title: Spt5-FRB_rapa_RNA-seq_rep2

description: DEseq2_RNAseq_analysis_DMSO_vs_Spt5AA.txt

data_processing:
Paired sequencing was performed, but only read1 FASTQ files were processed using usegalaxy.org. Illumina adapters were trimmed using Trim Galore!. Second trimming was performed to remove poly(A) (sequence to be trimmed off: AAAAAAAAAA) using Trim Galore!. Reads were aligned to a combined fasta file of S.cerevisiae and S.pombe genomes using TopHat (Kim et al., 2013). The aligned reads were filtered to remove PCR duplicates using RmDp and filtered for quality reads MAPQ > 49 using Filter SAM or BAM.
Counts table was created for S.cerevisiae and S.pombe genes using RStudio/Bioconductor. For spike-in normalisation, the estimateSizeFactors function in the DEseq2/RStudio package was applied to S.pombe counts table to calculate the relative amounts of S.pombe reads (i.e. normalisation ratio) in each sample (Love et al.,2014). The normalisation ratio obtained from S.pombe reads was then used as sizefactors value to calibrate S.cerevisiae counts table. Differential enrichment analysis was performed using the DEseq2/RStudio package (Love et al.,2014).
genome build: SacCer3 (R64) and ASM294v2
processed data file: Differential enrichment table from DEseq2 analysis.

growth_protocol: Cells were grown in YPD (30°C, 160 rpm) from OD600 0.2 to 0.65.

extract_protocol:
Cells were filtered and flash frozen in liquid nitrogen. 4 parts of the frozen S.cerevisiae pellet were spiked-in with one part of frozen S.pombe (containing a FLAG-tagged Rpb9) pellet (4:1 by weight). The combined pellet was ground with mixer mill (6 cycles, 3 min, 15 hz). The grindate was lysed in 20 mM HEPES (pH 7.4), 110 mM KOAc, 0.5 % Triton-X-100, 0.1 % Tween 20, 10 mM MnCl2, 1x proteinase inhibitors (Roche; complete, EDTA-free), 50 U/ml SUPERase.In RNase inhibitors (Invitrogen), 132 U/ml DNase I (Promega) in ice for 20 min, and cleared from cell debris (16,000 g, 10 min). Total RNA was extracted from supernatant using Qiagen miRNA kit according to the manufacturer’s instructions.
Large rRNA was depleted using Ribominus transcriptome isolation kit for yeast (Invitrogen) and standard NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

value: BY4741 tor1-1; fpr1<delta>; RPL13-2xFKBP12; SPT5-FRB-eGFP; RPB3-3xFLAG

value: Rapamycin (1mg/ml final in DMSO) addition 180 min prior to cell harvest

value: Total RNA


title: Spt5-FRB_DMSO_RNA-seq

status: Public on Sep 27 2021

type: SRA

city: Oxford

first: Ulku

last: Uzun

address: South Parks Rd

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

description: DEseq2_RNAseq_analysis_DMSO_vs_Spt4AA.txt

library_source: transcriptomic

molecule: total RNA

organism: Saccharomyces cerevisiae

tag: genotype

tag: treatment

value: DMSO treatment 120 min prior to cell harvest

tag: extracted molecule


title: WT_Sua7-FLAG_rep1

library_source: genomic

data_processing:
Paired FASTQ files were processed using usegalaxy.org. Illumina adapters were trimmed using Trim Galore!. Reads were aligned to SacCer3 and Pombe  genome using Bowtie2. Aligned reads were filtered to remove PCR duplicates using RmDp and filtered for quality reads MAPQ > 20 using Filter SAM or BAM.
To normalise reads to Pombe spike-ins, normalisation ratio was calculated to obtain the same amount of filtered Pombe BAM reads in each sample, and SacCer3 BAM reads were calibrated using Downsample SAM/BAM accordingly.
ChIP-seq peaks were obtained using MACS2 callpeak and the background signal was subtracted using MACS2 bdgcmp.
genome build: SacCer3 (R64) and ASM294v2
processed data file: bigwig files from MACS2 analysis

molecule: genomic DNA

growth_protocol: Cells were grown in YPD (30°C, 160 rpm) from OD600 0.2 to 0.6-0.8.

extract_protocol:
Cells were crosslinked as described in (Brown, Howe et al., 2018). Crosslinked cells were resuspended in cold FA‐150 buffer (10 mM HEPES pH 7.9, 150 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X‐100) and mixed with pre-crosslinked with S.pombe in 5:1 ratio (final S.pombe percentage being 16.7 %). The cell suspension was lysed with glass beads using the MagnaLyser (Roche; 6 x 45 s runs, 2500 g, 4°C). The lysate was sheared 30-40 min with a bioruptor sonicator 30 sec ON/30 sec OFF at high setting. The sheared lysate was cleared by centrifuge (10,000 g, 15 min, 4°C) and the supernatant was incubated with anti-FLAG (M2) antibody for 15–20 h rotating at 4°C. Bound chromatin was immunoprecipitated for 90 min at 22°C with pre‐blocked Dynabeads protein G. Beads and attached chromatin were pelleted, washed, and immunoprecipitated chromatin was eluted from the beads as described in (Brown, Howe et al., 2018). DNA was eluted with Zymoclean ChIP concentrator kit according to the manufacturer’s instructions.
standard NEBNext Ultra II DNA Library Prep Kit for Illumina

value: BY4741 SUA7-3xFLAG

value: no treatment

value: DNA


title: DAPT1 0h rep1

city: Planegg-Martinsried

first: Jasmin

last: Moneer

state: Munich

address: Grosshadernerstrasse

department: Biologie II

country: Germany

institute: LMU

description: The reads were demultiplexed. Illumina adapters and polyA sequences were trimmed and splice leader sequences (Stover and Steele, 2001) were removed from both forward and reverse reads. The tool ‘fastqfilter’ was used to ensure the paired nature of the filtered dataset, to filter out reads with a quality score lower than 20 and to exclude reads with a read length shorter than 30bp . Reads that contained ‘N’s were also removed from the dataset. Uploaded are the final reads.

data_processing:
Illumina adapters and polyA sequences were trimmed and splice leader sequences (Stover and Steele, 2001) were removed from both forward and reverse reads. The tool ‘fastqfilter’ was used to ensure the paired nature of the filtered dataset, to filter out reads with a quality score lower than 20 and to exclude reads with a  read length shorter than 30bp . Reads that contained ‘N’s were also removed from the dataset.
All forward and all reverse reads from all sequencing libraries were concatenated. The two resulting files were then used as input to the Trinity (version 2.8.4; Grabherr et al., 2011) de novo transcriptome assembler.
The assembly was run with the following parameters: -strand-specific library, in silico normalisation, -min_contig_length 300, -min_kmer_cov 1, no genome guided mode and no Jaccard Clip options.
The processed reads of the 36 RNA-seq libraries (timepoints 0, 3 and 6 h, DAPT and control samples, six replicates) were separately mapped to the de novo assembled transcriptome reference, within the Galaxy platform. The reads were mapped as strand-specific and with a maximum insert size of 800. RSEM (Li and Dewey, 2011) - with Bowtie2 (Langmead and Salzberg, 2012; Langmead et al., 2009) as alignment method- was used as the abundance estimation method.
The raw counts were used as input for differential expression (DE) analysis by DESeq2 (version 1.18.1).

organism: Hydra vulgaris

source_name: whole animals

growth_protocol: Animals of the strain Hydra vulgaris (Basel) were grown in Hydra medium (0.1 mM KCl, 1 mM NaCl, 0.1 mM MgSO4, 1 mM Tris and 1

extract_protocol: RNA-seq libraries were prepared for six biological replicates for each experimental condition. cDNA libraries were synthesized from total RNA using the strand specific SENSE mRNA-Seq Library Prep Kit V2 for Illumina (Lexogen) and the Purification Module with Magnetic Beads (Lexogen). The samples were multiplexed and sequenced on three lanes on Illumina Hiseq2000 with a 100 bpsequencing strategy.

treatment_protocol: Regularly fed animals were starved for 24 h and incubated in either 20 μM DAPT with 1% DMSO in Hydra medium or in only 1% DMSO in Hydra medium (control sample) for 48 h. DAPT and DMSO were renewed every 12 h. Animals were collected, and total RNA was isolated at three different time points: directly at the end of 48 h (0 h), 3 h after DAPT removal (3 h) and 6 h after DAPT removal (6 h). After 48 h incubation, DAPT was removed and replaced with 1% DMSO in Hydra medium for the samples 3 h and 6 h. About 25 animals were collected per sample

value: DAPT

tag: replicate

tag: tissue

value: basel

tag: time point


title: DMSO3 0h rep3

value: DMSO (control)


title: S14

city: Athens

first: Maria

middle: G.

last: Tektonidou

state: Please choose a State

address: Mikras Asias 75

country: Greece

institute: National and Kapodistrian University of Athens

data_processing:
Basecalling on Illumina NextSeq550
Alignement with STAR on hg38 with pipeline provided by Lexogen and BlueBee
Bam files summarised to 3’UTR count table with GenomicRanges R package
Gene count table normalised with DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: bigWig constructed through metaseqR2 with stranded=FALSE, normTo=1e+08

organism: Homo sapiens

extract_protocol:
Total RNA was isolated from whole blood, stored in paxgene, using the ExtractionMonarch® Total  RNA Miniprep Kit (NEB #T2010). Upon blood isolation, Monarch DNA/RNA Protection Reagent  (supplied as a 2x concentrate) was added undiluted to an equal volume of blood. Addition of the  protection reagent and the following RNA isolation was performed as described in the Kit's manual  for Total RNA Purification from Mammalian Whole Blood Samples.
After quantification on a NanoDrop ND-1000 (Thermofisher) and Bioanalyzer RNA 6000 Nano  assay (Agilent), 140-300ng of total RNA from samples passing quality control were processed  using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, 015.96) for library  preparation. Libraries were assessed for molarity and median library size using Bioanalyzer High  Sensitivity DNA Analysis (Agilent, 5067-4626)
RNA sequencing. The kit creates Illumina compatible libraries of sequences close to the 3’ end of polyadenylated RNA.

tag: subject status

value: anti-SARS-CoV2 antibody positive healthy individual

tag: age

tag: gender

value: F

tag: status

value: S

value: Whole Blood


title: S15

value: M


title: Spt5-FRB_rapa_RNA-seq_rep1


title: A16

value: A


title: S13


title: S12


title: WT_RNA-seq_rep1

description: DEseq2_RNAseq_analysis_WT_vs_spt4del.txt

value: BY4741 RPB3-3xFLAG


title: Spt4-FRB_rapa_RNA-seq_rep2

value: BY4741 tor1-1; fpr1<delta>; RPL13-2xFKBP12; SPT4-FRB-eGFP; RPB3-3xFLAG

value: Rapamycin (1mg/ml final in DMSO) addition 140 min prior to cell harvest


title: Spt4-FRB_DMSO_RNA-seq

value: Total RNA


title: S10


title: spt4del_Spt5_TEF-seq_rep2

data_processing:
Library strategy: TEF-seq
Single-end FASTQ files were processed using usegalaxy.org and RStudio. Reads were groomed using FASTQ groomer for Sanger & Illumina 1.8 + (Blankenberg et al., 2010). Adapter sequence ATCTCGTATGCCGTCTTC were trimmed and reads < 15 nt were discarded using Clip function. Reads were aligned to a combined fasta file of S.cerevisiae and S.pombe genomes using Bowtie for Illumina (Langmead, 2011). SAM files were converted to BAM files using SAM-to-BAM (Li, 2011).
Using RStudio/Bioconductor packages, multiply aligned reads were filtered, and reads were narrowed to the 3’ends. For spike-in normalisation, counts table was created for S.pombe genes using RStudio/Bioconductor. The estimateSizeFactors function in the DEseq2/RStudio package was applied to calculate the relative amounts of S.pombe reads (i.e. normalisation ratio) in each sample (Love, Huber, and Anders 2014). NET-seq data were calibrated by dividing S.cerevisiae reads by the normalisation ratios.
For no tag normalisation, NET-seq was performed on strains without a FLAG-tag to detect background signal during the IP. The SCR1 gene is transcribed by RNAPIII and gives a high non-specific signal in the TEF-seq IPs, and this locus was used for no-tag normalisation. The reads on chrV [442007:442458] were split into 10 nt bins and FLAG-tag over no tag sample ratio is calculated for each bin. The mean SCR1 ratio then multiplied by the no tag data and subtracted from the FLAG-tagged samples.
genome build: SacCer3 (R64) and ASM294v2
processed data file: normalised bigwig file for positive strand
processed data file: normalised bigwig file for negative strand

extract_protocol:
Cells were filtered and flash frozen in liquid nitrogen. 4 parts of the frozen S.cerevisiae pellet were spiked-in with one part of frozen S.pombe (containing a FLAG-tagged Rpb9) pellet (4:1 by weight). The combined pellet was lysed, and immunoprecipitation of the FLAG-tagged proteins was performed at 4°C as described in (Fischl et al., 2017). RNA was isolated with Qiagen miRNA kit according to the manufacturer’s instructions.
The isolated RNA was adapter ligated, fragmented, reverse transcribed, circularized, barcoded, and amplified as described in (Fischl et al., 2017).

value: BY4741 spt4<delta>;SPT5-3xFLAG

value: native RNA


title: A17


title: Spt4-FRB_rapa_RNA-seq_rep1


title: DMSO2 0h rep2


title: WT_RNA-seq_rep2

value: no treatment


title: Spt4_TEF-seq_rep1

value: BY4741 SPT4-3xFLAG


title: A15


title: spt4del_RNA-seq_rep2

value: BY4741 spt4<delta>;RPB3-3xFLAG


title: S9


title: S11


title: spt4del_Spt5_TEF-seq_rep1


title: spt4del_RNA-seq_rep1


title: A11


title: No-FRB_rapa_NET-seq

data_processing:
Library strategy: NET-seq
Single-end FASTQ files were processed using usegalaxy.org and RStudio. Reads were groomed using FASTQ groomer for Sanger & Illumina 1.8 + (Blankenberg et al., 2010). Adapter sequence ATCTCGTATGCCGTCTTC were trimmed and reads < 15 nt were discarded using Clip function. Reads were aligned to a combined fasta file of S.cerevisiae and S.pombe genomes using Bowtie for Illumina (Langmead, 2011). SAM files were converted to BAM files using SAM-to-BAM (Li, 2011).
Using RStudio/Bioconductor packages, multiply aligned reads were filtered, and reads were narrowed to the 3’ends. For spike-in normalisation, counts table was created for S.pombe genes using RStudio/Bioconductor. The estimateSizeFactors function in the DEseq2/RStudio package was applied to calculate the relative amounts of S.pombe reads (i.e. normalisation ratio) in each sample (Love, Huber, and Anders 2014). NET-seq data were calibrated by dividing S.cerevisiae reads by the normalisation ratios.
genome build: SacCer3 (R64) and ASM294v2
processed data file: normalised bigwig file for positive strand
processed data file: normalised bigwig file for negative strand

value: BY4741 tor1-1; fpr1<delta>; RPL13-2xFKBP12; RPB3-3xFLAG

value: Rapamycin (1mg/ml final in DMSO) addition 90 min prior to cell harvest


title: Spt5-FRB_rapa_NET-seq_rep1

value: BY4741 tor1-1; fpr1<delta>; RPL13-2xFKBP12; SPT5-FRB-eGFP; RPB3-3xFLAG

value: Rapamycin (1mg/ml final in DMSO) addition 180 min prior to cell harvest


title: S8

value: anti-SARS-CoV2 antibody positive healthy individual

value: F

value: S


title: A12

value: A

value: Whole Blood


title: A14

value: M


title: Spt4-FRB_rapa_NET-seq_rep1

value: BY4741 tor1-1; fpr1<delta>; RPL13-2xFKBP12; SPT4-FRB-eGFP; RPB3-3xFLAG

value: Rapamycin (1mg/ml final in DMSO) addition 140 min prior to cell harvest


title: Spt4_TEF-seq_rep2


title: Spt5_TEF-seq_rep1

value: BY4741 SPT5-3xFLAG


title: Spt5_TEF-seq_rep2

value: native RNA


title: Spt5-FRB_DMSO_NET-seq

value: DMSO treatment 120 min prior to cell harvest


title: S5


title: Spt5-FRB_rapa_NET-seq_rep2


title: A10


title: spt4del_notag_NET-seq

data_processing:
Library strategy: NET-seq
Single-end FASTQ files were processed using usegalaxy.org and RStudio. Reads were groomed using FASTQ groomer for Sanger & Illumina 1.8 + (Blankenberg et al., 2010). Adapter sequence ATCTCGTATGCCGTCTTC were trimmed and reads < 15 nt were discarded using Clip function. Reads were aligned to a combined fasta file of S.cerevisiae and S.pombe genomes using Bowtie for Illumina (Langmead, 2011). SAM files were converted to BAM files using SAM-to-BAM (Li, 2011).
Using RStudio/Bioconductor packages, multiply aligned reads were filtered, and reads were narrowed to the 3’ends. For spike-in normalisation, counts table was created for S.pombe genes using RStudio/Bioconductor. The estimateSizeFactors function in the DEseq2/RStudio package was applied to calculate the relative amounts of S.pombe reads (i.e. normalisation ratio) in each sample (Love, Huber, and Anders 2014). NET-seq data were calibrated by dividing S.cerevisiae reads by the normalisation ratios.
For no tag normalisation, NET-seq was performed on strains without a FLAG-tag to detect background signal during the IP. The SCR1 gene is transcribed by RNAPIII and gives a high non-specific signal in the NET-seq IPs, and this locus was used for no-tag normalisation. The reads on chrV [442007:442458] were split into 10 nt bins and FLAG-tag over no tag sample ratio is calculated for each bin. The mean SCR1 ratio then multiplied by the no tag data and subtracted from the FLAG-tagged samples.
genome build: SacCer3 (R64) and ASM294v2
processed data file: normalised bigwig file for positive strand
processed data file: normalised bigwig file for negative strand

value: BY4741 spt4<delta>

value: no treatment


title: Spt4-FRB_rapa_NET-seq_rep2


title: A9


title: A13


title: S7


title: A8


title: dst1del_NET-seq_rep2

value: BY4741 dst1<delta>;RPB3-3xFLAG


title: WT_notag_NET-seq


title: S4


title: dst1del_NET-seq_rep1


title: Spt4-FRB_DMSO_NET-seq


title: dst1del_notag_NET-seq

value: BY4741 dst1<delta>


title: S6


title: S3


title: A7


title: spt4del_NET-seq_rep2

value: BY4741 spt4<delta>;RPB3-3xFLAG


title: A6


title: A5


title: spt4del_NET-seq_rep1


title: S2


title: KU812_shNC_2

city: Shanghai

first: Wei

last: Yusheng

state: New York

address: 227,South Road of Chongqian,Shanghai,China

country: China

institute: Shanghai Jiao Tong University of Medicine

data_processing:
The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina HiSeqXTen.
The clean reads were then aligned to  genome (mouse version:GRCm38 NCBI; human version:GRCh38 NCBI) using the hisat2. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.HTseqwas used to count gene and lncRNA counts and RPKM method was used to determine the gene expression.
We applied DESeq algorithm to filter the differentially expressed genes, after the protocol significant analysis
Genome_build: GRCm38 NCBI;GRCh38 NCBI
Supplementary_files_format_and_content: text files include FPKM values for each Sample

source_name: Peripheral blood

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: chronic myelogenous leukemia cell line

tag: transfection

value: shNC


title: spt4del_MNase-seq_rep3

data_processing:
Paired FASTQ files were processed using usegalaxy.org. Illumina adapters were trimmed using Trim Galore!. Reads were aligned to SacCer3 genome using Bowtie2.
Aligned reads were filtered to remove PCR duplicates using RmDp and filtered for quality reads MAPQ > 20 using Filter SAM or BAM.
BAM files were further analysed using a peak calling software DANPOS2 (Chen et al., 2013).
genome build: SacCer3
processed data file: bigwig files showing peaks from DANPOS2 software
processed data file: bigwig files showing nucleosome centres from DANPOS2 software

growth_protocol: Cells were grown in YPD (30°C, 160 rpm) from OD600 0.2 to 0.6.

extract_protocol:
Cells were harvested and incubated in 2.8 mM EDTA, pH 8, 0.7 M 2-mercaptoethanol (30°C, 30 min). Then samples were pelleted and washed with 1 M sorbitol. The pellet was resuspended in 1 M sorbitol, 5 mM 2-mercaptoethanol solution and zymolase solution (30°C for 30 min). The lysate was pelleted and washed with 1 M sorbitol. Nuclei were resuspended in 18% Ficoll, 20 mM KH2PO4, 1 mM MgCl2, 0.25 mM EGTA, 0.25 mM EDTA and stored as pellet. Nuclei was digested with 80U of MNase (Nuclease S7; 37°C, exactly 10 min). Reaction was quenched with 5% SDS, 50 mM EDTA solution (65°C). Following protein and RNA digestion, DNA was eluted with Zymoclean ChIP concentrator kit according to the manufacturer’s instructions. Isolated DNA was run on a 1.5% agarose-TBE gel and the mononucleosomal DNA band was gel extracted.
standard NEBNext Ultra II DNA Library Prep Kit for Illumina

value: mononucleosomal DNA


title: WT_NET-seq_rep1

value: BY4741 RPB3-3xFLAG


title: A3

value: anti-SARS-CoV2 antibody positive healthy individual

value: A


title: A2

value: M

value: Whole Blood


title: S1

value: F

value: S


title: A4


title: A1


title: WT_MNase-seq_rep2


title: E13.5 male input for H3K9me3 rep3

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
raw reads were aligned to UCSC mm9 mouse genome obtained from iGenome with BWA (0.7.5a)
aligned reads were sorted by Picard SortSam tool (1.9)
duplicated reads were removed by Picard MarkDuplicates tool (1.9)
using samtools view (0.1.18) with -F 4 -f 0x02, we only kept properly paired reads for downstream analysis
bamCoverage function from deeptools (3.3.0) were applied to generated bigwig files with arguments -blackListFileName mm9-blacklist.bed --effectiveGenomeSize 2620345972 --normalizeUsing CPM
Peak calling was performed using MACS2 (2.1.0) with arguments -f BAMPE --broad -g mm
Genome_build: mm9
Supplementary_files_format_and_content: bigwig and BED6+3 format

organism: Mus musculus

source_name: Primordial germ cells

extract_protocol:
PGCs were FACS sorted into cold PBS and were lysed by nuclei isolation buffer (Sigma, NUC-101). For E10.5, PGCs were pooled from different embryos. 1000 PGCs were used for each ChIP reaction. Samples were permeabilized with 0.1% Triton-X-100 /0.1% deoxycholate in PBS on ice. Samples were digested with 200 U of micrococcal nuclease (New England Biolabs, M0247S) in digestion buffer at 21 °C for 7.5 mins and the reaction was stopped with 100 mM EDTA. An aliquot of chromatin (10%) was used as an input control. Samples were pre-cleaned by protein A/G beads for 2 hours at 4°C. Meanwhile, 250 ng anti-H3K9me3 (Diagenode, C15410056) and anti-H3K27me3 (Millipore, 07-449) antibodies were incubated with protein A/G beads for 2 hours at 4°C. Chromatin samples were incubated with antibody-bound beads overnight at 4°C. Samples were washed by two low-salt washes and one high salt wash and eventually DNA was eluted from the beads for 1.5 hours at 60°C. For sizes selection, AMPure XP beads were used at 1.8:1 ratio.
Library preparation was performed using a MicroPlex Library Preparation kit v2 (Diagenode, C05010013) following manufacturer’s recommendations. Libraries were further purified by AMPure XP beads at 1:1 ratio. Library quality was measured with a 2100 Bioanalyzer Instrument (Agilent) and library size was assessed with a Kapa library qPCR quantification kit (Roche, KK4824). Library sequencing was performed in a 100bp paired-end mode with a HiSeq 2500 System (Illumina) following manufacturer’s recommendations.

tag: genetic background

value: C57BL/6 x GOF18delta_PE-EGFP

value: Primordial germ cells

tag: Stage

value: wild type

tag: Sex

value: male


title: spt4del_MNase-seq_rep2

value: no treatment


title: Y2_Veh

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

institute: Tianjin Medical University

data_processing:
Basecalls performed using BGISEQ-500
SOAPnuke was used to get the "clean reads".
Mapping clean reads to Mus_musculus whole genome using BWA.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: Mus musculus (mm39)
Supplementary_files_format_and_content: fpkm, counts, tpm values for each Sample

source_name: MSC

growth_protocol: MSCs was cultured in DMEM medium with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using BGISEQ500 protocol

treatment_protocol: MSCs was 1 µM melatonin treated for 24 hours.

value: mouse bone marrow

tag: cell type

value: MSCs

value: young


title: Y5_Veh


title: O5_Veh

value: old

value: vehicle


title: O9_Veh


title: O8_Veh


title: WT_NET-seq_rep2

value: BY4741 RPB3-3xFLAG

value: native RNA


title: E13.5 female input for H3K9me3 rep3

value: female


title: O5_Mel

value: melatonin


title: O2_Veh


title: WT_MNase-seq_rep1

value: mononucleosomal DNA


title: Infection 3

city: Rochester

first: Roberto

last: Cattaneo

state: MN

address: 222 3rd Ave SW

department: Molecular Medicine

country: USA

institute: Mayo Clinic

description:
total RNA (ribosomal depleted)
iPSC-CMs_Infec-3_48h.FCHKNLJBBXY_L2_R*_ICTAGCGCT-GTGTAGAC

data_processing:
Base-calling was performed using Illumina’s RTA version 2.7.7
The quality of the raw RNA-seq data was assessed by fastqp v0.20.1, and quality reads were filtered and aligned against human genome (hg19) using STAR alignment (v2.7.8a) in 330 galaxy platform (https://usegalaxy.org). The aligned reads were counted using htseq-count 331 v0.9.1 and and 0.5 read counts per million (CPM) in at least two samples was used as an expression threshold.
Trimmed mean of M values normalized (TMM) (58) and log2 transformed 333 data was used for plotting heatmaps and differential analysis in limma (59).
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Differentiated hiPSC-CMs were maintained in Gibco™ Cardiomyocyte Maintenance Medium

extract_protocol:
Direct-zol RNA Miniprep kit (R2050)
Illumina TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold (Illumina, San Diego, CA).

value: human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs)

value: SARS-CoV-2/UW001/Human/2020/Wisconsin (UW-001) at MOI of 0.01 for 48hrs


title: WT_MNase-seq_rep3


title: E13.5 female input for H3K27me3 rep3

value: C57BL/6 x GOF18delta_PE-EGFP


title: E13.5 male input for H3K27me3 rep3

value: Primordial germ cells


title: Y4_Veh


title: O3_Veh


title: O1_Veh


title: O3_Mel


title: spt4del_MNase-seq_rep1

value: BY4741 spt4<delta>;RPB3-3xFLAG


title: E10.5 input rep3

value: wild type


title: Infection 1

description:
total RNA (ribosomal depleted)
iPSC-CMs_Infec-1_48h.FCHKNLJBBXY_L2_R*_ICGTCTGCG-TTCACAAT


title: E13.5 male H3K9me3 rep3

value: male


title: O1_Mel

value: mouse bone marrow


title: E13.5 male H3K27me3 rep3


title: Bacteria (GB00112) exposed to cells for 24hr

city: East Lansing

first: Shannon

middle: D

last: Manning

state: MI

address: 1129 Farm Lane

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v1.18.64
The output of RTA was demultiplexed and converted to FastQ files with Illumina Bcl2fastq, v1.8.4
Analysis was carried out on the CLC Genomics workbench using the RNAseq analysis tool by mapping the reads to the GB00112 (AKXO00000000.1) genome
Differential expression analysis was performed using EdgeR using the following comparisons: 1hr vs media alone, 24hr vs media alone, and 1hr vs 24hr. A significant difference in expression was accepted for genes with at least a 2 fold change in expression and P < 0.05
Genome_build: GB00112 genome,AKXO00000000.1
Supplementary_files_format_and_content: xls file containing EdgeR data

organism: Streptococcus agalactiae

source_name: Bacteria

growth_protocol: THP-1 cells were maintained in RPMI 1640 medium without antibiotics and were infected with GB0112 at a multiplicity of infection (MOI) of 10:1.

extract_protocol:
RNA samples were collected from bacterial culture in liquid medium by adding two volumes of RNAprotect Bacteria Reagent (Qiagen) or from bacteria inside macrophages by washing the cells twice with PBS then adding 1 mL RNAprotect Bacteria Reagent directly to the cells. RNA was extracted using the RNeasy minikit (Qiagen) using enzymatic lysis, Proteinase K digestion, and mechanical disruption. Residual genomic DNA was removed using the Turbo DNA-free kit (Ambion).
Illumina TruSeq Stranded mRNA Library Prep Kit was used. The protocol was modified to skip the oligo-dT bead step and proceeded directly to fragmentation and first strand synthesis

treatment_protocol: Cocultured cells were incubated at 37°C in air supplemented with 5% carbon dioxide for 1 to 24h prior to RNA extraction.

tag: strain

tag: exposure

value: THP-1 24 hour


title: Bacteria (GB00112) exposed to cells for 1hr

value: THP-1 1 hour


title: Infection 2

description:
total RNA (ribosomal depleted)
iPSC-CMs_Infec-2_48h.FCHKNLJBBXY_L2_R*_ITCGATATC-ACACGAGT

tag: treatment


title: E10.5 H3K27me3 rep3

tag: genotype


title: Treg KO female CSF1, 3

city: San Francisco

first: Ilia

middle: D.

last: Vainchtein

state: California

address: 1550 4th street

department: Psychiatry

institute: UCSF

data_processing:
QC with FASTQC (all samples passed)
Alignment with STAR version 2.5.4b
Reads counted with HTSeq (version 0.9.0)
Read normalization and DEGs calculated using DESeq2 version 1.24.0
Genome_build: GRCm38
Supplementary_files_format_and_content: excel, contains DEGs at adjusted p<0.05

source_name: lumbar dorsal horn spinal cord

extract_protocol:
Microglia were isolated using a tissue homogenizer and 22% Percoll gradient, all on ice or 4C, and collected with FACS.
Libraries were generated using the Nugen Trio RNA-Seq kit

treatment_protocol: CSF1 i.t. injection for 3 days

value: 8-12 weeks

value: Microglia

value: Treg KO


title: E13.5 female H3K27me3 rep3


title: ApoE4

city: Boston

first: I-Hsiu

last: Lee

state: Massachusetts

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

data_processing:
Base-calling was carried out with Illumina proprietary software
Sequencing reads were aligned to the mouse reference genome GRCm38.p6 with STAR 2.7.3a.
Read count per gene was obtained from STAR’s “quantMode” with the “GeneCounts” option using the mouse genome annotations from Ensembl database release 98
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text file includes gene-level raw counts for each sample

source_name: bone marrow

extract_protocol:
Bone marrow was flushed and enzymatically digested in Dulbecco’s Modified Eagle’s Medium without phenol red (D1145, Sigma-Aldrich, St. Louis, MO, USA) containing 1mg/mL Collagenase Type 4 (LS004188, Worthington Biochemical Corporation, Lakewood Township, NJ, USA) and 2mg/mL Dispase II (D4693, Sigma-Aldrich) for 30min at 37°C with gentle agitation. RNA was extracted from flow sorted bone marrow endothelial cells using the NucleoSpin RNA XS Kit (740902.50, Takara Bio, Kusatsu, Japan).
Total isolated RNA was subjected to polyA selection, followed by NGS library construction using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA).

value: 20 weeks

tag: group

value: atherosclerotic Apoe knockout mice (ApoE)

value: endothelial cells


title: E13.5 female H3K9me3 rep3

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling. Fastq Screen (0.13.0) was applied to ChIP-seq E13.5 Female H3K9me3 replicate 3 to remove the reads that uniquely aligned to human genome using arguments "--tag --inverse --filter 3000000". In the fastq_screen.conf, we set genomes from Human:Mouse:Yeast:Adaptor:Contaminant:Worm:Fly.
Filtered reads were aligned to UCSC mm9 mouse genome obtained from iGenome with BWA (0.7.5a)
aligned reads were sorted by Picard SortSam tool (1.9)
duplicated reads were removed by Picard MarkDuplicates tool (1.9)
using samtools view (0.1.18) with -F 4 -f 0x02, we only kept properly paired reads for downstream analysis
bamCoverage function from deeptools (3.3.0) were applied to generated bigwig files with arguments -blackListFileName mm9-blacklist.bed --effectiveGenomeSize 2620345972 --normalizeUsing CPM
Peak calling was performed using MACS2 (2.1.0) with arguments -f BAMPE --broad -g mm
Genome_build: mm9
Supplementary_files_format_and_content: bigwig and BED6+3 format

tag: tissue

value: female


title: Mock 2

description:
total RNA (ribosomal depleted)
iPSC-CMs_Mock-2_48h.FCHKNLJBBXY_L1_R*_IACGCACCT-GGTGAAGG

source_name: human fibroblast-derived iPSCs_mock

value: human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs)

value: mock infection


title: Mock 3

description:
total RNA (ribosomal depleted)
iPSC-CMs_Mock-3_48h.FCHKNLJBBXY_L1_R*_ITACTCATA-CCTGTGGC


title: Mock 1

description:
total RNA (ribosomal depleted)
iPSC-CMs_Mock-1_48h.FCHKNLJBBXY_L1_R*_IGTATGTTC-AACAGGAA


title: Treg KO female CSF1, 2


title: Bacteria (GB00112) only

value: RPMI 1640 control


title: Treg KO female CSF1, 4


title: ApoE3


title: ApoE2


title: Treg KO female CSF1, 1


title: WT female CSF1, 2

value: WT


title: HTN3

value: hypertensive mice with chronic angiotensin II treatment


title: Et-sprayed, experiment 1, biological rep3

type: RNA

city: Girona

first: Emilio

last: Montesinos

state: Girona

address: c/Pic de Peguera, 15. PCiT. Edif. Jaume Casademont, porta E, 4t pis

department: INTEA

country: Spain

institute: Universitat de Girona

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Tomato Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The microarray gene expression data was analyzed using GeneChip Expression Consol software (Affimetrix). Raw data (.cel files) were imported and processed, using Robust Multiarray Averaging (RMA) background correction, quantile normalization. Pre-processed data was analyzed by the web-base Babelomics (Medina et al., 2010) for gene expression analysis as the ratio of normalized fluorescence value between two compared treatments. This ration was then scaled using base 2 logarithm to obtain the log2 ratio, which in absolute terms is known as fold-change.

label: biotin

organism: Solanum lycopersicum

source_name: Leaves of Solanum lycopersicum 24 hours after spray treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seeds of tomato plants cv. Rio Grande were sown in hydroponic seed plugs (rockwool), germinated and grown under controlled greenhouse conditions (25±2 ºC, 16 h light/ 15±2 ºC, 8 h dark, and 60% RH). Two-week old seedlings (two cotyledons) were transplanted into Rockwool plugs (7.5x7.5x6.5 cm).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions after homogenization using TissueLyzerII system

treatment_protocol: After two weeks from transplanting, plants were sprayed with aqueous solutions of BP178 BP100 or flg 15 at 125 µM, SA and JA at 2.5 mM, to the run-off point.

value: leaves

value: Et-sprayed


title: flg15-sprayed, experiment 2, biological rep1


title: Et-sprayed, experiment 1, biological rep2


title: flg15-sprayed, experiment 2, biological rep2


title: Et-sprayed, experiment 1, biological rep1


title: JA-sprayed, experiment 1, biological rep2

value: JA-sprayed


title: SA-sprayed, experiment 1, biological rep3

value: SA-sprayed


title: HTN4


title: flg15-sprayed, experiment 2, biological rep3


title: WT female CSF1, 1


title: Male Saline

data_processing:
QC with FASTQC (all samples passed)
Alignment with STAR version 2.5.4b
Reads counted with HTSeq (version 0.9.0)
Read normalization and DEGs calculated using DESeq2 version 1.24.0
FPKM values were generated using Cufflinks v2.2.1
Genome_build: GRCm38
Supplementary_files_format_and_content: excel, FPKMs of all genes for each sample
Supplementary_files_format_and_content: excel, DEGs at adjusted p<0.01

extract_protocol:
Microglia were isolated using a tissue homogenizer and 22% Percoll gradient, all on ice or 4C, and collected with FACS.
Nugen Ovation RNA-Seq System V2 kit

treatment_protocol: CSF1 or saline i.t. injection for 3 days

tag: agent

value: Saline

value: male


title: JA-sprayed, experiment 1, biological rep3


title: JA-sprayed, experiment 1, biological rep1


title: Female CSF1, 3

value: 8-12 weeks

value: Microglia

value: Female


title: HTN2

value: 20 weeks


title: E10.5 H3K9me3 rep3

value: C57BL/6 x GOF18delta_PE-EGFP

value: Primordial germ cells

value: wild type


title: SA-sprayed, experiment 1, biological rep1


title: BP178-sprayed, experiment 1, biological rep3


title: BP178-sprayed, experiment 1, biological rep2


title: MI4

value: 2 days after acute myocardial infarction

value: endothelial cells


title: mock-sprayed, experiment 2, biological rep1

value: mock-sprayed


title: SA-sprayed, experiment 1, biological rep2


title: BP178-sprayed, experiment 1, biological rep1


title: mock-sprayed, experiment 2, biological rep3


title: mock-sprayed, experiment 1, biological rep3


title: MI3


title: MI2


title: Input-O7-V_FKDL210126322-1a

data_processing:
Basecalls performed using HiSeqX
ChIP-seq reads were aligned to the mm39 genome assembly using BWA version 0.7.13 with the following configurations -q 5 -l 32 -k 2
Data were filtered using Picard-tools version 1.126
peaks were called using macs2 version 2.1.0 with the following setting: -pvalue 0.01 --keep-dup all --extsize -1 --shift 0
Genome_build: Mus musculus (mm39)
Supplementary_files_format_and_content: narrowpeak files

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to the TruePrep® DNA Library Prep Kit V2 for Illumina (TD503-02). Briefly, TruePrep Tagment Enzyme Mix (TTEMix) contains transposase and two kinds of adapters (Adapter 1 and Adapter 2) with equal molar. Input DNA are fragmented and linked with adapters on both ends just by mixing with TTE Mix, followed by a 10-minute incubation at 55℃. The tagged DNA fragments can be further amplified with two pairs of primers N5 (N5XX) / N7 (N7XX) and P5 / P7 (PCR Primer Mix, PPM).  After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq X following the manufacturer's protocols.

value: mouse bone marrow

value: MSCs

value: untreated

tag: chip antibody


title: ChIP-O7-V_FKDL210126324-1a


title: Ctr4

tag: age

value: naive control


title: mock-sprayed, experiment 1, biological rep2

value: leaves


title: LSK_KO_1

source_name: Bone marrow

tag: genotype/variation


title: Adult Smooth Muscle Cells [SMC]

city: München

first: Stefanie

middle: A

last: Doppler

address: Lazarettstraße 36

department: Department of Cardiovascular Surgery

institute: German Heart Center Munich at the Technische Universität München

data_processing:
Raw sequencing reads were converted to FASTQ files using Cell Ranger (version 3.1.0) mkfastq command.
The CellRanger count command was used to generate gene expression matrix
Additional downstream analysis was done by Seurat R package
Genome_build: GRCh38
Supplementary_files_format_and_content: Barcode, feature and expression matrix file of each sample

source_name: Adult human vessel

extract_protocol:
Cultured cells were detached using trypsin-EDTA and further processed according the protocols of Chromium Single Cell 3’ Reagent Kits v2 and v3.1 (10x Genomics, Pleasanton, CA) to extract RNA from single cells.
Libraries were prepared according to protocols of Chromium Single Cell 3’ Reagent Kits v2 and v3.1 (10x Genomics, Pleasanton, CA).

tag: diagnosis

value: atherosclerotic heart disease

tag: surgery

value: coronary artery bypass graft

tag: gender

value: 66 years

value: Adult human vessel

value: Adult Smooth Muscle Cells

tag: passage

tag: molecule subtype

value: cytoplasmic RNA


title: LSK_WT_2

value: WT


title: m1_str_GFP+

city: New York

first: Panos

last: Roussos

state: NY

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
We combined fluorescence activated cell sorting (FACS) followed by 8 ATAC-seq libraries prepared from 4 animals
We generated a consensus set of 69,220 OCRs by taking the union of peaks called in the individual cells
For annotation of OCRs: we used the gene annotations form the org.Mm.eg.db (version 3.8.2) package.
The genomic context was defined as promoter (+/- 3kb of any TSS), 5’-UTR, 3’-UTR, exon, intron, distal intergenic and downstream.
Genome_build: GRCh38-mm10
Supplementary_files_format_and_content: After removing peaks overlapping the blacklisted genomic regions, 69,229 peaks remained. We subsequently quantified read counts of all the individual non-merged samples within these peaks, again, using the featureCounts function in RSubread (Liao et al. 2014) (v.1.15.0). We counted fragments (defined from paired-end reads), instead of individual reads, that overlapped with the final consensus set of peaks.

source_name: FACS sorted EGFP(+) cells from the PND3 striatum from GENSAT Nr4a1-EGFP mice

extract_protocol: GFP positive and negative cells were isolated by FACS using a FACSAria flow cytometer (BD Biosciences). ATAC-seq reactions were performed using an established protocol (Buenrostro et al PMID: 25559105) (Illumina Cat #FC-121-1030) and the resulting libraries generated using the Nextera index kit (Illumina Cat #FC-121-1011). Libraries were amplified for a total of 14–16 cycles of PCR. Following PCR, ATACseq libraries were resolved on 2% agarose gels and fragments ranging in size from 100bp-1Kbp were excised and purified (Qiagen Minelute Gel Extraction Kit – Qiagen Cat#28604). Libraries were quantified by Qubit HS DNA kit (Life technologies) and by quantitiative PCR (KAPA Biosystems Cat#KK4873) prior to sequencing. Finally, ATACseq libraries were sequenced on Hi-Seq2500 (Illumina) obtaining 2x50 paired-end reads.

value: postnatal day 3

value: GENSAT Nr4a1-EGFP

value: striatum

tag: yield of nuclei

value: M

tag: atacseq input (cells)

tag: barcode combination

value: GGACTCCT-CTCTCTAT

tag: total pcr cycles

tag: ab

value: GFP+

tag: dna stain

value: DAPI


title: Ctr3

tag: strain

value: 20 weeks

tag: group

tag: cell type

value: endothelial cells


title: mock-sprayed, experiment 2, biological rep2

tag: tissue

value: leaves

tag: treatment

value: mock-sprayed


title: Male CSF1, 3

tag: agent

tag: age

value: 8-12 weeks

value: Microglia

tag: Sex

value: male


title: Female Saline, 4

value: Saline

value: Female


title: Input-O7-M_FKDL210126323-1a

value: mouse bone marrow

value: MSCs

value: treated with 1 µM melatonin for 24 hours

tag: chip antibody


title: Ctr2

value: naive control


title: LSK_KO_2

tag: genotype/variation


title: Female Saline, 2


title: Female Saline, 3


title: LOF1

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

description: Gene expression data from Nr2f2 LOF

hyb_protocol: Microarray analysis was performed at the IRB Functional Genomics Core, Barcelona. cDNA synthesis, library preparation and amplification were performed as described in Gonzalez-Roca, E. et al., 2010. A Mouse Genome 430pm strip Affymetrix array was used and the data were normalized using RMA algorithm

data_processing: To normalize the data, the Robust Multi-array Average expression (RMA) method from the affy package was used.

source_name: LOF carcinoma 1

extract_protocol: RNA extraction from FACS isolated cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer ́s recommendations.

tag: tumor type

value: Carcinoma

tag: genotype

value: NR2F2 KO


title: ChIP-O7-M_FKDL210126325-1a


title: f3_str_GFP-

source_name: FACS sorted EGFP(-) cells from the PND3 striatum from GENSAT Nr4a1-EGFP mice

value: postnatal day 3

value: GENSAT Nr4a1-EGFP

value: striatum

tag: yield of nuclei

tag: gender

value: F

tag: atacseq input (cells)

value: TCCTGAGC-CTCTCTAT

value: GFP-


title: Male CSF1, 1

value: 8-12 weeks


title: f2_str_GFP+

tag: barcode combination

value: TCCTGAGC-TATCCTCT

tag: total pcr cycles

tag: ab

value: GFP+

value: DAPI


title: f3_str_GFP+

value: GGACTCCT-AGAGTAGA

tag: dna stain


title: f2_str_GFP-

value: TCCTGAGC-AGAGTAGA


title: Female CSF1, 2

tag: cell type

value: Microglia

value: Female


title: Adult Endothelial Cells [EC]

tag: diagnosis

value: atherosclerotic heart disease

tag: surgery

value: coronary artery bypass graft

value: male

value: 63 years

tag: tissue

value: Adult human vessel

value: Adult Endothelial Cells

tag: passage

tag: molecule subtype

value: cytoplasmic RNA


title: m1_str_GFP-

tag: age

value: postnatal day 3

value: GENSAT Nr4a1-EGFP

value: striatum

value: M

value: GGACTCCT-TATCCTCT


title: LOF_Control2

description: Gene expression data from Nr2f2 control corresponding to LOF

scan_protocol: Microarray analysis was performed at the IRB Functional Genomics Core, Barcelona. cDNA synthesis, library preparation and amplification were performed as described in Gonzalez-Roca, E. et al., 2010. A Mouse Genome 430pm strip Affymetrix array was used and the data were normalized using RMA algorithm

source_name: Ctrl carcinoma 2

value: Carcinoma

value: NR2F2 WT


title: Adult Cardiac Fibroblast Cells [CF]

source_name: Adult human cardiac apprendage tissue

value: Adult human cardiac apprendage tissue

value: Adult Cardiac Fibroblast Cells


title: LSK_WT_1

tag: strain

tag: genotype/variation

value: WT


title: Female CSF1, 1

tag: agent

value: 8-12 weeks

value: Microglia

tag: Sex

value: Female


title: Male CSF1, 4

value: male


title: GOF_Control2

description: Gene expression data from Nr2f2 control corresponding to GOF

source_name: Ctrl papilloma 2

label_protocol: Microarray analysis was performed at the IRB Functional Genomics Core, Barcelona. cDNA synthesis, library preparation and amplification were performed as described in Gonzalez-Roca, E. et al., 2010. A Mouse Genome 430pm strip Affymetrix array was used and the data were normalized using RMA algorithm

tag: tumor type

value: Papilloma

tag: genotype


title: mock-sprayed, experiment 1, biological rep1

value: leaves

tag: treatment

value: mock-sprayed


title: Female Saline, 1

value: Saline


title: f1_str_GFP-

value: postnatal day 3

value: GENSAT Nr4a1-EGFP

tag: yield of nuclei

tag: gender

value: F

tag: atacseq input (cells)

tag: barcode combination

value: AGGCAGAA-TATCCTCT

tag: total pcr cycles

value: GFP-

value: DAPI


title: Male Saline, 3

tag: cell type


title: OEEV47 1-2 6h wound B

city: Beltsville

first: Jonathan

last: Shao

state: MD

address: 10300 Baltimore Ave.

department: ARS

institute: USDA-ARS-Beltsville

hyb_protocol: not provided

scan_protocol: not provided

data_processing: MAS5 processing

organism: Arabidopsis thaliana

source_name: genotype:OEEV471-2 (pooled OEEV47-1 and OEEV47-2  lines); tissue:leaf;treatment wounding 6hr

label_protocol: not provided

extract_protocol: RNA extraction

tag: tissue

value: leaf

value: wounding 6hr


title: OEEV47 1-2 6h wound A

value: OEEV471-2 (pooled OEEV47-1 and OEEV47-2  lines)


title: LOF2

description: Gene expression data from Nr2f2 LOF

source_name: LOF carcinoma 2

value: Carcinoma

value: NR2F2 KO


title: Butyrate_4

city: Copenhagen

first: Nils

last: Billestrup

address: Blegdamsvej

country: Denmark

institute: University of Copenhagen

data_processing:
Fastq files were generated using bcl2fastq v2.19.1 and aligned to the GRCm38 (mm10) genome using STAR v2.5.3a (Dobin et al., 2013).
Transcript expression levels were estimated with the --quantMode GeneCounts option and gencode.GRCm38p5.vM15.primary_assembly annotations.
FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for QC metrics, and multiqc v1.7 (Ewels et al., 2016) for reporting.
Differential gene expression was performed using the R package DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Deseq2_processed_data.xlsx: Matrix table with raw and DESeq2-normalized gene counts for every gene and every sample. Statistics are also found in the file. Relevant comparisons are found in separate worksheets.
Supplementary_files_format_and_content: STAR_counts.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: Pancreatic Islet

growth_protocol: Mouse islets (500 per condition) were cultured for 10 days in RPMI 1640 medium with GlutaMAX supplemented with 2% Human serum and 1% penicillin/streptomycin (100 U/ml penicillin, 100 μg/mL streptomycin). At day 5 media was changed.

extract_protocol:
Mouse islets were lyzed in Trizol reagent and RNA was extracted using the RNeasy® Micro Kit (Qiagen).
Single-end sequencing libraries were constructed from 250 ng of isolated RNA using the NEBNext® Ultra™ II RNA Library Prep Kit #E7770S (Illumina®).
RNA sequencing was performed on a HiSeq 4000 System (Illumina®).

treatment_protocol: Mouse islets were exposed to recombinant mouse 50 pg/ml IL-1β (cat. 554577, BD Biosciences), 0.2 mM sodium butyrate ( B5887, Sigma), the combination or left unexposed.

value: Male

value: 12 weeks

value: Pancreatic Islet

value: Butyrate


title: Ezh2 Ctrl male PGC rep3

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
trimmomatic  (0.33) was applied for trimming adapter and low quality reads
Trimmed reads were mapped to mm9 whole genome using tophat2 (2.0.11) with default settings
Gene annotations were obtained from iGenome NCBIM37. Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: NCBIM37
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

source_name: Primordial germ cells

extract_protocol:
E13.5 PGCs from each embryo were sorted separately and centrifuged at 2,000 rpm for 3 min following liquid nitrogen snap freezing. Total RNA was extracted using ZR-Duet DNA and RNA Mini Prep kit (Zymo). The genotype of embryos was determined by PCR. RNA quality was measured by 2100 bioanalyzer (Agilent technologies).
To prepare cDNA libraries, 1 ng total RNA was used for cDNA synthesis amplification (11 cycles) using SMART-seq V4 Ultra Low input RNA kit (Clone Tech), according to the manufacturer’s instructions. The cDNA was sheared by Covaris S2 sonicator (peak: 175, Duty: 10, cycle: 200, duration: 240 secs)(Covaris). Fragmented cDNA was indexed and converted to sequencing libraries using NEBNext Ultra II DNA library Prep Kit (NEB) following the manufacturer’s instructions.

tag: genetic background

value: Primordial germ cells

tag: embryonic day

value: Ctrl


title: Male CSF1, 2

tag: age

value: 8-12 weeks

value: Microglia

value: male


title: LOF_Control1

source_name: Ctrl carcinoma 1

value: NR2F2 WT


title: OEEV47 1-2 6h wound C


title: OEEV47 1-2 1h wound A

source_name: genotype:OEEV471-2 (pooled OEEV47-1 and OEEV47-2  lines); tissue:leaf;treatment wounding 1hr

value: wounding 1hr


title: GOF1

description: Gene expression data from Nr2f2 GOF

source_name: GOF papilloma 1

value: Papilloma

value: NR2F2 GOF


title: Butyrate_3

tag: strain


title: GOF2

description: Gene expression data from Nr2f2 GOF

source_name: GOF papilloma 2


title: Butyrate_2


title: OEEV47 1-2 Control B

source_name: genotype:OEEV471-2 (pooled OEEV47-1 and OEEV47-2  lines); tissue:leaf;treatment control

value: leaf

value: control


title: Male Saline, 2

source_name: lumbar dorsal horn spinal cord

value: Saline


title: Male Saline, 1


title: Butyrate_1


title: OEEV47 1-2 1h wound C

value: OEEV471-2 (pooled OEEV47-1 and OEEV47-2  lines)


title: Ezh2 Ctrl male PGC rep4

value: Male


title: Ezh2 Ctrl male PGC rep1


title: Ezh2 Ctrl male PGC rep2


title: OEEV47 1-2 1h wound B


title: GOF_Control1

source_name: Ctrl papilloma 1


title: IL-1_Butyrate_4

description:
IL1_Butyrate_rep4_S16_R1_001
IL-1β and Butyrate

value: 12 weeks

value: IL-1beta and Butyrate


title: Ezh2 Ctrl female PGC rep3

value: Female


title: IL-1_Butyrate_3

description:
IL1_Butyrate_rep3_S12_R1_001
IL-1β and Butyrate

value: Pancreatic Islet


title: ZT19_4

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

institute: Ludwig-Maximilians-Universität München

data_processing:
obtained transcriptome profiles were processed on a Galaxy web interface hosted by LAFUGA (Gene Center, Munich)
After demultiplexing and trimming data was mapped against the mouse genome (mm10) using RNA-STAR mapper (Galaxy Version 2.5.2b-0). Abundant reads were counted using HTSeq-count (Galaxy Version 1.0.0)
Afterwards, gene expression analysis to detect differentially expressed genes was performed using DESeq2 (Galaxy Version 2.11.40.6), setting the false discovery rate (FDR) <0.05
Genome_build: mm10
Supplementary_files_format_and_content: HTSeq count data, tabular

source_name: Skin, sorted lymphatic endothelial cells

extract_protocol:
Ear samples of mice were digested using collagenase IV and DNAse I for 30 min, before being stained and used for sorting. Lymphatic endothelial cells were sorted. RNA of sorted dermal LECs harvested in TriZol-LS was purified using Direct-zol RNA mini Prep Kit (ZymoResearch) following manufacturer’s instructions. Isolated RNA was quantified using the Nanodrop (Thermofisher) and analyzed on a Bioanalyzer (Agilent) using the RNA 6000 Nano or Pico Kit (Agilent). 75 ng of eluted total RNA was digested with DNase (Thermofisher) to remove DNA contaminations. An additional purification step with RNAClean XP Beads (Agencourt) was performed
The purified, bead-bound RNA was directly used as input in the SMART-Seq v4 Ultra Low Input RNA Kit (TaKaRA Bio). Full-length cDNA was generated following manufacturer’s instructions. Full-length cDNA was quantified using the Qubit dsDNA HS Assay Kit (Invitrogen) with the Qubit fluorometer. Finally,equencing libraries were generated using 500 pg full-length cDNA following the NexteraXT protocol (Illumina).

value: Skin

value: post natal day 56

value: wild type

tag: time poine


title: Ezh2 Ctrl female PGC rep1

value: Primordial germ cells

value: Ctrl


title: IL-1_Butyrate_2

description:
IL1_Butyrate_rep2_S8_R1_001
IL-1β and Butyrate


title: IL-1_Butyrate_1

description:
IL1_Butyrate_rep1_S4_R1_001
IL-1β and Butyrate


title: ZT19_5


title: ZT19_3


title: Col 6h wound C

source_name: genotype: Col-0; tissue:leaf;treatment:wounding 6hr

value: wounding 6hr


title: Col 6h wound B


title: OEEV47 1-2 Control C


title: Col 1h wound C

source_name: genotype: Col-0; tissue:leaf;treatment:wounding 1hr

value: wounding 1hr


title: Col 6h wound A


title: Col 1h wound A


title: Col 1h wound B


title: Col Control A


title: OEEV47 1-2 Control A


title: Col Control B


title: ZT19_2


title: ZT13_4


title: IL-1_4

description:
IL1_rep4_S15_R1_001
IL-1β


title: ZT19_1


title: ZT13_5


title: IL-1_3

description:
IL1_rep3_S11_R1_001
IL-1β


title: Col Control C


title: Ezh2 CKO male PGC rep3

value: CKO


title: Ezh2 CKO male PGC rep2


title: Ezh2 Ctrl female PGC rep2


title: ZT13_3


title: IL-1_1

description:
IL1_rep1_S3_R1_001
IL-1β


title: Ezh2 CKO male PGC rep1


title: ZT13_2


title: ZT7_5


title: ZT13_1


title: Ezh2 CKO female PGC rep1


title: ZT7_4


title: ZT7_3


title: ZT7_2


title: Control_4


title: E13.5 male H3K9me3 rep2

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
raw reads were aligned to UCSC mm9 mouse genome obtained from iGenome with BWA (0.7.5a)
aligned reads were sorted by Picard SortSam tool (1.9)
duplicated reads were removed by Picard MarkDuplicates tool (1.9)
using samtools view (0.1.18) with -F 4 -f 0x02, we only kept properly paired reads for downstream analysis
bamCoverage function from deeptools (3.3.0) were applied to generated bigwig files with arguments -blackListFileName mm9-blacklist.bed --effectiveGenomeSize 2620345972 --normalizeUsing CPM
Peak calling was performed using MACS2 (2.1.0) with arguments -f BAMPE --broad -g mm
Genome_build: mm9
Supplementary_files_format_and_content: bigwig and BED6+3 format

value: C57BL/6 x GOF18delta_PE-EGFP

tag: Stage


title: Ezh2 CKO female PGC rep2

tag: Sex


title: ZT7_1


title: Control_3


title: ZT1_4


title: Control_2


title: ZT1_5


title: IL-1_2

description:
IL1_rep2_S7_R1_001
IL-1β


title: ZT1_3


title: E13.5 male H3K27me3 rep2


title: ZT1_1


title: E13.5 male input rep2


title: ZT1_2


title: Control_1


title: replicate 3 of mdx_IL5Tg condition

city: Bethesda

first: Philip

last: Murphy

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw fastq files were then trimmed for quality and adapter contamination using Cutadapt v2.10 and trimmed reads were mapped to the mm10 mouse reference genome and Gencode M25 transcriptome using STAR v2.5.3 in 2-pass mode.
Gene-level expression quantification was performed using RSEM v1.3.0
Prior to differential expression and downstream time course analysis, genes were filtered to include <1 counts per million (CPM) across <3 samples.
Standard differential expression was performed using the R package limma with voom normalization
Genome_build: mm10
Supplementary_files_format_and_content: raw expression (expected counts) text file generated from RSEM

source_name: eosinophils isolated from quadricep muscle infiltrates

extract_protocol:
Eosinophils from infiltrates in mouse quadriceps muscle were isolated by fluorescence-activated cell sorting (FACS); live eosinophils (CD45+CD11c-Gr1-MHCII-SiglecF+) were sorted directly into TRIZOL-LS (Life Technologies, Frederick, MD, USA) at a 3:1 ratio of TRIZOL-LS to sorted cell sample which was then equilibrated with chloroform. Total RNA was purified from the aqueous phase, combined with equal volumes of 70% ethanol, and purified with the RNeasy Cleanup kit (Qiagen, Germantown, MD, USA).
RNA libraries were prepared using the NEBnext Ultra Low Input Total RNA Library Prep Kit (New England BioLabs, Beverly, MA, USA) following the manufacturer’s instructions.

value: mdx

tag: developmental stage

value: adult


title: E13.5 female H3K9me3 rep2

extract_protocol:
PGCs were FACS sorted into cold PBS and were lysed by nuclei isolation buffer (Sigma, NUC-101). For E10.5, PGCs were pooled from different embryos. 1000 PGCs were used for each ChIP reaction. Samples were permeabilized with 0.1% Triton-X-100 /0.1% deoxycholate in PBS on ice. Samples were digested with 200 U of micrococcal nuclease (New England Biolabs, M0247S) in digestion buffer at 21 °C for 7.5 mins and the reaction was stopped with 100 mM EDTA. An aliquot of chromatin (10%) was used as an input control. Samples were pre-cleaned by protein A/G beads for 2 hours at 4°C. Meanwhile, 250 ng anti-H3K9me3 (Diagenode, C15410056) and anti-H3K27me3 (Millipore, 07-449) antibodies were incubated with protein A/G beads for 2 hours at 4°C. Chromatin samples were incubated with antibody-bound beads overnight at 4°C. Samples were washed by two low-salt washes and one high salt wash and eventually DNA was eluted from the beads for 1.5 hours at 60°C. For sizes selection, AMPure XP beads were used at 1.8:1 ratio.
Library preparation was performed using a MicroPlex Library Preparation kit v2 (Diagenode, C05010013) following manufacturer’s recommendations. Libraries were further purified by AMPure XP beads at 1:1 ratio. Library quality was measured with a 2100 Bioanalyzer Instrument (Agilent) and library size was assessed with a Kapa library qPCR quantification kit (Roche, KK4824). Library sequencing was performed in a 100bp paired-end mode with a HiSeq 2500 System (Illumina) following manufacturer’s recommendations.

tag: genotype


title: WT rep 4

city: Tucson

first: Deepta

last: Bhattacharya

state: Arizona

address: 1656 E. Mabel Street, MRB 217

department: Department of Immunobiology

institute: University of Arizona

data_processing:
Reads were mapped and transcript abundances were calculated using Salmon v1.5.1
Differentially expressed genes were quantified with DESeq2 v2.11.40.6
Genome_build: Gencode M27 transcriptome
Supplementary_files_format_and_content: Salmon generated .tabular files containing TPM values for all transcripts
Supplementary_files_format_and_content: DESeq2 generated a .tabular file containing a list of genes differentially regulated between Mpc2 KO and WT granulocyte-macrophage progenitors. Columns from left to right are gene id, mean normalized counts, log2 fold change, SE for log2 fold change, Wald stat, p value, and p value with FDR

source_name: granulocyte-macrophage progenitors

extract_protocol:
NucleoSpin RNA XS (Macherey-Nagel)
SMARTseq V4  (Takara Bio) by Novogene

value: ROSA26 CreER+/-

tag: time after gene deletion

value: ~10 weeks


title: WT rep 5


title: E13.5 female input rep2


title: replicate 2 of mdx_IL5Tg condition


title: replicate 1 of mdx_IL5Tg condition


title: WT rep 3


title: Adult Cardiosphere-Derived Cells

source_name: Adult human cardiac apprendage tissue

tag: diagnosis

value: atherosclerotic heart disease

tag: surgery

value: coronary artery bypass graft

value: male

value: 61 years

value: Adult human cardiac apprendage tissue

value: Adult Cardiosphere-Derived Cells

tag: passage

tag: molecule subtype

value: cytoplasmic RNA


title: E13.5 female H3K27me3 rep2

value: Primordial germ cells

value: wild type

value: Female


title: WT rep 1


title: WT rep 2


title: E13.5 male H3K9me3 rep1

value: Male


title: replicate 3 of mdx condition


title: replicate 1 of mdx condition


title: ChIPseq_INPUT_H3K27me3_Embryo_26_S2_rep1

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

description: ChIP-sequencing, Input (INPUT) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 2 (S2) from seeds produced at 26°C

data_processing:
TrimGalore to trim short reads (remove adapters)
Fastqc to check sequencing quality control
STAR mapper to map reads against the genome: STAR --readFilesIn read1.fq.gz read2.fq.gz --genomeDir genome index --outFileNamePrefix results_file --runThreadN 20 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06 --alignIntronMax 1 --outSAMtype BAM SortedByCoordinate --readFilesCommand 'gunzip -c'
Read deduplication using Picard Markduplicates algorithm
BAMcoverage to transform raw data in bigwig
Peak calling using macs2 callpeak function to statistically identify binding sites using INPUT and IP files. Broad peak calling setting for H3K27me3 and narrow peak calling setting for H3ac according to ENCODe recommendations.
Genome_build: MtrunA17r5.0-20161119-ANR.fasta

organism: Medicago truncatula

source_name: embryos S2, 26C

growth_protocol: Plants were grown in a culture room in trays containing a sterile soil at 20°C/18°C, with a 16 h light photoperiod at 150 μmol photons m -²s-²

extract_protocol:
Extraction protocol as explained in Cortijo et al, 2018 (https://doi.org/10.1007/978-1-4939-7747-5_18)
Library construction by Microplex diagenode protocol. Samples were sent to BGI, Hong Kong, for sequencing. https://www.diagenode.com/en/p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns

treatment_protocol: All plants grew in control conditions (as indicated above) at 20°C/18°C (day/night) then at flowering half of plants stayed in control conditions (20°C/18°C), and half of them were moved to heat stress with a constant 26°C/24°C (day/night) temperature conditions. Then seeds were collected at S1, S2, S3 and S4 from both conditions and embryos were dissected then frozen in liquid nitrogen.

tag: line

value: seeds from 2017 and 2018

tag: chip antibody

tag: expt

value: H3K27me3 INPUT


title: Mpc2 KO rep 4

value: Mpc2fl/fl; ROSA26 CreER+/-


title: E13.5 female H3K9me3 rep1

tag: genetic background

value: C57BL/6 x GOF18delta_PE-EGFP

tag: tissue


title: ChIPseq_INPUT_H3K27me3_Embryo_26_S4_rep1

description: ChIP-sequencing, Input (INPUT) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 4 (S4) from seeds produced at 26°C

source_name: embryos S4, 26C


title: replicate 3 of IL5Tg condition

value: mdx

value: adult


title: ChIPseq_INPUT_H3K27me3_Embryo_20_S4_rep1

description: ChIP-sequencing, Input (INPUT) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 4 (S4) from seeds produced at 20°C

source_name: embryos S4, 20C


title: ChIPseq_INPUT_H3K27me3_Embryo_26_S3_rep1

description: ChIP-sequencing, Input (INPUT) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 3 (S3) from seeds produced at 26°C

source_name: embryos S3, 26C


title: Mpc2 KO rep 3

value: ~10 weeks


title: E13.5 female input rep1

source_name: Primordial germ cells


title: replicate 2 of IL5Tg condition


title: ChIPseq_INPUT_H3K27me3_Embryo_26_S1_rep1

description: ChIP-sequencing, Input (INPUT) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 1 (S1) from seeds produced at 26°C

source_name: embryos S1, 26C


title: Mpc2 KO rep 5


title: replicate 2 of mdx condition


title: Mpc2 KO rep 2


title: E13.5 male H3K27me3 rep1


title: E13.5 male input rep1


title: E10.5 H3K9me3 input rep2


title: replicate 1 of IL5Tg condition


title: Neonatal Cardiosphere-Derived Cells

source_name: neonatal human cardiac apprendage tissue

value: Hypoplastic left heart syndrome

value: Norwood I procedure for single-ventricle patients

tag: gender

value: female

tag: age

value: 7 days

tag: cell type

value: Neonatal Cardiosphere-Derived Cells


title: Gls Mpc2 DKO rep 5

value: Glsfl/fl Mpc2fl/fl; ROSA26 CreER+/-

tag: strain


title: ChIPseq_INPUT_H3K27me3_Embryo_20_S2_rep1

description: ChIP-sequencing, Input (INPUT) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 2 (S2) from seeds produced at 20°C

source_name: embryos S2, 20C


title: f1_str_GFP+

source_name: FACS sorted EGFP(+) cells from the PND3 striatum from GENSAT Nr4a1-EGFP mice

value: postnatal day 3

value: GENSAT Nr4a1-EGFP

value: striatum

tag: yield of nuclei

value: F

tag: atacseq input (cells)

tag: barcode combination

value: AGGCAGAA-CTCTCTAT

tag: total pcr cycles

tag: ab

value: GFP+

tag: dna stain

value: DAPI


title: E13.5 female H3K27me3 rep1

value: C57BL/6 x GOF18delta_PE-EGFP

value: Primordial germ cells

tag: Stage

tag: genotype

value: wild type

tag: Sex

value: Female


title: ChIPseq_INPUT_H3K27me3_Embryo_20_S1_rep1

description: ChIP-sequencing, Input (INPUT) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 1 (S1) from seeds produced at 20°C

source_name: embryos S1, 20C

tag: line

value: seeds from 2017 and 2018

tag: chip antibody

value: H3K27me3 INPUT


title: Nipponbare Sheath HNT

city: Potsdam

first: Ellen

last: Zuther

address: Am Muehlenberg 1

department: Transcript Profiling

institute: MPI of Molecular Plant Physiology

description:
STAR_raw_count_table.txt
AV

data_processing:
Filtered fastq files with trimmomatic 0.36 (adapter removal, min. length of reads 80bp)
Alignment with STAR 2.7.1a against the Nipponbare reference genome
Generated raw count matrix based on STAR geneCount output (4th column)
Genome_build: EnsemblePlants Oryza_sativa.IRGSP-1.0.dna.toplevel.fa
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Oryza sativa

source_name: Leaf

growth_protocol: Seed germination, planting and stress treatment were performed as previously described (Glaubitz et al. 2014; http://dx.doi.org/10.1071/FP13132).

extract_protocol:
Homogenized plant material of five replicate samples per cultivar, segment and treatment was pooled to 100 mg resulting into 48 samples for the analysis. Total RNA was isolated using a TRIzol protocol based on the ‘single step’ method (Sprenger, Kurowsky, Horn, Erban, Seddig, Rudack, Fischer, Walther, Zuther, Köhl, Hincha & Kopka, 2016). Four μg of each RNA sample was further treated with DNase (RapidOut DNA-removal Kit, Thermo Scientific). Absence of genomic DNA contamination was confirmed by qRT-PCR using intron-specific primers (At5g65080). Finally, RNA quality and integrity were verified with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Library preperation with NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs) and library type RNA library including polyA enrichment.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Experiments were performed in a controlled climate chamber with 12 h light regime with 70% relative humidity and a temperature setting of 26°C in the light and 22°C at night for control conditions or 28°C constant in the light and at night.

tag: cultivar

value: Nipponbare

value: Sheath

tag: hnt-sensitivity

value: tolerant

tag: subspecies

value: japonica

tag: treatment

value: HNT


title: Gls Mpc2 DKO rep 4

value: Glsfl/fl Mpc2fl/fl; ROSA26 CreER+/-

tag: time after gene deletion

value: ~10 weeks


title: M202 Sheath HNT

description:
STAR_raw_count_table.txt
AU

tag: tissue

value: sensitive


title: Mpc2 KO rep 1

value: Mpc2fl/fl; ROSA26 CreER+/-

tag: strain


title: IR72 Sheath HNT

description:
STAR_raw_count_table.txt
AT

value: indica


title: E10.5 H3K27me3 input rep2

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

institute: MRC London Institute of Medical Sciences

tag: genetic background


title: ChIPseq_INPUT_H3K27me3_Embryo_20_S3_rep1

description: ChIP-sequencing, Input (INPUT) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 3 (S3) from seeds produced at 20°C

source_name: embryos S3, 20C

tag: expt


title: IR57311 Sheath HNT

description:
STAR_raw_count_table.txt
AS


title: ChIPseq_IP_H3K27me3_Embryo_26_S4_rep1

description: ChIP-sequencing, Immunoprecipitated (IP) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 4 (S4) from seeds produced at 26°C

value: H3K27me3 antibodies

value: H3K27me3 IP


title: E10.5 H3K27me3 rep2

value: C57BL/6 x GOF18delta_PE-EGFP

value: Primordial germ cells


title: IR62266-42-6-2 Sheath HNT

description:
STAR_raw_count_table.txt
AR


title: ChIPseq_IP_H3K27me3_Embryo_26_S3_rep1

description: ChIP-sequencing, Immunoprecipitated (IP) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 3 (S3) from seeds produced at 26°C


title: Gls Mpc2 DKO rep 3


title: Gls Mpc2 DKO rep 2


title: E10.5 H3K9me3 input rep1

value: wild type


title: ChIPseq_IP_H3K27me3_Embryo_26_S2_rep1

description: ChIP-sequencing, Immunoprecipitated (IP) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 2 (S2) from seeds produced at 26°C

value: seeds from 2017 and 2018


title: E10.5 H3K9me3 rep1


title: E10.5 H3K9me3 rep2


title: CT9993-5-10-1M Sheath HNT

description:
STAR_raw_count_table.txt
AQ


title: Gls Mpc2 DKO rep 1


title: Gls KO rep 5

value: Glsfl/fl; ROSA26 CreER+/-


title: ChIPseq_IP_H3K27me3_Embryo_26_S1_rep1

description: ChIP-sequencing, Immunoprecipitated (IP) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 1 (S1) from seeds produced at 26°C


title: Nipponbare Base HNT

description:
STAR_raw_count_table.txt
AP

value: Nipponbare

value: Base


title: ChIPseq_IP_H3K27me3_Embryo_20_S4_rep1

description: ChIP-sequencing, Immunoprecipitated (IP) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 4 (S4) from seeds produced at 20°C


title: E10.5 H3K27me3 input rep1


title: ChIPseq_IP_H3K27me3_Embryo_20_S2_rep1

description: ChIP-sequencing, Immunoprecipitated (IP) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 2 (S2) from seeds produced at 20°C


title: ChIPseq_IP_H3K27me3_Embryo_20_S3_rep1

description: ChIP-sequencing, Immunoprecipitated (IP) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 3 (S3) from seeds produced at 20°C


title: KDM4A-OE.ATAC.G2.rep2

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

data_processing:
Reads were aligned to hg19 using BWA, and PCR duplicates were removed using samtools rmdup.
Peak calling was performed using the Homer package (HOMER v4.8) with matched inputs.
Genome_build: hg19
Supplementary_files_format_and_content: peak files (bed) generated by findpeaks (Homer)

source_name: Retinal Pigmented Epithelial

growth_protocol: 15 cm plates of 2 million RPE cells were seeded for 48 hours, in order to be harvested at ~70% confluency

extract_protocol:
Sorted cells were pelleted and resuspended in 250 ml cold RBS buffer (10 mM Tris-HCl pH 7.4 – 10 mM NaCl – 3 mM MgCl2) before being pelleted by centrifugation. Pellet was resuspended in 250 ml cold RBS buffer – 0.1% NP-40, incubated 5 minutes on ice and pelleted by centrifugation. Pellet was reuspended in 50 ml Tagmentation mix (22.5 ml H2O – 25 ml 2X Tagment DNA buffer – 2.5 ml Tagment DNA enzyme, Nextera Illumina FC-121-1030) and incubated 30 minutes at 37 degrees before being placed ion ice.
Protocol was adapted from (Buenrostro et al Nat Methods 2013). Purified DNA was amplified by PCR by adding 2.5 ml 25 mM Primer Ad2 and 37.5 ml PCR mix (10 ml H2O – 2.5 ml 25 mM Primer Ad1 – 25 ml 2X NEBnext master mix, NEB E6040S) and incubated as follows: 72 degrees 5 minutes, 98 degrees 30 seconds, [98 degrees 10 seconds, 63 degrees 30 seconds, 72 degrees 1 minute] x 12 cycles, 4 degrees. Amplified DNA was purified using a Promega Gel Purification Kit following supplier’s instructions and eluted in 25 ml H2O. Library length distribution were assessed by TapeStation (Agilent) and quantified with Qubit (ThermoFisher). Libraries were paired-end sequenced (43 cycles each way) using a NextSeq500 (Illumina).

tag: cell type

value: RPE

tag: genotype/variation

tag: cell cycle phase


title: ChIPseq_IP_H3K27me3_Embryo_20_S1_rep1

description: ChIP-sequencing, Immunoprecipitated (IP) fraction using H3K27me3 antibodies of DNA extracted from embryo at Stage 1 (S1) from seeds produced at 20°C


title: IR62266-42-6-2 Base HNT

description:
STAR_raw_count_table.txt
AL


title: Gls KO rep 1


title: M202 Base HNT

description:
STAR_raw_count_table.txt
AO

value: japonica


title: CT9993-5-10-1M Base HNT

description:
STAR_raw_count_table.txt
AK

value: HNT


title: IR72 Base HNT

description:
STAR_raw_count_table.txt
AN

value: tolerant


title: KDM4A-OE.ATAC.LS.rep2

value: late S


title: KDM4A-OE.ATAC.LS.rep1


title: ChIPseq_INPUT_H3Ac_Embryo_26_S2_rep1

description: ChIP-sequencing, Input (INPUT) fraction using H3 pan-acetyl antibodies of DNA extracted from embryo at Stage 2 (S2) from seeds produced at 26°C

value: H3Ac INPUT


title: Gls KO rep 3

value: ~10 weeks


title: Gls KO rep 4


title: Gls KO rep 2


title: sod1 5

city: Madrid

first: Silvia

last: Corrochano

address: Calle del Prof Martín Lagos

department: Neurología

institute: Instituto de Investigación Sanitaria del Hospital Clínico San Carlos

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 Version 2.1.0
featureCounts version 2.0.2 was used for counting reads to genes
Differential expression analysis was performed with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with the results of the differential expression analysis

source_name: spinal cord

extract_protocol:
RNA was isolated from dissected spinal cords of wild-type and SOD1G93A female mice at 90 days, using Qiazol followed by the mini Lipid tissue RNAeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spinal cord

value: sod1 g93a

tag: gender

value: female

tag: age

value: 90 days


title: KDM4A-OE.ATAC.G2.rep1


title: Nipponbare Middle HNT

description:
STAR_raw_count_table.txt
AJ

value: Middle


title: ChIPseq_INPUT_H3Ac_Embryo_20_S1_rep1

description: ChIP-sequencing, Input (INPUT) fraction using H3 pan-acetyl antibodies of DNA extracted from embryo at Stage 1 (S1) from seeds produced at 20°C


title: KDM4A-OE.ATAC.G1.rep2


title: M202 Middle HNT

description:
STAR_raw_count_table.txt
AI

value: sensitive


title: sod1 3

tag: genotype


title: E10.5 H3K27me3 rep1

value: C57BL/6 x GOF18delta_PE-EGFP

value: Primordial germ cells

tag: Stage

value: wild type


title: KDM4A-OE.ATAC.ES.rep2

value: early S


title: KDM4A-OE.ATAC.ES.rep1

value: RPE


title: ChIPseq_INPUT_H3Ac_Embryo_20_S2_rep1

description: ChIP-sequencing, Input (INPUT) fraction using H3 pan-acetyl antibodies of DNA extracted from embryo at Stage 2 (S2) from seeds produced at 20°C

tag: line

value: seeds from 2017 and 2018

tag: chip antibody


title: ChIPseq_IP_H3Ac_Embryo_26_S2_rep1

description: ChIP-sequencing, Immunoprecipitated (IP) fraction using H3 pan-acetyl antibodies of DNA extracted from embryo at Stage 2 (S2) from seeds produced at 26°C

value: H3Ac antibodies

value: H3Ac IP


title: IR72 Middle HNT

description:
STAR_raw_count_table.txt
AH

tag: cultivar

tag: hnt-sensitivity

value: tolerant

value: indica

value: HNT


title: ChIPseq_INPUT_H3Ac_Embryo_26_S1_rep1

description: ChIP-sequencing, Input (INPUT) fraction using H3 pan-acetyl antibodies of DNA extracted from embryo at Stage 1 (S1) from seeds produced at 26°C

value: H3Ac INPUT


title: sod1 1

value: spinal cord

value: sod1 g93a


title: KDM4A-OE.ATAC.G1.rep1


title: wt 5

value: female

value: 90 days


title: ChIPseq_IP_H3Ac_Embryo_26_S1_rep1

description: ChIP-sequencing, Immunoprecipitated (IP) fraction using H3 pan-acetyl antibodies of DNA extracted from embryo at Stage 1 (S1) from seeds produced at 26°C


title: ChIPseq_IP_H3Ac_Embryo_20_S2_rep1

description: ChIP-sequencing, Immunoprecipitated (IP) fraction using H3 pan-acetyl antibodies of DNA extracted from embryo at Stage 2 (S2) from seeds produced at 20°C


title: Ctrl.ATAC.G2.rep2

value: Control


title: sod1 2


title: wt 4


title: IR62266-42-6-2 Middle HNT

description:
STAR_raw_count_table.txt
AF

value: Middle

value: sensitive

tag: subspecies

tag: treatment


title: Ctrl.ATAC.LS.rep2

value: late S


title: CT9993-5-10-1M Middle HNT

description:
STAR_raw_count_table.txt
AE

tag: tissue

value: japonica


title: Ctrl.ATAC.G1.rep2

value: RPE


title: wt 2

tag: strain

value: wild type


title: M202 Tip HNT

description:
STAR_raw_count_table.txt
AC

value: Tip


title: IR72 Tip HNT

description:
STAR_raw_count_table.txt
AB


title: Chronic Beryllium Disease [45]

city: Aurora

first: Ivana

last: Yang

state: CO

address: 1635 Aurora Ct

institute: University of Colorado

description:
45
CBD
single cell RNA

data_processing:
Raw sequencing reads were demultiplexed, mapped to the human reference genome (build GRCh38) as appropriate and gene-expression matrices were generated using CellRanger (version 3.1.0).
The resulting count matrices were further filtered in Seurat 4.0.1 (https://satijalab.org/seurat/) to remove cell barcodes with less than 500 or more than 7000 genes, more than 20% of UMIs derived from mitochondrial genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.tar: UMI count matrices and associated cell-level metadata; barcodes.tsv, features.tsv, matrix.mtx.

source_name: bronchoalveolar lavage

extract_protocol: Live cells were then processed on the 10X Chromium instrument in the Genomics Core.

treatment_protocol: Aliquots from May/Kristyin and performed dead cell removal with the Miltenyi kit: https://www.miltenyibiotec.com/US-en/products/dead-cell-removal-kit.html#gref

tag: diagnosis

value: Chronic Beryllium Disease

value: bronchoalveolar lavage


title: Beryllium Sensitized  [29]

description:
29
BeS
single cell RNA

value: Non-diseased


title: wt 3


title: wt 1


title: IR57311 Middle HNT

description:
STAR_raw_count_table.txt
AG

value: tolerant

value: indica

value: HNT


title: Ctrl.ATAC.LS.rep1


title: Ctrl.ATAC.G2.rep1


title: sod1 4

value: spinal cord

value: sod1 g93a


title: IR57311 Tip HNT

description:
STAR_raw_count_table.txt
AA


title: Ctrl.ATAC.ES.rep1

value: early S


title: Non-progressive Sarcoidosis  [29715]

description:
29715
SarcR
single cell RNA

value: Non-progressive Sarcoidosis


title: Progressive Sarcoidosis  [4276]

description:
4276
SarcP
single cell RNA

value: Progressive Sarcoidosis


title: ChIPseq_IP_H3Ac_Embryo_20_S1_rep1

description: ChIP-sequencing, Immunoprecipitated (IP) fraction using H3 pan-acetyl antibodies of DNA extracted from embryo at Stage 1 (S1) from seeds produced at 20°C

value: seeds from 2017 and 2018

value: H3Ac antibodies

tag: expt

value: H3Ac IP


title: miPSC rep3

city: Tsukuba

first: Yohei

last: Hayashi

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

country: Japan

institute: RIKEN

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using CLC Genomics Workbench (Qiagen) software.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Name, Chromosome, Region, Expression value, TPM, RPKM,,, for each Sample

source_name: mouse iPS cells

extract_protocol:
RNA was extracted using FastGene RNA Premium Kit (Nippon Genetics) with on-column Dnase I treatment
RNA-seq library was generated using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) and NEBNext rRNA Delepletion Kit (New England Biolabs)
Paired-end sequencing of the libraries was performed using Novaseq 6000 SP Sequencing system using SP 100 cycle kit (Illumina).

tag: strainn

tag: cell type

value: Nanog-GFP MEF-derived cells


title: miPSC rep2


title: IR62266-42-6-2 Tip HNT

description:
STAR_raw_count_table.txt
Z

value: sensitive


title: Nipponbare Tip HNT

description:
STAR_raw_count_table.txt
AD

value: Nipponbare

value: Tip

value: japonica


title: Ctrl.ATAC.ES.rep2

value: RPE

tag: genotype/variation

value: Control

tag: cell cycle phase


title: miPSC rep1


title: Progressive Sarcoidosis  [24703]

description:
24703
SarcP
single cell RNA

value: bronchoalveolar lavage


title: CT9993-5-10-1M Tip HNT

description:
STAR_raw_count_table.txt
Y

value: HNT


title: IR57311 Base HNT

description:
STAR_raw_count_table.txt
AM

value: Base

value: tolerant

value: indica


title: Ctrl.ATAC.G1.rep1


title: Non-progressive Sarcoidosis  [42787]

description:
42787
SarcR
single cell RNA

value: Non-progressive Sarcoidosis


title: SeVdp_L507A_d10 rep3

source_name: Reprogramming MEF day 10


title: Chronic Beryllium Disease [2578]

description:
2578
CBD
single cell RNA

value: Chronic Beryllium Disease


title: SeVdp_L507A_d10 rep2


title: Nipponbare Sheath Control

description:
STAR_raw_count_table.txt
X

value: Sheath


title: sihnRNP LL rep3

city: Kansas City

first: Ning

last: Zhang

state: MO

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

data_processing:
Raw reads are demultiplexed into fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.
For RNA-seq samples, reads are aligned to UCSC genome hg38 with STAR aligner (version STAR_2.7.3a ), using Ensembl 102 gene models.
Transcript per million (TPM) values are generated by RSEM (version 1.3.0).
Genome_build: hg38
Supplementary_files_format_and_content: RNA-seq gene TPM in tab delimited text file

source_name: HEK293T cells

growth_protocol: HEK293T from were maintained as adherent cells in DMEM supplemented with 10% FBS and 2 mM L-glutamine at 37 °C with 5% CO2.

extract_protocol:
Total RNA was isolated from exponentially growing 293T cells and treated with DNaseI.
Sequencing libraries were prepared using High Throughput Library Prep Kit (KAPA Biosystems) following the manufacturer’s instructions. For RNA-Seq, ribodepletion and polyA enrichment was performed before library preparation.

treatment_protocol: Cells were treated with siRNA for 72 hours.

value: hnRNP LL siRNA treated


title: sihnRNP LL rep2


title: Chronic Beryllium Disease [1154]

description:
1154
CBD
single cell RNA


title: SeVdp_L507A_d10 rep1


title: siScramble rep4

value: scramble siRNA treated


title: M202 Sheath Control

description:
STAR_raw_count_table.txt
W


title: Beryllium Sensitized  [2954]

description:
2954
BeS
single cell RNA

value: Non-diseased


title: IR72 Sheath Control

description:
STAR_raw_count_table.txt
V


title: siScramble rep3


title: IR57311 Sheath Control

description:
STAR_raw_count_table.txt
U


title: SeVdp_WT_d10 rep3

value: Nanog-GFP MEF-derived cells


title: SeVdp_WT_d10 rep2


title: SeVdp_WT_d10 rep1


title: PNX0010 cells overexpressing PARG Rep3

city: Grand Forks

first: Yaroslava

last: Karpova

state: ND

address: 501 Columbia Road

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Illumina FQ sequencing files were imported into CLC Genomics Workbench version 12.0.
The reads were trimmed to remove adapters then the trimmed reads were mapped to the Human genome using CLC’s default parameters (mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, auto-detect paired distanc-es, maximum number of hits per read = 10).
All samples have a minimum of 50 million reads with 92% or greater mapping in pairs to the genome.  At least 97% of the mapped reads mapped to genes.
N=3 for both treatment groups.  Differential expression for RNA-seq analyses was performed in CLC Genomics Workbench 12.0 on the gene-level expression tracks using whole transcriptome RNA-seq with TMM normalization.
Differential expression due to treatment (hPARG+ or control) was tested with the comparison against the control group.
Supplementary_files_format_and_content: csv, Gene RPKM and expression changes

source_name: ccRCC cell line PNX0010

growth_protocol: PNX0010_pLVX_TetOne-Puro cells were cultured in RPMI-1640 (Bio-Whittaker, Walkersville, MD) supplemented with 10% FCS (Hyclone, Logan, UT), gentamicin (50 mg/l), sodium pyruvate (1mM) and non-essential amino acids (0.1mM)

extract_protocol:
RNeasy kit (Qiagen), mRNA was enriched via Poly(A) selection.
Novogene libraries were prepared using NEB’s Ultra II RNA library kit

treatment_protocol: PNX0010 cells were transduced with lentivirus construct encoding PARG cDNA with cleavable mClover3 under TetOne Doxycycline inducible promoter. Cells were plated to single well of 6 well plate, grown at 37°C in 5% CO2 for 72 hours without or with 500ng/ml Doxycycline and RNA isolated. 3 wells for untreated control group, 3 wells for treated inducible experimental group.

tag: parg status

value: PARG overexpression

value: renal cell carcinoma

tag: cell line


title: CT9993-5-10-1M Sheath Control

description:
STAR_raw_count_table.txt
S

value: sensitive

value: japonica


title: PNX0010 cells overexpressing PARG Rep1


title: PNX0010 cells overexpressing PARG Rep2


title: PNX0010 cells not induced Rep3

value: control


title: IR62266-42-6-2 Sheath Control

description:
STAR_raw_count_table.txt
T

value: Control


title: M202 Base Control

description:
STAR_raw_count_table.txt
Q


title: Nipponbare Base Control

description:
STAR_raw_count_table.txt
R

value: Nipponbare


title: SeVdp_L507A_d2 rep2

source_name: Reprogramming MEF day 2


title: SeVdp_L507A_d2 rep1


title: IR72 Base Control

description:
STAR_raw_count_table.txt
P

value: Base


title: A431-NR2F2-KD2-DOX-2

data_processing:
Adaptors sequences were removed with TrimmomaticPE using options “ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:8”
Reads were mapped against the human reference genome (Grch38.87) using STAR software
Duplicate reads were removed by Picard tools, MarkDuplicates module.
After transcripts assembling, gene level counts were obtained using Htseq with annotations GRCh38.87 and normalized to 20 millions of aligned reads.
Genome_build: Grch38.87
Supplementary_files_format_and_content: .txt / rawcount of gene expression

source_name: Skin squamous cell carcinoma

growth_protocol: Cells were grown in EMEM culture medium, with 10% FBS tetracycline-free.

extract_protocol:
RNA extraction from cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer ́s recommendations.
Indexed cDNA libraries were obtained using the Truseq Standard mRNA library prep kit (Illumina) .

treatment_protocol: NR2F2 KD induced cells were exposed to 1µg/mL Doxycycline for 72h.

value: Skin squamous cell carcinoma

value: Doxycycline


title: PNX0010 cells not induced Rep1


title: PNX0010 cells not induced Rep2


title: IR57311 Base Control

description:
STAR_raw_count_table.txt
O

value: tolerant

value: indica


title: Pap_CD34p_1

description: Gene expression data from Nr2f2 Papilloma

hyb_protocol: Microarray analysis was performed at the VIB MicroArray Facility in Leuven. cDNA synthesis, library preparation and amplification were performed as described in Gonzalez-Roca, E. et al., 2010. A Mouse Genome 430pm strip Affymetrix array was used and the data were normalized using RMA algorithm

data_processing: To normalize the data, the Robust Multi-array Average expression (RMA) method from the affy package was used.

source_name: CD34+ tumor cells from DMBA tumor

extract_protocol: RNA extraction from FACS isolated cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer ́s recommendations.

tag: tumor type

value: Papilloma


title: Pap_CD34p_2

scan_protocol: Microarray analysis was performed at the VIB MicroArray Facility in Leuven. cDNA synthesis, library preparation and amplification were performed as described in Gonzalez-Roca, E. et al., 2010. A Mouse Genome 430pm strip Affymetrix array was used and the data were normalized using RMA algorithm


title: Car_CD34p_2

description: Gene expression data from Nr2f2 carcinoma

label_protocol: Microarray analysis was performed at the VIB MicroArray Facility in Leuven. cDNA synthesis, library preparation and amplification were performed as described in Gonzalez-Roca, E. et al., 2010. A Mouse Genome 430pm strip Affymetrix array was used and the data were normalized using RMA algorithm

value: Carcinoma


title: SeVdp_WT_d2 rep2


title: IR62266-42-6-2 Base Control

description:
STAR_raw_count_table.txt
N


title: A431-NR2F2-KD2-DOX-1


title: Car_CD34p_3


title: Pap_CD34p_GFP


title: SeVdp_WT_d2 rep1


title: SeVdp_L507A_d2 rep3


title: A431-NR2F2-KD1-DOX-72h-2


title: CT9993-5-10-1M Base Control

description:
STAR_raw_count_table.txt
M


title: A431-NR2F2-KD1-DOX-72h-1


title: Nipponbare Middle Control

description:
STAR_raw_count_table.txt
L

value: Middle


title: SeVdp_WT_d2 rep3


title: MEF rep2

source_name: Mouse Embryonic Fibroblasts


title: M202 Middle Control

description:
STAR_raw_count_table.txt
K


title: Car_CD34p_GFP


title: MEF rep3


title: Car_CD34p_1


title: A431-NR2F2-KD2-NO-DOX-2


title: MEF rep1


title: A431-NR2F2-KD2-NO-DOX-1


title: IR72 Middle Control

description:
STAR_raw_count_table.txt
J


title: MB49 cells

city: Shen Zhen

first: Kang

last: Wu

state: Guang Dong

address: 47 Youyi Road, Luohu District

department: Urology

institute: The Third Affiliated Hospital of Shenzhen University (LuoHu Hospital Group)

description: Tumour

data_processing:
Illumina Casava1.7 software used for basecalling.
raw sequencing data were timmed for adaptor sequence, and masked for low complexity or low-quanlity sequence.
trimmed data were mapped to mm10 genome using Hisat2.
Fragments Per Kilobase of gene or Transcript model per Million mapped fragments(FPKM) were calculated for analysis differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with FPKM for every gene in P group samples
Supplementary_files_format_and_content: Matrix table with FPKM for every gene in Bladder and Tumour samples

source_name: tumor

growth_protocol: in vivo

extract_protocol:
The whole RNA of tissue was harvested using Trizol reagent.Total RNA of the sample was subjected to test the RNA integrity using agarose gel electrophoresis, then quantified and examined by NanoDrop ND-1000.1-2 ug of total RNA was selected for each sample for sequencing library construction.
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina NovaSeq 6000 Sequencer.
RNA libraries were prepared for sequencing using standard Illumina Hiseq protocols.

treatment_protocol: non treatment

tag: sample type

value: tumor-bearing mice


title: IR62266-42-6-2 Middle Control

description:
STAR_raw_count_table.txt
H


title: A431-NR2F2-KD1-NO-DOX-2


title: IR57311 Middle Control

description:
STAR_raw_count_table.txt
I


title: A431-NR2F2-KD1-NO-DOX-1


title: AKP::Keap1 mouse (female) KPKF2

city: Sendai

first: Shin

last: Hamada

state: Miyagi

address: 1-1 Seiryo-machi, Aobaku

department: Division of Gastroenterology

institute: Tohoku University Graduate School of Medicine

description: AKP::Keap1 mouse (female)

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: Data was obtained using the Agilent Feature Extraction software (v10.1), using default for all parameters.  The data were analyzed using GeneSpring GX software (v11.5) (Agilent).

source_name: Whole liver tissue

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from whole livers using Sepazol-RNA I Suger G (Nacalai Tesque).

tag: gender

value: female

value: liver


title: CD71+ TER119+ cells

source_name: spleen


title: AKP::Keap1 mouse (female) KPKF1

description: AKP::Keap1 mouse (female)


title: CT9993-5-10-1M Middle Control

description:
STAR_raw_count_table.txt
G

tag: cultivar


title: CD71- TER119- cells


title: AKP mouse (female) KPF2

description: AKP mouse (female)


title: Nipponbare Tip Control

description:
STAR_raw_count_table.txt
F

value: Tip

tag: hnt-sensitivity


title: IR72 Tip Control

description:
STAR_raw_count_table.txt
D

tag: subspecies


title: Ezh2 KO PGCLC d4 rep3

department: Bioinformatics Core

data_processing:
Illumina CASAVA 1.8.4 software used for basecalling.
trimmomatic  (0.33) was applied for trimming adapter and low quality reads
Trimmed reads were mapped to mm9 whole genome using tophat2 (2.0.11) with default settings
Gene annotations were obtained from iGenome NCBIM37. Gene-based read count were obtained using featureCounts function from Rsubread Bioconductor package
Genome_build: NCBIM37
Supplementary_files_format_and_content: csv file includes Gene counts for each Sample

source_name: Primordial germ cell like cells

growth_protocol: Ezh2f/f, Cre-ERT2 ES cells were cultured in serum-free media containing N2B27 supplemented with 1 μM 7u7jPD0325091 (Cambridge Bioscience, 1643-5) and 3 μM CHIR99021 (Cambridge Bioscience, SM13-10) and 1200 U/ml LIF (ESG1107, Sigma)

extract_protocol:
PGCLC aggregates were trypsinased and sorted into cold PBS. The cells were centrifuged at 2,000 rpm for 3 min following liquid nitrogen snap freezing. Total RNA was extracted using ZR-Duet DNA and RNA Mini Prep kit (Zymo). The genotype of embryos was determined by PCR. RNA quality was measured by 2100 bioanalyzer (Agilent technologies).
RNA and cDNA were prepared by NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® according to the manufacturer’s instructions.

treatment_protocol: EpiLC induction and PGCLC induction were performed as previously described (Hayashi and Saitou, 2013). In brief, 1 × 10e5 cells were seeded in one well of a fibronectin-coated 12-well plate in EpiLCs differentiation medium (N2B27 medium supplemented with 12 ng/ml bFGF (Thermo Fisher, 13256-029), 20 ng/ml Activin A (Peprotech, 120-14E-10) and 1 % KSR (Gibco, 10828). Cells were kept in the plate at 37 °C in a CO2 incubator for 2 days and the media was changed at day 1 of culture. After 2 days EpiLCs were trypsinized. The cell suspension was diluted with PGCLC differentiation medium (GK15 medium containing 500 ng/ml BMP2 (Qkine, Qk007), 100 ng/ml mSCF (R&D Systems, 455-MC-010), 1,000 U/ml LIF and 50 ng/ml EGF (R&D Systems, 2028-EG-010) to a final concentration of 2 × 10e4 cells per ml. 100 µl of the cell suspension was pipetted into a 96-well PrimeSurface® 3D Culture Spheroid plate (MoBiTec, MS-9096VZ) and cultured for 4 days. To induce the depletion of Ezh2, 1 µl of 1 mM 4-Hydroxytamoxifen (H7904, Sigma) dissolved in ethanol was added to 10 ml PGCLC differentiation medium. 1 µl of ethanol was added to 10 ml PGCLC differentiation medium as control. After 2 days of culture, 50 µl of fresh PGCLC differentiation medium (without ethanol or 4-Hydroxytamoxifen) was added to the cells.

tag: genetic background

value: Primordial germ cell like cells

tag: genotype

value: Ezh2-/-, CreERT2

tag: group

value: Ezh2 KO

tag: time

value: day 4