogonia was isolated from Lin28-YFP knockin mice. Testes from 3-week-old Lin28-YFP knockin mice were collected and digested by type I collagenase and 0.25% Trypsin as described previously1. After centrifugation, the pellet was resuspended in DMEM containing 2% BSA at a concentration of 1×106 cells/40 μL, followed by incubating with PE-conjugated anti-CD117 antibody (0.1 μg/106 cells; Molecular probes) for 30 min on ice. The undifferentiated spermatogonia (YFP-positive, PE-negative population) was collected using FACS (BD). The type A1 spermatogonia was isolated from synchronous Stra8-GFPCre mice. Testes were collected and digested. The type A1 spermatogonia (GFP-positive population) was collected using FACS. The type B spermatogonia and different stages of spermatocytes were isolated from synchronous Lin28-YFP and Vasa-tdTomato double positive mice. To isolate the type B spermatogonia, testes were digested and the synchronous advanced spermatogenic cells (tdTomato positive population) were collected using FACS. To isolate different stages of spermatocytes, testes were digested and the cell suspensions were stained with Hoechst 33342. The tdTomato positive 4N population were collected using FACS. The identity of sorted spermatocytes were validated using surface spreading and immunofluorescence.

extract_protocol:
genomic DNA
ChIP assay was carried out as previously described. The sorted homogenous synchronous spermatogenic cells were crosslinked with 1% formaldehyde for 10 mins and then stopped by adding 125 mM Glycine. Chromatin samples were lysed with lysis buffer (20 mM Tris-HCl pH8.0, 500 mM NaCl, 1 mM EDTA, 1% TritonX-100 and 0.1% SDS) and sonicated with Qsonica. Histone modification specific antibody was incubated with chromatin samples overnight at 4 ℃.0.5 ug spike-in antibody (Active motif #61686) and 25 ng spike-in chromatin (Active motif #53083) were used in this ChIP assay according to the manufacture’s guidelines.DNA samples were analyzed using real time PCR and prepared for deep sequencing according to the manufacture’s guidelines (KAPA Biosystems KK8503 and VAHTS Universal DNA Library Prep Kit for Illumina V3 ND607). Finally, libraries were pooled and sequenced on the Illumina HiSeq 2500 sequencer for 150-bp paired-end sequencing.

treatment_protocol: Spermatogenesis was synchronized and validated as previously described.

tag: strain

tag: developmental stage

tag: genotype

value: Wild type

tag: chip antibody

value: Rpb1 NTD (D8L4Y) Rabbit mAb#14958


title: Pol2-NTD.RS4.Setd1bKO.rep2

description:
Pol2-NTD.RS4.Setd1bKO.ext150.bigWig
Pol2-NTD_RS4_Setd1bKO_peaks.bed

value: Homogenous synchronous spermatogenic cells

value: Setd1b KO


title: Lobaria pulmonaria thallus, 11th day of experiment, replicate 3

city: Kazan

first: Ilya

last: Leksin

address: 2 Lobachevsky str.

country: Russia

institute: Federal Research Center Kazan Scientific Center of Russian Academy of Sciences

library_source: transcriptomic

data_processing:
The quality of the fastq files was checked using FastQC v. 0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapters, low quality, and short reads were removed using the Trimmomatic v 0.39 tool with the custom parameter set «SE MINLEN:40 LEADING:3 TRAILING:3».
Genome sequences and annotations hosted in the Mycocosm database (https://mycocosm.jgi.doe.gov/Lobpul1/Lobpul1.home.html) for mycobiont and Phycocosm for photobiont (https://phycocosm.jgi.doe.gov/Dicre1/Dicre1.home.html) were used for reads mapping and DEGs annotation. The GFF3 genome annotation file was converted to GTF format using gffread for exons «hisat2_extract_exons.py» and splicing sites extraction by Python scripts «hisat2_extract_splice_sites.py». We generated an index needed to map quality-filtered reads by the HISAT2 program using reference genomes of Lobaria pulmonaria and Symbiochloris reticulate, and files containing exons and splicing-sites information with the additional parameters (‐‐rna-strandness R, --ss, --exon).
Reads aligned to individual genes were counted using htseq-count v. 0.5.4
Genes with counts fewer than 10 per sample in at least seven samples were removed from our study. The R package edgeR was applied to determine DEGs using normalization by the TMM method. Genes were considered differentially expressed with an adjusted Benjamini–Hochberg p-value (FDR) < 0.05 and log2FC > |1|.
Assembly: Lobaria pulmonaria Scotland reference genome v1.0
Assembly: Symbiochloris reticulata Spain reference genome v1.0
Supplementary files format and content: File in csv format with the raw counts data matrix of mycobiont.
Supplementary files format and content: File in csv format with the raw counts data matrix of photobiont.

molecule: polyA RNA

organism: Lobaria pulmonaria

source_name: Lobaria pulmonaria thallus, ultraviolet B dose 158.4 kJ/m2

growth_protocol: The lichen Lobaria pulmonaria was collected from trunks of aspens (Populus tremuloides) in woodlands on the outskirts of Syktyvkar, Komi Republic, Russia (latitude 61о34' N, longitude 50о33' E). Thalli were air dried at room temperature between sheets of filter paper. Dried material was stored at -20 °C until use. The thalli were hydrated by placing them on wet filter paper and then transferred to a climate chamber (Binder KBWF-720, Germany) with the following conditions: temperature +15 °C, relative humidity (RH) 40% and 12/12 h (light/dark) photosynthetically active radiation (PAR) 80 μmol quanta m-2 s-1, corresponding to typical conditions in forest habitats during spring and summer seasons. The samples were constantly maintained in a hydrated, functionally active state throughout the experiment. The thalli were at room temperature during UV-B exposure.

extract_protocol:
Samples for RNA extraction were collected after the UV treatment of lichen thalli, immediately fixed in liquid nitrogen and stored at -80 °C until further use. Extraction of RNA was performed using the RNeasy Plant Mini Kit (QIAGEN) with an on-column DNase digestion step (DNase 1, QIAGEN) according to the manufacturer’s protocol. The quality of the extracted RNA was assessed using a Bioanalyzer 2100 (Agilent Technologies, USA). RNA concentrations were measured using a NanoDrop–1000 (Thermo Scientific, USA) and a Qubit fluorimeter (Life Technologies, Carlsbad, USA) with the RNA HS assay kit (QIAGEN).
The NEBNext® Poly(A)+ mRNA isolation module (NEB, USA) with magnetic particles was used to isolate the mRNA fraction from 1 μg total RNA. cDNA libraries were prepared using a NEBNext® Ultra™ II Directional Kit (NEB, USA). PCR enrichment was carried out as follows: 98 °C for 30 s for initial denaturation followed by eight cycles of 98 °C for 10 s and 65 °C for 75 s with a final elongation 65 °C for 4 min. The quality of cDNA libraries was monitored using a Bioanalyzer 2100 (Agilent Technologies, USA) and a Qubit fluorimeter (Life Technologies, Carlsbad, USA) with the DNA HS assay kit (QIAGEN). Sequencing of cDNA libraries was carried out on the HiSeq 2500 platform using a HiSeq SR Cluster Kit v4 cBot and a HiSeq SBS Kit V4 50 cycle kit with 50-bp single-ended reads.

treatment_protocol: The thalli from the experimental group were irradiated with UV-B fluorescent erythema lamps (3 W/m2) for 80 min daily for 14 days. The thalli received a daily UV dose of 14.4 kJ/m2, a 3-fold increase of the dose they would receive in natural forest habitats and equivalent to the UV dose in the middle taiga subzone during the summer months under clear weather conditions.

value: thallus

tag: condition

value: ultraviolet B dose 158.4 kJ/m2

tag: time

value: day 11


title: Lobaria pulmonaria thallus, 2nd day of experiment, replicate 3

source_name: Lobaria pulmonaria thallus, ultraviolet B dose 28.8 kJ/m2

value: ultraviolet B dose 28.8 kJ/m2

value: day 2


title: Lobaria pulmonaria thallus, 11th day of experiment, replicate 1


title: iPSC-CM Differentiation, Control, Day 9A

value: iPSC-CM Differentiation

value: CA1 D09A cells for scRNA-seq


title: Lobaria pulmonaria thallus, 7th day of experiment, replicate 1

source_name: Lobaria pulmonaria thallus, ultraviolet B dose 100.8 kJ/m2

value: ultraviolet B dose 100.8 kJ/m2

value: day 7


title: iPSC-CM Differentiation, Control, Day 2

value: CA1-A iPSC

value: CA1 D02 cells for scRNA-seq


title: Pol2-NTD.RS4.WT.rep2

description:
Pol2-NTD.RS4.WT.ext150.bigWig
Pol2-NTD_RS4_WT_peaks.bed


title: Pol2-NTD.RS8.WT.rep1


title: Lobaria pulmonaria thallus, 7th day of experiment, replicate 2


title: Lobaria pulmonaria thallus, 11th day of experiment, replicate 2


title: iPSC-CM Differentiation, Control, Day 9B

value: CA1-B iPSC

value: CA1 D09B cells for scRNA-seq


title: Lobaria pulmonaria thallus, 2nd day of experiment, replicate 2


title: iPSC-CM Differentiation, Control, Day 0

value: CA1 D00 cells for scRNA-seq


title: iPSC-CM Differentiation, Control, Day 4

value: CA1 D04 cells for scRNA-seq


title: Pol2-NTD.RS4.Setd1bKO.rep1

value: Homogenous synchronous spermatogenic cells

value: Rpb1 NTD (D8L4Y) Rabbit mAb#14958


title: iPSC-CM Differentiation, Patient, Day 19

value: PA1 iPSC

value: PA1 D19 cells for scRNA-seq


title: Pol2-NTD.LS10.WT.rep1

description:
Pol2-NTD.LS10.WT.ext150.bigWig
Pol2-NTD_LS10_WT_peaks.bed

value: Wild type


title: Pol2-NTD.RS4.WT.rep1


title: Lobaria pulmonaria thallus, UV-untreated, replicate 2

source_name: Lobaria pulmonaria thallus, ultraviolet B dose 0 kJ/m2

value: thallus

value: ultraviolet B dose 0 kJ/m2 (control)

value: day 0


title: Lobaria pulmonaria thallus, UV-untreated, replicate 3


title: Lobaria pulmonaria thallus, UV-untreated, replicate 1


title: Pol2-NTD.Unsynchronized_RS.Setd1bKO.rep2

description:
Pol2-NTD.Unsynchronized_RS.Setd1bKO.merged.ext150.bigWig
Pol2-NTD_Unsynchronized_RS_Setd1bKO_peaks.bed

source_name: Unsynchronous spermatogenic cells

value: RS

value: Unsynchronous spermatogenic cells

value: Setd1b KO


title: Control-2

city: Mueang Khon Kaen

first: Todsapol

last: Techo

state: Khon Kaen

department: Biology

country: Thailand

institute: Khon Kaen University

data_processing:
Base calling was performed using the HiSeq Control Software (HCS) along with OLB and GAPipeline-1.6 (Illumina)
Cutadapt (version 1.9.1) was used to trim the paired-end raw reads, removing adapters, PCR primers, and low-quality bases (Q score <20)
Bowtie2 (v2.2.6) was used to align the clean data to the assembled genome of the E324 strain (GCF_026226235.1)
HTSeq (v0.6.1p1) was employed to estimate gene expression levels.
Assembly: The assembled genome of the E324 strain (GCF_026226235.1)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample with gene annotations

organism: Cupriavidus nantongensis

source_name: Log-phase cells

growth_protocol: The E324 cells were cultivated and maintained in nutrient broth (NB) media at 30 °C with shaking at 200 rpm.

extract_protocol:
The total RNA of each sample was extracted using RiboPure RNA Purification Kit (Thermo Fisher 168 Scientific).
The library was constructed using NEBNext Ultra™ RNA Library Prep Kit for Illumina (New England BioLabs Inc.).

treatment_protocol: Log-phase E324 cells were inoculated into nutrient broth (NB) media in the presence and absence of  4 mM CdCl2 (IC90) with an initial OD600 of 0.1, and incubated at 30 °C with shaking at 200 rpm. After 2 h of incubation (2 doubling times), the cells from three biological replicates were harvested by centrifugation.

value: Log-phase cells

value: WT

tag: treatment

value: Control


title: HEp-2 cells; RSV-infected; polysomal RNA; biological replicate 3

city: Toronto

first: Kyra

last: Kerkhofs

state: ON

address: 4700 Keele Street

country: Canada

institute: York University

description: polysomal poly(A)-tail enriched RNA

library_source: other

data_processing:
Raw reads in .fastq format were trimmed using Trim Galore v.0.5.0 with Cutadapt v.1.10 (with following parameters: -q 25, --clip_R1 6, --clip_R2 6, --stringency 5, --length 40, --paired).
The raw trimmed reads were aligned to the concatenated GRCh38 GENCODE release 36, and RSV genome (GenBank: KT992094.1) using STAR aligner v.2.6.0c.
Gene expression analysis was done using htseq-count v.0.6.1p2 (mode “intersection_nonempty”) to obtain raw counts.
Assembly: Concatenated GRCh38 GENCODE and RSV genome (GenBank: KT992094.1).
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample.

molecule: other

growth_protocol: HEp-2 cells were grown in high glucose DMEM containing 10% FBS.

extract_protocol:
Next, polysome profiling was performed. In brief, 100 μg/mL cycloheximide was added to the cells for 5 minutes at 37°C prior to collection. The cells were washed twice in PBS containing 100 μg/mL cycloheximide. The cell pellets were stored at -80°C until use. Next, the cell pellets were lysed in 485 μL hypotonic buffer [5 mM Tris-HCl (pH 7.5), 2.5 mM MgCl2, 1.5 mM KCl, 1X Halt™ Protease Inhibitor Cocktail, 100 μg/mL cycloheximide, 2 mM DTT, 200 Units/mL SUPERase In™ RNase Inhibitor, 0.5% (v/v) Triton X-100 and 0.5% (w/v) sodium deoxycholate], followed by centrifugation for 5 minutes at 20,000g at 4°C to obtain cytoplasmic extracts. A fraction of the lysate was taken as the total protein samples. The remaining sample (500 μL of 20 A260 units) was fractionated on a 7-step 20-50% sucrose gradient prepared in sucrose buffer [20 mM HEPES (pH 7.6), 100 mM KCl, 5 mM MgCl2 and 100 μg/mL cycloheximide] by centrifugation at 30,000 RPM for 3 hours in a Beckman SW41Ti rotor at 4°C (acceleration: max., deceleration: no brake). Heavy polysome fractions were collected (800 μL each, fraction numbers 7-11). RNA extraction of polysome fractions was performed by adding 2 parts 100% ethanol containing 80 mM NaOAc, pH 5.1 and 300 μg GlycoBlue overnight at -80°C to precipitate the RNA. RNA pellets were collected by centrifugation at 20,000g for 30 minutes at 4°C, followed a 70% ethanol wash and resuspension in ddH2O. Both polysomal RNA and total RNA were extracted using Trizol according to manufacturer’s instruction.
RNA extracted from total and polysomal RNA was subjected to stranded cDNA library preparation by poly(A) tail selection (poly(A)+) (NEBNext) and paired end 50 bp sequencing using the Illumina NovaSeq 6000 at The Centre for Applied Genomics (TCAG, Hospital for Sick Children).

treatment_protocol: The RSV P3 stock was quickly thawed at 37°C and diluted in FBS-free DMEM to a multiplicity of infection (MOI) of 1. The cells were washed once with PBS, followed by incubation with a small volume of RSV-containing FBS-free DMEM (infection medium) (15 cm plates: 5 mL) and incubated for 2 hours with frequent rocking to redistribute the infection medium evenly. Mock treatment included, PBS wash and 2 hour incubation in infection medium. Following infection, the cells were maintained in DMEM containing 5% (HEp-2) inactivated FBS (30 minutes at 56°C) for 24 hour.

value: RSV-infected (24h)


title: Control-3


title: HEp-2 cells; RSV-infected; polysomal RNA; biological replicate 2

description: polysomal poly(A)-tail enriched RNA


title: Lobaria pulmonaria thallus, 2nd day of experiment, replicate 1

value: ultraviolet B dose 28.8 kJ/m2

value: day 2


title: HEp-2 cells; mock-infected; polysomal RNA; biological replicate 3

description: polysomal poly(A)-tail enriched RNA

value: mock-infected (24h)


title: HEp-2 cells; mock-infected; polysomal RNA; biological replicate 2

description: polysomal poly(A)-tail enriched RNA


title: HEp-2 cells; mock-infected; polysomal RNA; biological replicate 1

description: polysomal poly(A)-tail enriched RNA


title: Pol2-NTD.Unsynchronized_RS.WT.rep1

description:
Pol2-NTD.Unsynchronized_RS.WT.merged.ext150.bigWig
Pol2-NTD_Unsynchronized_RS_WT_peaks.bed

value: Rpb1 NTD (D8L4Y) Rabbit mAb#14958


title: CdCl2-3


title: CdCl2-2


title: iFlpMosaic-YFPN123_WT

city: Madrid

first: Rui

last: Benedito

state: Madrid

address: C. de Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
The demultiplexing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (RbpjLOF and RbpjWt) and v7.1.0 (N123LOF and N123Wt) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
For alignment and quantification of gene expression the reference transcriptome was built using mouse genome GRCm38 and ensembl gene build version 98 (sep2019.archive.ensembl.org). The Cre, PhiYFP, Tomato or WPRE transgenes sequences expressed in the samples were added to the reference
Single cell analysis was based on the Seurat R 50 package. Low quality cells were filtered out using the following criteria: total counts > 1000 and below 55000, genes detected > 500 and < 7500, Mitochondrial transcripts content < 15%, Haemoglobin transcripts < 1% and Ribosomal transcripts < 35%, where doublets were filtered out using the DoubletFinder package. Counts were log-normalized. In order to carry out ratiometric analysis, for the RbpjLOF each dataset was normalized to 10k cells and 8853 for the N123LOF datasets.
Assembly: mm10
Supplementary files format and content: fasta file
Supplementary files format and content: gtf file
Supplementary files format and content: csv expression matrix
Supplementary files format and content: csv metadata

source_name: embryos

extract_protocol:
For RNA-seq analysis, embryos were dissociated using Miltenyi Biotec Tissue Dissociation Kit 2 following the instructions. A volume of 1,2ml of dissociation solution was used per embryo inside a 2ml round bottom tube. Following a 5 minutes incubation in a 37C water bath, tubes were put inside a pre-warmed 50ml falcon and incubated for 25 minutes in the MACSmix Tube Rotor. After cells were resuspended with a Gilson P1000 pipet for 30 times. Starting slow and increasing speed gradually. To the 1.2ml of cells, 3ml of sorting buffer (10% FBS in DPBS -Ca2-Mg2-) was added and this solution transferred to a 5ml syringe. This volume was pressed slowly through a small 70 μm strainer to remove clumps. Each embryo gave around 30 million cells at this stage. Cells suspensions were spinned at 400g for 6 minutes. Pellet was detached and ressuspended in 300μl sorting buffer containing DAPI. DAPI negative, single, and live Tomato+ and YFP+ cells were sorted to Eppendorf tubes containing 300ul of Sorting buffer. 66k Tomato+ and 30k YFP+ cells were sorted using a 100 μm Nozzle, 20 PSI and high purity scale and low flow rate (1) to preserve cell viability and decrease contamination. At the end sorted cells were spinned at 500g for 5min, and resuspended in 30-40μl Cell Capture Buffer (DPBS (-)Ca2+ (-)Mg2+ with 0.04%BSA). After counting cells in Countess III, two independent 10x genomics ports were loaded with either 16k Tomato+ cells (90% vaibility) or 16k YFP+ cells (88% viability).
Single cell suspensions of freshly isolated ECs were resuspended in Cell Capture buffer to a final concentration of 800 to 1600 cells/μl. scRNA-seq libraries were prepared using the Chromium Single Cell 3´ Reagent Kits v3.1 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions.

treatment_protocol:
Notch1/2/3: Embryos were induced with 4OHT at E7.5 and collected at E13.5
Rbpj embryos: Embryos were induced with 4OHT at E9.5 and collected at E13.5

value: embryos

value: CAG-FlpoER2 + iFlpMosaic

tag: age


title: Pol2-NTD.Unsynchronized_RS.WT.rep2

value: Wild type


title: HEp-2 cells; RSV-infected; polysomal RNA; biological replicate 1

description: polysomal poly(A)-tail enriched RNA


title: H3K4me3.RS4.Setd1bKO

description:
H3K4me3.RS4.Setd1bKO.ext150.bigWig
H3K4me3_RS4_Setd1bKO_peaks.bed

value: Homogenous synchronous spermatogenic cells


title: iFlpMosaic-YFPRbpj_WT


title: CdCl2-1


title: HEp-2 cells; RSV-infected; total RNA; biological replicate 3

description: total poly(A)-tail enriched RNA


title: iFlpMosaic-TomatoRbpj_KO


title: Xenograft Human Metastasis Macro Tumor 6

city: New York

first: Elena

last: Piskounova

state: NY

address: 52 East 78th Street, Apt 4A

institute: Weill Cornell Medicine

data_processing:
Trimming to remove low quality and adaptor contamination by Trim Galore v0.6.10
Remove mouse reads using Bbmap v38.90
Non-coding RNA removal using custom reference and STAR v2.7.9a keeping non mapped reads,
Mapping to GRCh38 primary assembly genome using MANE v1.2 annotation file and EndToEnd alignment mode.
gene raw counts generation based on CDS region using featureCounts v 2.0.1  and normalization by DESeq2 packages.
Assembly: GRCh38 primary assembly
Supplementary files format and content: tab delimited file with raw counts for each sample
Supplementary files format and content: tab deleimited file with normalized values for each sample

source_name: Xenograft Liver

extract_protocol:
Tissue was manually homegenized and lysed in 1% TritonX-100 lysis buffer with 100ug/mL cyclohexamide and tigecycline.
TruSeq Stranded Total RNA Library Preparation (rRNA depletion and Stranded RNA-Seq)

value: Xenograft Liver

tag: disease

value: melanoma

value: Metastasis

tag: model

value: PDX metastasis model


title: HEp-2 cells; RSV-infected; total RNA; biological replicate 1

description: total poly(A)-tail enriched RNA


title: Xenograft Human Metastasis Micro Tumor 5


title: HEp-2 cells; RSV-infected; total RNA; biological replicate 2

description: total poly(A)-tail enriched RNA


title: H3K4me3.RS8.WT


title: H3K4me3.RS8.Setd1bKO

value: Setd1b KO


title: H3K27ac.RS4.Setd1bKO

description:
H3K27ac.RS4.Setd1bKO.ext150.bigWig
H3K27ac_RS4_Setd1bKO_peaks.bed

value: H3K27ac (Active Motif 39133)


title: iFlpMosaic-TomatoN123_KO


title: Xenograft Human Metastasis Macro Tumor 5


title: Control-1

value: Log-phase cells

value: WT


title: H3K4me3.RS4_WT

description:
H3K4me3.RS4.WT.ext150.bigWig
H3K4me3_RS4_WT_peaks.bed


title: Xenograft Human Primary Tumor 6

value: Primary Tumor


title: H3K27ac.RS4.WT

description:
H3K27ac.RS4.WT.ext150.bigWig
H3K27ac_RS4_WT_peaks.bed


title: Pol2-NTD.Unsynchronized_RS.Setd1bKO.rep1

value: RS

value: Unsynchronous spermatogenic cells


title: Xenograft Human Metastasis Micro Tumor 6


title: Input.RS4.Setd1bKO


title: HEp-2 cells; mock-infected; total RNA; biological replicate 1

description: total poly(A)-tail enriched RNA

value: mock-infected (24h)


title: Xenograft Human Primary Tumor 5


title: HEp-2 cells; mock-infected; total RNA; biological replicate 2

description: total poly(A)-tail enriched RNA


title: Xenograft Human Metastasis Micro Tumor 4


title: Input.RS8


title: Xenograft Human Metastasis Macro Tumor 4


title: Input.RS4.WT


title: HEp-2 cells; mock-infected; total RNA; biological replicate 3

description: total poly(A)-tail enriched RNA


title: Xenograft Human Metastasis Micro Tumor 3


title: Input.RS2


title: Input.RS4


title: ZIKV 48h (2) [B_60]

city: Gießen

first: Torsten

last: Hain

state: Hessen

address: Schubertstraße 81

department: Institute for Medical Microbiology

country: Germany

institute: Justus-Liebig University

data_processing:
The generated sequence reads were basecalled, and demultiplexed prior to analysis
All sequence reads obtained were filtered by mapping against their respective virus genome (Dengue virus 2 (NC_001474.2); Tick-borne encephalitis virus (NC_001672.1); West Nile virus isolate NY99 (MZ605381.2); Yellow fever virus 17D/Tiantan (FJ654700.1); Zika virus strain PRVABC59 (KU501215.1)), before aligning them to the human genome sequence GRCh38.p14 (RefSeq GCF_000001405.40) using STAR
Aligned sequence reads were sorted by position using samtools
Sequence read counts per gene or transcript were calculated for each library using the subread function featureCounts
Differential gene expression analyses were performed with the R-package DESeq2. Data were normalized per regularized log transformation and shrunk using the adaptive shrinkage estimator for the ashr package. Genes were considered differentially expressed when the adjusted p-value was below 0.05 and the log2 fold change was above 1 or below −1.
Assembly: GRCh38.p14 (RefSeq GCF_000001405.40)
Supplementary files format and content: Tab-delimited files including counts for each sample

growth_protocol: HEK293T and Vero E6 were obtained from the American Type Culture Collection, BHK21 from C. Munoz-Fontela, and Huh7 from R. Bartenschlager. Cells were grown under standard cell culture conditions in high glucose DMEM supplemented with 10% FCS, GlutaMax, and Pen/Strep (Gibco). Cell viability was determined by CellTiter96 Aqueous One Solution Reagent (Promega).

extract_protocol:
Total RNA was isolated using TriReagent (Sigma-Aldrich) following the manufacturer’s protocol followed by DNA digestion with the TURBO DNA-free DNase kit Hehner, Schneider et al. (Ambion).
Depletion of ribosomal rRNA with the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat) (New England Biolabs) and Agencourt RNAClean XP beads (Beckman Coulter). Library preparation was performed according to the manufacturer’s protocol by using NEB Next Ultra II Directional RNA Library Prep Kit for Illumina. To barcode the libraries and therefore facilitate multiplex sequencing, Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) (New England Biolabs) were used. Libraries were further purified with Agencourt AMPure XP Reagent (Beckman Coulter).

treatment_protocol: Transfection for lentivirus production was performed by calcium phosphate precipitation.

value: hepatocyte derived cellular carcinoma

value: ZIKV 48h


title: H3K9me3.RS8.rep2

description:
H3K9me3.RS8.merged.ext150.bigWig
H3K9me3_RS8_peaks.bed

value: H3K9me3 (Active Motif 39161)


title: ZIKV 24h (3) [B_62]

value: ZIKV 24h


title: ZIKV 24h (2) [B_59]


title: Xenograft Human Primary Tumor 3


title: H3K9me3.RS8.rep1

value: Homogenous synchronous spermatogenic cells

value: Wild type


title: H3K9me3.RS4.rep2

description:
H3K9me3.RS4.merged.ext150.bigWig
H3K9me3_RS4_peaks.bed


title: Xenograft Human Metastasis Micro Tumor 2

value: Xenograft Liver

value: melanoma


title: ZIKV 12h (2) [B_58]

value: ZIKV 12h


title: Xenograft Human Metastasis Macro Tumor 3

value: Metastasis

value: PDX metastasis model


title: ZIKV 48h (1) [B_57]


title: H3K9me3.RS4.rep1


title: Xenograft Human Metastasis Macro Tumor 2


title: Xenograft Human Primary Tumor 2


title: ZIKV 24h (1) [B_56]


title: ZIKV 48h (3) [B_63]


title: Xenograft Human Primary Tumor 4


title: ZIKV 12h (1) [B_55]


title: ZIKV 12h (3) [B_61]


title: H3K9me3.RS2.rep2

description:
H3K9me3.RS2.merged.ext150.bigWig
H3K9me3_RS2_peaks.bed


title: YFV 48h (3) [B_54]

value: YFV 48h


title: Xenograft Human Metastasis Micro Tumor 1


title: H3K9me2.RS8.rep2

value: H3K9me2 (Abcam ab1220)


title: Xenograft Human Primary Tumor 1

value: Primary Tumor


title: YFV 24h (3) [B_53]

value: WT

value: YFV 24h


title: H3K9me2.RS8.rep1


title: KO1_3 Selenium Supplementation

data_processing:
Trimming to remove low quality and adaptor contamination by Trim Galore v0.6.10
Removal of duplicated reads  based on UMI using CTK tool kit
Non-coding RNA removal using custom reference and STAR v2.7.9a keeping non mapped reads,
Mapping to GRCh38 primary assembly genome using MANE v1.2 annotation file and EndToEnd alignment mode.
gene raw counts generation based on CDS region in-frame psite counts using riboWaltz and normalization using DESeq2 packages.
Assembly: GRCh38 primary assembly
Supplementary files format and content: tab delimited file with raw counts for each sample
Supplementary files format and content: tab delimited file with normalized values for each sample
Library strategy: Ribo-seq

molecule: cytoplasmic RNA

source_name: melanoma cell line

extract_protocol:
cells were snap-frozen and  lysed in buffer containing 5 mM Mg2+ and 1% TritonX-100 with 100 μg/mL cycloheximide and tigecycline
The Ribo-seq libraries were generated as previously described with following modifications (McGlincy et al.).  Cells were snap-frozen and allowed to thaw on ice, then lysed in lysis buffer [50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 μg/mL cycloheximide, 100 μg/mL tigecycline, 15 U/mL DNaseI (ThermoFisher, 89836)].  RNA was quantified using Qubit Broad range RNA kit (ThermoFisher, Q10211).  Ribosome footprint was generated using 15 U RNase I (Biosearch Technologies, N6901K) to 300 ug RNA in 200 μL reaction volume at room temperature for 45 min.  The ribosome was collected by ultracentrifugation and ribosome footprint was purified using TRIzol (ThermoFisher, 15596018).  RNA was then dephosphorylated and subjected to size selection from 17-40 nt range from 15% polyacrylamide TBE-Urea gel.  Ribosome footprint was extracted from the gel in the extraction buffer [50 mM Tris-HCl (pH 7.0), 300 mM NaCl, 1 mM EDTA, 0.25 % SDS] and subjected to rRNA depletion using Human/Mouse/Rat riboPOOL kit (Galen Molecular, dp-K024-000050) by following the manufacture’s instruction.  rRNA-depleted ribosome footprint was precipitated in 80% ethanol at -20 °C overnight. rRNA-depleted ribosome footprint was then ligated to a pre-adenylated linker (rApp-WWAGATCGGAAGAGCACACGTC-3ddC).  The footprint was reverse transcribed by SuperScript III reverse transcriptase (ThermoFisher, 18080044) with a 5’ phosphorylated primer that contains eight-nucleotide unique molecular identifiers and two spacer residues (Phos-NNNNNNNNAGATCGGAAGAGCGTCGTGTA-iSp18-AA-iSp18-TAGACGTGTGCTC).  cDNA was run on 10% non-denaturing gel to remove the non-ligated linker and the reverse transcription primer.  cDNA was the circularized using CircLigase I in the presence of 1 mM ATP.  The library was PCR amplified using KAPA HiFi HotStart ReadyMix (FisherScientific, 50-196-5217) and NEBNext® Multiplex Oligos for Illumina® Dual Index Primers Set 1 (NEB, E7600S).  The library was purified twice using 1x AMPure XP Bead (BeckmanCoulter, A63881).  The library was sequenced for single-end 100 cycles on Illumina NextSeq 2000.

value: melanoma cell line

value: human melanoma

value: FTS1 KO

value: 30nM Sodium Selenite


title: YFV 48h (2) [B_51]

value: hepatocyte derived cellular carcinoma


title: H3K9me2.RS4.rep2

value: Homogenous synchronous spermatogenic cells


title: KO1_2 Selenium Supplementation


title: Xenograft Human Metastasis Macro Tumor 1


title: KO1_1 Selenium Supplementation


title: YFV 12h (3) [B_52]

value: YFV 12h


title: WT_3 Selenium Supplementation


title: YFV 24h (2) [B_50]


title: YFV 12h (2) [B_49]


title: WT_2 Selenium Supplementation


title: YFV 48h (1) [B_48]


title: H3K4me3.RS8.rep2

description:
H3K4me3.RS8.merged.ext150.bigWig
H3K4me3_RS8_peaks.bed

value: Wild type


title: WT_1 Selenium Supplementation


title: YFV 24h (1) [B_47]


title: H3K9me2.RS2.rep2


title: H3K4me3.RS8.rep1


title: H3K9me3.RS2.rep1

value: H3K9me3 (Active Motif 39161)


title: YFV 12h (1) [B_46]


title: KO1_3 No Selenium Supplementation

value: No Selenium


title: H3K4me3.RS4.rep2

description:
H3K4me3.RS4.merged.ext150.bigWig
H3K4me3_RS4_peaks.bed


title: KO1_2 No Selenium Supplementation


title: H3K4me3.RS4.rep1


title: Mock 48h (6) [B_45]

value: Mock 48h


title: H3K9me2.RS4.rep1


title: H3K9me2.RS2.rep1


title: H3K4me3.RS2.rep2

description:
H3K4me3.RS2.merged.ext150.bigWig
H3K4me3_RS2_peaks.bed


title: Mock 24h (6) [B_44]

value: Mock 24h


title: Mock 12h (6) [B_43]

value: Mock 12h


title: KO1_1 No Selenium Supplementation


title: WT_3 No Selenium Supplementation


title: WT_2 No Selenium Supplementation


title: WT_1 No Selenium Supplementation


title: H3K4me1.RS8.rep1

description:
H3K4me1.RS8.merged.ext150.bigWig
H3K4me1_RS8_peaks.bed

value: H3K4me1 (Active Motif 39297)


title: Mock 24h (5) [B_41]


title: Mock 12h (5) [B_40]


title: cpr-6 S4

city: Jerusalem

first: Atif

last: Ahmed

state: Jerusalem

address: Botnar building, Room 132, First floor, Faculty of medicine, Institute of medical research Israel-Canada (IMRIC), Hebrew University, Ein Kerem campus

department: Biochemistry and Molecular biology

country: Israel

institute: Hebrew University

data_processing:
Quality trimming was done at the 3’ end using cutadapt (v2.10),with the quality cutoff 10. Also using cutadapt,  adapter and poly-A sequences were removed. The error rate (-e parameter) was set to zero. Reads that became shorter than 28 nt were filtered out (-m parameter).
The processed fastq files were aligned to the Caenorhabditis elegans transcriptome and genome using TopHat (v2.1.1 ). The genome version was WBcel235 with annotations from Ensembl Metazoa release 46. Strand information was taken into consideration (--library-type fr-secondstrand). Alignment allowed up to 2 mismatches per read, and a total edit distance of 5.
Quantification was done using htseq-count (v0.12.4 ). Only uniquely aligned reads were counted. Strand information was taken into consideration (--stranded=’yes’).
Differential expression analysis was done with the DESeq2 package (v1.30.1). Genes with a mean of counts less than 3 over all samples were filtered out.
An experimental batch effect was present. Control samples EV S1,EV S2 and treatment cpr-6 S1,cpr-6 S2 belonged to one group, while EV S3,EV S4 together with cpr-6 S3,cpr-6 S4 belonged to another group. Differential expression was calculated with the batch effect incorporated into the statistical model  (~Batch+Condition). Default parameters were used except not using the independentFiltering algorithm.
Significance threshold was taken as padj<0.1 (default).
Assembly: WBcel235
Supplementary files format and content: An Excel file. 'rawc.' columns are raw counts,  'normc_noBatch.' are columns are the values after DESeq2 normalization.  'baseMean, Log2FoldChange, lfcSE, stat, pvalue, padj' are corresponding results of DESeq2 analysis. 'sig' indicates significance according to the threshold (padj<0.1).

organism: Caenorhabditis elegans

source_name: pool of whole worms

growth_protocol: Synchronized CL2006 worms were grown at 20C on the indicated RNAi (EV or cpr-6) to day 1 of adulthood and were bleached again. Eggs were placed on the same RNAi (EV or cpr-6). Worms of the second generation were washed and transferred onto new plates every day to remove progeny and harvested at day 6 of adulthood.

extract_protocol:
RNA was extracted using the NucleoSpin® RNA kit (MACHEREY-NAGEL; 740955) according to the manufacturer instructions.
Libraries were prepared and sequenced by the Technion Genome Center (Technion, Haifa, Israel) using the CEL-Seq2 protocol

value: pool of whole worms

value: harvested at day 6 of adulthood

value: Grown on cpr-6 RNAi expressing bacteria


title: cpr-6 S3

value: WT


title: H3K4me1.RS8.rep2


title: H3K4me3.RS2.rep1


title: H3K4me1.RS4.rep2

description:
H3K4me1.RS4.merged.ext150.bigWig
H3K4me1_RS4_peaks.bed


title: Mock 48h (4) [B_39]


title: VP64_Untransfected, replicate 3

city: Barcelona

first: Eulalia

last: Marti

address: Passeig de la Vall d’Hebron, 171

department: Institute of Neurosciences

institute: University of Barcelona

data_processing:
Basecalling with Illumina bcl2fastq
Salmon transcript quantification using Homo sapiens Gencode annotation version 26
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Text files: raw counts per transcript obtained by Salmon using Homo sapiens Gencode annotation version 26

source_name: SH-SY5Y VP64

growth_protocol: SH-SY5Y cells were transfected with a construct consisting of dCas9 coupled to VP64 and, when indicated, a sgRNA construct.

extract_protocol:
RNA isolation was performed with the miRNeasy kit (QIAGEN) following manufacturer’s instructions. RNA was reverse transcribed using Transcriptor First Strand cDNA Synthesis Kit (Roche).
starting material 500ng RNA total. Kit Truseq Stranded mRNA (illumina) - Single Read, 50nts (1x50, v4). HiSeq2500.

tag: sgrna

tag: expressing

value: SH-SY5Y expressing dCas9 coupled to VP64.


title: H3K4me1.RS4.rep1


title: cpr-6 S2


title: Mock 24h (4) [B_38]


title: VP64_Untransfected, replicate 2


title: H3K4me1.RS2.rep2

description:
H3K4me1.RS2.merged.ext150.bigWig
H3K4me1_RS2_peaks.bed


title: cpr-6 S1


title: Mock 12h (4) [B_37]


title: H3K4me1.RS2.rep1


title: VP64_Untransfected, replicate 1


title: Mock 48h (5) [B_42]


title: EV S4

value: Grown on control RNAi expressing bacteria


title: VP64_Untransfected, replicate 4


title: EV S3


title: H3K36me3.RS8.rep2

description:
H3K36me3.RS8.merged.ext150.bigWig
H3K36me3_RS8_peaks.bed


title: VP64_sgRNA_LINC01007, replicate 3

source_name: SH-SY5Y VP64 sgRNA LINC01007

value: SH-SY5Y expressing dCas9 coupled to VP64 and a sgRNA construct targeting LINC01007.


title: WNV 48h (3) [B_36]

value: hepatocyte derived cellular carcinoma

value: WNV 48h


title: VP64_sgRNA_LINC01007, replicate 4


title: WNV 24h (3) [B_35]

value: WNV 24h


title: WNV 12h (3) [B_34]

value: WNV 12h


title: H3K36me3.RS4.rep2

description:
H3K36me3.RS4.merged.ext150.bigWig
H3K36me3_RS4_peaks.bed

value: Homogenous synchronous spermatogenic cells

value: Wild type


title: EV S1


title: H3K36me3.RS4.rep1


title: EV S2


title: WNV 24h (2) [B_32]


title: VP64_sgRNA_LINC01007, replicate 1


title: H3K36me3.RS8.rep1


title: VP64_sgRNA_LINC01007, replicate 2


title: High fat diet fed mouse, Exercise, tumor tissue, mouse4

city: Osaka-City

first: Kanae

last: Echizen

state: Osaka

address: Asahimachi 1-4-3, Abeno-Ku

department: Graduate School of Medicine

country: Japan

institute: Osama Metropolitan University

data_processing:
The libraries were sequenced on NextSeq 500 platform in a 76 base single read mode.
Fastq files were trimmed by Trim Galore version 0.6.10.. The low quality reads, the TrueSeq adapter sequences and short reads (shorter than 20bps) were removed.
Sequenced reads were mapped to the mouse reference genome sequences (GRCm39) using STAR_2.7.11a.
Raw count matrixes were generated by featureCounts function from the Subread v2.0.5 package.
Assembly: Gencode GRCm39 Release M32
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted from frozen liver using RNAiso Plus (Takara Bio).
Library preparation was performed using the TruSeq Stranded mRNA sample prep kit (Illumina), according to the manufacturer’s instructions.

treatment_protocol: The mice were maintained under specific pathogen-free conditions, on a 12-h light-dark cycle, free drinking and fed a normal diet (ND, CE-2 from CLEA, composed of 12 kcal% fat, 29 kcal% protein, 59 kcal% carbohydrates) or  a high-fat diet (HFD, D12492, Research Diet, composed of 60 kcal% fat, 20 kcal% protein, 20 kcal% carbohydrates). All the mice used in the experiments are male mice, the obese mice with a body weight exceeding 45g at 35 weeks of age. DMBA (7,12-dimethylbenz(a)anthracene, D3254, Sigma-Aldrich) treatments were performed. In brief, 50 μL of 0.5% DMBA in acetone was applied to the dorsal surface on postnatal day 4–5. The neonatal mice used for carcinogenesis experiments were shuffled from their littermates when grouping to avoid any littermate tendency. Afterwards, the mothers and pups were fed ND or HFD. At 4 weeks old, pups were weaned and continuously fed ND or HFD until euthanized. The neonatally DMBA-treated, HFD-fed WT mice were divided into non-exercise and exercise groups at the age of 20 weeks. At the beginning of the running experiment, the mice of the exercise group were gradually trained to run on a treadmill running machine by exposing them to increase speed and time running. At the first training week, the running speed was set at 10 m/min and it was increased week by week, the maximum speed which the majority of obese mice could continue running was 18m/min. After the first 5 training weeks, the mice ran at a speed of 18 m/min for 20 min/day, 5 days/week, at the last 10 weeks during the 35-week protocol. The non-exercise mice were kept in their cages and put in the same room as the exercise mice. Both the exercise and non-exercise mice were followed the body weight each three weeks. At the age of 35 weeks, the exercise and non-exercise mice were euthanized on the same day within 2 hours after the final exercise.

value: liver

value: 35 weeks

value: wild type


title: H3K36me3.RS2.rep2

description:
H3K36me3.RS2.merged.ext150.bigWig
H3K36me3_RS2_peaks.bed


title: VP64_sgRNA_GFP, replicate 4

source_name: SH-SY5Y VP64 sgRNA GFP

value: GFP

value: SH-SY5Y expressing dCas9 coupled to VP64 and a sgRNA construct targeting GFP.


title: VP64_sgRNA_GFP, replicate 3


title: H3K36me3.RS2.rep1


title: High fat diet fed mouse, Exercise, tumor tissue, mouse2


title: H3K27me3.RS8.rep2

description:
H3K27me3.RS8.merged.ext150.bigWig
H3K27me3_RS8_peaks.bed


title: VP64_sgRNA_GFP, replicate 2


title: High fat diet fed mouse, Exercise, tumor tissue, mouse3


title: High fat diet fed mouse, Exercise, tumor tissue, mouse1


title: WNV 48h (1) [B_30]


title: WNV 12h (2) [B_31]


title: WNV 24h (1) [B_29]


title: H3K27me3.RS8.rep1


title: WNV 12h (1) [B_28]


title: High fat diet fed mouse, Exercise, non-tumor tissue, mouse3


title: Frontal_cortex, Control, replicate 7

description: Individual  without neuropathological lesions or neurological signs

source_name: Frontal Cortex, post-mortem sample, Control

growth_protocol: All samples were obtained from the Institute of Neuropathology Brain Bank (IDIBELL), in accordance with the standards of the local ethics committee.

extract_protocol:
RNA isolation was performed with the miRNeasy kit (QIAGEN) following manufacturer’s instructions. RNA was reverse transcribed using Transcriptor First Strand cDNA Synthesis Kit (Roche).
Starting material 500ng RNA total. Kit Truseq Stranded mRNA (illumina) - Paired End, 125nts (2x125, v4). HiSeq2500.

treatment_protocol: Brain samples were frozen at -80ºC.

value: Frontal Cortex

tag: diagnosis

value: Control

tag: braak stage


title: H3K27me3.RS4.rep2

description:
H3K27me3.RS4.merged.ext150.bigWig
H3K27me3_RS4_peaks.bed


title: H3K27me3.RS4.rep1


title: High fat diet fed mouse, Exercise, non-tumor tissue, mouse2

tag: tissue


title: Frontal_cortex, Parkinson disease, replicate 7

description: Parkinson Disease

source_name: Frontal Cortex, post-mortem sample, Parkinson Disease

value: Parkinson disease


title: VP64_sgRNA_GFP, replicate 1

tag: cell line


title: H3K27me3.RS2.rep2

description:
H3K27me3.RS2.merged.ext150.bigWig
H3K27me3_RS2_peaks.bed

source_name: Homogenous synchronous spermatogenic cells

tag: cell type


title: High fat diet fed mouse, Exercise, non-tumor tissue, mouse1

tag: strain


title: H3K27me3.RS2.rep1

tag: developmental stage


title: High fat diet fed mouse, Non exercise, tumor tissue, mouse4

tag: genotype


title: Frontal_cortex, Control, replicate 6


title: TBEV 12h (3) [B_25]

value: WT

value: TBEV 12h


title: WNV 48h (2) [B_33]


title: Frontal_cortex, Control, replicate 5


title: TBEV 48h (2) [A_24]

value: TBEV 48h


title: H3K27ac.RS8.rep2

description:
H3K27ac.RS8.merged.ext150.bigWig
H3K27ac_RS8_peaks.bed

tag: chip antibody

value: H3K27ac (Active Motif 39133)


title: TBEV 24h (2) [A_23]

value: hepatocyte derived cellular carcinoma

value: TBEV 24h


title: High fat diet fed mouse, Exercise, non-tumor tissue, mouse4


title: TBEV 12h (2) [A_22]


title: Frontal_cortex, Control, replicate 4


title: TBEV 48h (3) [B_27]


title: High fat diet fed mouse, Non exercise, tumor tissue, mouse2


title: H3K27ac.RS8.rep1


title: H3K27ac.RS4.rep2

description:
H3K27ac.RS4.merged.ext150.bigWig
H3K27ac_RS4_peaks.bed


title: Frontal_cortex, Parkinson disease, replicate 8

description: Parkinson Disease


title: Frontal_cortex, Control, replicate 3


title: TBEV 24h (3) [B_26]


title: Frontal_cortex, Control, replicate 2


title: High fat diet fed mouse, Non exercise, tumor tissue, mouse1


title: H3K27ac.RS4.rep1


title: High fat diet fed mouse, Non exercise, non-tumor tissue, mouse4


title: Frontal_cortex, Parkinson disease, replicate 6

description: Parkinson Disease


title: TBEV 12h (1) [A_19]


title: High fat diet fed mouse, Non exercise, non-tumor tissue, mouse3


title: High fat diet fed mouse, Non exercise, non-tumor tissue, mouse2


title: H3K27ac.RS2.rep1

description:
H3K27ac.RS2.merged.ext150.bigWig
H3K27ac_RS2_peaks.bed


title: Frontal_cortex, Control, replicate 1


title: H3K27ac.RS2.rep2


title: Frontal_cortex, Parkinson disease, replicate 5

description: Parkinson Disease


title: High fat diet fed mouse, Non exercise, non-tumor tissue, mouse1


title: High fat diet fed mouse, Non exercise, tumor tissue, mouse3


title: R36_331317

city: Baltimore

first: Alan

middle: L

last: Scott

address: 615 N Wolfe St

department: Molecular Microbiology and Immunology

institute: Johns Hopkins University

data_processing:
Sequencing QA/QC (NovoGene):
Remove reads containing adapters;
Remove reads containing N > 10% (N represents base that could not be determined);
Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
Mapping (NovoGene):
STAR aligner was used.
Assembly: mm10
Supplementary files format and content: tab-delimited text files with TPM-normalized absolute count data (per sample)

source_name: rIL-33/rIL-13/rIL-17A stimulation

extract_protocol:
Rneasy micro plus kit (Qiagen)
manufacturer's protocols/reagents for NovaSeq6000 (ILLUMINA)

value: primary

value: alveolar macrophage

value: WT (Strain:BALB/cJ)

value: 20 hours post-stimulation


title: R23_331317


title: DENV 24h (3) [A_17]

value: DENV 24h


title: Frontal_cortex, Parkinson disease, replicate 4

description: Parkinson Disease


title: Normal diet fed mouse, Non exercise, mouse3

value: liver

value: 35 weeks

value: wild type

value: Normal diet fed mouse, Non exercise


title: Normal diet fed mouse, Non exercise, mouse4


title: TBEV 48h (1) [A_21]


title: DENV 12h (3) [A_16]

value: DENV 12h


title: R22_331317


title: DENV 48h (2) [A_15]

value: DENV 48h


title: TBEV 24h (1) [A_20]

value: WT


title: Frontal_cortex, Parkinson disease, replicate 3

description: Parkinson Disease

value: Frontal Cortex

value: Parkinson disease


title: R21_3313

source_name: rIL-33/rIL-13 stimulation


title: R20_3313


title: Frontal_cortex, Parkinson disease, replicate 1

description: Parkinson Disease


title: Frontal_cortex, Parkinson disease, replicate 2

description: Parkinson Disease


title: DENV 24h (2) [A_14]


title: Normal diet fed mouse, Non exercise, mouse2


title: DENV 48h (3) [A_18]


title: R19_3313


title: R32_3317

source_name: rIL-33/rIL-17A stimulation


title: DENV 12h (2) [A_13]


title: ShamTx

city: Mohali

first: Sharvan

last: Sehrawat

state: Punjab

address: SAS Nagar

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research

data_processing:
self-written python scripts were used for data processing and analysis
Raw fastq files were assessed for quality using FASTQC and the 5’ end reads were trimmed accordingly using an in-house python script. The trimmed fastq files were subsequently mapped to the reference genome assembly mm10 of Mus musculus using Hi-SAT2. The output Bam files were processed using sam-tools and the processed bam files were used to count the number of reads that map to each gene in the mm10 assembly using HT-Seq count. Genes with raw counts of ≤10 were eliminated from the analysis before normalization and calculation of FPKM values. The raw read counts were then converted to FPKM+1 values using an in-house python script. Log2FoldChange for all the genes were calculated with respect to Sham and used for Gene Set Enrichment Analysis (GSEA) using GSEApy
Assembly: mm10
Supplementary files format and content: csv file containing raw counts

source_name: Spleen

growth_protocol: Mice were housed in polysulfone cages and fed labdiet under a 10 hrs light and 14 hrs dark cycle

extract_protocol:
RNA was extracted by Trizol method.
The RNA-Seq paired end sequencing libraries were prepared from the QC passed RNA samples using illumina TruSeq Stranded mRNA sample Prep kit as per the manufacturer’s protocol.

treatment_protocol: Mice were infected intraperitoneally with MHV68-SIINFEKL. While one group of mice was intraperitoneally administered dexamethasone from 4-6 days post infection, another group was administered the diluent. The animals were then sacrificed at 8 days post infection. The spleens from each group were pooled and CD8+CD44+ cells were FACS purified. This was followed by RNA extraction.

value: Spleen

value: CD8+CD44+ cells

value: sham treatment


title: DexaTx

value: dexamethasone treatment


title: DENV 48h (1) [A_12]

value: hepatocyte derived cellular carcinoma


title: Mouse_FNRMS_ATACseq_miR449a340_1

city: Leuven

first: Maurilio

last: Sampaolesi

address: Herestraat 49, ON4 - box 804

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

data_processing:
ATAC-seq reads were analysed using the ENCODE ATAC-seq pipeline (http://doi.org/10.5281/zenodo.156534) developed by Anshul Kundaje’s laboratory, which performs quality and adapter trimming, alignment, deduplication, peak calling and quality control in a fully automated manner. The resulting peak files and alignment files were used by DiffBind (v3.0.15) to find differentially accessible regions (DARs). Profile plots and heatmaps were made using DeepTools (v3.4.3) from bigwig files generated from merged replicate reads with the ATAC-seq pipeline.
Assembly: GRCh38 (RD18) / mm10 (KMR46)
Supplementary files format and content: bigwig file per sample
Supplementary files format and content: bigwig file for pooled reads
Supplementary files format and content: bed file with differentially accessible regions (open)
Supplementary files format and content: bed file with differentially accessible regions (close)

extract_protocol:
Cells were collected and washed with ice-cold PBS, 50.000 cells were pelleted in a pre-cooled 1.5 ml tube by centrifugation for 5 minutes at 600 rcf at 4 ºC in a microcentrifuge. The supernatant was removed and 50 µl of ATAC-lysis buffer was added (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40) and the nuclei were pelleted for 10 minutes at 600 rcf at 4 ºC in a microcentrifuge. Subsequently, the supernatant was removed and nuclei were resuspended in 50 µl transposition reaction buffer (27.5 µl H2O, , 25 µl TD buffer, 2.5 µl Tagment DNA Enzyme 1) (Tagment DNA Enzyme and Buffer Small Kit, Illumina, 20034197) and incubated for 30 minutes at 37 ºC at 1000 rpm in a thermomixer. The transposed DNA was cleaned up immediately following transposition using the ZymoDNAClean & Concentrator-5 kit (Zymo, WA, USA, D4014) and amplified in one pre-amplification step (5 cycles) and a final amplification (5 to 7 cycles) in the same 50 µl reaction using 1x NEBNext High-fidelity PCR master mix (New England Biolabs, MA, USA, M0541S).
Following amplification, the libraries were purified using the ZymoDNAClean & Concentrator-5 kit (Zymo, D4014) followed by 0.55x-1.75x dual size selection using AMPure XP beads (Beckman Coulter, CA, USA). The quality of the libraries was assessed using an Agilent Bioanalyzer 2100 with the High Sensitivity DNA analysis kit (Agilent Technologies, 5067-4626) and the concentration was determined using Qubit™ dsDNA HS Assay kit (Invitrogen, Q32854). The libraries were diluted to 4 nM and pooled together for SE50 sequencing on an Illumina HiSeq4000, aiming for minimally 25 million mapped and unique reads.

value: Mouse FN-RMS cell line

value: MyoD-Cre x p53 F/+ x KRasG12D


title: Mouse_FNRMS_ATACseq_miR449a340_2


title: DENV 24h (1) [A_11]

value: DENV 24h


title: Mouse_FNRMS_ATACseq_vehicle_2


title: R31_3317

value: primary

value: alveolar macrophage

value: WT (Strain:BALB/cJ)

value: 20 hours post-stimulation


title: H3K27 acetyl, Input

city: New york

first: Yurii

last: Chinenov

state: New York

address: 535 E 71 str, Hospital for Special Surgery

department: Research Division

institute: Hospital for special surgery

data_processing:
Single-end reads are pre-processed using fastp which supports adapter trimming, low quality base trimming, and calculation of additional quality control metrics.
Trimmed reads were aligned to the mm10 genome using bowtie2  with --very-sensitive-local -q -p options set. Low quality, improper, multimapping alignments, and PCR duplicates are filtered using SAMtools .
Peaks are called on each sample (replicas are not pooled) with MACS2  sing macs2 callpeak --nomodel --shift -100 --extsize 200 -q 0.05 options. After peak calling, all peaks from all samples called separately were combined and adjacent peaks (within 10bp) were merged. Reads from each sample within the combined set of peaks are then counted using featureCounts to produce an initial reads-per-peak count matrix
Assembly: mm10
Supplementary files format and content: bigwig files for each sample
Supplementary files format and content: csv peak count matrices

source_name: Bone Marrow

growth_protocol: BMDM were prepared from 8- to 10-week-old male mice as previously describe . Briefly, bone marrow was flushed from the femurs and tibiae of mice and differentiated for 5 days in the DMEM (1 g/l glucose) supplemented with 20% bovine serum and 10% L-cell conditioned media

extract_protocol:
Macrophages were crosslinked with 1% methanol-free formaldehyde (Thermo) for 10 min (H3K27ac) or double-crosslinked with 2 mM disuccinimidyl glutamate (Proteochem, c1104) (GR) for 30 min followed by 1% methanol-free formaldehyde for 10 min at room temperature (GR). Nuclear extracts were prepared  and chromatin DNA was sonicated using Bioruptor Pico (Diagenode, 8 cycles, 30s on/off bursts) to generate DNA fragments ~130-600 bp. (200-700 bp – reconcile). After sonication, 10% of nuclear extract was saved as input and rest incubated with protein A/G agarose (Santa Cruz) for 30 min at 4 °C. Precleared extracts were incubated with 40 μL of 50% protein A/G agarose and 5 g of normal rabbit IgG (Santa Cruz Biotech), H3K27ac (Active Motif, 39133), GR (Thermo Fisher Scientific, PA1-511A) at 4 °C overnight. The following day, beads were washed 8x with modified RIPA buffer containing 500 mM LiCl and 2x with TE + 50 mM NaCl buffer. DNA was extracted after reversing crosslinks and purified with Qiagen PCR purification kit. Resulting DNA was analyzed by qPCR (primer sequences are listed in Supplementary Data 1) with 28S as an internal control and occupancies expressed relative to the normal IgG baseline.
Libraries were prepared using NEBNext Ultra II Library Prep Kit for Illumina (NEB), size selected (150-500 bp), and PCR-amplified for 15 cycles

treatment_protocol: Adherent cells were scraped, seeded into 150 mm or 6-well plates and polarized for 24 h with 10 ng/ml IL4, 500 nM Cort or 100 nM Dex

value: Bone Marrow

value: primary cells

value: Bone marrow derived macrophages

value: vehicle


title: DENV 12h (1) [A_10]

value: WT

value: DENV 12h


title: Mouse_FNRMS_ATACseq_vehicle_1


title: R16_3317


title: Mock 48h (3) [A_9]

value: Mock 48h


title: Mouse_FNRMS_RNAseq_miR449a340_4

data_processing:
50 bp single-end reads were generated. An average of 20 million reads were obtained from all samples. Quality control of raw reads was performed with theFastQC v0.11.5. The adapters were filtered with ea-utils v1.2.2.18. The splice-aware alignment was performedwith TopHat v2.0.13 against the mouse genome mm10. The number of allowed mismatches was 2. Reads that mapped to more than one site to the reference genome were discarded. The minimal score of alignment quality to be included in count analysis was 10. Resulting SAM and BAMalignment files were handled with Samtools v0.1.19.24. Quantification of reads per gene was performed with HT-Seq count v0.5.3p3.
Count-based differential expression analysis was done with R-based (The R Foundation for Statistical Computing, Vienna, Austria) Bioconductor package DESeq2.
Assembly: mm10
Supplementary files format and content: csv file containing matrix with read counts normalized by the library size for all samples

extract_protocol:
RNA was isolated using Total RNA isolation kit and post isolation DNAase (Thermo Fisher Scientific)- 2µg were processed
Library preparation was performed with the Illumina TruSeq Stranded mRNA Sample Preparation Kit, according to the manufacturers protocol. Denaturation of RNA was performed at 65oC in a thermocycler and cooled down to 4oC. Samples were indexed to allow for multiplexing. Sequencing libraries were quantified using the Qubit fluorometer (Thermo Fisher Scientific, Massachusetts, USA). Library quality and size range was assessed using the Bioanalyzer (Agilent Technologies) with the DNA 1000 kit (Agilent Technologies, California, USA) according to the manufacturer’s instructions. Libraries were diluted to a final concentration of 2nM and sequenced on Illumina HiSeq4000 sequencing system, according to the manufacturer’s recommendations.


title: H3K27 acetyl, IL4, 24 h, rep 3


title: Mouse_FNRMS_RNAseq_miR449a340_3


title: H3K27 acetyl, IL4, 24 h, rep 1


title: Normal diet fed mouse, Non exercise, mouse1

value: liver

value: 35 weeks

value: wild type

value: Normal diet fed mouse, Non exercise


title: R14_33

source_name: rIL-33 stimulation


title: Mock 24h (3) [A_8]

value: hepatocyte derived cellular carcinoma

value: Mock 24h


title: H3K27 acetyl, IL4, 24 h, rep 2


title: R13_33

value: primary


title: Mock 12h (3) [A_7]

value: Mock 12h


title: H3K27 acetyl, Dexamethasone, 24 h, rep 3

value: Dexamethasone


title: Mock 48h (2) [A_6]


title: Mouse_FNRMS_RNAseq_miR449a340_2

value: Mouse FN-RMS cell line

value: MyoD-Cre x p53 F/+ x KRasG12D


title: R12_1713

source_name: rIL-13/rIL-17A stimulation

value: alveolar macrophage

value: WT (Strain:BALB/cJ)

value: 20 hours post-stimulation


title: Mock 24h (2) [A_5]

value: WT


title: H3K27 acetyl, Dexamethasone, 24 h, rep 2

value: Bone Marrow

value: primary cells

value: Bone marrow derived macrophages


title: R11_1713


title: Mouse_FNRMS_RNAseq_vehicle_4


title: H3K27 acetyl, Dexamethasone, 24 h, rep 1


title: R10_1713


title: Mock 48h (1) [A_3]

value: Mock 48h


title: Mouse_FNRMS_RNAseq_vehicle_2


title: H3K27 acetyl, Corticosterone, 24 h, rep 3

value: Corticosterone


title: R30_33


title: Mock 24h (1) [A_2]


title: Mouse_FNRMS_RNAseq_vehicle_1


title: H3K27 acetyl, Corticosterone, 24 h, rep 2


title: R7_17

source_name: rIL-17A stimulation


title: Mock 12h (1) [A_1]


title: H3K27 acetyl, Corticosterone, 24 h, rep 1


title: R8_17


title: H3K27 acetyl, vehicle, rep 3

value: vehicle


title: H3K27 acetyl, vehicle, rep 2


title: R6_13

source_name: rIL-13 stimulation


title: Mouse_FNRMS_RNAseq_miR449a340_1


title: NK-92, OA treated

city: Jinan

first: Deyan

last: Jiao

address: wenhuaxi road

institute: shandong university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Clean reads were mapped to the reference genome using Bowtie2 software. And reads from organelle, mapping quality smaller then 30, PCR duplicated reads all removed. Those high quality mapping reads were subjected to further peak calling.
Macs2 was used to call peaks with qvalue < 0.05.
Peaks were annotated by ChIPseeker package.
Assembly: hg38
Supplementary files format and content: bw

extract_protocol:
50 μL pre-cooled RSB (containing 0.1% NP40 [Thermo Scientific, 85,124], 0.1% Tween-20 [Thermo Scientific, 28,320], 0.01% digitalis saponin [MedChemExpress, HYN4000]) was added to 5 × 104 living cells, which were incubated on ice for 3 min. Then, 1 mL pre-cooled RSB only contained 0.1% Tween-20 was added and centrifuged at 500 g for 5 min. The supernatant was removed. The precipitate was resuspended with 50 μL transposition mix (TD, 2× reaction buffer from Nextera kit [Illumina, FC-121-1030], 25 μL; TDE1, Nextera Tn5 Transposase from Nextera kit, 2.5 μL; and nuclease-free H2O 22.5 μl; total volume 50 μL), and placed into a mixometer (Youning, Hangzhou China) at 177 × g for 30 min. The DNA was first purified with Qiagen MinElute PCR Purification Kit (QIAGEN, 28,004), and was further purified with Zymo DNA Clean and Concentrator-5 Kit (ZYMO RESEARCH, D4004). Then PCR was performed in a 50 μL final volume as follows: 7 cycles of 98°C for3 min, 98°C for 15s, and 63°C for 30s, finally, 72°C for 30s, 72°C for 5 min. The PCR product was sequenced by illuminaHiSeq/NextSeq platform. Subsequently, the data was analyzed using unique mapped reads.
Around 50,000 living cells were taken for each library preparation. The cells were lysed in1×Lysis Buffer to get the nuclei, and TruePrep™DNA Library Prep Kit V2 for Illumina(Vazyme Biotech) was used to construct the transposase-treated libraries.The mass concentration and molar concentration of libraries weredetected by Qubit 3.0 Fluorometer and StepOnePlus™Real-Time PCR system,respectively, and lengthsof inserted fragmentswere detect with Agilent HS 2100 Bioanalyzer. Qualified libraries were sequencing by Illumina HiSeq X tenplatformin pair-end 150 bp style.

treatment_protocol: NK-92 cells were treated with or without OA (0.2mM oleic acid (OA) for 36h. The treatment processed only once.)

value: NK cell

value: OA treated


title: NK-92, control

value: control


title: Mouse_FNRMS_RNAseq_vehicle_3


title: R5_13

value: primary


title: Mock 12h (2) [A_4]

value: hepatocyte derived cellular carcinoma

value: Mock 12h


title: LNCaP_VP64_ERa_4h_rep3

first: Xuanrong

last: Chen

address: 1300 York Ave

data_processing:
Briefly, the quality of the raw reads (FASTQ files) was validated using FastQC software (Version 0.11.7), and single-end reads with a score > 29 were aligned to the hg19 human reference genome using Bowtie2 software (v2.2.9) with default parameters.
The resulting SAM files were converted to BAM format, sorted, PCR duplicates removed, ENCODE blacklist regions eliminated, and final BAM files indexed using Samtools (v1.7).
Replicate BAM files were then combined to generate RPKM-normalized bigwig files for each factor using Deeptools (v3.0).
Peaks were called using MACS2 with a p value < 10-8 or q = 0.05 (replicates combined) using the narrow peak caller and matched input as background. Peak overlap and Venn diagrams were generated using pybedtools and bedtools intersect function and werewas defined as overlap (more than or equal to) 1 bp.
Assembly: hg19
Supplementary files format and content: bigWig (except for Input sample)

extract_protocol:
For each replicate, 20 million cells were fixed with 1% formaldehyde for 10 minutes at 24°C, quenched with 0.125 M glycine for 5 minutes, washed 2x with PBS, and stored at -80°C until use. The fixed pellets were lysed in 1% SDS lysis buffer and sonicated for 30 cycles (30s on/off) in a temperature-controlled Bioruptor 3000 to obtain a size range of 250-400 bp. After centrifugation at 15000 RPM for 20 minutes to remove debris, individual samples were incubated with Protein A/antibody-conjugated beads overnight while rocking at 4°C. The samples were washed six times with increasing salt buffers and DNA was eluted at 65°C overnight. All samples were treated with RNase A for 30 minutes at 37°C followed by Proteinase K at 65°C for 1 hour. DNA was purified using phenol chloroform.
ChIP sequencing libraries were constructed using the KAPA Hyper Prep Kit (Roche; cat. 08278539001) following the manufacturer's instructions, using 20 ng DNA per sample. The libraries were assessed for quality, purity, and size using DNA High Sensitivity Bioanalyzer chips (Agilent; cat. 5067-4626), and those passing quality control (with an equal size distribution between 250-400 bp, no adapter contamination peaks, and no degradation peaks) were quantified using the Library Quantification Kit (Roche; cat. 07960298001). Finally, the libraries were pooled to a final concentration of 10nM and sequenced at the WCM Genomics Core on a NovaSeq 6000. The ChIP-seq utilized the ERalpha (ERa) antibody from Santa Cruz Biotechnology (Cat# sc-8002, AB_627558) to generate MACC peaks, along with the H3K27ac antibody from Abcam (Cat# ab4729, AB_2118291).

treatment_protocol: The LNCaP MACC cells were treated with 2.5uM Tamoxifen for 4 hours or 18 hours.

value: ectopic Activating MACC construct (VP64) expressed LNCaP cell line

value: human prostate cancer cell line

value: Ectopic expression of Activating MACC construct (VP64)

value: 2.5uM Tamoxifen, 4h


title: Plasma_Control_Rep6

type: RNA

city: liverpool

first: Iain

middle: M

last: Dykes

state: Select...

address: James Parson Bl, Byrom Street,

department: Pharmacy & Biomolecular science

country: United Kingdom

institute: Liverpool John Moores University

hyb_protocol: Samples were hybridised using the NanoString nCounter rat miRNA Expression Assay kit. See nCounter miRNA Expression Assay User Manual for protocol.

scan_protocol: Standard protocol

data_processing: The data shown in the matrix table is the unprocessed raw count data. We used a total of 14 different methods to process this data and, as described in the paper, the method chosen changes the output of the system. These methods differ in the method of background correction, the level of background set and in the method of content normalisation. There is no single established method in the literature to process nCounter data.

organism: Rattus norvegicus

source_name: Plasma, Non-pregnant control

label_protocol: Samples were labelled using the NanoString nCounter rat miRNA Expression Assay kit. See nCounter miRNA Expression Assay User Manual for protocol.

growth_protocol: Twelve Wistar female rats were divided into a control and a pregnant group of equal size (n=6). The oestrous cycle of the pregnant group was monitored using daily vaginal smears. Females in proestrus were paired overnight with a male. Pregnancy was confirmed by presence of a mucosal plug in the cage and presence of sperm in the vaginal smear. Pregnant rats were sacrificed at midday 14 days post mating (day E14.5) by Schedule 1 methods (CO2 inhalation followed by cervical dislocation to ensure death).

extract_protocol: Whole rat blood was immediately centrifuged at 3,000 rpm (1,811 rcf) for 30 minutes at room temperature in an Eppendorf Centrifuge 5810R to pellet cells. The top layer (plasma) was then transferred into RNase-free 1.5 ml microcentrifuge tubes and centrifuged at 13,000 rpm (14,549 rcf) for 30 minutes at 4°C in a benchtop Eppendorf Centrifuge 5418 to remove platelets. The supernatant was centrifuged a second time at 13,000 rpm (14,549 rcf) for 5 minutes at 4°C to ensure complete platelet removal and the supernatant was then transferred to a fresh tube. Plasma was stored at -80°C. Total RNA was prepared from 1.5ml of plasma using the Norgen Biotek Plasma/Serum RNA Purification Midi Kit (Norgen Biotek, Ontario, Canada) following the manufacturer’s protocol. 5μl (200pM) of an exogenous spike-in miRNA control from rice (osa-miR-414) was added to each sample at the start of the protocol. Following purification, the volume of the sample was reduced to 20μl using an Amicon Ultra-0.5mL centrifugal filter (3kDa cutoff) (Merck, Cork, Ireland).

value: Wistar

tag: Sex

value: female

value: Blood plasma

tag: pregnant?

value: No

tag: age (days)

tag: gestational age


title: H3K27 acetyl, vehicle, rep 1

value: Bone Marrow

value: primary cells

value: Bone marrow derived macrophages

tag: treatment


title: Plasma_Control_Rep5


title: R4_13

value: alveolar macrophage

value: WT (Strain:BALB/cJ)

tag: time

value: 20 hours post-stimulation


title: R9_17

value: primary


title: Glucocorticoid Receptor, IL4, 24 hours, rep3, batch 2


title: LNCaP_VP64_ERa_4h_rep2

value: ERalpha (ERa) antibody from Santa Cruz Biotechnology (Cat# sc-8002, AB_627558)


title: Plasma_Control_Rep3


title: LNCaP_VP64_ERa_4h_rep1


title: R3_ctrl

source_name: Untreated

value: Untreated


title: Glucocorticoid Receptor, IL4, 24 hours, rep2, batch 2


title: R2_ctrl


title: Plasma_Control_Rep4


title: Glucocorticoid Receptor, IL4, 24 hours, rep1, batch 2


title: Plasma_Pregnant_Rep6

source_name: Plasma, Pregnant (E14.5)

value: Yes


title: R1_ctrl


title: LNCaP_VP64_H3K27ac_18h_rep2

value: ectopic Activating MACC construct (VP64) expressed LNCaP cell line

value: human prostate cancer cell line

value: 2.5uM Tamoxifen, 18h

value: H3K27ac antibody from Abcam (Cat# ab4729, AB_2118291)


title: Plasma_Pregnant_Rep5

value: Wistar

value: female


title: LNCaP_VP64_H3K27ac_18h_rep3

value: Ectopic expression of Activating MACC construct (VP64)


title: Glucocorticoid Receptor, Dexamethasone, 24 hours, rep3, batch 2

value: Bone Marrow

value: Dexamethasone


title: Glucocorticoid Receptor, Dexamethasone, 24 hours, rep4, batch 2

value: primary cells

value: Bone marrow derived macrophages


title: R14

data_processing:
Sequencing QA/QC:
Remove reads containing adapters;
Remove reads containing N > .1% (N represents base that could not be determined);
(3) Remove low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 20.
Mapping:
HISAT2 aligner was used.
Assembly: mm10
Supplementary files format and content: tab-delimited text files with TPM-normalized absolute count data (per sample)

extract_protocol:
Rneasy mini plus kit (Qiagen)
manufacturer's protocols/reagents for NovaSeq6000 (ILLUMINA)

value: primary lung fibroblasts

value: WT (Strain:BALB/cJ)

value: untreated


title: LNCaP_VP64_H3K27ac_4h_rep3

value: 2.5uM Tamoxifen, 4h


title: Plasma_Pregnant_Rep3

value: Blood plasma


title: LNCaP_VP64_H3K27ac_18h_rep1


title: Plasma_Pregnant_Rep2

value: Yes


title: R13

value: 20 hours post-stimulation


title: Glucocorticoid Receptor, Corticosterone, 24 hours, rep4, batch 2

value: Corticosterone


title: Plasma_Control_Rep2

value: No


title: Plasma_Pregnant_Rep1


title: R12


title: LNCaP_VP64_H3K27ac_4h_rep2

value: ectopic Activating MACC construct (VP64) expressed LNCaP cell line

value: human prostate cancer cell line

value: H3K27ac antibody from Abcam (Cat# ab4729, AB_2118291)


title: Glucocorticoid Receptor, vehicle, 24 hours, rep4, batch2

value: vehicle


title: Glucocorticoid Receptor, vehicle, 24 hours, rep3, batch2

value: Bone Marrow


title: LNCaP_VP64_H3K27ac_4h_rep1

value: Ectopic expression of Activating MACC construct (VP64)


title: R11


title: R10


title: Plasma_Control_Rep1

description:
NS_R_miR_1.5
R5

value: Wistar

value: female


title: Human_FNRMS_ATACseq_miR449a340_2

value: Human FN-RMS cell line


title: LNCaP_VP64_Input

source_name: Input

value: 2.5uM Tamoxifen, Input


title: Glucocorticoid Receptor, Dexamethasone, 24 hours, rep2, batch 1

value: primary cells

value: Bone marrow derived macrophages

value: Dexamethasone


title: R15

value: primary lung fibroblasts

value: WT (Strain:BALB/cJ)

value: untreated


title: LNCaP_KRAB_ERa_4h_rep3

value: ectopic Repressive MACC construct (KRAB) expressed LNCaP cell line

value: Ectopic expression of Repressive MACC construct (KRAB)

value: 2.5uM Tamoxifen, 4h

value: ERalpha (ERa) antibody from Santa Cruz Biotechnology (Cat# sc-8002, AB_627558)


title: Plasma_Pregnant_Rep4

value: Blood plasma

value: Yes


title: Human_FNRMS_ATACseq_miR449a340_1


title: Glucocorticoid Receptor, Dexamethasone, 24 hours, rep1, batch 1

value: Bone Marrow


title: R9

value: 20 hours post-stimulation


title: LNCaP_KRAB_ERa_4h_rep2

value: human prostate cancer cell line


title: R8


title: Glucocorticoid Receptor, Corticosterone, 24 hours, rep3, batch 2

value: Corticosterone


title: Human_FNRMS_ATACseq_vehicle_2

value: Human FN-RMS cell line


title: LNCaP_KRAB_ERa_4h_rep1


title: Human_FNRMS_ATACseq_vehicle_1


title: Glucocorticoid Receptor, Corticosterone, 24 hours, rep2, batch 1

value: primary cells


title: R7


title: LNCaP_KRAB_H3K27ac_18h_rep3

value: 2.5uM Tamoxifen, 18h

value: H3K27ac antibody from Abcam (Cat# ab4729, AB_2118291)


title: Glucocorticoid Receptor, Corticosterone, 24 hours, rep1, batch 1

value: Bone marrow derived macrophages


title: Human_FNRMS_miR449a340_4

data_processing:
50 bp single-end reads were generated. An average of 20 million reads were obtained from all samples. Quality control of raw reads was performed with theFastQC v0.11.5. The adapters were filtered with ea-utils v1.2.2.18. The splice-aware alignment was performedwith TopHat v2.0.13 against the mouse genome GRCh38. The number of allowed mismatches was 2. Reads that mapped to more than one site to the reference genome were discarded. The minimal score of alignment quality to be included in count analysis was 10. Resulting SAM and BAMalignment files were handled with Samtools v0.1.19.24. Quantification of reads per gene was performed with HT-Seq count v0.5.3p3.
Count-based differential expression analysis was done with R-based (The R Foundation for Statistical Computing, Vienna, Austria) Bioconductor package DESeq2.
Assembly: GRCh38
Supplementary files format and content: csv file containing matrix with read counts normalized by the library size for all samples


title: LNCaP_KRAB_H3K27ac_18h_rep2


title: R6

value: primary lung fibroblasts

value: WT (Strain:BALB/cJ)


title: Human_FNRMS_miR449a340_3


title: LNCaP_KRAB_H3K27ac_18h_rep1

value: ectopic Repressive MACC construct (KRAB) expressed LNCaP cell line


title: Human_FNRMS_miR449a340_2


title: R4


title: Glucocorticoid Receptor, vehicle, 24 hours, rep1, batch1

value: vehicle


title: LNCaP_KRAB_H3K27ac_4h_rep3

value: Ectopic expression of Repressive MACC construct (KRAB)

value: 2.5uM Tamoxifen, 4h


title: Human_FNRMS_miR449a340_1


title: XDP NPCs 517, Q, rep2

city: Padova

first: Giulia

last: Nicoletto

address: Via Gabelli 63

department: Molecular Medicine

country: Italy

institute: UNIPD

data_processing:
Sequence reads were quality checked with FASTQC (v0.11.9) and align to hg38 or XDP custom genome with STAR (v2.7.10).
Alignments were sorted and indexed with samtools. Bigwig were generated with deeptools (v3.5.4) ( parameters - bamCoverage --normalizeUsing RPKM -bs 10)
RNA-seq raw count were generated with HT-seq (v0.11.2) (parameters --nonunique all -s no -a 10 -t exon -f bam -r name)
DE analyses was performed with DESeq2 R package.
Assembly: hg38
Supplementary files format and content: tab-delimited file includes raw counts for each Sample

source_name: Neuronal progenitor cells

growth_protocol: Cells were grown in standard conditions in NPM medium and geltrex coated wells.

extract_protocol:
RNA was harvested using Total RNA Purification Plus Micro Kit (Norgen Biotek, #NR48500).
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep (Illumina) following manufacturer's protocols.

treatment_protocol: Cells were seeded at 70% confluence. The next day, cells were treated with B19 or Q. After 24 hours, RNA was harvested.

value: Neuronal progenitor cells

value: XDP

value: G4 ligand treatment Q


title: R3

value: 20 hours post-stimulation


title: R2


title: LNCaP_KRAB_H3K27ac_4h_rep1

value: human prostate cancer cell line


title: XDP NPCs 517, Q, rep1


title: Human_FNRMS_vehicle_3


title: LNCaP_KRAB_H3K27ac_4h_rep2


title: Human_FNRMS_vehicle_4


title: R1


title: XDP NPCs 517, B19, rep3

value: G4 ligand treatment B19


title: LNCaP_KRAB_Input

value: 2.5uM Tamoxifen, Input


title: Human_FNRMS_vehicle_2

value: Human FN-RMS cell line


title: Low carbon_replicat3

city: Haikou

first: Li

last: WEI

state: Hainan

address: No. 99 Longkun South Road, Haikou City

institute: Hainan normal university

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw data (2×150 bp PE reads) were quality controlled using Trim-Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
The remaining high quality Illumina reads were aligned to our previously published N. oceanica IMET1 genome (Gong, Kang, Kim, Wang, Wei, Xin, Shen, Wang, You, Lim, Jeong, Park, Oh, Pan, Poliner, Yang, Li-Beisson, Li, Hu, Poetsch, Farre, Chang, Jeong, Jeong, Xu, 2020) with STAR (Dobin, Davis, Schlesinger, Drenkow, Zaleski, Jha, Batut, Chaisson, Gingeras, 2013) with duplication marked using Picard (https://broadinstitute.github.io/picard/).
The abundance of expression was quantified using featureCounts (Liao, Smyth, Shi, 2014) and StringTie (Kovaka, Zimin, Pertea, Razaghi, Salzberg, Pertea, 2019). For each of the mRNA-Seq datasets under each experimental condition, gene expression was measured as the numbers of aligned reads to annotated genes by featureCounts (Liao, Smyth, Shi, 2014) and normalized to CPM, FPKM (fragments per kilobase of exon model per million mapped fragments) and TPM values. Besides, raw counts from featureCounts (Liao, Smyth, Shi, 2014) were used for the differential gene expression analysis with edgeR (R package)
Genome_build: Nannochloropsis oceanica IMET1
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

organism: Nannochloropsis oceanica

source_name: Cells

growth_protocol: Nannochloropsis oceanica IMET1 was inoculated into the modified f/2 liquid medium, which was prepared with 35 g L-1 sea salt (Realocean, USA), 1 g L-1 NaNO3, 67 mg L-1 NaH2PO4*H2O, 3.65 mg L-1 FeCl3*6H2O, 4.37 mg l-1 Na2EDTA*2H2O, trace metal mix (0.0196 mg L-1 CuSO4*5H2O, 0.0126 mg L-1 NaMoO4*2H2O, 0.044 mg L-1 ZnSO4*7H2O, 0.01mg L-1 CoCl2, and 0.36 mg L-1 MnCl2*4H2O), and vitamin mix (2.5 µg L-1 VB12, 2.5 µg L-1 biotin, and 0.5 µg L-1 thiamine HCl).The cells were first cultured in f/2 medium at 25°C with 80±5 μmol m-2 s-1 continuous irradiation in a 1 L column reactor (inner diameter: 5cm).

extract_protocol:
Total microalgal RNA was extracted using Trizol reagents (Invitrogen, USA). The concentration and purity of the RNA were determined spectrophotometrically (NanoDrop-1000, Thermo Scientific, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In total, six identical column reactors were employed. Each reactor contains 800 ml of fresh modified f/2 liquid medium, which was supplemented with 10 mM Tris-HCl buffer (pH=8.2) in order to accurately control the pH during the culture. Equal numbers of the seed cells were re-inoculated into each of the six column reactors to an OD750 of 1.5. The light intensity was maintained at 80±5 μmol m-2 s-1. The six algal cultures were first aerated with air enriched with 5% CO2 (“High CO2” conditions, or HC) for one hour. After the pre-adaption phase, three of the algal cultures proceeded under HC as the control condition, whereas the other three were switched to aeration with 0.04% CO2 (“Low CO2” conditions, or LC).After being transferred to the designated conditions, cell aliquots were taken at 24 h from each column by syringe for  transcriptomic profiling.

tag: condition

value: low carbon


title: XDP NPCs 517, B19, rep2


title: Glucocorticoid Receptor, vehicle, 24 hours, rep2, batch 1

value: Bone Marrow

value: primary cells


title: R5

value: primary lung fibroblasts


title: XDP NPCs 517, B19, rep1


title: Low carbon_replicat2


title: Human_FNRMS_vehicle_1


title: LNCaP_3X_ERa_4h_rep2

value: ectopic Neutral MACC construct (3X) expressed LNCaP cell line

value: Ectopic expression of the neutral MACC construct (3X)

value: ERalpha (ERa) antibody from Santa Cruz Biotechnology (Cat# sc-8002, AB_627558)


title: XDP NPCs 517, Q, rep3


title: Low carbon_replicat1


title: RNASeq_PleD4_repetition

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

institute: Helmholtz Centre for Infection Research

data_processing:
RiboSeq
clipping using cutadapt (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
bowtie -m 1
RNASeq
Reference genome: NC_002516.2 (Pseudomonas aeruginosa PA01)
bowtie --trim3 1 -m 1
RNASeq_repetition
cutadapt --nextseq-trim=20 -g 'TTTTT;min_overlap=1' -G 'GGGGGGG;min_overlap=3' -m 36
Reference genome: NC_002516.2 (Pseudomonas aeruginosa PA01)
bowtie2 --very-sensitive-local -I 100 -X 1200
Genome_build: Reference genome: NC_002516.2 (Pseudomonas aeruginosa PA01)
Supplementary_files_format_and_content: contains RiboSeq_EV[1-2], RiboSeq_PleD[1-2], RNASeq_EV[1-2], and RNASeq_PleD[1-2] data
Supplementary_files_format_and_content: contains RNASeq repetition samples
Supplementary_files_format_and_content: raw count data

organism: Pseudomonas aeruginosa PAO1

source_name: RNA-seq of planktonic culture of Pseudomonas aeruginosa PA01  treated with 0.2% arabinose from 45 min after inoculation (OD of 0.05) to OD 0.5-0.7

growth_protocol: Bacterial cultures were grown in liquid LB supplemented with 400 µg/ml carbenicillin at 37 °C and 180 rpm. Cultures were inoculated with OD600 of 0.05.

extract_protocol: Total RNA was extracted by mixing bacterial cells 1:1 with RNAprotect Bacteria Reagent (Qiagen) and by using the RNeasy® Mini Kit (Qiagen) in combination with QIAshredderTM (Qiagen) according to the manufacturer’s instructions. Genomic DNA was removed by DNase treatment (DNA-free™ Kit DNase Treatment & Removal, ambion). Tag-seq was used for library preparation including rRNA removal by treatment with RiboZero (Illumina).

treatment_protocol: Expression of pHERD20T based plasmids was induced with 0.2 % arabinose after 45 min of growth. Cells were harvested between OD600 of 0.5 - 0.7.


title: RNASeq_PleD3_repetition


title: XDP NPCs 517, NT, rep3

value: NT


title: LNCaP_3X_ERa_4h_rep1

value: 2.5uM Tamoxifen, 4h


title: XDP NPCs 517, NT, rep1

value: Neuronal progenitor cells


title: RNASeq_PleD2_repetition


title: LNCaP_3X_H3K27ac_18h_rep2

value: 2.5uM Tamoxifen, 18h

value: H3K27ac antibody from Abcam (Cat# ab4729, AB_2118291)


title: High carbon_replicat2

value: high carbon


title: Ctrl NPCs 362, Q, rep3

value: XDP

value: G4 ligand treatment Q


title: 42 DAP seed inoculated by Xcf (Xanthomonas) rep3 (RNA-seq)

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

data_processing:
After quality control, high‐quality reads were mapped on Phaseolus vulgaris transcriptome version 2.1 (https://phytozome-next.jgi.doe.gov/info/Pvulgaris_v2_1) using quasi‐mapping alignment and quantification methods of Salmon algorithm v.1.2 (Patro et al. 2017). For gene expression analysis, raw RNA‐Seq data were first normalized as transcripts per kilobase million (TPM).
Assembly: Phaseolus vulgaris transcriptome version 2.1 (https://phytozome-next.jgi.doe.gov/info/Pvulgaris_v2_1)
Supplementary files format and content: Count and TPM files

organism: Phaseolus vulgaris

source_name: Seed developmental stages

growth_protocol: Experiments were performed with a variety of common bean (Phaseolus vulgaris L. cv. Flavert) susceptible to common bacterial blight. Seeds were sown in pots containing one liter of soil substrate (Tray substrat, NF U 44–551, Klasmann- Deilmann GmbL, Rippert France). Plants were grown in a controlled growth chamber with 16 h of light at 23 °C and 8 h of darkness at 20 °C and a relative humidity (RH) of 70%. Plants were watered twice a week during the first three weeks and then with a nutrient solution (N/P/K=15/10/30).

extract_protocol:
Seed samples from Common bean plants were frozen in liquid nitrogen immediately after harvest. Seed samples from three biological replicates were ground in liquid nitrogen at the three different seed developmental stages (i.e. 24, 35 and 42 DAP) using a mechanical grinder (XXXX) during 1 min at 30 Hertz. Total RNA were extracted using the NucleoSpin® RNA Plant and Fungi Kit (Macherey‐Nagel, Düren, Germany), according to the manufacturer instructions. RNA quantity and quality was measured using a NanoDrop ND‐1000 (NanoDrop Technologies, Wilmington, DE, USA).
RNA sequencing including cDNA library preparation and paired-end sequencing (SE50, 20M) was outsourced to the Beijing Genomics Institute (BGI, https://www.bgi.com). using the Illumina Hiseq 2500 technology.

treatment_protocol: Plants were spray-inoculated with water or bacterial suspension(106 CFU/ml) at the flower bud stage (R5 stage, Michael 1994). The day prior to inoculation, temperature (day 25°C/night 23°C) and relative humidity (RH, 95%) were increased. Inoculation was performed in a two-step protocol. First, small green flower buds were sprayed. Three days later, flower buds at the pollination stage were tagged. Then, a second inoculation was performed at one DAP (day after pollination) when tagged organs became open flowers. RH was reduced to 70% the day after to limit symptom development and seed abortion. Three independent replicates of 15 plants per treatment were inoculated. Tagged pods of five plants per repeat were harvested at 24, 35 and 42 DAP. Seeds were collected aseptically from pods to avoid contamination by contact with external bacterial populations on pods (Darsonval et al., 2008).

tag: cultivar

value: Flavert

value: Seed developmental stages

value: Xcf CFBP7767R

value: Phaseolus vulgaris Flavert

value: Inoculated with Xcf 10power6 CFU ml-1 by spray-inoculation


title: Ctrl NPCs 362, Q, rep2


title: High carbon_replicat1


title: RNASeq_PleD1_repetition


title: LNCaP_3X_ERa_4h_rep3

value: human prostate cancer cell line


title: RNASeq_EV4_repetition


title: LNCaP_3X_H3K27ac_4h_rep3

value: ectopic Neutral MACC construct (3X) expressed LNCaP cell line


title: RNASeq_EV3_repetition


title: RNASeq_EV2_repetition


title: 42 DAP seed inoculated by Xcf (Xanthomonas) rep1 (RNA-seq)


title: 42 DAP seed inoculated by Xcf (Xanthomonas) rep2 (RNA-seq)


title: Ctrl NPCs 362, Q, rep1


title: LNCaP_3X_H3K27ac_4h_rep1

value: Ectopic expression of the neutral MACC construct (3X)


title: Ctrl NPCs 362, B19, rep3

value: G4 ligand treatment B19


title: Ctrl NPCs 362, B19, rep2


title: LNCaP_3X_H3K27ac_18h_rep3


title: High carbon_replicat3


title: RNASeq_EV1_repetition


title: LNCaP_3X_Input

value: 2.5uM Tamoxifen, Input


title: 35 DAP seed inoculated by Xcf (Xanthomonas) rep3 (RNA-seq)


title: RNASeq_PleD2


title: XDP NPCs 517, NT, rep2

value: NT


title: 35 DAP seed inoculated by Xcf (Xanthomonas) rep2 (RNA-seq)


title: Ctrl NPCs 362, B19, rep1

value: Neuronal progenitor cells


title: 35 DAP seed inoculated by Xcf (Xanthomonas) rep1 (RNA-seq)


title: LNCaP_3X_H3K27ac_18h_rep1

value: 2.5uM Tamoxifen, 18h


title: Ctrl NPCs 362, NT, rep3


title: RNASeq_EV2


title: 24 DAP seed inoculated by Xcf (Xanthomonas) rep3 (RNA-seq)


title: 24 DAP seed inoculated by Xcf (Xanthomonas) rep2 (RNA-seq)


title: Ctrl NPCs 362, NT, rep2


title: Ctrl NPCs 362, NT, rep1


title: 24 DAP seed inoculated by Xcf (Xanthomonas) rep1 (RNA-seq)


title: 42 DAP seed inoculated by water rep3 (RNA-seq)

value: no strain

value: Inoculated by water


title: Ctrl hFib, Q, rep3

source_name: foreskin fibroblasts

value: foreskin fibroblasts

value: ctrl


title: Negative control mimic, replicate 2 [NCM2]

city: Ghent

first: Yannick

last: Gansemans

address: Ottergemsesteenweg 460

department: Pharmaceutical Sciences

institute: Ghent University

description: Element Biosciences AVITI was used as the sequencing instrument

data_processing:
Raw read QC was done using FastQC (v0.11.9)
Adapter and quality trimming was done using cutadapt (v3.7)
Mapping of the trimmed reads on the reference genome was done using STAR (v2.7.10a)
UMI-based removal of mapped PCR duplicates was done using umi_tools (v1.1.4)
Expression quantification was done using rsem-calculate-expression (RSEM v1.3.3)
Assembly: Bos taurus ARS-UCD1.2 (Ensembl release 109)
Supplementary files format and content: all_samples_rsem_gene_counts.tsv: raw expression count table in tab separated format, with genes as rows and samples as columns

organism: Bos taurus

source_name: blastocyst

extract_protocol:
Total RNA was isolated from cells and purified using RNeasy Micro kit (Qiagen) following the manufacturer protocol.
Modified Smart-seq3xpress for 5’-end mRNA sequencing

value: blastocyst

value: Negative control mimic


title: Negative control mimic, replicate 1 [NCM1]


title: Ctrl hFib, B19, rep3


title: 42 DAP seed inoculated by water rep2 (RNA-seq)

value: Flavert

value: Seed developmental stages


title: Negative control inhibitor, replicate 3 [NCI3]

value: Negative control inhibitor


title: Ctrl hFib, NT, rep3


title: 35 DAP seed inoculated by water rep3 (RNA-seq)

value: Phaseolus vulgaris Flavert


title: Negative control inhibitor, replicate 1 [NCI1]


title: XDP hFib, NT, rep3

value: XDP


title: 42 DAP seed inoculated by water rep1 (RNA-seq)


title: RNASeq_PleD1


title: XDP hFib, Q, rep3

value: G4 ligand treatment Q


title: Negative control inhibitor, replicate 2 [NCI2]


title: 35 DAP seed inoculated by water rep2 (RNA-seq)


title: 35 DAP seed inoculated by water rep1 (RNA-seq)


title: Inhibitor, replicate 3 [I3]

value: microRNA-34c inhibitor supplementation


title: NMC hFib, Q, rep3


title: RNASeq_EV1


title: 24 DAP seed inoculated by water rep3 (RNA-seq)


title: NMC hFib, B19, rep3

value: G4 ligand treatment B19


title: Negative control mimic, replicate 3 [NCM3]


title: Inhibitor, replicate 1 [I1]


title: 24 DAP seed inoculated by water rep2 (RNA-seq)


title: 24 DAP seed inoculated by water rep1 (RNA-seq)


title: Mimic, replicate 5 [M5]

value: microRNA-34c mimic supplementation


title: XDP hFib, B19, rep3


title: XDP NPCs, Q, rep2

value: Neuronal progenitor cells


title: Kbu_low-carbon_replicat2

data_processing:
In brief, reads were trimmed using Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), then aligned against the N. oceanica reference genome using BWA (Li, Durbin, 2009). The mapped reads were with duplication marked using Picard and analyzed by DeepTools (Ramirez, Dundar, Diehl, Gruning, Manke, 2014) and MACS2 (Liu, 2014; Zhang, Liu, Meyer, Eeckhoute, Johnson, Bernstein, Nusbaum, Myers, Brown, Li, Liu, 2008). The “--broad” flag was on for peak calling, with reads from the input samples used as controls. Besides, differential analysis was performed using diffReps (Shen, Shao, Liu, Maze, Feng, Nestler, 2013), the resulting differential peaks were annotated using ChIPpeakAnno package (Zhu, Gazin, Lawson, Pages, Lin, Lapointe, Green, 2010).
Genome_build: Nannochloropsis oceanica IMET1 genome
Supplementary_files_format_and_content: bedgraph were generated.
Supplementary_files_format_and_content: differential peak text files

source_name: cells

extract_protocol:
N. oceanica cells (1-2 million cells · mL−1) from 400 mL culture were fixed under vacuum for 30 min with 1% formaldehyde (Sigma)at room temperature. After fixation, cells were incubated at room temperature for ten min under vacuum with 0.15 M glycine. Nuclei were isolated as described (Wei, Xu, 2018).
All subsequent end repairing, A-tailing, adaptor ligation, and library amplification steps were done following a standard protocol (Illumina). The final library was sequenced on an Illumina HiSeq 2500 instrument with 1×150-bp reads.

treatment_protocol: In total, six identical column reactors were employed. Each reactor contains 800 ml of fresh modified f/2 liquid medium, which was supplemented with 10 mM Tris-HCl buffer (pH=8.2) in order to accurately control the pH during the culture. Equal numbers of the seed cells were re-inoculated into each of the six column reactors to an OD750 of 1.5. The light intensity was maintained at 80±5 μmol m-2 s-1. The six algal cultures were first aerated with air enriched with 5% CO2 (“High CO2” conditions, or HC) for one hour. After the pre-adaption phase, three of the algal cultures proceeded under HC as the control condition, whereas the other three were switched to aeration with 0.04% CO2 (“Low CO2” conditions, or LC).After being transferred to the designated conditions, cell aliquots were taken at 24 h from each column by syringe for histone modification  profiling.

value: Kbu

value: low carbon


title: LNCaP_3X_H3K27ac_4h_rep2

value: ectopic Neutral MACC construct (3X) expressed LNCaP cell line

value: human prostate cancer cell line

value: Ectopic expression of the neutral MACC construct (3X)

value: 2.5uM Tamoxifen, 4h

value: H3K27ac antibody from Abcam (Cat# ab4729, AB_2118291)


title: Kbu_Low-carbon_replicat1


title: XDP NPCs, Q, rep1


title: Mimic, replicate 3 [M3]

value: blastocyst


title: Kbu_High-carbon_replicat2

value: High carbon


title: Mimic, replicate 2 [M2]


title: Mimic, replicate 1 [M1]


title: Kbu_High-carbon_replicat1


title: XDP NPCs, B19, rep2


title: XDP NPCs, B19, rep3


title: Control, replicate 4 [CTR4]

value: Untreated


title: K9m2_low-carbon_replicat2


title: Inhibitor, replicate 2 [I2]