title: SMAD2 ChIP-seq HMCESKO-mESC rep2

city: Beijing

first: Qiaoran

last: Xi

address: Haidian District

institute: School of Life Sciences, Tsinghua University

data_processing:
ChIP-seq reads were quality checked with FastQC v0.11.5 and mapped to the mouse (mm10) genome with Bowtie2 v2.3.3 using standard settings for paired reads. The .sam and .bam files were manipulate with samtools v1.9. Peaks were called using macs2 2.1.4 with default settings. The visualizations of detected peaks were performed using deeptools 3.4.3, and downstream analyses were performed using DiffBind 3.2.4.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data provided as supplementary file

source_name: mouse embryonic stem cell

growth_protocol: Mouse ESCs E14Tg2a.IV, CCE lines were cultured and maintained in feeder free leukemia inhibitory factor (LIF) -supplemented medium (Keller, 1995), which 15% FBS, 100 U of Penicillin-Streptomycin, β-me, NEAA, and sodium pyruvate were also added in.Media was changed daily.

extract_protocol:
For HMCESchip experiment, HMCES-GFP mESCs were cross-linked with 1% formaldehyde at 37 °C for 10 min and quenched with 0.125 M glycine for 5 min at room temperature. Then cells were scraped and GFP-trap-beads assisted ChIP was performed and DNA were extracted using a ChIP assay kit (Millipore) as described. For SMAD2chip, 20 million mESCs were collected for cut&tag experiment followed manuals (Yeason) using anti-SMAD2 antibody (CST: D43B4) to got SMAD2-enriched DNA.
For library construction and sequencing, ChIP DNA samples were quantified and quality assessed by Qubit 2.0 and Agilent 2100. DNA fragments range from 200-600bp were selected constructed for ChIP-Seq library with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions. After scraped from plate, embryonic stem cells were washed with PBS and incubated in lysis buffer.

treatment_protocol: No treatment

value: embryonic stem cell

tag: chip antibody


title: 5_KO_H2O2

status: Public on Sep 14 2022

type: SRA

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

country: USA

institute: NCI

library_source: transcriptomic

data_processing:
Illumina software RTA 2.4.11 was used for basecalling.
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Mouse_mm10) and the annotated transcripts using  STAR and RSEM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts and  RPKM values for each Sample

molecule: total RNA

organism: Mus musculus

extract_protocol:
Cells with/without 1uM H2O2 treatement were lysed with RLT lysis buffer containing 1% beta mercaptoethanol after 24 hours and RNA was harvased using QIAcube as per Rneasy kit from Qiagen.
RNA libraries were prepared for sequencing using llumina TruSeq Stranded mRNA Library Prep.
The mRNA-Seq samples were sequenced on NextSeq using paired-end sequencing.

tag: strain background

tag: cell line

tag: cell type

value: mammary cancer cell line

tag: genotype/variation

tag: treatment

value: treated with 1uM H2O2


title: WID2V_0009_K

city: Lausanne

first: Gaby

last: El Alam

state: Vaud

address: Station 15

department: SV LISP

country: Switzerland

institute: École polytechnique fédérale de Lausanne

description: Influenza H1N1 PR8 H1N1 PR8 virus infected

data_processing:
FastQC (default parameters) was used to verify the quality of the mapping. No low-quality reads were present and no trimming was needed.
generate STAR (version 2.73a) genome indexes with following parameters: STAR --runThreadN 16 --runMode genomeGenerate --limitGenomeGenerateRAM 33524399488 --genomeFastaFiles FASTA_FILE.fa --sjdbGTFfile GTF_FILE.gtf --sjdbOverhang 99
Map reads for each sample using STAR (version 2.73a) aligner with the following parameters: STAR --runThreadN 16 --genomeDir ./Data/stargenome/$STARGENOMENAME --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesIn $R1 $R2 --outFileNamePrefix ./Data/mapped/$SAMPLE
Counts for each sample features (outputed by STAR) where read into R
The obtained STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package edgeR (version 3.24.3) using a generalized-linear model. The trimmed mean of M values (TMM) method was chosen to normalize the counts and the Cox-Reid common dispersion method for computing the dispersion parameter (tag wise dispersion was also computed).
The RUV R package was used to remove batch effects.
A threshold of 1 log2 absolute fold change and p-value larger than 0.05 were considered when identifying the differentially expressed genes.
The clusterProfiler (version 3.10.1) package was then used to perform various Enrichment Analysis on the obtained results.
Genome_build: rnm10
Supplementary_files_format_and_content: tab-delimited text files include raw mapped read counts per feature (generated by STAR - per strand and combined strands)

source_name: Kidney

growth_protocol: We subjected 8 week-old female BALB/cN mice to either mock  or intranasal inoculation with 175 PFU of the IFV H1N1 PR8 strain

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen) and then extracted and cleaned using Direct-zol-96 RNA kit (Zymo Research). 1 ug of total RNA was used for the construction of sequencing libraries.
Transcriptome Library construction Protocol

treatment_protocol: The 3 infected groups were given vehicle, Tet1 (at 40 mpkd) or Tet2 (at 1 mpkd) by daily intraperitoneal injection (mock group respectively injected with vehicule as well).

tag: strain

value: BALB/C

tag: age (weeks)

tag: tratment

value: Vehicule


title: hMus_H3K9me3_2

city: Schwerzenbach

first: Ferdinand

last: von Meyenn

state: Zurich

address: Schorenstrasse 16

department: Health Sciences and Technology

institute: ETH Zurich

description: DNA marked by H3K9me3 and cut by Tn5

library_source: genomic

data_processing:
Library strategy: Cut&Tag
FastQC v0.11.0 used for quality control
TrimGalore v0.6.6 used for trimming low quality bases + adapter sequences
Bowtie2 v2.4.4 used for read mapping
samtools v1.13 used for sorting bam files
bedtools v2.30 used for converting sorted bam files into bedgraph files
bedtools v2.30 used for merging replicate specific bedgraph files for each histone mark
SEACR v1.3 used for calling peaks
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited called peak regions on merged bedgraph files

molecule: genomic DNA

organism: Homo sapiens

source_name: Human vastus lateralis muscle

extract_protocol:
Muscle samples were thawed and sliced in small pieces on ice. Subsequently, the pieces were transferred to an ice-cold dounce homogenizer (7 mL) and 3 mL of nucleus extraction buffer (1× prelysis buffer from the EpiQuick Total Histone Extraction Kit (EpiGentek)) was added before douncing, on ice, 10× with pestle A and 10× with pestle B. To stop the lysis reaction, 3 mL of PBS+1%BSA was added. After 5’ centrifugation at 4˚C, 500 rpm, the supernatant was removed, the nuclei were resuspended in PBS+1%BSA and a sample was visually inspected for viability, purity and abundance of nuclei under the microscope. CUT&Tag was performed according to the published CUT&Tag sequencing protocol for nuclei.All buffers were supplemented with 5 mM sodium-butyrate and 1X complete protease inhibitor (Merck, 1187358000). Protein lo-bind tubes (Eppendorf, EP0030108116) were used to reduce sample loss.  Antibodies against H3K18la (PTM-Bio, PTM-1406), H3K4me3 (Abcam, ab8580), H3K27me3 (Cell Signaling Technology, C36B11), H3K27ac (Abcam, ab4729) and H3K9me3 (Abcam, ab8898) were used in this study.
PCR was performed with 21 μL DNA + 2 μL Universal i5 primer (10 μM) + 2 μL uniquely barcoded i7 primers (10 μM) in a thin-wall 0.5 ml PCR tube, using a different barcode for each sample. *Nextera primers or indexed primers described by Buenrostro, J.D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523:486 (2015).To this mixture,  25 μL NEBNext HiFi 2x PCR Master mix was added. The samples were mixed, quick spinned and placed in  a thermocycler with heated lid. The following program was used: Cycle 1: 72 °C for 5 min (gap filling) Cycle 2: 98 °C for 30 sec.Cycle 3: 98 °C for 10 sec.Cycle 4: 63 °C for 10 sec.Repeat Cycles 3-4 13 times 72°C for 1 min and hold at 8 oC.

treatment_protocol: control

tag: biological replicate

tag: antibody


title: WID2V_0008_K


title: SMAD2 ChIP-seq HMCESKO-mESC rep1

country: China

value: untreated


title: 4_KO_NT


title: hMus_H3K9me3_1

description: DNA marked by H3K9me3 and cut by Tn5


title: SMAD2 ChIP-seq WT-mESC rep2


title: hMus_H3K4me3_2

description: DNA marked by H3K4me3 and cut by Tn5


title: 3_KO_NT


title: WID2V_0007_K


title: WID2V_0006_K


title: SMAD2 ChIP-seq WT-mESC rep1


title: hMus_H3K4me3_1

description: DNA marked by H3K4me3 and cut by Tn5


title: 2_KO_NT


title: HMCES ChIP-seq HMCES-GFP-mESC rep2

value: GFP-trap


title: WID2V_0042_K


title: EndoC-βH1, IFNa 24h, siCT (exp175)

city: Anderlecht

first: Florian

last: Szymczak

state: Brussels

address: Route de Lennik 808 - CP618

department: Faculty of Medicine

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Raw RNA-seq data (2x150bp paired-end with a depth >200M reads) was quality checked with fastp to remove reads with poor quality and trim remaining adapters.
The quality control (QC) of the passing reads was assessed with FastQC (Babraham Bioinformatics). One paired experiment for the IFNα treatment at 24h did not pass our QC (insufficient read quality) and was removed from the subsequent analyses.
Gene expression was quantified in TPM (Transcripts per Millions) using Salmon v1.4  with additional parameters “--seqBias --gcBias --validateMappings”.
We used GENCODE v35  as the reference genome and indexed it with default k-mer values. Differential Gene Expression (DGE) analysis was performed with DESeq2 v1.30.1
Assembly: GENCODE v35 (GRCh38.p13)
Supplementary files format and content: Tab Separated Values (TSV) file containing TPM values at the gene level

growth_protocol: The EndoC-βH1 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) with 5.6 mmol/L glucose (Gibco, Thermo Fisher Scientific), 2% fatty acid-free BSA fraction V, 50 μmol/L 2-mercaptoethanol (Gibco, Thermo-Fisher Scientific), 10 mmol/L nicotinamide (Sigma-Aldrich), 5.5 μg/mL transferrin (Sigma-Aldrich), 6.7 ng/mL selenite (Sigma-Aldrich), 100 U/mL penicillin + 100 μg/mL streptomycin in matrigel–fibronectin–coated plates (60).

extract_protocol:
Total RNA was isolated from EndoC-βH1 samples using the RNeasy Plus Micro kit (Qiagen) and quantified using a Nanodrop (NanoDrop ND-1000; Thermo Fisher Scientific).
A minimum of 500ng of high-quality RNA with RNA integrity number > 9 (as determined by Agilent Bioanalyzer) per sample and replicate was used for library preparation. RNA-seq was performed on a NovaSeq 6000 (Eurofins).

treatment_protocol: NLRC5 gene expression was silenced using two independent siRNA (Thermo Fisher Scientific; siNL#1 (siRNA HSS130675): 5’-GGACACCUGGCAGUCUUUCAUUCAU-3’; siNL#2 (siRNA HSS130676): 5’-GCAGUUGGCAGAGUCUCUCGUUCUU-3’). Allstars Negative Control siRNA (siCTL) (Qiagen) was used as a negative control; the siRNA control does not interfere with β-cell gene expression, function, or viability. Cells were transfected using the Lipofectamine RNAiMAX lipid reagent (Invitrogen, Life Technologies) in OptiMEM (Gibco, Thermo Fisher Scientific) reduced serum medium, according to the manufacturer's instructions. EndoC- βH1 were transfected using 30 nmol/L of each siRNA, overnight. Dispersed human islets and iPSC-derived β-like cells were transfected with 60 nmol/L of each siRNA, also during an overnight incubation period. After transfection, EndoC-βH1  were kept in culture for a 48h recovery period and subsequently exposed or not to human IFNα (2,000 U/mL; PeproTech) for 8 or 24h.

value: IFNa (Interferon Alpha)

tag: knock-down (kd)

value: siCT

tag: time


title: WID2C_0041_K

description: Influenza H1N1 PR8 H1N1 PR8 virus uninfected

value: Control


title: 1_KO_NT


title: hMus_H3K27me3_2

description: DNA marked by H3K27me3 and cut by Tn5


title: EndoC-βH1, IFNa 24h, siCT (exp166)


title: WID2C_0005_K


title: hMus_H3K27me3_1

description: DNA marked by H3K27me3 and cut by Tn5


title: HMCES ChIP-seq HMCES-GFP-mESC rep1


title: WID2C_0004_K


title: hMus_H3K27ac_2

description: DNA marked by H3K27ac and cut by Tn5


title: WGBS Ultrasound treated wheat seedling 1

city: Martonvásár

first: Norbert

middle: Tibor

last: Hidvégi

address: Brunszvik street 2.

department: Department of Biological Resources

country: Hungary

institute: HUN-REN Centre for Agricultural Research Agricultural Institute

data_processing:
FastQ files were quality checked with FastQC v0.11.9. Adapter and quality trimming were done with TrimGalore v0.6.7. Trimmed reads were aligned to Triticum aestivum IWGSC v52 genome from Ensembl Plants with bismark v0.23.1 by followed the manufacturer's instructions.
Aligned and methylation extracted bismark.cov files were analysed in SeqMonk v1.48.1. Chi-squared test and EdgeR were used to identified the significantly differently methylated regions in CpG, CHG and CHH contexts.
Assembly: IWGSC CS RefSeq v2.1
Supplementary files format and content: DNA methylation levels in percentage in tab-delimited TXT file

organism: Triticum aestivum

source_name: seedling

extract_protocol:
Plant materials were homogenized with Bertin Precellys Minilys. Genomic DNA was isolated with Macherey-Nagel NucleoSpin Plant II mini kit based on the manufacturer's user manual. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the firs strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina NovaSeq 6000 and MGI DNBSEQ-G400 platform.
WGBS library was constructed with NEBNext® Enzymatic Methyl-seq Kit by the manufacturer's protocols
Whole Genome Bisulfite Sequencing

treatment_protocol: In present experiments, the germination of a breeding line of winter wheat (Triticum aestivum L. cv. SE15) was investigated. The water content of the seeds was 13.6%. Half of the seeds (100 seeds) were ultrasonicated before germination at 30 kHz, 70 W for 5 minutes. The seeds were placed into open Petri dishes 4 cm away from the ultrasound head. The parameters of the ultrasound treatment have been optimized previously in preliminary experiments. The other half of the seeds (100 seeds) served as control and were non-ultrasonicated. Thereafter, winter wheat seeds were germinated at 20 °C in darkness for a week, in accordance with the Hungarian standard of MSZ 6354-3:2008 describing the determination of germination.

tag: tissue

value: seedling

value: 7 days after germination

tag: genotype

value: Ultrasound teated


title: WID2C_0003_K


title: WGBS Control, untreated wheat seedling 1


title: hMus_H3K27ac_1

description: DNA marked by H3K27ac and cut by Tn5


title: Ultrasound treated wheat seedling 3

data_processing:
FastQ files were quality checked with FastQC v0.11.9. Adapter and quality trimming were done with TrimGalore v0.6.7.
Trimmed reads were aligned to Triticum aestivum IWGSC v52 genome from Ensembl Plants with STAR v2.7.10a.
Aligned bam files were analysed with SeqMonk v1.48.1
Statistical analysis was made in DESeq2 and SeqMonk.
Assembly: RefSeq GCF_018294505.1
Supplementary files format and content: Logarithmic fold changes in tab-delimited TXT file

source_name: leaf

extract_protocol:
Plant materials were homogenized with Bertin Precellys Minilys. Genomic DNA was isolated with Macherey-Nagel NucleoSpin Plant II mini kit based on the manufacturer's user manual.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the firs strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina NovaSeq 6000 platform.

value: leaf

value: ultrasound treated


title: hMus_H3K18la_2

description: DNA marked by H3K18la and cut by Tn5


title: WID2D_0046_L

source_name: Liver

value: Dox at 40mpkd


title: Ultrasound treated wheat seedling 1


title: WID2C_0001_K


title: hMus_H3K18la_1

description: DNA marked by H3K18la and cut by Tn5


title: WID2D_0030_L


title: WID2D_0028_L


title: Ultrasound treated wheat seedling 2


title: WID2D_0027_L


title: Control, untreated wheat seedling 3

value: not treated, control


title: WID2D_0029_L


title: HOTTIP-KO-small-RNA-seq_1

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end small RNA-seq reads from human AML cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for small RNA-seq

source_name: MOLM13 leukemia cells

growth_protocol: Human MOLM13 leukemia cells were culture at RMPI1640 medium with 10% FBS media.

extract_protocol:
Norgen Biotek RNA purification kit was used to isolate RNA as per manufacturer’s instructions. cDNA (reverse transcription - RNA to cDNA) was made using High Capacity RNA to cDNA kit (Life Technologies, Grand Island, NY).
Small RNA-seq libraries were prepared using BioO from Perkin Elmer and Qiagen kits. Small RNAs were sequenced using a TruSeq Small RNA Sequencing Kit (Illumina, San Diego, CA, USA) according to manufacturer instructions.

treatment_protocol: Immediately extract small RNA from MOLM13 AML cells without any treatment

value: Human-derived acute myeloid leukemia cell line

tag: tissue source

value: peripheral blood

value: HOTTIP-KO


title: HOTTIP-KO-small-RNA-seq_2


title: WID2D_0026_L

value: BALB/C


title: WT-small-RNA-seq_1

value: wild type


title: Control, untreated wheat seedling 2


title: Control, untreated wheat seedling 1


title: WT-small-RNA-seq_2


title: S2_WT3_GFP_RNAi_mRNA

city: Cambridge

first: David

last: Bartel

state: MA

address: 455 Main St

institute: Whitehead Institute, MIT

description:
RNAseq following knockdown of Ago1 (or GFP) in WT and dora S2 cells
S2_RNAi_mRNA_rawreads.csv

data_processing:
RNAseq reads were aligned to the genome (UCSC dm6.08 reference assembly) using STAR (V2.4, with the paramaters “--alignIntronMax 1 --runThreadN 30 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated –outSJfilterReads”) (Dobin et al., 2013), and alignments to all chromosomal genes were counted using htseq-count (with the parameters “-m union -s reverse -r name") (Anders et al., 2015). TPM values were determined by dividing these htseq-determined counts for each gene by the median length for all isoforms of that gene, and then normalizing these values for library depth.
Assembly: dm6
Supplementary files format and content: All processed .csv files contain non-normalized mRNA counts for the indicated samples

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: Drosophila S2 cells were grown at 26°C in Schneider’s Drosophila Medium (Life Technologies) supplemented with 10% heat-inactivated FBS (Life Technologies). Cells were passaged 1:5 every 3–5 days. For knockdown experiments, each well of a 6-well plate was transfected twice with 2 µg of dsRNA, with the second transfection occurring 3 days after the first. Transfections were with effectene, according to the manufacturer’s protocol. Cells were collected for RNA extraction 4 days after the second transfection.

extract_protocol:
RNA was extracted with TRI Reagent (Life Technologies), according to the manufacturer’s protocol. Briefly, samples were homogenized in TRI reagent, and RNA was phase-separated by the addition of chloroform (J.T. Baker Analytical) at a ratio of 250 µL per 1 mL TRI Reagent. RNA was then precipitated with isopropanol, with GlycoBlue (Life Technologies) added as a co-precipitant when necessary, and pellets were washed twice with 70% ethanol prior to resuspension in water.
RNAseq libraries were prepared with the Kapa RNA Hyperprep Kit with mRNA capture (Roche diagnostics). These libraries were sequenced on an Illumina NovaSeq platform with 50-nt paired-end reads

value: WT

tag: RNAi target

value: GFP


title: WID2T_0025_L

value: 9TB at 1mpkd


title: S2_WT2_GFP_RNAi_mRNA


title: H1155, GFI1KO_3

city: Tianjin

first: Hao

last: Wang

address: Tianjin Medical University, 22 Qixiangtai Road, Heping District, Tianjin 300070, China

institute: Tianjin Medical University

description: GFI1-KO H1155 rep 3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie2.
HTseq was used to quantify gene count.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: H1155 cell line knock out GFI1

growth_protocol: Wildtype and GFI1-KO H1155 cell line were cultred in DMEM medium containg 10%FBS

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA sequencing libraries were prepared using NovaSeq™ 6000 v1.5.

treatment_protocol: untreatment

value: neuroendocrine large cell lung cancer

value: GFI1 knockout


title: WID2T_0045_L


title: S2_Dora2_GFP_RNAi_mRNA

value: Dora


title: S2_WT1_GFP_RNAi_mRNA


title: T20;Digoxin  5µM rep 3

type: RNA

city: Lille

first: Philippe

last: Lefebvre

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: INSERM UMR 1011, Université Lille-Nord de France

description:
Samples from untreated AC16 cells collected 4 hours (T20) after 5µM digoxin treatment
24_T20_Digo_5uM_rep3

hyb_protocol: Following fragmentation, 5,5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip Human Transcriptome Array 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: Raw data were processed further using GIANT (Galaxy-based interactive tools for Analysis of Transcriptomic data). This user-friendly tool suite was developed in-house for microarray and RNA-seq differential data analysis. It consists of modules allowing to perform quality control (QC), Robust Multi-Average method normalization, LIMMA differential analysis, volcano plot and heatmaps.

label: biotin

source_name: AC16 cells human ventricular cardiomyocytes

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: The AC16 human cardiomyocyte cell line was obtained from Millipore (SCC109). Cells were maintained in DMEM/F12 Ham (Sigma-Aldrich) supplemented with 2mM L-Glutamine (Thermo Fisher  Scientific), 12.5% of fetal bovine serum (FBS) and 1% penicillin-streptomycin (Thermo Fisher Scientific).Cells were synchronized with 100nM dexamethasone for 2h followed by PBX washes. Cells were treated with digoxin (0.5 or 5µM) and cells were lysed 4, 16 and 20 hours after the treatment

extract_protocol: RNA  extraction  from  cultured  cells  was  carried  out  using  the  NucleoSpin®  RNA  Midi  kit  according  to  the  manufacturer’s  instruction  (Macherey-Nagel).

treatment_protocol: Digoxin 0.5µM or 5µM

tag: cell line/type

value: AC16  human ventricular cardiomyocytes

tag: treatment/time point


title: H1155, GFI1KO_2

description: GFI1-KO H1155 rep 2

tag: cell line


title: T20;Digoxin 0.5µM rep1

description:
Samples from untreated AC16 cells collected 4 hours (T20) after 0.5µM digoxin treatment
19_T20_Digo_0.5uM_rep1


title: T20;Digoxin  5µM rep 1

description:
Samples from untreated AC16 cells collected 4 hours (T20) after 5µM digoxin treatment
22_T20_Digo_5uM_rep1


title: T20;Digoxin  5µM rep 2

description:
Samples from untreated AC16 cells collected 4 hours (T20) after 5µM digoxin treatment
23_T20_Digo_5uM_rep2


title: S2_Dora3_GFP_RNAi_mRNA


title: T20;Digoxin 0.5µM rep3

description:
Samples from untreated AC16 cells collected 4 hours (T20) after 0.5µM digoxin treatment
21_T20_Digo_0.5uM_rep3


title: H1155, GFI1KO_1

description: GFI1-KO H1155 rep 1

tag: cell type


title: WID2T_0022_L


title: T20;Digoxin 0.5µM rep2

description:
Samples from untreated AC16 cells collected 4 hours (T20) after 0.5µM digoxin treatment
20_T20_Digo_0.5uM_rep2


title: WID2T_0024_L


title: H1155, WT_3

description: Wildtype H1155 rep 3

value: Wildtype


title: H1155, WT_1

description: Wildtype H1155 rep 1


title: WID2T_0023_L


title: S2_Dora1_GFP_RNAi_mRNA


title: H1155, WT_2

description: Wildtype H1155 rep 2


title: S2_WT3_Ago1_RNAi_mRNA


title: T20; Vehicule rep2

description:
Samples from untreated AC16 cells collected 4 hours (T20) after vehicule treatment
17_T20_veh_rep2


title: S2_WT2_Ago1_RNAi_mRNA


title: T20; Vehicule rep3

description:
Samples from untreated AC16 cells collected 4 hours (T20) after vehicule treatment
18_T20_veh_rep3


title: WID2V_0042_L

value: Vehicule


title: Floating_A549_GFI1_3

description: Floating GFI1-expressing A549 rep 3

source_name: A549 cell line overexpress GFI1

growth_protocol: Control and GFI1-expressing A549 cell line were cultred in RPMI1640 medium containg 10%FBS

treatment_protocol: Cells in floating group were forced into suspension for 48hrs.

value: Lung adenocarcinoma

value: GFI1 overexpression

value: force into suspension for 48hrs


title: Floating_A549_GFI1_1

description: Floating GFI1-expressing A549 rep 1


title: Floating_A549_GFI1_2

description: Floating GFI1-expressing A549 rep 2


title: Floating_A549_Ctrl_3

description: Floating control A549 rep 3

value: control


title: WID2V_0009_L


title: WID2V_0008_L


title: S2_Dora1_Ago1_RNAi_mRNA


title: WID2T_0021_L


title: WID2V_0006_L


title: T16; Untreated rep2

description:
Samples from untreated AC16 cells collected 16 hours (T16) after synchronization
14_T16_rep2


title: T16; Untreated rep3

description:
Samples from untreated AC16 cells collected 16 hours (T16) after synchronization
15_T16_rep3


title: T4;Digoxin  5µM rep3

description:
Samples from untreated AC16 cells collected 4 hours (T4) after 5µM digoxin treatment
12_T4_Digo_5uM_rep3


title: T20; Vehicule rep1

description:
Samples from untreated AC16 cells collected 4 hours (T20) after vehicule treatment
16_T20_veh_rep1


title: T16; Untreated rep1

description:
Samples from untreated AC16 cells collected 16 hours (T16) after synchronization
13_T16_rep1


title: S2_WT1_Ago1_RNAi_mRNA


title: WID2V_0010_L


title: S2_Dora2_Ago1_RNAi_mRNA


title: S2_Dora3_Ago1_RNAi_mRNA


title: Floating_A549_Ctrl_2

description: Floating control A549 rep 2


title: WID2C_0041_L

value: Control


title: Attached_A549_GFI1_3

description: Attached GFI1-expressing A549 rep 3

value: untreated


title: WID2C_0003_L

value: BALB/C


title: Day 30 epicardial cells 2

city: Palo Alto

first: Laksshman

last: Sundaram

state: California

address: stanford

department: Computer science

institute: Stanford University

description: Day 30 epicardial cells aligned tn5 insertion fragments

data_processing:
fastqs generated using bcl2fastq utility
scATAC reads aligned to hg38 using cellranger-atac v1 software
Assembly: hg38
Supplementary files format and content: fragment files indicating tn5 insertions along with the single cell barcode

source_name: iPS derived epicardial cells

extract_protocol:
The iPSC-derived epicardial cells were differentiated in a chemically defined medium (CDM), which is composed of 50% IMDM, 50% Ham’s F-12 Nutrient Mix, 1% chemically defined lipid concentrate, 2 mM Glutamax, 1 mg/ml PVA, 15 μg/ml transferrin, and 450 μM monothioglycerol. When hiPSCs reached ~80% confluency they were dissociated with 1 ml of Accutase (Sigma) and replated a density of 1.5 x104 cells/cm2 in 6-well plates and cultured in iPS-Brew medium (Miltenyi Biotech) supplemented with 10 μM Y27632. The next day (day 1),  each well was washed with D-PBS, and epicardial cells differentiation was initiated by adding the mid-primitive streak induction medium (consisting of 10 ng/ml Activin A, 6 μM CHIR99021, 50 ng/ml BMP4, 20 ng/ml FGF2, and 2 μM LY294002 in CDM). On day 2, each well was refreshed with the lateral plate mesoderm induction medium (consisting of 1 μM A83-01, 30 ng/ml BMP4, and 1 μM C59 in CDM). On days 3-4, each well was refreshed with the splanchnic mesoderm induction medium (consisting of 1 μM A83-01, 30 ng/ml BMP4, 1 μM C59, 20 ng/ml FGF2, and 2 μM retinoic acid in CDM). On days 5-8, the media was refreshed with the septum transversum induction medium (consisting of 2 μM retinoic acid and 40 ng/ml BMP4 in CDM). On day 9, cells were dissociated using Accutase and sparsely seeded (104 cells/cm2) on gelatin-coated 6-well plates in the proepicardium induction medium (consisting of 100 μg/ml ascorbic acid, 2 μM of retinoic acid, and 0.7 μg/ml insulin in CDM) for 2 days without medium change. Starting at day 11, each well was refreshed every other day with the epicardial cell induction/maintenance medium (consisting of 100 μg/ml ascorbic acid, 10 μM SB431542, and 0.7 μg/ml insulin in CDM). The iPSC-derived epicardial cells can preserve their cell type-specific markers (e.g., TBX18, WT1, and TCF21) for at least 18 passages in the epicardial cell induction/maintenance medium.
Libraries were constructed using the 10X Genomics scATAC-seq kits

tag: differentiation day

value: Day 30


title: IgG_rep2

description: GFI1-Flag-expressing IgG_rep_2

data_processing:
Basecalls performed using CASAVA version 1.4
Data were filtered using Trimmomatic
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2-2.3.5
Determination of the normalized factor using deeptools
peaks were called using MACS2
Assembly: hg38

growth_protocol: GFI1-Flag-expressing A549 cell line were cultred in RPMI1640 medium containg 10%FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and GFI1-Flag-DNA complexes were isolated with anti-Flag affinity gel.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Samples Prep Kit. Briefly, DNA fragment end repair, add A base to 3'end, and connect sequencing adapter. PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

tag: chip antibody

value: anti-IgG (I8765,Sigma-Aldrich)

tag: treatment

value: untreatment


title: WID2C_0005_L

tag: strain

tag: age (weeks)


title: WID2C_0002_L

tag: tratment


title: IP_rep2

description: GFI1-Flag-expressing ChIP-seq IP_rep_2

data_processing:
Basecalls performed using CASAVA version 1.4
Data were filtered using Trimmomatic
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2-2.3.5
Determination of the normalized factor using deeptools
peaks were called using MACS2
Genome_build: hg38

tag: genotype/variation

value: expressing GFI-FLAG

value: anti-Flag affinity gel (A2220, Sigma-Aldrich)


title: Attached_A549_GFI1_1

description: Attached GFI1-expressing A549 rep 1


title: Input_rep2

description: GFI1-Flag-expressing Input_rep_2


title: IgG_rep1

description: GFI1-Flag-expressing IgG_rep_1


title: WID2C_0001_L


title: Control

city: Durham

first: Purushothama Rao

last: Tata

email: pt93@duke.edu, tata.lab@yahoo.com

state: NC

address: 303 Research Dr., Alexander Sands Building, Room- 451, BOX 3709

department: Department of Cell Biology

institute: Duke University School of Medicine

description: Single-cell RNA-seq (3' enrichment)

data_processing:
FASTQ files were processed using Cell Ranger v3.0.0 (10x Genomics) and mapped to the mm10 reference genome.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.h5 files: Expression matrices.

molecule: polyA RNA

source_name: Mouse lungs

extract_protocol:
Lungs were collected three days after final dose of Tamoxifen. Briefly, lungs were inflated with dissociation solution (450U/mL Collagenase I (Worthington, LS004197), 5U/mL Dispase (Corning, 354235), and 0.33U/mL DNase I (Roche, 10104159001), in DMEM). Separated lung lobes were minced and incubated in enzyme solution at 37°C for 25 minutes. Dissociation was quenched with equivalent volume 10% FBS/DMEM and passed through a 100 µm strainer. Cell pellet was resuspended in red blood cell lysis buffer (100 µm EDTA, 10 mM KHCO3, 155 mM NH4Cl) for 2 minutes, followed by quenching with 10%FBS/DMEM and filtration through a 40 µm strainer. The cells were pelleted, then resuspended in 500µL 2%FBS/DMEM and split into three fractions: CD45/31/140a, CD45, and bulk sample. For MACS, cells were incubated for 30 minutes with the following antibodies: CD45 (Miltenyi Biotech, 130-052-301), CD31 (Miltenyi Biotech, 130-097-418), and CD140a (Miltenyi Biotech, 130-101-547). MACS depletion was performed as per manufacturer protocol using LD columns (Miltenyi Biotech, 130-042-901). For AT2 ablation scRNA-seq, we aimed to enrich epithelial cell populations. For this, we combined different cell populations as follows: 11,200 cells from CD31/CD45/CD140a-depleted cells, 3200 cells from CD45-depleted cells, and 1600 cells from bulk fractions and resuspended in PBS supplemented with 0.01% BSA. For control lung scRNA-seq, we used CD31/CD45-depleted population only.
Followed the protocol of 10x Genomics Chromium v3.1 chemistry.

treatment_protocol: Sftpc-CreER;Rosa26R-DTA mice treated with Tamoxifen for three consecutive days.

value: Lung cells

value: Wild type

tag: age

value: Adult


title: Attached_A549_Ctrl_2

description: Attached control A549 rep 2


title: Attached_A549_GFI1_2

description: Attached GFI1-expressing A549 rep 2


title: Input_rep1

description: GFI1-Flag-expressing Input_rep_1


title: Attached_A549_Ctrl_3

description: Attached control A549 rep 3


title: T4;Digoxin  5µM rep2

description:
Samples from untreated AC16 cells collected 4 hours (T4) after 5µM digoxin treatment
11_T4_Digo_5uM_rep2

value: AC16  human ventricular cardiomyocytes


title: IP_rep1

description: GFI1-Flag-expressing ChIP-seq IP_rep_1


title: Floating_A549_Ctrl_1

description: Floating control A549 rep 1


title: WGBS Ultrasound treated wheat seedling 2

value: seedling

tag: time

value: 7 days after germination

value: Ultrasound treated


title: AT2 cell ablation

description: Single-cell RNA-seq (3' enrichment)


title: dksA ES2

status: Public on Sep 13 2022

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Basecalling was done using bcl2fastq2 V2.20 (Illumina, USA).
QC was performed using fastQC (v0.11.9)
Reads were trimmed using bbduk (v38.79) using the adapters.fa file provided with bbduk and parameters ktrim=r k=23 mink=11 hdist=1 qtrim2=t trimq=10 tpe tbo
Reads were mapped using bbmap (v38.79) with parameters k=13 and ambig=toss against the Acinetobacter baumannii genome (accession CP000522) and plasmids (accessions CP000523, CP012004, CP012005)
Reads were sorted using samtools (v1.6)
Reads over CDS features were quantified using HTSeq (v0.12.4)
Genome_build: CP000522.1, CP000523.1, CP012004.1, CP012005.1
Supplementary_files_format_and_content: Tab separated values containing read counts per feature in each condition

organism: Acinetobacter baumannii

source_name: Batch culture Mueller Hinton broth

extract_protocol:
Bacterial cells were collected, flash frozen on dry ice ethanol bath, and RNA was harvested using Trizol (Ambion) reagent. For isolation and purification of total RNA from cells, RNeasy Qiagen was used.
Libraries were constructed using Universal Prokaryotic RNA-Seq Library preparation kit (Tecan, USA) according to the manufacturer protocol.

tag: growth phase

value: Late exponential

value: No treatment


title: dksA ES3

tag: genotype


title: WGBS Control, untreated wheat seedling 2

tag: tissue

value: Control


title: WT ES1

value: Wild-type


title: dksA Cu3

value: Exponential


title: dksA ES1


title: dksA Zn3


title: dksA Cu2


title: dksA Zn2


title: dksA2


title: dksA Cu1


title: WT ES3


title: dksA Zn1


title: WT Cu3


title: Attached_A549_Ctrl_1

description: Attached control A549 rep 1

value: Lung adenocarcinoma

value: control

value: untreated


title: dksA1


title: WT ES2


title: T4; Vehicule rep2

description:
Samples from untreated AC16 cells collected 4 hours (T4) after vehicule treatment
5_T4_veh_rep2


title: WT Cu2


title: dksA3


title: WT Cu1


title: T4;Digoxin 0.5µM rep3

description:
Samples from untreated AC16 cells collected 4 hours (T4) after 0.5µM digoxin treatment
9_T4_Digo_0.5uM_rep3


title: T4; Vehicule rep3

description:
Samples from untreated AC16 cells collected 4 hours (T4) after vehicule treatment
6_T4_veh_rep3


title: T4;Digoxin  5µM rep1

description:
Samples from untreated AC16 cells collected 4 hours (T4) after 5µM digoxin treatment
10_T4_Digo_5uM_rep1


title: T4;Digoxin 0.5µM rep1

description:
Samples from untreated AC16 cells collected 4 hours (T4) after 0.5µM digoxin treatment
7_T4_Digo_0.5uM_rep1


title: T4;Digoxin 0.5µM rep2

description:
Samples from untreated AC16 cells collected 4 hours (T4) after 0.5µM digoxin treatment
8_T4_Digo_0.5uM_rep2


title: WT Zn3


title: T4; Vehicule rep1

description:
Samples from untreated AC16 cells collected 4 hours (T4) after vehicule treatment
4_T4_veh_rep1


title: T0; Untreated rep3

description:
Samples from untreated AC16 cells collected (T0) after synchronization
3_T0_rep3

value: collected (T0) after synchronization


title: WT Zn1


title: WT Zn2


title: WT3


title: T0; Untreated rep1

description:
Samples from untreated AC16 cells collected (T0) after synchronization
1_T0_rep1


title: WT2


title: T0; Untreated rep2

description:
Samples from untreated AC16 cells collected (T0) after synchronization
2_T0_rep2


title: D8W_5

city: Shanghai

first: Chun-Xiao

last: Huang

address: 65 Chifeng Road, Yangpu District

department: School of Medcine, Tongji University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: danRer11
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

organism: Danio rerio

source_name: spinal cord

extract_protocol:
Spinal cord tissue were dissected out. V2a interneurons were isolated from Tg(Chx10:GFP) line by FAC-sorting, flash frozen on dry ice. Total RNA was isolated using SMART-SeqTM v4 UltraTM Low Input RNA Kit for Sequencing (Clontech). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spinal cord segments 1 to 7

value: V2a interneurons with regrown-axon

tag: disease state

value: 8 weeks after spinal cord injury


title: D8W_4


title: D8W_6


title: WT1


title: D8W_2


title: D8W_1


title: Zfp7 RNA-seq

first: Jeremy

last: Ratiu

state: North Carolina

address: 328 Jones Bldg, Box 3010

department: Immunology

institute: Duke University

data_processing:
Reads were mapped using Hisat2, sam files converted to bam and sorted using samtools and raw counts matices generated using featureCounts.
Differential expression was performed using edgeR and DeSeq2 implemented through iDep.91.
Genome_build: mm10
Supplementary_files_format_and_content: Raw read count matrices are provided as basic TSV files.

source_name: Zfp335 cKO DP 1

growth_protocol: Mice were maintained under specific pathogen-free conditions

extract_protocol:
DP thymocytes were isolated by FACS sorting. Cells were lysed in trizol and total RNA isolated using the Zymo Direct-zol RNA Microprep kit.
Libraries were constructed at BGI genomics

tag: strain background

value: Zfp335 cKO

value: DP Thymocyte


title: Zfp8 RNA-seq

source_name: Zfp335 cKO DP 2


title: Zfp10 RNA-seq

source_name: Zfp335 cKO DP 3


title: G8W_2

value: V2a interneurons without regrown-axon


title: D8W_3


title: G8W_1


title: Con1 RNA-seq

source_name: Zfp335 WT DP 1

value: Zfp335 WT


title: Con3 RNA-seq

source_name: Zfp335 WT DP 3


title: G8W_3


title: D3W_5

value: 3 weeks after spinal cord injury


title: G8W_5


title: Con2 RNA-seq

source_name: Zfp335 WT DP 2


title: G8W_4


title: FTF1

city: Hangzhou, Zhejiang, China

first: Xiaowei

last: Li

address: No. 298 Deshengzhong road

institute: Zhejiang Academy of Agricultural Sciences

data_processing:
A cDNA library was sequenced run with Illumina Novaseq 6000 sequence platform.
Firstly, Cutadapt [1] and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.
De novo assembly of the transcriptome was performed with Trinity 2.4.0 [2]. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
Salmon [4] was used to perform expression level for Unigenes by calculating TPM
Assembly: Trinity.gene.fasta
Supplementary files format and content: xlsx files include TPM values for each Sample

organism: Frankliniella intonsa

source_name: female, antennae, rep1

extract_protocol:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribe™ Reverse Transcriptase reaches the 5’ end of the mRNA, the enzyme’s terminal transferase activity adds a few additional nucleotides to the 3’ end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5’ end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase(NEB, M0348S) by incubate at 37°C for 30min.Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand,indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR.

value: antennae

tag: Sex

value: female


title: FTF3

source_name: female, antennae, rep3


title: WFTM3

organism: Frankliniella occidentalis

source_name: male, antennae, rep3

value: male


title: D3W_4


title: D3W_3


title: D3W_2


title: WFTF2

source_name: female, antennae, rep2


title: WFTM2

source_name: male, antennae, rep2


title: G3W_5


title: D3W_1


title: WFTF1


title: G3W_2


title: G3W_3


title: WFTF3


title: G3W_1


title: FTF2


title: G3W_4


title: S2-09

city: PULLMAN

first: Eric

middle: Aaron

last: Shelden

state: WA

address: 1770 NE Stadium Way

department: School of Molecular Biosciences

institute: Washington State University

description: RNA extracted from a canine soft tissue sarcoma

data_processing:
RNA seq reads were aligned to a recent canine reference genome (ROS-canfam-01) using STAR2 and counted using htseq-count.
Assembly: ROS-canfam-01
Supplementary files format and content: comma separated values (csv) file containing counts of aligned reads produced by htseq-count

organism: Canis lupus familiaris

source_name: soft tissue sarcoma

extract_protocol:
Two 50 micron thickness sections were obtained from each FFPE tumor sample and processed for total RNA extraction using an Qiagen RNeasy FFPE kit. One microgram of total RNA was enriched for mRNA using Ribominus Eukaryotic V2.
Sequencing libraries were constructed using 200 nanograms of enriched mRNA and the Ion Total RNA-Seq Kit V2 without further fragmentation while all purification and size selection were performed using AMPureXP beads.

value: soft tissue sarcoma

tag: histological diagnosis

value: perivascular wall tumor

tag: molecular identity

tag: tumor grade

tag: tumor size

value: 5 cm in diameter, multi-nodular

tag: reproductive status

value: FS

tag: breed

value: Mixed Breed Dog

tag: tumor location

value: Right lateral thora


title: S2-11

value: 6 x 5 x 2 cm (6.0 x 4.0 x 2.0 cm @ processing)

value: MN

value: Labrador Retriever

value: Craniolateral aspect of right carpus


title: Dcon_4

tag: strain

value: spinal cord segments 1 to 7

tag: cell type

value: retrogradely labeled V2a interneurons

value: uninjured


title: S2-08

value: fibrosarcoma

value: 3 x 5 cm (8 x 5 x 5 cm sample @ processing)

value: Great Pyrenees

value: Ventral thorax


title: S2-07

value: soft tissue sarcoma

value: peripheral nerve sheath tumor

value: American Cocker Spaniel

value: Interdigit 3-4 left forelimb


title: Dcon_3


title: Dcon_5


title: S2-06

value: 8 x 6.2 x 2.7 cm (13 x 9 x 4 cm @ processing)

value: FS

value: Golden Retriever

value: Right hip


title: S2-04

value: perivascular wall tumor

value: Tibetan Terrier

value: Left antebrachium


title: S2-03

value: Head


title: Dcon_2

value: spinal cord segments 1 to 7

value: retrogradely labeled V2a interneurons

value: uninjured


title: S1-11

value: fibrosarcoma

value: MN

value: Right lateral stifle


title: WFTM1

source_name: male, antennae, rep1

value: antennae

value: male


title: Gcon_4

value: non-labeled V2a interneurons


title: Gcon_5


title: S1-12

value: soft tissue sarcoma

value: 2 cm

value: Whippet

value: Left metacarpus


title: S1-10

value: perivascular wall tumor

value: peripheral nerve sheath tumor

value: 4 x 4 cm

value: Australian Cattle Dog

value: Proximal thigh


title: S1-09

value: Australian Shepherd

value: Left ilum


title: Gcon_3

value: spinal cord segments 1 to 7

value: uninjured


title: Gcon_2


title: S1-04

value: FS

value: Standard Poodle

value: Knee


title: S1-07

value: Plott hound mix

value: Thoracic wall


title: Library B - gate 4

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

data_processing:
Illumina Casava 1.8 software was used for basecalling and demultiplexing.
Reads were quality checked and filtered to retain only those sequences that were not shifted (starting codon: CCA/CNA). Furthermore, only reads with no mismatch in the translation starting codon (ATG/CTG) were retained. Finally, the 11 bases of Kozak sequences library were extracted from the reads. The library (sequenceIdentifier.fa) is composed of 5539 sequences, of which 231 are wild-type, 5306 are variants and 2 are control sequences. BAG1 wild type and variant sequences were excluded due to an error in the wild type sequence. FXN variant sequences were excluded becuase the wild type sequence was missing in the library. Finally, 230 wild-type sequences, corresponding to 226 unique sequences, and 5261 variant sequences corresponding to 4621 unique sequences, were obtained.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text files include raw read counts for each sequence of the library
Library strategy: DNA-seq

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM), supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, and 100U/ml antibiotics (PenStrep). The cells were maintained at 37°C in a 5% CO2. humidified atmosphere.

extract_protocol:
After cell sorting, the Kozak sequences from the subpopulations were PCR amplified. Genomic DNA was extracted from the subpopulations using the DNeasy Blood & Tissue Kit (Qiagen, #69504).
The DNA from each population was loaded in PCR reactions with 400ng input each. A second PCR was performed for the ligation of standard Illumina adapters. The PCR products were purified with Ampure XP beads and mixed in equimolar ratios

treatment_protocol: The Kozak sequence variants were synthesised as oligonucleotides on a custom Agilent 244K microarray designed for this purpose. The oligonucleotides designed were 98nt long. 11 central nucleotides in each oligo (4 before and 4 after the ATG) represent the Kozak sequence and the variable part of each oligonucleotide. The oligonucleotides library was cloned in the linearised vector using NEBuilder® HiFi DNA Assembly Master Mix.

value: wild type


title: Gcon_1

value: non-labeled V2a interneurons


title: S1-03

value: soft tissue sarcoma

value: 9 x 9 x 7 cm

value: F

value: Boxer

value: Right caudal hip


title: Gcon_6


title: S1-05

value: peripheral nerve sheath tumor


title: Dcon_1

value: retrogradely labeled V2a interneurons


title: Library B - gate 3


title: S1-02

value: fibrosarcoma

value: Beagle

value: Right prescapular, subcutaneous (shoulder)


title: Library A - gate 3


title: Library B - gate 2


title: Library B - gate 1


title: liver tissue, Dengue, Day8 3

city: Guangzhou

first: zheng

last: wenjiang

state: Guangdong

department: The First Clinical Medical School

institute: Guangzhou University of Chinese Medicine

data_processing:
Libraries were sequenced on the Illumina HiSeq X Ten platform, and 150 bp paired-end reads were generated.
The raw data were first pre-processed by removing primer splice sequences and double-checking and screening the base quality and length of sequenced fragments.
We used cutadapt software (version 1.14) to remove the splice sequences and screen out sequences between 15 and 41 nt in length, and then used fastx toolkit software (version 0.0.13) to perform Q20 quality control on the sequences, retaining those with 80% Q20 and above.
NGSQCToolkit (version 2.3.3) was used to filter out reads containing N bases, and the obtained high-quality CleanReads were distributed according to the type, quantity, and sequence length, and finally the sequences were annotated against databases (Rfam database (version 10.0) , cDNA sequences, RepeatMasker, miRBase database) using bowtie software to obtain the final small RNA distribution data for the six mice samples.
We used the TPM formula (transcript per million) to calculate the expression of known miRNAs and newly predicted miRNAs. “N” is the number of reads per miRNA, “M” is the total number of reads compared to the sample (CleanReads). For the TPM result see the document named: "TPM-microRNA expression in each sample.xls"
Differential gene expression analysis was performed using the DESeq2 (2014) R package
Assembly: http://www.mirbase.org/cgi-bin/browse.pl?org=mmu
Supplementary files format and content: tab-delimited text files include TPM and count values for each Sample
Supplementary files format and content: A total of 1078 known miRNAs were found in these six samples. For the annotation result see the document named: "annotation.xls"

source_name: liver

growth_protocol: IFNAR-/- mice on the C57BL/6J background were generated and bred in-house under specific pathogen-free conditions in our laboratory at 21 °C in 55% humidity on a 12:12 h light: dark cycle.

extract_protocol:
Total RNA was extracted from mouse liver tissue using mirVana™ miRNA ISOlation Kit (Ambion-1561) according to the manufacturer’s protocol. 0.5 ug of total RNA was used for the construction of sequencing libraries.
samall RNA libraries for RNA-seq were prepared using TruSeq Small RNA Sample Prep Kits (Cat. No. RS-200-0012, Illumina, USA.) following the manufacturer’s recommendations.  Briefly, total RNA was ligated to adapters at each end. Then the adapter-ligated RNA was reverse transcribed to cDNA and performed PCR amplification. The PCR products ranging from 140-160 bp were isolated and purified as small RNA libraries. Library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.

treatment_protocol:
Male mice (6-8 weeks old) were challenged intraperitoneally (i.p.) with the DENV-2 TSV01 strain (dengue virus infection group, n=3, 1×105 PFU)
Mice injected with an equivalent volume of PBS (mock infection) were used as negative controls (n=3).

value: liver

value: IFNAR knockdown

tag: treatment

value: dengue virus serotypes -2 (TSV01) i.p.

value: Day 8


title: liver tissue, Control, Day8 3

value: PBS i.p.

tag: time


title: liver tissue, Dengue, Day8 1


title: liver tissue, Dengue, Day8 2


title: Library A - gate 1

value: wild type


title: liver tissue, Control, Day8 2


title: liver tissue, Control, Day8 1


title: MELA_0469 Tumour

type: genomic

city: Herston

first: Felicity

last: Newell

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer Medical Research Institute

hyb_protocol: Illumina protocol

scan_protocol: iScan Illumina

data_processing:
2021
The raw data in the form of IDAT files for 144 samples were imported filtered and normalized using the ChAMP package implemented in R .  Probes were primarily filtered out if detection p-value > 0.01 or there were fewer than three beads in 5% or more of samples.  A β-mixture quantile normalisation (BMIQ) was performed to account for probe type 1 and type 2 biases, followed by a quantile normalisation.  Further filtering was performed to remove probes if they were located in non-CpG sites, X and Y chromosomes, single nucleotide polymorphism-related polymorphisms and probes that map to multiple locations.

source_name: Tumour

label_protocol: Illumina protocol

growth_protocol: not applicable

extract_protocol: All prep DNA/RNA/miRNA Universal kit

treatment_protocol: not applicable

value: melanoma tumour


title: Library A - gate 4


title: D28 post-depletion, WT tendon 2

city: Rochester

first: Antonion

last: Korcari

state: NY

address: 142 Westminster Rd, Appartment number 914 9th floor

institute: University of Rochester Medical Center

data_processing:
Data normalization and differential expression analysis of DTRScxLin relative to WT at a given time point was performed using DESeq2-1.22.1 with an adjusted p-value threshold of 0.05 on each set of raw expression measures. The ‘lfcShrink’ method was applied, which moderates log2 fold-changes for lowly expressed genes. DeSeq2 data was uploaded to Enrichr (https://maayanlab.cloud/Enrichr/) to perform pathway analysis of the DEGs in DTRScxLin vs WT. Additionally, StringDB (https://string-db.org/) was utilized to identify potential interactions between the DEGs.
Supplementary files format and content: Processed data_file _DEG.xlsx (DEG analysis of DTR vs WT groups)

source_name: D28 post-depletion, WT tendon

extract_protocol:
FDL tendons (1 tendon per biological sample; N=3 biological samples per genotype) were harvested at D28 post-surgery and flash frozen in liquid nitrogen. Total RNA was isolated using the Powermasher II (DIAGNOCINE) to homogenize the tissue. RNA was isolated from the extract using Trizol (Life Technologies, Carlsbad, CA) and the RNeasy Plus Micro Kit (Qiagen, Valencia, CA) per manufacturer’s recommendations. The total RNA concentration was determined with the NanoDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The RNA integrity number (RIN) for all harvested samples was 7.73 ± 0.22 (mean ± standard deviation). The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next-generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 200 ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double-stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200–500 bp in size. The amplified libraries were hybridized to the Illumina flow cell and single end reads were generated for each sample using Illumina NovaSeq6000.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: FDL tendons

value: Scx-Cre-; DTR F/+

value: DT

value: 5 daily injections of DT 2 weeks prior to harvesting


title: D28 post-depletion, WT tendon 1


title: MELA_0472 Tumour


title: D28 post-depletion, DTR tendon 3

source_name: D28 post-depletion, DTR tendon

value: Scx-Cre+; DTR F/+


title: MELA_0329 Tumour


title: MELA_0328 Tumour


title: MELA_0308 Tumour


title: D28 post-depletion, DTR tendon 2


title: Library A - gate 2


title: MELA_0309 Tumour


title: MELA_0307 Tumour


title: MELA_0310 Tumour


title: MELA_0305 Tumour


title: D28 post-depletion, DTR tendon 1


title: Embryonic forelimb field, e3.5, rep 1

city: Clayton

first: Axel

middle: H

last: Newton

state: Victoria

address: 19 Innovation Walk

institute: Monash University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0
Assembly: GRCg6a
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, genes.tsv, matrix.mtx)

organism: Gallus gallus

source_name: embryonic forelimb field e3.5 (HH18), pooled male and female

growth_protocol: Fertile chicken eggs were incubated in a 37 degree humidified incubator

extract_protocol:
Forelimb field tissues were microdissected from the body, lateral to the somites.
Library was performed according to the manufacter’s instructions (single cell 3’ V3.1, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode.

value: embryonic forelimb field

value: pooled male and female

value: Various cell types from embryonic ectoderm, mesoderm and endoderm

value: Wildtype

tag: Stage


title: Embryonic forelimb field, e1.5, rep 1

description: 10x Genomics

source_name: embryonic forelimb field e1.5 (HH10), pooled male and female

tag: genotype


title: Jun, CY2

city: Lanzhou

first: Xingdong

state: 未选择

address: No.335 Jiangouyan, Qilihe District

institute: CAAS: Chinese Academy of Agricultural Sciences

data_processing:
Clean reads were obtained from the raw data after quality control processing. The 3' adaptors were removed from the clean reads, and the length was screened to retain the sequence with a base length of 18-26nt.
the remaining sequences are aligned with various RNA database sequences (excluding miRNAs), such as mRNA database, Rfam database (including rRNA, tRNA, snRNA, snoRNA, etc.) and RepBase database, and filtered.
the data obtained is effective data, which can be used for subsequent small RNA data analysis.
Assembly: LU_Bosgru_v3.0
Supplementary files format and content: normalized counts

organism: Bos grunniens x Bos taurus

source_name: cattle-yak milk in June

extract_protocol:
Extraction of exosome RNA from yak and Jersey cattle-yak in June and December with reference to the instructions of Norgen 58000 kit.
The experimental procedure was performed according to the standard steps provided by Illumina, including library preparation and sequencing experiments. Small RNA sequencing libraries were prepared using the TruSeq Small RNA Sample PrepKits (Illumina, San Diego, USA) kit. After library preparation, the constructed libraries were sequenced using Illumina instrument with a single-end 1X50bp read length.

tag: tissue

value: milk exosomes

value: June


title: Embryonic forelimb field, e2.5, rep 1

description: 10x Genomics

source_name: embryonic forelimb field e2.5 (HH14), pooled male and female


title: Jun, CY1


title: MELA_0304 Tumour


title: Jun, CY3


title: MELA_0395 Tumour


title: Dec, CY2

source_name: cattle-yak milk in December

value: December


title: Dec, CY3


title: D28 post-depletion, WT tendon 3


title: MELA_0311 Tumour


title: Dec, CY1


title: MELA_0327 Tumour


title: MELA_0393 Tumour


title: ZT12 sample 0 run FGC2199

city: Philadelphia

first: Garret

middle: A.

last: FitzGerald

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

description: 10x Genomics

data_processing:
mm10
Assembly: Tab-separated values files and matrix files

source_name: Whole aorta

extract_protocol:
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)

treatment_protocol: Freshly dissected whole aortas from C57BL6 mice were rinsed with ice-cold PRMI1640 to remove blood residue. Aortic cells isolation was performed by incubation of tissue with enzyme digestion buffer (PRMI1640 medium containing DNase, 120U/mL, Liberase, 4U/mL and hyaluronidase, 60U/mL)  at 37 °C for 40 min. Isolated cell suspension was filtered through a 40 um cell filter to remove undigested tissue, and enzymatic digestion was stopped by resuspending the cells in PRMI1640 medium+ 10% FBS. Cells were washed 2X with FACS buffer (DPBS+ FBS 2%+ EDTA 5mM+ HEPES 20mM+ sodium pyruvate 1mM) and resuspended in DMEM/F12 +10% FBS for cell viability test using trypan blue.

value: Whole aorta

tag: age

value: 6-8 weeks old


title: ZT6 sample 0 run FGC2199

description: 10x Genomics


title: MELA_0326 Tumour


title: stool, MG78.01, NEC, DOL49

city: Pittsburgh

first: David

last: Peters

address: 204 Craft Avenue

institute: Magee-Womens Research Institute

data_processing:
DNA sequence reads were quality trimmed and adaptor sequences were removed using Trim-Galore.
The reads were aligned to the human refrence sequence using Bismark Bisulfite Read Mapper in paired-end, bowtie2 mode. Any unmapped reads were aligned in single-end, bowtie2 mode.
Read duplicates were removed using Bismark.
Methylation was called on paired-end and single-end files and then merged to determine the methylation status for each CpG site.
DNA methylation signatures were determined using the beta-binomial test implemented in the R packages methylSig and DSS.
Assembly: GRCh38
Supplementary files format and content: Bismark Coverage output merged from PE and SE methylation extractor outputs. <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

source_name: stool

extract_protocol:
Snap-frozen specimens were mounted on appropriate embedding molds with clear Optimal Cutting Temperature Embedding Medium and cryostat sectioned at 7 um. These sections were mounted on memebrane slides, stained with toluidine blue and air dried. Tissue DNA was extracted using the Nucleospin Tissue XS Kit. Extracted DNA was quantified by using the KAPA hgDNA Quantification and QC Kit. Stool DNA was extracted using the NucleoSpin DNA Stool, Mini Kit. Human and bacterial DNA content were measured using Femto Human and Femto Bacterial DNA Quantification Kits.
DNA was sheared with Covaris to a size of ~175bp. Libraries were prepared using the KAPA HyperPrep Kit. Libraries were bisulfite converted post-ligation using the EZ DNA Methylation-Direct Kit and amplified 13-15 cycles. Bisulfite-converted DNA libraries underwent targeted capture using the SeqCap Epi CPGiant Enrichment Kit and amplified 10 cycles. Samples were sequenced on a HiSeq with 100 bp paired-end reads to a mean targeted read depth of ~24x.

treatment_protocol: Intestinal tissue samples were procured if resected for NEC or other noninflammatory indications, such as reanastomosis, spontaneous intestinal perforation or anorectal malformation. Resections of intestinal tissue were snap frozen and stored at -80 degrees Celsius until further analysis. Non-NEC tissue samples were healed NEC tissue obtained during surgical reanastomosis. Stool was collected from diapers and identified as being from cases with NEC or premature control infants. The diapers were initially placed at 4 degrees Celsius, transferred to the laboratory within 12-24 h, aliquoted into barcoded tubes and stored at -80 degrees Celsius until processing.

value: stool

tag: disease state

value: NEC

tag: race

value: W

value: male

tag: dol (days_of_life)_at_sampling

tag: age at_nec_onset

tag: dol at_nec_onset


title: stool, MG63.01, control, DOL11

value: control

tag: Sex

value: female


title: stool, MG02.01, NEC, DOL61


title: stool, MG67.01, NEC, DOL22


title: CUT&TAG_NG

city: Beijing

first: Ting

last: Peng

address: Beijing haidiang

institute: PKU

data_processing:
Fastq files were trimmed using TrimGalore and aligned to the human genome assembly (hg19) with Bowtie2. Then peaks were called by MACS2 v2.2.5 with parameters ‘-p 0.01 --nomodel --extsize 200’
Assembly: hg19
Supplementary files format and content: bigwig file
Library strategy: CUT&Tag

source_name: bone marrow

extract_protocol:
NK cells were separated from NG-BM and G-BM using FACS
100000 cells were washed twice gently with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail). 10μL Concanavalin A coated magnetic beads (Bangs Laboratories) were added per sample and incubated at RT for 10min. Remove unbound supernatant and resuspended bead-bound cells with dig wash buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin; 2mM EDTA) and a 1:50 dilution of GR (G-5,sc-393232,SantaCruz) or IgG control antibody (Millipore cat.no. 12-371) incubated on a roating platform overnight at 4°C. The primary antibody was removed using magnet stand. Secondary antibody (abcam,ab6709) was diluted 1:100 in dig wash buffer and cells were incubated at RT for 60 min. Cells were washed using the magnet stand 2-3 times in dig wash buffer . A 1:100 dilution of pA-Tn5 adapter complex was prepared in Dig-med buffer (0.01% Digitonin; 20mM HEPES pH 7.5; 300mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail) and incubated with cells at RT for 1h. Cells were washed 2-3× for 5 mins in 1 mL Dig-med buffer. Then cells were resuspended in tagmentation buffer (10mM MgCl2 in Dig-med Buffer) and incubated at 37 °C for 1 h. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. To amplify libraries, 21μL DNA was mixed with 2μL of a universal i5 and a uniquely barcoded i7 primer. A volume of 25μL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72 °C for 5 min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30 s; final extension at 72 °C for 1 min and hold at 8 °C. Libraries clean-up was performed using XP beads (Beckman Counter).

treatment_protocol: Steady state bone marrow (NG-BM) was obtained from allogeneic donors before G-CSF in vivo treatment. Then these donors received 5ug/kg body weight of G-CSF (filgrastim; Kirin Co., Ltd., Tokyo, Japan) for 5 consecutive days and G-CSF-primed bone marrow (G-BM) was collected on the 4th day after mobilization.

value: bone marrow

tag: cell line

value: primary cells

value: NK cells

value: WT

value: after G-CSF treatment


title: MELA_0325 Tumour

value: melanoma tumour


title: MELA_0306 Tumour


title: MELA_0303 Tumour


title: ZT18 sample 0 run FGC2199

description: 10x Genomics


title: CUT&TAG_G


title: ZT18 sample 0 run FGC2193

description: 10x Genomics


title: ZT0 sample 0 run FGC2199

description: 10x Genomics


title: NG4

data_processing:
Paired end RNA-seq reads were aligned to the human genome assembly (hg19) with STAR v2.7.2b, and gene expression levels were counted using HTSeq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw count values for each sample

extract_protocol:
NK cells were separated from NG-BM and G-BM using FACS
Total RNA with polyA tail was extracted with RNeasy Micro Kit (QIAGEN). Then reverse transcribed to cDNA and for sequencing. All sequencing was performed on an Illumina HiSeq X Ten with 2 ×150 bp cycles.

value: before G-CSF treatment


title: NG2


title: ZT12 sample 0 run FGC2193

description: 10x Genomics


title: NG5


title: NG6


title: NG1


title: MELA_0324 Tumour


title: NG3


title: ZT6 sample 0 run FGC2193

description: 10x Genomics


title: MELA_0392 Tumour


title: G6


title: ZT0 sample 0 run FGC2193

description: 10x Genomics


title: MELA_0447 Tumour


title: ZT18 sample 0 run FGC2191

description: 10x Genomics


title: G4


title: G3


title: MELA_0301 Tumour


title: G2


title: G1


title: p2_NG

data_processing:
The raw sequenced reads were analyzed using the Hi-C-Pro (v2.11.1) pipeline
Assembly: hg19
Supplementary files format and content: .hic file can be visualized by Juicebox

extract_protocol:
NK cells were separated from NG-BM and G-BM using FACS
2 million cells per sample were fixed with 1% formaldehyde and suspended in Hi-C lysis buffer, then 100U MobI restriction enzyme (NEB, R0147) was added. After overnight chromatin digestion, biotin was used to fill ends before DNA proximity ligation and crosslink. Then DNA was sheared to 300-500 bp using sonicator. Finally, biotin-labeled DNA was pulled down and libraries were prepared using the NEBNext primer set and sequenced on Illumina HiSeq X Ten.


title: MELA_0444 Tumour


title: p2_G


title: ZT0 sample 0 run FGC2191

description: 10x Genomics


title: p1_NG


title: ZT6 sample 0 run FGC2191

description: 10x Genomics


title: p1_G


title: MELA_0317 Tumour


title: MELA_0298 Tumour


title: NG3_Rep1

data_processing:
ATAC-seq reads were trimmed using TrimGalore v0.4.5 and aligned to the human genome assembly (hg19) with Bowtie2 v2.3.5, and peaks were called by MACS2 v2.2.5  with parameters ‘-B -p 1e-5 -g hs --nomodel --shift -100 --extsize 200’
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw count values for each sample

extract_protocol:
NK cells were separated from NG-BM and G-BM using FACS
The ATAC-seq (assay for transposase-accessible chromatin with high-throughput sequencing) experiment was performed as previously (Buenrostro et al., 2013) described.


title: NG3_Rep2


title: MELA_0297 Tumour


title: NG2_Rep2


title: NG2_Rep1


title: G5


title: NG1_Rep2


title: MELA_0391 Tumour


title: Rag1 KO, Batch 2, White Matter_1

city: Bonn

first: Ozgun

last: Gokce

address: Venusberg-Campus 1/99

institute: UKB-DZNE

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4
Assembly: mm10
Supplementary files format and content: Tab-separated expression matrices of raw counts for each dataset

source_name: White Matter

extract_protocol:
The mice were deeply anesthetized and perfused with cold HBSS between 9am-11am (to decrease circadian fluctuations). Each brain was removed and under a dissection microscope individually micro-dissected; grey matter was isolated from the frontal cortex and white matter form optic tract, medial lemniscus and corpus callosum (attached grey matter and choroid plexus were removed carefully) isolated. We developed and established a microglia isolation protocol that prevents ex-vivo transcription and automatizes the mechanical isolation parts using GentleMacs with the Neural Tissue Dissociation Kit (Papain) (Miltenyi Biotec). We added actinomycin D (Act-D, Sigma, No. A1410) to a final concentration of 45 μM into the dissociation solution and enzyme mix to prevent ex-vivo transcription. To collect enough cells for loading onto the 10x Genomics Chromium chip, two gray matter/ white matter tissue samples were combined into one sample. After tissue dissociation, SYTOX Blue negative cells were sorted into a 2 mL Eppendorf tube with 1 mL RPMI+5% FBS. Sorted cells were centrifuge at 300xg for 10min at 4ºC. Cell pellets were resuspended in 0.04% BSA+PBS catching media at a concentration of 700-900 cells per μl.
Single-cell suspensions were loaded onto the Chromium Single Cell Controller using the Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (10X Genomics) chemistry following the manufacturer’s instructions. Sample processing and library preparation was performed according to manufacturer instructions using AMPure beads (Beckman Coulter).

value: Brain cells

value: White Matter

value: 24 months old


title: G3_Rep2


title: NG1_Rep1


title: microglia of 16-week old MRL/MpJ 3

city: Sapporo

first: Kohei

last: Karino

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

country: Japan

institute: Hokkaido university

data_processing:
The resultant libraries were then quantified and sequenced using the Illumina NovaSeq (Illumina, San Diego, CA, USA), according to the manufacturer’s instructions, with 150 bp paired-end configuration.
The raw sequencing reads with low quality, and adapter sequences were removed using Cutadapt v 2.1.
The trimmed reads were mapped to the mm10 (Ensembl 99) and quantified using STAR v 2.7.1a.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: microglia

growth_protocol: The murine brains were removed and enzymatically digested using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec). Cell suspensions were positively selected for CD11b expression using the magnetic-activated cell sorting system.

extract_protocol:
RNA was isolated using the RNeasy Mini kit (QIAGEN Inc., Hilden, Germany).
Libraries were prepared by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs), according to the manufacture’s protocol.

treatment_protocol: The isolated microglia from neonatal mice were incubated in DMEM nutrient mixture F-12 (DMEM/ F-12) containing 10% FBS, penicillin, and streptomycin for 48 h and stimulated with each cytokine for 6h.

value: MRL/MpJ

value: untreated


title: MELA_0296 Tumour


title: G3_Rep1


title: ZT12 sample 0 run FGC2191

description: 10x Genomics

value: Whole aorta

value: 6-8 weeks old


title: microglia of 16-week old MRL/MpJ 2


title: Rag1 KO, Batch 2, White Matter_2


title: MELA_0300 Tumour


title: G2_Rep1


title: G2_Rep2


title: MELA_0295 Tumour


title: G1_Rep2


title: MELA_0294 Tumour


title: microglia of 16-week old MRL/lpr 1

value: MRL/lpr


title: G1_Rep1


title: microglia of 16-week old MRL/lpr 2


title: microglia of 16-week old MRL/lpr 3


title: neonatal microglia stimulated with TNFa 3

value: neonatal

value: TNFa


title: neonatal microglia stimulated with IFNa 3

value: IFNa


title: MELA_0434 Tumour


title: MELA_0291 Tumour


title: neonatal microglia stimulated with IL6 3


title: MELA_0436 Tumour


title: MELA_0433 Tumour


title: MELA_0561 Tumour


title: MELA_0387 Tumour


title: neonatal microglia stimulated with IFNg 3

value: IFNg


title: neonatal microglia unstimulated 3


title: MELA_0292 Tumour


title: microglia of 16-week old MRL/MpJ 1


title: neonatal microglia stimulated with all cytokine 2

value: IFNg IL6 IFNa TNFa


title: MELA_0386 Tumour


title: MELA_0388 Tumour


title: neonatal microglia stimulated with TNFa 2


title: neonatal microglia stimulated with IL6 2


title: neonatal microglia stimulated with IFNg 2


title: MELA_0315 Tumour


title: MELA_0385 Tumour


title: MELA_0430 Tumour


title: MELA_0711 Tumour


title: MELA_0384 Tumour


title: MELA_0290 Tumour


title: neonatal microglia stimulated with TNFa 1


title: neonatal microglia stimulated with all cytokine 3


title: neonatal microglia stimulated with all cytokine 1


title: neonatal microglia unstimulated 2


title: MELA_0382 Tumour


title: neonatal microglia stimulated with IFNa 1


title: MELA_0323 Tumour


title: MELA_0425 Tumour


title: MELA_0381 Tumour


title: MELA_0071 Tumour


title: neonatal microglia stimulated with IFNg 1


title: neonatal microglia stimulated with IL6 1


title: neonatal microglia stimulated with IFNa 2


title: neonatal microglia unstimulated 1


title: MELA_0380 Tumour


title: Wild Type mouse 3 [F3]

city: Augusta

first: Ganesh

middle: Daulatrao

last: Warthi

state: Georgia

address: 1460 Laney Walker BLVD

department: Vascular biology Center

institute: Augusta University

data_processing:
Sequencing Platform: Illumina NovaSeq6000
Data Formatting: bcltofastq-2.19.0
Data Cleaning: fastp 0.20.0, --in1 ../${SAMPLE}_R1.fastq.gz --out1 clt_${SAMPLE}_R1.fastq.gz --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -w 8 -y -r -j ${SAMPLE}_fastp.json
Genome Alignment: STAR_2.7.0f, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification1: subread-1.6.4, featurecounts, -s 2 -t exon -g gene_name
Read Quantification3: salmon-0.13.1, --seqBias --gcBias --posBias
Assembly: GRCm38.p6 + Gencode-M22 Annotation
Supplementary files format and content: deSeq2_counts; normcounts

source_name: Aorta

extract_protocol:
Aortae were removed, flash frozen via liquid nitrogen, and Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, Valencia, CA) per manufacturer’s recommendations. The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina flow cell and single end reads of 75nt were generated for each sample using Illumina’s NovaSeq 6000 sequencer.
Library Preparation by TruSeq Stranded mRNA

tag: genotype/variation

value: Wild Type

value: Aorta


title: Wild Type mouse 2 [F2]


title: Myh11-Cre mouse 3 [D3]


title: MELA_0015 Tumour

value: melanoma tumour


title: MELA_0289 Tumour


title: Wild Type mouse 1 [F1]


title: L20

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

description: Low fertility

data_processing:
FASTQC software (v0.11.8) was used to check the quality of the raw sequencing reads.
Sequencing indexing adapters were removed using Cutadapt (v2.6)
Input reads were then aligned to the bovine reference genome (UMD3.1) using STAR (v2.6.1), incorporating the quantmode function to determine the number of mapped reads.
The R (v3.4) Bioconductor package, EdgeR (v3.5), was applied to identify statistically significant differentially expressed genes.
Genome_build: ARS1.2
Supplementary_files_format_and_content: Tab delimited txt file of merged gene read counts

organism: Bos taurus

source_name: Spermatozoa

growth_protocol: Frozen-thawed semen from Holstein Friesian bulls

extract_protocol:
RNA was  precipitated and purified from spermatozoa using trizol according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
cDNA libraries were prepared from high quality RNA  using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA), following the manufacturer’s instructions.

treatment_protocol: High and Low fertility bulls were selected using an animal adjusted statistical model

tag: fertility status

value: Low fertility

value: Spermatozoa

tag: breed

value: Holstein-Friesian


title: Myh11-Cre mouse 2 [D2]

tag: strain


title: Myh11-Cre mouse 1 [D1]


title: MELA_0014 Tumour


title: Itga8-Cre mouse 3 [B3]


title: MELA_0288 Tumour


title: L8

description: Low fertility


title: MELA_0379 Tumour


title: L11

description: Low fertility


title: L7

description: Low fertility


title: MELA_0287 Tumour


title: L1

description: Low fertility


title: MELA_0070 Tumour


title: L4

description: Low fertility


title: Itga8-Cre mouse 2 [B2]


title: MELA_0421 Tumour


title: Zfp335cKO scRNA-seq

city: Durham

data_processing:
Conversion of base call logs to fastq, alignment and generation of raw count matrices were performed using Cellranger v3.0.1 with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts in gene-barcode matrix in Market Exchange Format (MEX). Columns correspond to individual cells(barcodes), while rows correspond to genes. *barcodes.tsv = Barcode sequences that correspond to column indices in matrix.mtx. *features.tsv = Gene IDs.

source_name: Zfp335 cKO DN4 thymocytes

growth_protocol: Mice were maintained under specific pathogen-free conditions.

extract_protocol:
DN4 thymocytes were isolated by FACS sorting. Single-cell suspensions were loaded on the 10x Genomics Chromium controller, and mRNA converted to cDNA lirbaries. Single-cell libraries were sequenced on a Novaseq 6000 150PE S-Prime flowcell. Libraries were seuqenced in single index mode with the following read lengths: 28x8x91
10x Genomics 3' kit v3

tag: strain background

value: Zfp335 KO

tag: cell type

value: DN4 thymocyte


title: Zfp335WT scRNA-seq

source_name: Zfp335 WT DN4 thymocytes

value: Zfp335 WT


title: MELA_0286 Tumour

source_name: Tumour


title: H15

description: High ferility

value: High ferility


title: MELA_0378 Tumour


title: L5

description: Low fertility


title: L19

description: Low fertility


title: MELA_0562 Tumour


title: H14

description: High ferility


title: H10

description: High ferility


title: L13

description: Low fertility


title: MELA_0066 Tumour


title: H17

description: High ferility


title: H9

description: High ferility


title: H3

description: High ferility


title: H6

description: High ferility


title: MELA_0377 Tumour


title: H2

description: High ferility


title: L18

description: Low fertility


title: Itga8-Cre mouse 1 [B1]


title: 20

data_processing:
FASTQC software (v0.11.8) was used to check the quality of the raw sequencing reads.
Sequencing indexing adapters were removed using Cutadapt (v2.6)
Input reads were then aligned to the bovine reference genome (ARS1.2) using the miRDeep2 package (version 2.00.8), the miRDeep2 quantifier module was used to quantify all expressed miRNAs in the sequence data, producing read counts for each individual sample.
The R (v3.4) Bioconductor package, EdgeR (v3.5), was applied to identify statistically significant differentially expressed genes.
Genome_build: ARS1.2
Supplementary_files_format_and_content: Tab delimited txt file of merged gene read counts

extract_protocol:
RNA was  precipitated and purified from spermatozoa using trizol according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
cDNA libraries were prepared from high quality RNA  using the NEBNext® Multiplex Small RNA Library Prep kit for Illumina (NEB), following the manufacturer’s instructions.

tag: group


title: 18


title: H16

description: High ferility


title: 13


title: MELA_0322 Tumour


title: 19


title: MELA_0064 Tumour


title: 11


title: 7


title: MELA_0063 Tumour


title: 4


title: MELA_0314 Tumour


title: H12

description: High ferility


title: 5


title: 8


title: 17


title: 15


title: 1


title: MELA_0285 Tumour


title: 10


title: MELA_0336 Tumour


title: MELA_0061 Tumour


title: 12


title: 16


title: 9


title: MELA_0065 Tumour


title: 3


title: 6


title: MELA_0060 Tumour


title: MELA_0284 Tumour


title: 14


title: MELA_0013 Tumour


title: TKO mES, ChrMeRIP rep2

city: Madrid

first: Maria

last: Gomez

address: Nicolas Cabrera, 1

country: Spain

institute: CBMSO(CSIC/UAM)

description:
H1-TKO_ChrMeRIP_IP_Watson.bw
H1-TKO_ChrMeRIP_IP_Crick.bw

data_processing:
Raw reads were aligned to mm10 genome using TopHat2 (for RNA samples) or BWA mem (for DNA samples), using standard parameters
Low score alignments were filtered using samtools view
bigwig files were generated with bedtools genomeCoverageBed
Differential expression analysis was carried out with DEseq2
Mnase data combing was performed with NucWave
Genome_build: mm10
Supplementary_files_format_and_content: bigwig for coverage files for each experiment, and a bed file containing a list of differential transcripts in H1-TKO cells

source_name: Embryonic stem cells

growth_protocol: Mouse embryonic stem cells were grown in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Biosera), 1x non-essential aminoacids (Gibco), 1mM sodium piruvate (Gibco), 2mM L-glutamine (Gibco), 50 uM B-mercaptoethanol (Gibco), 103 U/mL LIF (ESGRO), 100 U/mL penicillin (Invitrogen) and 100 ug/mL streptomycin (Invitrogen), at 37ºC and 5% CO2

extract_protocol:
RNA fragmentation and meRIP were performed as described in Dominissini et al. (2013) and Zeng et al. (2018), with the following modifications. Aliquots containing 2 g of CheRNAs in 18L of DEPC H2O were fragmented by incubation with 2 L of 100 uL Tris pH 7, 100 uL ZnCl2 1M, 800 uL DEPC water, at 70ºC for 8 minutes, and reactions were stopped by adding 2 L of 0.5M EDTA. A total of 50 g of pooled fragmented CheRNAs were incubated with 5 g of anti-m6A antibodies (Synaptic Systems) previously bound to A/G protein agarose beads (SantaCruz) in IP buffer (10 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.1% Igepal CA-630), and supplemented with RiboLockTM (Thermo Scientific), during 6 hours at 4ºC. Beads were washed three times with IP buffer, meRNAs were eluted in elution buffer (10 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.1% Igepal CA-630, 6.67mM m6A) and purified through RNeasy columns (Qiagen) following the manufacturers protocol
TruSeq Stranded total RNA, Libraries 1x75 reads

value: Embryonic stem cells

tag: genotype

tag: merip antibody

value: anti-m6A, Synaptic Systems (202003)

tag: molecule subtype

value: chromatin enriched RNA


title: TKO mES, ChrMeRIP rep1


title: WT mES, ChrMeRIP rep2

description:
WT-mES_ChrMeRIP_IP_Watson.bw
WT-mES_ChrMeRIP_IP_Crick.bw

value: WT


title: H1-TKO mES, cheRNA input rep2

description:
H1-TKO_ChrMeRIP_Input_Watson.bw
H1-TKO_ChrMeRIP_Input_Crick.bw

extract_protocol:
40x106 mES cells were lysed in 800 uL ice-cold Lysis Buffer A (10 mM Tris pH 7.5, 0.1% NP-40, 150 mM NaCl) for 5 minutes on ice. Nuclei were collected by sucrose cushion centrifugation (24% sucrose in lysis buffer A), rinsed with ice-cold PBS + 1mM EDTA, and resuspended in 500uL ice-cold Glycerol Buffer (20 mM Tris pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 0.125 mM PMSF, 50% glycerol). Nuclei were lysed by adding one volume of ice-cold Lysis Buffer B (10 mM HEPES pH 7.6, 1mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3M NaCl, 1M urea, 1% NP-40) and kept on ice for 10 minutes, with periodic vigorous shaking. Insoluble chromatin was sedimented by centrifugation at 15000g and 4ºC for 2 minutes, rinsed twice with cold PBS + 1mM EDTA, and resuspended in 100 uL PBS. At this point, 10 pg of an in vitro transcribed m6A methylated luciferase RNA was added to the chromatin samples as a spike-in control. RNAs were purified using TRIzolTM, following manufacturer’s instructions
TruSeq Stranded total RNA, Libraries 1x75 reads


title: H1-TKO mES, cheRNA input rep1


title: MELA_0418 Tumour

data_processing:
2021
The raw data in the form of IDAT files for 144 samples were imported filtered and normalized using the ChAMP package implemented in R .  Probes were primarily filtered out if detection p-value > 0.01 or there were fewer than three beads in 5% or more of samples.  A β-mixture quantile normalisation (BMIQ) was performed to account for probe type 1 and type 2 biases, followed by a quantile normalisation.  Further filtering was performed to remove probes if they were located in non-CpG sites, X and Y chromosomes, single nucleotide polymorphism-related polymorphisms and probes that map to multiple locations.

extract_protocol: All prep DNA/RNA/miRNA Universal kit

tag: tissue


title: MELA_0321 Tumour


title: WT mES, cheRNA input rep2

description:
WT-mES_ChrMeRIP_Input_Watson.bw
WT-mES_ChrMeRIP_Input_Crick.bw


title: MELA_0282 Tumour


title: MELA_0283 Tumour


title: H1-TKO cells - Ttseq -rep2

data_processing:
Raw reads were aligned to mm10 genome using TopHat2 (for RNA samples) or BWA mem (for DNA samples), using standard parameters
Low score alignments were filtered using samtools view
bigwig files were generated with bedtools genomeCoverageBed
Differential expression analysis was carried out with DEseq2
Mnase data combing was performed with NucWave
Genome_build: mm10
Supplementary_files_format_and_content: bigwig for coverage files for each experiment,  and a bed file containing a list of differential transcripts in H1-TKO cells

source_name: H1-TKO cells

extract_protocol:
4-thiouridine (4sU) was added to sub-confluent cell cultures at a final concentration of 1 mM for 10 min before cell harvest. Cells were lysed directly on a plate with 5 ml of TRIzol (Invitrogen), total RNA was isolated following manufacturerÂ´s protocol and sonicated by two pulses of 30 seconds in a Bioruptor instrument. A total of 100 ug of sonicated RNA per cell line was used for biotinylation and purification of 4sU-labeled nascent RNAs. Biotinylation reactions consisted of total RNA and EZ-Link HPDP-Biotin dissolved in dimethylformamide (DMF) and were performed in labeling buffer (10 mM Tris pH 7.4, 1 mM EDTA) for 2 h with rotation at RT. Unbound Biotin-HPDP was removed by chloroform/isoamylalcohol (24:1) extraction in MaXtract tubes (Qiagen). RNA was precipitated with 10th volume of 5M NaCl and 1 volume of isopropanol. Following one wash in 80% ethanol, the RNA pellet was left to dry and resuspended in 100 uL RNase-free water. Biotinylated RNA was purified using uMacs Streptavidin kit, eluted twice using 100 mM DTT and recovered using RNeasy MinElute Cleanup column (Qiagen) according to instructions
cDNA libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturerâ€™s instructions. Libraries were pooled and sequenced by 2x75 single-reads

value: Histone H1 triple KO

value: Nascent RNA


title: WT mES, cheRNA input rep1


title: MELA_0281 Tumour


title: MELA_0058 Tumour


title: MELA_0374 Tumour


title: mES WT cells - Mnase - rep1

source_name: mES WT cells

extract_protocol:
Cells were washed twice with PBS, and crosslinked by a 10 minutes incubation with PBS + 1% formaldehyde at room temperature. Crosslinking reactions were stopped by the addition of 125 mM glycine and additional rocking for 5 minutes. Cells were collected by scrapping in 2 mL ice-cold PBS + protease inhibitors (10 uM leupeptin, 100 uM PMSF, 1uM pepstatin, 2 ug/mL aprotinin), collected by centrifugation at 180g for 5 minutes at 4oC, resuspended in Homogenization Buffer (10 mM Tris pH 7.4, 1mM EDTA, 0.1mM EGTA, 15 mM NaCl, 50 mM KCl, 0.15mM spermine, 0.5 mM spermidine, 0.2% NP-40, 5% sucrose) at a concentration of 2x106 cells/mL and incubated on ice for 3 minutes. Nuclei were then placed on top of a 3.5 mL sucrose cushion (Homogenization Buffer + 10% sucrose), and centrifuged for 20 minutes at 900g and 4oC. The nuclei pellet was resuspended in ice-cold Wash Buffer (10mM Tris pH 7.4, 15mM NaCl, 50 mM KCl, 0.15 mM spermine, 0.5 mM spermidine, 8.5% sucrose) at a concentration of 2x106 nuclei/mL, and divided in 1 mL aliquots. Two of these aliquots were treated with 0 and 600 units of MNase (Thermo Fisher) after adding 1mM CaCl2 for 6 minutes at 25oC. Enzymatic reactions were stopped by adding 9mM EDTA and 3.5 mM EGTA and placing the samples at 4oC.Next, samples were purified and those treated with 600 units of MNase loaded in a 1.2% agarose gel. The fragments corresponding to the mononucleosomal fraction (around 150 bp) were sliced from the agarose gel and purified using a Speedtools PCR Clean Up Kit (Biotools) following manufacturerâ€™s instructions
Libraries were generated with the NEBNext DNA Library Prep Kit (New England Biolabs) and sequenced by 2x75 paired-end reads


title: H1-TKO cells - RNAPII-ChIP - rep1

extract_protocol:
Crosslinkings were performed in culture medium with 1% formaldehyde during 15 minutes at RT. After stopping the reactions with 125 mM glycine for 5 minutes, cells were washed twice with PBS and collected by scrapping in ice-cold PBS supplemented with protease and phosphatase inhibitors (10 uM leupeptin, 100 uM PMSF, 1uM pepstatin, 2 ug/mL aprotinin, 5 mM NaF, 1mM NaVO3). Cells were centrifuged at 200g for 5 minutes, resuspended in cold Lysis Buffer (50 mM Tris pH 8, 1% SDS, 10 mM EDTA, protease and phosphatase inhibitors) at a concentration of 2x107 cells/mL and incubated on ice for 20 minutes. Soluble chromatin was fragmented on a Covaris sonication system by 40 cycles at 20% intensity, during 20 minutes. 100 ug of the fragmented chromatin was diluted 1:10 in Dilution Buffer (20 mM Tris pH 8, 1% Triton X-100, 2mM EDTA, 150mM NaCl, protease and phosphatase inhibitors), and 5 ug of human chromatin, obtained from a MCF10A cell line following the same protocol, was added as spike-in control. Precleared chromatin was incubated overnight with 25 ug of anti-RNApolII antibody (Millipore) at 4ÂºC with gentle agitation, followed by a 2 hours incubation with 200 ÂµL of A/G protein beads. Immunocomplexes were washed sequentially with four different buffers, all supplemented with protease and phosphatase inhibitors: low salt buffer (10 mM Tris pH 8, 0.1% SDS, 1% Triton X-100, 2mM EDTA, 150 mM NaCl), high salt buffer (20 mM Tris pH 8, 0.1% SDS, 1% Triton X-100, 2mM EDTA, 500 mM NaCl), LiCl buffer (10 mM Tris pH 8, 0.25M LiCl, 1% NP40, 1% Na-deoxycholate, 1mM EDTA) and TE buffer (10 mM Tris pH 8, 1mM EDTA). Finally, chromatin was eluted with elution buffer (0.1M NaHCO3, 1% SDS), crosslinkings were reverted, and DNA was purified with phenol-chloroform extraction and ethanol precipitation
Libraries were generated with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) following the manufacturerâ€™s recommendations and sequenced by 1x75 single-reads


title: H1-TKO cells - RNAPII-ChIP - rep2


title: mES WT cells - Ttseq - rep1


title: mES WT cells - Ttseq - rep2


title: mES WT cells - RNAPII-ChIP - rep2


title: mES WT cells - Mnase - rep2


title: H1-TKO cells - Mnase - rep1


title: MELA_0059 Tumour


title: MELA_0335 Tumour


title: MELA_0280 Tumour


title: mES WT cells - RNAPII-ChIP - rep1